B16-EvolveC.txt

Graham L. Kendall
All these files are available on
http://www.grahamkendall.net/
Modified 6/9/2008
I am found on IRC Efnet/Undernet as glk
Email grahamkendall74135@yahoo.com
All are free to use any of this material without limit.
*******************************************************************************
==
Weaknesses of evolution
Starting this summer, the state education board will determine the curriculum
for the next decade and decide whether the "strengths and weaknesses" of
evolution should be taught. The benign-sounding phrase, some argue, is a
reasonable effort at balance. But critics say it is a new strategy taking
shape across the nation to undermine the teaching of evolution, a way for
students to hear religious objections under the heading of scientific
discourse.
---
Already, legislators in a half-dozen states -- Alabama, Florida, Louisiana,
Michigan, Missouri and South Carolina -- have tried to require that classrooms
be open to "views about the scientific strengths and weaknesses of Darwinian
theory," according to a petition from the Discovery Institute, the
Seattle-based strategic center of the intelligent design movement.
---
The story mainly covers the local Texas aspects of the story, with quotes from
the state education board chairman ("I believe a lot of incredible things") and
some pro-evolution opponents.
I looked at the website where the Texans for Better Science Education lay out
examples of the "weaknesses" that should be taught. They're pretty weak, all
right. I think that most of these could be included in a science course as
"common myths about evolutionary theory."
Consider these:
---
The Cambrian explosion quickly produced all of the basically different body
structures, and some of these have since become extinct. This is very
different from the evolutionary tree of life, which suggests a slow and
gradual increase in body structures.
---
No, no it doesn't. Evolutionary theory provides no reason to think that body
structures should change at a slow constant rate. The synthetic theory
emphasizes why bursts of adaptive change should happen episodically.
---
Many life forms persist through large expanses of geologic time with
essentially no change. Evolution theory suggests that mutations occur randomly
over time and are selected to produce continuing change as the environment
continually changes.
---
No, no it doesn't. Some organisms may well have relatively constant
environments for millions of years.
---
Selective breeding has produced only very limited change with no new
structures occurring over thousands of years and multitudes of generations of
selection.
---
Umm... teosinte? I think that biology texts should devote a lot more attention
to selective breeding, as the best concrete examples of evolution in action.
So, that reflects on the basic problem with the idea of teaching evolution's
"weaknesses": A real weakness is not a matter of ignorance, but a matter of
evidence weighing in favor of some alternative hypothesis. We don't have that
here.


==
Cell manufacture
http://www.scienced aily.com/ releases/ 2008/06/08060414 0959.htm
[go to link for full article]

New Way To Think About Earth's First Cells

A team of researchers at Harvard University have modeled in the
laboratory a primitive cell, or protocell, that is capable of
building, copying and containing DNA.

Since there are no physical records of what the first primitive cells
on Earth looked like, or how they grew and divided, the research
team's protocell project offers a useful way to learn about how
Earth's earliest cells may have interacted with their environment
approximately 3.5 billion years ago.
The protocell's fatty acid membrane allows chemical compounds,
including the building blocks of DNA, to enter into the cell without
the assistance of the protein channels and pumps required by today's
highly developed cell membranes. Also unlike modern cells, the
protocell does not use enzymes for copying its DNA.
Led by Jack W. Szostak of the Harvard Medical School, the research
team published its findings in the June 4, 2008, edition of the
journal Nature's advance online publication.
"Szostak's group took a creative approach to this research challenge
and made a significant contribution to our understanding of small
molecule transport through membranes," said Luis Echegoyen, director
of the NSF Division of Chemistry.
When the team started its work, the researchers were not sure that the
building blocks required for copying the protocell's genetic material
would be able to enter the cell.
"By showing that this can happen, and indeed happen quite efficiently,
we have come a little closer to our goal of making a functional
protocell that, in the right environment, is able to grow and divide
on its own," said Szostak.
"We have found that membranes made from fatty acids and related
molecules -- the most likely components of primitive cell membranes --
have properties very different from those of the modern cell membrane,
which uses specialized pumps, channels or pores to control what gets
in and out," says Jack Szostak, PhD, of the MGH Department of
Molecular Biology and Center for Computational and Integrative
Biology, the report's senior author. "Our report shows that very
primitive cells may have absorbed nutrients from their environment,
rather than having to manufacture needed materials internally, which
supports one of two competing theories about fundamental properties of
these cells."
Szostak's team carefully analyzed vesicles comprised of different
fatty acid molecules and identified particular features that made
membranes more or less permeable to potential nutrient molecules. They
found that, while large molecules such as strands of DNA or RNA could
not pass through fatty acid membranes, the simple sugar molecules and
individual nucleotides that make up larger nucleic acids easily
crossed the membrane.
To further explore the function of a fatty acid cell membrane, the
researchers used activated nucleotides they developed for this study
that will copy a DNA template strand without needing the polymerase
enzyme usually required for DNA replication. After placing template
molecules inside fatty-acid vesicles and adding the activated
nucleotides to the external environment, they found that additional
DNA was formed within the vesicles, confirming that the nucleotide
molecules were passing through the fatty-acid membranes.

Related references:

Jack W. Szostak, Ph.D.
http://www.hhmi. org/research/ investigators/ szostak_bio. html

Mineral Surface Directed Membrane Assembly
(Origins of life and evolution of the biosphere, Feb. 2008; 37(1):67-82)
http://genetics. mgh.harvard. edu/szostakweb/ publications/ Szostak_pdfs/
Hanczyc_et_ al_2006_OLEB. pdf
[link may be line-wrapped]

Structure and Evolutionary Analysis of a Non-biological ATP-binding
Protein
(Journal of Molecular Biology, Aug. 10 2007; 371(2):501-13)
http://genetics. mgh.harvard. edu/szostakweb/ publications/ Szostak_pdfs/
mansy_etal_ JMB_2007. pdf


==
Parasite turns host into bodyguard
Many parasites simply eat away at their hosts from the inside. That may be bad
enough. But some go further: they manipulate their hosts behavior to benefit
themselves, producing some of natures most cruel and strange spectacles.
One notable example is that of the hairworm, which somehow induces its insect
hosts to commit suicide by jumping into water, where the hairworms go to
reproduce.
In this experimental setup, a caterpillar knocks a small parasitic bug off its
twig. The bug is seen rapidly dropping down at the lower right of the twig; the
caterpillar still hasn't finished its violent swing. Above the caterpillar are
the lightcolored wasp cocoons. (Courtesy A.H. Grosman et al.)
A new study describes yet another strange case of apparently parasiteinduced
behavioral changes: a creature that turns its host into its own, suicidally
devoted bodyguard.
After the parasitic wasp Glyptapanteles completes an early life stage as an
uninvited guest in the body of a caterpillar, the caterpillar exhibits
stunning changes, according to researchers. It stops eating and stays close by
the wasps, which by then are cocoons. It wraps them in a protective web of silk
and defends them against approaching predators with violent, relentless
headswings.
It continues this until the wasps emerge from their cocoons, then it dies,
according to the scientists, from the University of Amsterdam and University
of Vicosa in Brazil.
In experiments, when presented with a small predatory insect, 17 out of 19
parasitized caterpillars lashed out at the bug with repeated violent
headswings, the investigators wrote in a paper describing their work.
By contrast, only one of 20 unparasitized caterpillars showed this behaviour,
they wrote. The others hardly responded to the presence of the predator, even
when it was walking on the host. The paper is published June 4 in the online
research journal PLoS One.
The wasps bizarre life cycle begins when an adult lays eggs inside the
caterpillar. These develop into larvae that live on the animals body fluids.
They eventually crawl out of the caterpillar, to become cocoons shortly in
preparation for adulthood.This is when the caterpillar, known as Thyrinteina
leucocerae, acts as a bodyguard, the researchers said. The cocoons and
caterpillar live next to each other on a twig as the drama plays out.
Strictly speaking, the wasp is called a parasitoid, not a parasite, because it
only spends part of its life cycle as a parasite.
The researchers found that parasitoid cocoons guarded by caterpillars in the
wild suffered half as much predation as those without a bodyguard.
Its unclear how the wasp changes the behaviour of its host. But interestingly,
the investigators said, one or two parasitoid larvae normally remained behind
in the host after the others left. These larvae may be the ones that change
the caterpillars behaviour, thus sacrificing themselves for their brothers and
sisters, the researchers speculated.
==
 Hominids by Robert J. Sawyer, This book looks at the history of humankind on
this planet and all we have done to it.
==
Yeast use many of the same enzymes and cofactor vitamins and
minerals as humans and are an excellent model for human metabolism.

There are over 600 human enzymes that use vitamins or minerals as cofactors
==
A mutation permitting tooth development in chicken
embryos shows not only avian archosaur ancestry but
also process by which toothlessness arose in birds:
==
Darwinian: Our species homo sapiens arose, like all other species, from the
ordinary processes of evolution, which have continued to the present day.
Human nature is a collection of characteristics all susceptible to biological
explanation. These characteristics show variation in any one population. A
human population that breeds mostly within itself for many generations will
develop distinctive profiles of variation, as a result of ordinary biological
laws, causing it to diverge from other such populations. Neither individual
human beings nor human populations are equal. Some human-nature
characteristics can be shaped to some degree by "cultural" (i.e. social or
environmental) forces; some cannot. Biology rules!
==
Self-assembled Viruses Efficiently Carry Genes And Drug Molecules Into
Tumor Cells
http://www.scienced aily.com/ releases/ 2008/05/08053010 2627.htm

ScienceDaily (Jun. 2, 2008) (I12(B Viruses are true experts at importing
genetic material into the cells of an infected organism. This trait is
now being exploited for gene therapy, in which genes are brought into
the cells of a patient to treat genetic diseases or genetic defects.
Korean researchers have now made an artificial virus. As described in
the journal Angewandte Chemie, they have been able to use it to
transport both genes and drugs into the interior of cancer cells.

Natural viruses are extremely effective at transporting genes into
cells for gene therapy; their disadvantage is that they can initiate
an immune response or cause cancer. Artificial viruses do not have
these side effects, but are not especially effective because their
size and shape are very difficult to control(I12(Bbut crucial to their
effectiveness. A research team headed by Myongsoo Lee has now
developed a new strategy that allows the artificial viruses to
maintain a defined form and size.

The researchers started with a ribbonlike protein structure ((IA(B-sheet)
as their template. The protein ribbons organized themselves into a
defined threadlike double layer that sets the shape and size. Coupled
to the outside are "protein arms" that bind short RNA helices and
embed them. If this RNA is made complementary to a specific gene
sequence, it can very specifically block the reading of this gene.
Known as small interfering RNAs (siRNA), these sequences represent a
promising approach to gene therapy.

Glucose building blocks on the surfaces of the artificial viruses
should improve binding of the artificial virus to the glucose
transporters on the surfaces of the target cells. These transporters
are present in nearly all mammalian cells. Tumor cells have an
especially large number of these transporters.

Trials with a line of human cancer cells demonstrated that the
artificial viruses very effectively transport an siRNA and block the
target gene.

In addition, the researchers were able to attach hydrophobic (water
repellant) molecules(I12(Bfor demonstration purposes a dye(I12(Bto the
artificial viruses. The dye was transported into the nuclei of tumor
cells. This result is particularly interesting because the nucleus is
the target for many important antitumor agents.


==
Modeling Hox gene regulation in digits: reverse collinearity and the molecular origin of thumbness
Abstract
During the development of mammalian digits, clustered Hoxd genes are expressed
following a collinear regulatory strategy, leading to both the growth of digits
and their morphological identities. Because gene dosage is a key parameter in
this system, we used a quantitative approach, associated with a collection of
mutant stocks, to investigate the nature of the underlying regulatory
mechanism(s). In parallel, we elaborated a mathematical model of quantitative
collinearity, which was progressively challenged and validated by the
experimental approach. This combined effort suggested a two-step mechanism,
which involves initially the looping and recognition of the cluster by a
complex including two enhancer sequences, followed by a second step of
microscanning of genes located nearby. In this scenario, the respective rank
of the genes, with respect to the 5 extremity of the cluster, is primordial,
as well as different gene-specific affinities. This model accounts for the
quantitative variations observed in our many mutant strains, and reveals the
molecular constraint leading to thumbness; i.e., why a morphological
difference must occur between the most anterior digit and the others. We also
show that the same model applies to the collinear regulation of Hox genes
during the emergence of external genitalia, though with some differences
likely illustrating the distinct functionalities of these structures in adults.

In vertebrates, Hox genes belonging to the HoxA and HoxD clusters are
necessary for the development of the limbs (see Zakany and Duboule 2007).
Genes of both clusters are expressed in a complex manner, mostly through two
different phases, which depend on distinct regulatory controls (Nelson et al.
1996; Deschamps and van Nes 2005; Tarchini and Duboule 2006). During early
limb budding, Hoxd gene transcription is activated in a collinear fashion,
starting with Hoxd1 and progressing toward the 5 end of the cluster (Hoxd13).
This early phase of activation leads to the concomitant restriction in the
expression of the most 5-located genes (from Hoxd10 to Hoxd13) into the most
posterior-distal cells of the developing limb bud. Eventually, these posterior
Hox gene products will activate transcription of the gene sonic hedgehog
(Tarchini et al. 2006), a key determinant of limb growth and polarity (Riddle
et al. 1993), necessary for the second phase of limb development to occur.

This early phase of Hox genes activation corresponds to the organization and
patterning of both the stylopodium (the arm) and the zygopodium (the forearm).
This phase is soon followed by the morphogenesis of the most distal parts of
the limbs (the autopodium; hands and feet), which is accompanied by a second
wave of Hox genes activation, involving Hoxa13 as well as the four posterior
most genes of the HoxD cluster (from Hoxd10 to Hoxd13). It is during this late
phase of expression that the Shh signaling pathway further impacts on the shape
of the expression domain, thus imposing the anterior-to-posterior (AP) polarity
of our limb extremities (Drossopoulou et al. 2000). The existence of these two
separate modes of Hox gene expression has been associated with the distinction
between the most distal pieces of the limbs and the rest of the appendages in
term of evolutionary history. In this view, the autopodium is a neomorphic
structure that appeared in tetrapods, subsequent to the appearance of proximal
limbs (Sordino et al. 1995), in parallel to either the de novo emergence, or
the full recruitment of the appropriate regulatory sequences (see Spitz et al.
2003; Davis et al. 2007; Freitas et al. 2007; Gonzalez et al. 2007).

The nature of the genetic control underlying the early phase of Hoxd gene
expression in limb buds remains to be determined. However, molecular genetic
approaches in the mouse have revealed that transcriptional activation likely
depends on sequences located outside from the cluster itself, on the telomeric
side; i.e., 3 from Hoxd1 (Spitz et al. 2005). In contrast, the regulatory
elements that control the late phase of activation appear to locate
centromeric to the cluster (5 from Hoxd13), as judged by extensive genetic and
transgenic analyses. On the one hand, both spontaneous and engineered large
inversions have clearly positioned digit-specific enhancer sequences upstream
of (centromeric from) the HoxD cluster (Spitz et al. 2003, 2005). On the other
hand, transgenic analyses involving BAC clones as well as shorter DNA fragments
have pointed to two regions of critical importance for the expression of
5-located Hoxd genes in developing autopods.

The first of these DNA segments, located some 180 kb upstream of Hoxd13,
contains several global enhancer sequences, one of which active in developing
digit cells. This global control region (GCR) is conserved among all
vertebrates including teleostei, even though the fish counterpart was not able
to elicit a digit-specific expression when introduced into transgenic mice
(Spitz et al. 2003). The second sequence (Prox) was identified subsequently,
and lies between the GCR and the 5 end of the HoxD cluster. It is also found
in birds and amphibian, although not detected in teleostei genomes (Gonzalez
et al. 2007). In transgenic animals, this sequence can drive expression in
developing digits with a specificity slightly distinct from, and complementary
to, that of the GCR. Therefore, expression of Hoxd genes during the late phase
of limb development likely results from the combined action of these two
regulatory sequences (Gonzalez et al. 2007). In contrast, little is known yet
on the transcriptional control of Hoxa13 expression during digit morphogenesis.

In wild-type embryonic day 12.5 (E12.5) mouse embryos, the four contiguous
genes Hoxd10, Hoxd11, Hoxd12, and Hoxd13 are expressed under the control of
the GCR and Prox sequences. While their expression profiles in digits are
virtually identical to one another, their transcriptional outputs seems to
follow a collinear distribution, at least when considering steady-state levels
of mRNAs (Dolle et al. 1991). Hoxd13, the gene lying at the 5 extremity of the
cluster, is transcribed with maximal efficiency, whereas Hoxd10 is only weakly
expressed. Hoxd12 and Hoxd11 have intermediate amounts of transcripts, as
assessed by in situ hybridization. This quantitative difference makes Hoxd13
expression detectable in presumptive cells of future digit I (the most
anterior digit; the thumb in mammals), unlike the other three genes, whose
transcripts are not detected in these cells, most likely due to lower
expression levels. Consequently, the Hoxd13 transcript domain encompasses
those of the three other genes, an observation in contrast to the general
expression strategy of Hox genes and referred to as reverse collinearity
(Nelson et al. 1996).

This difference between Hoxd13 and other Hox genes is of critical importance
as it may help to individualize the morphology of digit I from those of the
other digits. There is indeed an exact correlation between digit morphology
and Hox gene expression, such that all reported cases where the thumb is
replaced by a more posterior (longer) type of digits, also show a gain of
posterior Hoxd genes expression in the presumptive thumb domain.
Alternatively, forced expression of posterior Hox genes (e.g., Hoxd11)
throughout the limb budi.e., including presumptive digit I cellsleads to the
disappearance of the thumb and transformation toward a more elongated digit
morphology, resembling posterior digits (e.g., Morgan et al. 1992). Therefore,
the globally weaker dose of Hox function in presumptive digit I cells, mostly
due to the nonexpression of Hoxd12, Hoxd11, and Hoxd10 there, is likely a key
factor in the morphological difference that exists between this future digit
and more posterior digits, which express these latter genes in addition to
Hoxa13 and Hoxd13.

The nature of the molecular mechanism underlying reverse collinearity is
unknown, yet it must rely on quantitative collinearity, since the Hoxd gene
expressed at the highest level (Hoxd13) is the only one transcribed in
presumptive digit I cells. By using a set of deletion and duplication alleles
produced by targeted meiotic recombination (TAMERE) (Herault et al. 1998), we
previously showed that the respective position of a gene was important, rather
than the specificity of its promoter. For example, when Hoxd12 was
experimentally positioned at the end of the cluster, where Hoxd13 normally
stands, it was expressed with the same efficiency as Hoxd13 (Kmita et al.
2002a), including in presumptive digit I cells, where it is normally silent.
Also, the introduction of supernumerary promoters at the proximity of the HoxD
cluster induced regulatory reallocations in digits (Monge et al. 2003),
suggesting that collinear expression of Hoxd genes in developing autopods was
the result of a global regulatory equilibrium, controlled by upstream
sequences and involving both the number and respective positions of target
transcription units.

In this study, we investigate this collinear process by using a quantitative
approach to precisely determine the impact of several mutated configurations
on the relative amounts of the various Hoxd mRNAs. We use both experimental
and theoretical approaches to elaborate a model of collinear regulation, after
several rounds of predictions and validations, a process made possible by the
large number of various mutant alleles available at this locus. We conclude
that the best-fit model involves both a strong topological component, but also
calls for some differences in promoter-specific responses. This model also
indicates that the collinear Hoxd genes regulations underlying the development
of both digits and external genitalia are very similar and likely implemented
by the same elements, even though differences exist in the local control of
some genes. Finally, this model accounts for the impossibility for all Hoxd
genes to be expressed equally strongly in presumptive digits cells (reverse
collinearity), and hence, it links a clustered genetic topography and the
associated regulatory constraints, to a particularly important morphological
output, the emergence and maintenance of thumbness.

In E12.5 mouse limb buds, the four most 5-located Hoxd genes are transcribed
in developing digits, with virtually identical expression profiles (Fig. 1A).
However, Hoxd13 is expressed at a much higher level and extends within the
most anterior presumptive digit one (Fig. 1A, arrowhead; Kmita et al. 2002a),
unlike the three other neighbor genes, whose mRNAs steady-state levels seem to
decrease following their respective rank on the cluster (Fig. 1A, quantitative
collinearity). This expression pattern in digits is controlled by two
regulatory sequences located in cis (GCR and Prox) (Spitz et al. 2003;
Gonzalez et al. 2007), which also regulate expression of the Evx2 and lunapark
(Lnp) genes in the same digit domain, as a result of their location within this
regulatory landscape (Fig. 1A; Spitz et al. 2003).

Figure 1.
Quantitative collinearity in developing digits. (A, top) Posterior Hoxd genes
are expressed in developing digits following a gradient of transcriptional
efficiency: Hoxd13 is expressed robustly, whereas more 3-located genes display
progressively (more ...)

Quantitative collinearity
In order to assess the various quantities of steady-state mRNAs, and hence to
establish a baseline for the relative expression levels of these genes in the
wild-type condition, the most distal parts of developing E13.5 digits were
dissected out, mRNA extracted and quantified by real-time RTPCR. At the same
time and for comparative purposes, the emergent genital bud was also dissected
out and treated similarly (Fig. 1B), since quantitative collinearity was
originally described in this developing bud (Dolle et al. 1991). The accuracy
of this quantitative approach was verified using a mouse carrying a deletion
of the Hoxd13 locus. In heterozygous mice, presumptive digits expressed almost
exactly half the amount of the corresponding mRNAs, whereas Hoxd13 transcripts
were expectedly not scored in the homozygous mutant background (Fig. 1C). This
result as well as several other lines of evidence (data not shown), indicated
that cross-regulatory interactions occurring between posterior Hox genes and
their products, if any, were not importantly involved in the final amounts of
transcripts. Consequently, this particular collinear regulation mostly, if not
entirely, derives from interactions in cis.

We next quantified the relative amounts of transcripts between the various
genes, such as to better visualize quantitative collinearity and to have a
starting point for both the evaluation of our various mutant configurations
and theoretical modeling (see below). By using comparisons with known amounts
of RNA, the results depicted in Figure 1D were obtained. While they globally
confirmed the existence of a collinear distribution, they revealed some
unexpected aspects. Because the amount of Hoxd13 mRNAs was arguably the
highest, it was arbitrarily fixed to 1, the other values being expressed in
percentages of this amount. In this scale, Hoxd8 transcripts were not detected
and Hoxd9 mRNAs represented <5%, which was at the limit of significance. This
may reflect some weak activity, not easily detected by in situ hybridization.
While Hoxd10 was clearly expressed, although at a low level, Hoxd11 and Hoxd12
had surprisingly almost identical levels of mRNAs, in the range of 35% of the
Hoxd13 amount. Altogether, quantitative collinearity was confirmed, yet with
no clear application to Hoxd12 and Hoxd11. Unlike what previous expression
studies had suggested, the steady-state levels of both Lnp and Evx2 mRNAs were
low, barely >10% of that of Hoxd13 (Fig. 1D).

Regulatory reallocations
Once these wild-type quantifications were established, we processed a set of
mutant strains where both the number and respective order of the genes had
been modified (Fig. 2). We first used three mutant strains where the most
posterior gene Hoxd13 had been deleted, either alone (Fig. 3A, red bars), in
combination with Hoxd12 (Fig. 3A, yellow bars), or together with both Hoxd12
and Hoxd11 (Fig. 3A, green bars). In all cases, quantitative collinearity was
maintained, but shifted along with the number of genes deleted. For example,
in the absence of the Hoxd13 locus, Hoxd12 was overexpressed by a factor of
two- to threefold, to reach 80% of wild-type Hoxd13 expression level. Both
Hoxd11 and Hoxd10 transcripts were also increased in amounts, although to a
lesser extent. A slight increase in Hoxd9 expression was also scored, yet
still below the amount of Hoxd10 mRNAs in the wild-type configuration (i.e.,
at the same respective positions).

Figure 2.
Stocks of mutant mice used in this study with, at the top, a drawing of the
wild-type HoxD cluster. Posterior Hoxd genes are depicted by using a color
code, from Hoxd13 in red, to Hoxd9 in blue. The position of conserved RXII is
shown by the light-blue (more ...)

Figure 3.
Regulatory reallocations. Real-time PCR comparisons of gene expression levels
in presumptive digits of either wild-type embryos (light-blue bars) or embryos
homozygous for deletions of Hoxd loci located in 5 of the cluster. The levels
are always (more ...)

When all three Hoxd13 to Hoxd11 loci were removed, Hoxd10 was increased, yet
not to the expected level for the leading gene; i.e., the gene positioned at
rank number 1. In this case, a very significant increase in the amount of
Hoxd9 mRNAs was detected (Fig. 3A, green bars), although also below the amount
expected for a gene located at the second position with respect to the 5 end of
the cluster. Also, in all deleted configurations, Lnp was not significantly
modified, except for a slight up-regulation in the del(13-11) mice. The same
holds true for the regulation of Evx2, even though in this case, the magnitude
of the variations was much higher. In particular, removing the Hoxd13 to Hoxd11
DNA interval induced an almost 300% increase in the transcription of Evx2,
whereas the shorter deletions had a less pronounced effect, though stronger
than that seen for Lnp.

From this set of experiments, we concluded that the collinear response in
transcript amounts was mostly, although not entirely, dependent on the rank of
the gene. A collinear response was obtained regardless of which gene was
positioned first, yet the shape of the response was not identical in all
cases, as clearly shown by the expression of Hoxd9 in the del(13-12) mutant
limbs, which was much below the level of Hoxd10 (Fig. 3A, yellow bars), unlike
the expression of Hoxd12 and Hoxd11 in the wild-type condition, where these
latter two genes were at the same respective positions and are expressed in
similar amounts (Fig. 3A, light-blue bars).

Conserved region XII (RXII)
RXII, a region of high DNA homology between various vertebrate species and
located between Hoxd13 and Evx2 (Kmita et al. 2002b) was previously proposed,
using in situ hybridization data, to help potential enhancer sequences to
contact between Hoxd13 and Evx2, thereby favoring expression of Hoxd13 (Kmita
et al. 2002a). By using this quantitative approach, we could not confirm this
original observation, despite RXII having a genuine effect on the
transcription of these target genes. Rather than equalizing transcript amounts
among the various target genes, the deletion of RXII increased the
transcriptional activities of Hoxd13 to Hoxd10 (Fig. 3B, cf. dark-blue and
light-blue bars). When combined with the deletions of either the Hoxd13 locus,
or of both the Hoxd13 and Hoxd12 loci, the same tendency was observed and
quantitative collinearity was maintained (Fig. 3B, orange and green bars)more
obviously, in fact, than upon the mere deletion of RXII. In this latter case,
expression of Hoxd11 was not significantly different from that of Hoxd12 when
using the Students t-test (Fig. 3B, dark-blue bars).

Interestingly, the major modification caused by deletion of RXII was scored on
Evx2 regulation, whose transcript level dropped down to 50%. As observed also
in the presence of RXII (Fig. 3A), the deletion of RXII in combination with
either Hoxd13 or Hoxd13 and Hoxd12 lead to an increase in the transcription of
Evx2. In this case, however, the increase was much less pronounced than in the
presence of RXII, and the level of Evx2 mRNAs eventually reached the wild-type
level (Fig. 3B, green bar), whereas a robust increase was seen with the same
deletion but in the presence of RXII (Fig. 3A, green bar). Altogether, the
gain of expression observed on Hox genes upon deletion of RXII was clearly
more important than the concomitant loss of Evx2 expression, indicating that
the increase was not due to a mere redistribution of regulations.

Modeling quantitative collinearity
As different mechanisms could underlie both the collinear regulation in the
wild-type locus and its observed variations in our mutant configurations, we
tried to elaborate a theoretical model that would best fit this initial set of
experimental data. We considered two major classes of mechanisms: those relying
on a scanning process, and those involving direct initial contacts between the
enhancers and the target DNA region(s), through the formation of loops (e.g.,
see Bulger and Groudine 1999; Tolhuis et al. 2002). Based on the first set of
experimental data mentioned above, two important general observations were
taken into account: First, while the rank of the gene with respect to the 5
end of the cluster is a key parameter for the expression level, it is not the
only element to consider. For example, regardless of which gene was positioned
at the place of Hoxd13 (rank I), this gene was highly expressed. The absolute
levels of expression were nevertheless significantly different from gene to
gene (Fig. 4A). Generally, genes located 3 of the breakpoint were not as
highly expressed as was predicted by their new position. For example, in
del(13), Hoxd12 reached only 80% of the Hoxd13 wild-type level, despite its
first position within the cluster (Fig. 4A). However, no simple rule could be
drawn, as shown by Hoxd11 expression in the same deletion, which in contrast
was 1.4-fold that of the Hoxd12 wild-type level (Fig. 4A). Also, Evx2
expression increased strongly together with the size of the deletions, even
though the respective position of this gene remained unchanged (Fig. 3A).
These observations suggested that slightly different, gene-specific affinities
were also involved.

Figure 4.
Modeling quantitative collinearity. (A) Expression levels of Hoxd genes as a
function of their relative position with respect to the 5 extemity of the
cluster (their rank), in the various genetic configurations. While gene rank
(more ...)

Second, the overall transcriptional activity of the locus, as measured by
cumulative amounts of transcripts, was function of the number of transcription
units present, such that the deletion of one or several genes led to a
corresponding overall decrease of mRNAs produced at the locus (with the
exception of the codeletion of RXII, as described above). This observation was
subsequently confirmed by increasing the number of genes, through various
duplications (see below), leading to a quasilinear relationship between gene
number and total mRNAs levels (Fig. 4B). This unexpected observation indicated
that the regulatory system is not saturated in the wild-type condition, and
that regulatory reallocations, following genomic modifications, do not simply
reflect the redistribution of the same general regulatory potential among a
reduced or increased number of target units.

After considering various model outlines, a particular class of models was
found to fit the above-mentioned constraints, while not requiring an undue
number of estimated parameters. These models assume a two-step process: In the
first phase, a complex involving regulatory sequences (GCR, Prox), together
with their bound factors, will interact with the Evx2-Hoxd13 intergenic region
(Fig. 4C). The probability that the GCR/Prox complex will bind the locus is
proportional to the number of promoters present at the locus.

Once this interaction has occurred, various probabilities exist to activate
either Lnp, Evx2, or Hoxd genes. These probabilities depend on the affinities
of the various promoters and the probability that the GCR/Prox complex did not
stop previously at upstream promoters. We thus assumed that the five Hox genes
promoters are not equivalent in their capacity to attract and fix the GCR/Prox
complex. This second step could occur via a microscanning process, over the
~40-kb large DNA interval containing from Hoxd13 to Hoxd10. Since all
promoters are at the vicinity of the enhancers complex, this latter can
discriminate and select in function of the respective affinities. In this
class of models, the maximum number of estimated parameters is nine (see
Materials and Methods). Two parameters define the regression between the total
number of transcripts and the number of promoters at the locus, and seven
parameters at most are required to account for the affinities of the seven
loci considered (Lnp, Evx2, and Hoxd13 to Hoxd9). Such models successfully
passed the test of the three observed features (Fig. 5): (1) the decrease in
total transcripts amount together with promoter number, (2) the modulation of
ranking by promoter efficiency to determine the expression levels, and (3) the
up-regulation of Evx2 whenever Hox genes are deleted. After definition of the
various parameters, this model, which includes components of both scanning and
looping mechanisms, fit the first set of data much better than any other model
relying exclusively on either a general scanning process or gene-specific
affinities (data not shown).

Figure 5.
Predicted versus observed expression levels. Comparison between expression
levels predicted by the model (yellow bars) and observed values in either the
wild-type (light-blue bars) or mutant configurations (red bars). The various
configurations are depicted (more ...)

The application of this model generated a set of values, which were then
compared with both the wild-type condition and the three deleted
configurations described above. In the wild-type condition, a very good match
was obtained between the predicted and the observed values (Fig. 5A). When
either the Hoxd13 locus, both Hoxd13 and Hoxd12 or the Hoxd13 to Hoxd11
interval were deleted from the model, the predicted values for reallocations
also matched the observed data set within error bars (Fig. 5BD, cf. red and
yellow bars), with the exception, perhaps, of the gain of Evx2 expression,
which was slightly but systematically underestimated by the model. Once
established, the model was used to make a number of predictions, which were
verified by using the appropriate mutant strains. In turn, the new results
were not only used to test the resilience of the model, but also to further
constrain the parameter values, progressively, through several rounds of
adjustment and experimental validation. The values (predictions) of the model
given in the figures below, for comparison with the experimental data sets,
are extracted from the final version of the model.

Duplication alleles
This model made clear predictions regarding the effects of either gene
duplications, or internal deletions. We experimentally challenged these
predictions, starting with three duplications obtained via our TAMERE system
(Herault et al. 1998). The first duplication was that of the Hoxd13 locus
alone (Fig. 6A), the second was a duplication of the entire Hoxd13 to Hoxd11
interval (Fig. 6B), and the third allele was an internal duplication of the
Hoxd12 to Hoxd11 locus (Fig. 6C). Generally, the predictions of the model
turned out to be rather precisely validated by the experiments. In particular,
the duplication of the Hoxd13 locus, leading to two copies of Hoxd13 positioned
at ranks 1 and 2 did not elicit a double amount of Hoxd13 mRNAs, emphasizing
again the prime importance of the promoters rank over the promoters affinity.
In this same duplication, however, the impact on Evx2 transcription was once
again not faithfully predicted, the observed down-regulation being more
important than anticipated (Fig. 6A).

Figure 6.
Duplication alleles. Observed (red) and predicted (yellow) gene expression
levels in three duplications. Wild-type levels (light blue) are shown on each
panel for comparison. (A) dup(13). (B) dup(13-11). (C) dup(12-11). In all
cases, the expression of (more ...)

Also, in the duplication of Hoxd13 to Hoxd11, the predicted level for Hoxd11
mRNAs at first appeared too high when compared with the experimental data
(Fig. 6B), yet the Students t-test indicated that this difference was not
significant. Beside this point, the observed matching was good, as was the
case for the internal duplication of both the Hoxd12 and Hoxd11 loci, where
the amount of Hoxd13 transcripts remained expectedly stable. In this latter
duplication, a robust increase in Hoxd11 mRNAs was scored, as predicted by the
model. This increase would not be expected based on a rank-only model, since
after duplication, one copy of Hoxd11 is now in the respective position of
Hoxd9; i.e., in a virtually silent position with respect to digit enhancers
(see above). This increase thus illustrates the affinity component of the
system (as predicted by the model), Hoxd11 performing better than Hoxd9 when
placed at the same genomic position. In all duplicated configurations, the
observed decrease in the amount of Hoxd10 mRNAs matched the predictions.

Interestingly, in contrast to what was observed with the various deletions,
the overall level of Hoxd gene transcripts increased together with the
importance of the duplications. For instance, a mild increase in total
transcription was detected with the duplication of Hoxd13, whereas a more
robust increase was scored upon duplication of the Hoxd13 to Hoxd11 interval
(addition of three transcription units). As mentioned earlier, this
relationship between the number of genes and the total amount of transcripts
was nearly linear (Fig. 4B).

Internal deletions
The predictions of the model concerning a set of five internal deletionsi.e.,
deletions that did not remove Hoxd13 from its first rankwere also challenged
experimentally (Fig. 7). In all these deletions, the observed levels of Hoxd13
mRNAs were stable, as predicted, except for the case of the del(12-11) where an
~20% increase was detected. Therefore, the general decrease in the amount of
Hoxd genes transcripts did not lead to an increase in Hoxd13 transcription.
Likewise, neither Evx2 nor Lnp showed significant variations in their
transcriptions, in agreement again with the model.

Figure 7.
Deletions excluding Hoxd13. Observed and predicted gene expression levels in
five internal deletions. Colors and schemes are as in Figure 6. (A) del(12).
(B) del(12-11). (C) del(12-10). (D) del(11). (E) del(11-10). All deletions
lead (more ...)

The effects of these deletions were thus scored mostly on the 3 side of the
breakpoints. Here again, the observed transcript levels were in good agreement
with the predictions. For example, Hoxd10 transcription was only moderately
increased in the absence of the Hoxd12 locus (hence, at respective rank 3)
(Fig. 7A), whereas a robust increase was scored for the same gene when located
at respective rank 2, after deletion of both Hoxd12 and Hoxd11 (Fig. 7B), thus
emphasizing the importance of the rank. Interestingly, when Hoxd12, Hoxd11 and
Hoxd10 were deleted (Fig. 7C), and hence, Hoxd9 was now neighboring Hoxd13 in
rank 2, this latter gene was not activated at a very high absolute level,
showing once again that the overall transcriptional activity distributed over
the cluster was not simply reallocated among the number of resident promoters.

While the deletion of the Hoxd11 locus generated data in good agreement with
the predictions (Fig. 7D), the internal deletion of both Hoxd11 and Hoxd10
generated the only truly aberrant measure of the whole experimental series.
This internal deletion indeed induced a very robust increase of Hoxd9
transcription, reaching the level of endogenous Hoxd12 (Fig. 7E).
Interestingly, the same 3 breakpoint was used in the del(12-10) configuration,
which did not lead to a similar increase (Fig. 7; cf. red bars in C and E).

Regulation in the genital eminence
During the emergence and further development of the external genital organs
(the future penis and clitoris), the same Hoxd genes are expressed with a
similar quantitative collinear distribution of transcripts (Dolle et al.
1991). This observation, as well as subsequent genetic data, have highlighted
the developmental similarities between distal limb buds and genital buds
(Kondo et al. 1997; Cobb and Duboule 2005), and suggested that Hoxd gene
expression in both structures could be controlled by the same regulatory
circuitry (Dolle et al. 1991; e.g., see Cohn 2004; Suzuki et al. 2004). We
thus investigated whether the model could also be applied to both wild-type
and mutant situations in the developing external genital organs. However, when
the parameters of the model were adapted after considering the entire series of
alleles, the global fit with the experimental data set was not optimal. This
could mean that either the structure of the model was different between
developing limbs and genitals, or alternatively, some classes of genetic
configurations (5 deletions, duplications, internal deletions) could not be
accounted for by the actual model; hence, their consideration to adjust the
parameters would decrease the general fit.

Consequently, we tried to exclude specific classes of genetic rearrangements
in the adjustment of parameters, by keeping the same model structure.
Interestingly, when we ignored the data set obtained with the various internal
deletions (not containing Hoxd13) to adjust the various parameters, we obtained
an excellent fit with the data sets derived from both 5 deletions (including
Hoxd13) and duplications (Fig. 8). As for the digits, the match with the
wild-type condition was very good (Fig. 8A) and the same (almost linear)
relationship was observed between the overall level of transcription and the
absolute number of transcription units present in this DNA interval (Fig. 8F).
The match between the model and either two 5 deletions [del(13) and del(13-12)]
(Fig. 8B,C), or two duplications [dup(13-11) and dup(12-11)] (Fig. 8D,E) was
very good, indicating that the regulatory mechanisms at work in both
developing digits and external genitalia were most likely the same.

Figure 8.
Hoxd gene regulation in the developing genital tubercle. The same model
structure was applied to investigate Hoxd gene regulation in the genital
eminence. The various parameters of the model were optimized using expression
values observed in the genital (more ...)

Because internal deletions had to be ignored to adjust the parameters, their
fit with the model was expectedly rather poor. For example, in the del(12-11)
configuration, Hoxd10 transcripts were much less abundant than anticipated by
the model (Fig. 8G, yellow bar). Also, the deletion of both Hoxd11 and Hoxd10
loci induced a decrease of Hoxd12 mRNAs, which were thus below the predicted
amount (Fig. 8I). Only the deletion of the Hoxd11 locus matched fairly well
the predictions of the model (Fig. 8H). Finally, and similar to what was
observed in digits, the deletion of the Hoxd11 and Hoxd10 loci induced a large
and unexpected gain in the transcription of Hoxd9 (Fig. 8I, red bar) that could
neither be explained nor accounted for by the model.

We used a quantitative approach to analyze the regulatory mechanism underlying
collinear Hoxd gene regulation during mammalian digit development. Such an
approach is necessary due to the sensitivity of various digit morphologies to
both the dose and quality of Hox gene functions delivered during fetal
development (Zakany et al. 1997; Zakany and Duboule 2007). Variations in this
quantitative regulation have been proposed to partially account for important
morphological differences between mammalian digits (e.g., Chen et al. 2005);
hence, the understanding of this regulatory control may help explain what
determines the various digital formulae of mammalian hands and feet.

The ontogeny of mammalian thumbness; a dosage effect linked to gene topology
In mammals, a clear difference is observed between the morphology of the most
anterior digit (the thumb) and the other digitsthe former generally displaying
a reduced size due to the presence of two phalanges only. At the molecular
level, very few genes are differentially regulated in various presumptive
digit domains, and hence could determine digit identities. Among these few
candidates, Hox genes are the most promising for at least three reasons.
First, the inactivation of HoxA and HoxD gene functions lead to either a
reduction or a complete agenesis of digits, including the thumb (Dolle et al.
1993; Fromental-Ramain et al. 1996; Kmita et al. 2005). Second, gain of
expression of posterior Hoxd genes (e.g., Hoxd12 and Hoxd11) in presumptive
thumb cells lead to a more elongated morphology, resembling posterior digits
(Morgan et al. 1992; Zakany et al. 2004). Finally, naturally occurring
mutations, which homogenize digital morphologies, are all associated with a
homogenization of Hox genes expression domains.

Among Hox genes expressed in digits during development, Hoxa13, the only
member of the HoxA cluster expressed there, is equally transcribed in all
digit primordia, including the thumb. Therefore, this critical difference in
shape ought to be determined by Hoxd genes and indeed both Hoxd10, Hoxd11, and
Hoxd12 are expressed exclusively in presumptive digits 25, whereas excluded
from digit I (the thumb). In contrast, Hoxd13, like Hoxa13, is expressed
throughout all presumptive digit cells. Accordingly, mice mutant for Hoxd13
have an abnormal thumb (Dolle et al. 1993). Interestingly, however, Hoxd13 is
expressed originally with the same posterior restriction than its three
immediate neighbors, with an apparent peak in posterior-distal cells and an
exclusion from digit I cells. Because Hoxd13 is expressed more robustly than
its neighbors, transcription is nevertheless subsequently detected in
presumptive thumb cells, thus encompassing all five digital primordia, leading
to what was referred to as reverse collinearity (Nelson et al. 1996). In this
view, reverse collinearity is the mere topological translation of quantitative
collinearity.

Therefore, the subtle transcriptional regulation of Hoxd genes in these cells
is likely a crucial parameter in the determination of thumbness, mostly by
reducing the global dose of HOX products present in digit I. This dosage
effect appears to be linked to gene topology, since mice deleted for the
Hoxd13 locus expressed Hoxd12 in developing digit I (Kmita et al. 2002a),
indicating that the gene positioned at the extremity of the cluster is always
expressed with maximal efficiency, regardless of its own specific regulatory
sequences. Accordingly, genes located at the second, third, fourth, and fifth
ranks respond to this regulation too, yet with lower efficiencies, leading to
their nontranscription in presumptive digit I cells. The resulting dose of
HOXA and HOXD proteins is thus higher in developing digits 25 than in digit I,
which will impact on the future morphologies, Hox genes being involved in the
control of cell proliferation and digit patterning. This difference between
digit I and the others suggests a regulatory explanation for the existence of
two developmental modules underlying the evolution of anthropoid distal
forelimbs (Reno et al. 2007).

In an evolutionary context, it is likely that the recruitment of this
regulation was an important step to accompany either the emergence, or the
expansion of digits in an ancestral tetrapod. Because of the built-in
asymmetry of the system, based on gene order, we can speculate that
quantitative collinearity was already at work in these ancestral autopods.
Consequently, a morphological distinction between the most anterior digit (the
thumb in mammals) and the others must have existed from the start. In this
view, while Hox gene clustering was certainly an efficient evolutionary
opportunity, it may have also importantly constrained the system to impose
some heterogeneity in digital morphologies. These morphological differences
may have been a basis for further adaptive solutions and selection thereof,
either by further elaborating on them, or by subsequent digital deletions or
reductions.

While many mammals indeed display little if any difference in the morphologies
of more posterior digits (e.g., the human digits 25), some vertebrate species
exhibit remarkably different, although neighboring, digits; for example,
associated with their flying behavior. In both bat and chicken wings, digits
can be variable in sizes and number of phalanges, without obvious changes in
Hox gene expression. It is nonetheless possible that slight quantitative
modifications be responsible for this effect (Chen et al. 2005).
Alternatively, the exact timing in the expression of these Hox genes in every
presumptive digit territory may subsequently affect digital morphologies.
While our various analytical tools reflect a frozen situation, a more dynamic
view of the system may reveal the nature of such differences. It is equally
possible that the Hox system be not used after the initial morphological
distinction has occurred between the most anterior digit and the others.

Modeling quantitative collinearity
Our quantitative approach, associated with the large collection of mutant
strains at this locus, allowed us to elaborate a model of large-scale gene
regulation that accounts for most of the observed results. In order to model
this regulation, we considered some facts as established, such as the
importance of gene position (the rank), the fact that two other genes were
also affected by this regulation (Evx2 and Lnp), and the known presence and
locationupstream of the gene clusterof regulatory sequences that control gene
expression in developing distal limb buds (the GCR and Prox elements) (Spitz
et al. 2003; Gonzalez et al. 2007). Other parameters were readily excluded,
due to their incapacity to explain the observed results. For example,
differences in various mRNAs half-lives, if at all involved, would have a very
minor impact. Also, models involving the scanning of the landscape by a protein
complex, after initial recognition of enhancer sequences (see Blackwood and
Kadonaga 1998) were rapidly discarded due to the difficulty of reconciling
them with any available data set. We thus focused on models based on an
initial looping, followed by the construction of a particular regulatory
microarchitecture. The predictions formulated from an early model were
subsequently tested by using the appropriate set of mutant strains. In turn,
the new data were used to adjust the various parameters such as to improve the
fit of the model. This bilateral process led to a final formulation built on
nine different parameters, which could account for the 69 quantitative
observations made by using 12 different mouse strains.

Surprisingly, the model helped to clarify two issues raised previously on the
basis of in situ hybridization patterns. First, the gene rank alone cannot
account for the observed transcriptional efficiencies. While of primary
importance, this parameter is not sufficient to explain the various data sets.
In fact, even wild-type absolute transcript levels indicate no real difference
between Hoxd12 and Hoxd11. Second, while largely increased, the transcript
levels of either Hoxd12 or Hoxd11, when placed at the first rank, never
reached the wild-type level of Hoxd13 transcripts. Also, the total amounts of
Hoxd13 transcripts in duplicated configurations containing two copies of this
locus were the same regardless of the rank of the second Hoxd13 copy; i.e.,
when placed either at rank number 2 or number 4. Therefore, the importance of
gene rank has to be somehow modulated by specific affinities between the
enhancer complex and the various gene promoters. In the model, the
introduction of parameters reflecting this previously unanticipated feature
(see Kmita and Duboule 2003) was necessary to reach the requested global fit.
Interestingly, the affinities derived from the model for Lnp, Evx2, and Hoxd9
are very similar to each other (see Materials and Methods), possibly
reflecting a generic, baseline promoter affinity, whereas Hoxd10 to Hoxd13
promoters would have evolved more robust affinities for the enhancer complex.

The second issue concerns the DNA segment initially contacted by the enhancer
complex. Our various data sets suggested a model whereby enhancers, in a first
step, contact the Evx2 to Hoxd13 intergenic region via a loop. In a second
step, the enhancer complex scans (senses) the immediate environment
preferentially from the 5 toward the 3 part of the cluster, regulated by
promoter-specific affinities. While anticipated, the importance of the
Evx2-Hoxd13 intergenic region does not seem to rely on the presence of the
highly conserved sequence RXII, unlike originally reported based on in situ
hybridization patterns (Kmita et al. 2002a). In this latter case, expression
of genes located at ranks number 2 and 3 were also detected in presumptive
cells of digit I, which was interpreted as a break in the collinear response.
Our quantification of transcripts derived from mice deleted for this sequence
XII indeed revealed that quantitative collinearity was maintained despite a
generally elevated level of Hoxd gene expression, which likely explains their
transcription in presumptive digit I cells.

In support of this explanation, the deletion used by Kmita et al. (2002a)
removed both the RXII and the Hoxd13 locus. Our analysis of this genetic
condition revealed a very robust transcriptional increase (>100%) of the
remaining three genes, explaining their expression in presumptive digit I
cells and, hence, the misleading impression that all patterns were alike in
these embryos. In the absence of RXII, Evx2 transcription was down-regulated,
which suggests that this sequence may be part of the Evx2-specific
transcriptional requirements (in the promoter region or in the 5 untranslated
region). However, the effects observed upon Hoxd gene transcription cannot be
explained solely on this basis, and call for a specific function for RXII. For
example, this conserved DNA sequence may act as a switch for the direction of
scanning, once enhancers have recognized the Hoxd13-Evx2 intergenic region.
The factors that favor the contact between the GCR/Prox enhancers and this
intergenic region remain to be characterized.

Finally, the model integrated an interesting phenomenon observed with both
deleted and duplicated configurations; i.e., the fact that the total amount of
transcripts produced in digit cells by all genes present in the landscape is a
function of the number of genes. This has several implications regarding the
transcriptional mechanism at work, as it means that the system is not
saturated, and adding more transcription units will increase the global output
of the system. This suggests that the wild-type situation likely corresponds to
a particular equilibrium, as imposed by the regulatory architecture of the
locus. Likewise, the deletion of several promoters will not merely reallocate
the regulatory potential over the remaining units, but instead, will produce a
novel equilibrium that will use less of the global transcriptional potential
available. One possibility is that such equilibrium imposes a number of
constraints to the systemfor example, in the spatial organizationpreventing
situations in which any number of genes would use their full regulatory
potential.

While in good agreement with the vast majority of the data sets obtained
experimentally, our model showed some minor and acceptable discrepancies with
the reality (for example, the underestimation of Evx2 down-regulation in
Hoxd13 duplication), as well as one major problem that remains unsolved; i.e.,
the behavior of Hoxd9 in the internal deletion del(10-11). In this case, an
almost 20-fold increase was scored in the expression of Hoxd9, whereas the
model predicted only a slight increase (Fig. 7E). This particular result is
the only one suggesting the manifestation of a new phenomenon, such as the
emergence of a novel, increased affinity for Hoxd9 following the fusion with
the 3 part of the Hoxd12 locus. The validation of this hypothesis would
require yet another set of genetic modifications, not readily available.

The digits versus genitals connection
Because of similar Hox expression dynamics during the development of both
digits and external genitalia, it was proposed that these structures share
both ontogenetic principles and a phylogenetic history (Dolle et al. 1991;
Kondo et al. 1997). Since then, the conservation of developmental principles
during the emergence and growth of these various buds has been largely
documented, notably through the presence and function of the same key
regulatory molecules and signaling pathways (for reviews, see Cohn 2004;
Suzuki et al. 2004). In fact, quantitative collinearity was originally
described in the growing genital eminence (Dolle et al. 1991), and we thus
looked at whether the model constructed for the digits could equally account
for the results obtained with developing external genitalia.

Clearly, the same type of model could be applied to the results obtained with
RNA extracted from developing genital buds. In particular, the model had a
very good fit for the duplicated configurations and the deletions including
Hoxd13 (5 deletions). Also, the quasilinear relationship between the total
transcriptional readout of the system and the number of transcription units
was also observed in genitalia. Altogether, these results suggested that the
regulatory strategy leading to quantitative collinearity was identical in both
digits and genitalia, and that these various structures not only use the same
genes, but also the same regulatory circuitry.

However, the consideration of all experimental data, as obtained from genital
bud RNAs, did not fit well, at first, with the model elaborated for digit
RNAs, even after adaptation of some parameter values. Interestingly, the set
of internal deletionsi.e., those deletions excluding Hoxd13was systematically
at odds with the model. Whenever these deletions were ignored and parameters
values adapted accordingly, a close to perfect match with the model was
obtained. This observation ought to be interpreted in two different contexts.
First, Hox gene function and regulation in these structures must be compared
at slightly different developmental time points (see Cobb and Duboule 2005),
as the distal part of the limb buds should be compared with the distal part of
the developing genitalia (the future penis, in males, or clitoris, in females)
and not with more proximal parts of the bud, the labioscrotal, and preputial
swellings, giving rise to either the scrotum, the labia, or the prepuce.
Because there was no clear morphological landmark to dissociate these parts at
our dissection time point, unlike in subsequent developmental stages, it is
possible that a contamination of more proximal cells induced a bias in the
results.

Another, nonexclusive explanation is that additional regulatory sequences
evolved within the gene cluster (e.g., see Gould et al. 1997) to fine-tune or
accompany the evolution of the external genital apparatus, on top of
pre-existing mechanisms. Internal deletions may have a particularly pronounced
impact on the function of these genital-specific sequences, thus leading to
results that cannot possibly be accounted for by the model. Such targeted
differences in the regulation of these genes may not be so surprising, given
the end result that is achieved in both cases. Indeed, in the external
genitals, the adaptive value may reside in the elongation of the future organ.
In digits, however, the function of these genes is not restricted to the mere
growth of the structures but also, as documented above, to their patterning.
These slightly different and sex-dependent contexts ultimately had their own
adaptive values, and it is perhaps not surprising if each structure evolved
some additional regulation, on top of a shared and potentially ancestral
regulatory circuitry.

Stocks of mice
The various mutant strains used in this study were described previously (Kmita
et al. 2002a, b; Tarchini and Duboule 2006; Di-Poi et al. 2007). Besides the
deletion of RXII, all mutant alleles were produced by TAMERE (Herault et al.
1998). Genotyping of mice and embryos was performed using Southern blot and
PCR analysis, according to standard procedures. For duplicated alleles, a
real-time PCR strategy was used to quantify copy numbers of the duplicated
segments, in order to discriminate between heterozygous and homozygous mutant
embryos (Supplemental Material).

RNA samples and real-time RTPCR
For each mutant line, heterozygous mice were crossed to obtain wild-type,
heterozygous, and homozygous mutant embryos. Presumptive digits and genital
tubercles were dissected from E13.5 embryos and stored in RNA later reagent
(Qiagen), until genotyped. RNA was isolated from individual embryo samples
using the RNeasy microkit (Qiagen) after disruption and homogenization with a
Polytron device (Kinematica). Single-stranded cDNA was synthesized using
SuperScript II RT (Invitrogen)

Real-time PCR primers and TaqMan probes were designed using Primer Express 2.0
software (Applied Biosystems), and PCR efficiencies were measured using serial
dilutions of cDNA. cDNAs were PCR-amplified in a 7900HT SDS system (Applied
Biosystems). Results were comparable when using either TaqMan or SYBR green
strategies. Specificity of the SYBR green reactions was determined by
examination of product melting curves. Relative quantities (RQ) were
calculated from the threshold cycle (Ct) values with the formula RQ = (1 +
E)-Ct, where E is the PCR efficiency calculated from standard curves. A mean
quantity was calculated from triplicate reactions for each sample and
normalized to two or three similarly measured quantities of housekeeping genes
(Rps9, Tbp, and Tubb). Sequences of primers and probes used in this assay are
listed in Supplemental Table S1.

For the determination of absolute transcripts levels, external calibration was
performed using a standard consisting of known amounts of the various mRNAs.
Sense RNA was produced by in vitro transcription of full-length or partial
cDNA clones (Supplemental Material) using T7 or SP6 RNA polymerases (Promega).
Standard curves were obtained by serial dilution of known amounts of these
RNAs, and reverse transcription with Drosophila L2 cell total RNA as a
carrier. Absolute quantification was performed by parallel real-time PCR
amplification of digit and genital bud total cDNA together with this standard
curve. Similar results were obtained using serial dilutions of a BAC clone
covering the locus as a standard (data not shown).



Looping and tracking model in digits
A preliminary analysis of the data revealed two striking features of this
system: First, the total amount of transcriptsi.e., the sum of absolute levels
of expression for all genes in a given configurationstrongly correlated with
the number of promoters present at the locus (Fig. 4B). The Pearson
coefficient is 0.93 in digits for the eleven configurations [excluding
del(10-11), see the text]. Second, the five Hoxd genes showed a constant
pattern where, in any given pair, the 5-located gene is more robustly
expressed than its 3-located neighbor. However, rank alone is not a good
predictor of absolute levels of expression (see the text). Therefore, we
designed a two-step model assuming the existence of seven different promoter
efficiencies (Elnp, Eevx, E13 to E9), which would determine a probability for
the GCR/Prox transcription complex to interact with any of these promoters. In
the first step, the GCR/Prox elements loop over and bind the locus somewhere
between Evx2 and Hoxd13 (Fig. 4C). The probability of this event is assumed to
be proportional to the number of promoters present at the locus. This will
determine the overall level of transcription; i.e., the total number of
transcripts from all the genes present. In a second step, the frequency f of
interaction between the GCR/Prox complex and either Lnp, Evx2, or Hoxd13, is
proportional to the efficiency E of their respective promoters. A potential
interaction with any downstream-located Hoxd gene is processive and will
depend on (1) the intrinsic efficiency of its promoter and (2) the cumulative
effect of previous interactions with all upstream-located Hoxd promoters.
Thus, the theoretical frequency fi of interaction of GCR/Prox with a Hoxd
promoter i is

where Qi is the probability that the GCR did not stop upstream of i in the
sweep, computable from the Ei; i.e., Q12 = (1-E13); Q11 = [1 - E13 - E12 * (1
- E13)] and so forth. Relative activities may then be obtained by

where Sfj is the sum over the seven genes. Absolute levels of activity (ai)
are computed by applying this ratio to the predicted total number of
transcripts for a given configuration (TTc), as derived from the linear
regression

These absolute levels of activity are to be compared with the observed
absolute levels of expression. The best fit between this model and the data
sets was looked for by using an optimum set of nine parameters: two parameters
for the linear regression to account for the total number of transcripts, and
seven parameters to account for the efficiencies of the promoters. The seven
latter parameters were derived from minimizing the sum of weighted least
squares:

where aip and aio are the predicted and observed absolute levels of
expression, respectively, Vi is the variance of measurements for the gene i,
and SS is the sum over all configurations and all genes. All computations were
done using Matlab 7.0.4 (The MathWorks) software.

Among the 69 data points, one observation, Hoxd9 in the del(10-11)
configuration, significantly deteriorated the goodness-of-fit of both the
linear regression and the least-square fit: The weighted sum of least squares
was almost halved when Hoxd9 in del(10-11) was excluded. Not taking this
observation into account in the fit (see the text), we obtained the following
optimum model efficiencies:



Efficiencies Ei in digits

Lnp 0.035
Evx2 0.031
Hoxd13 0.347
Hoxd12 0.198
Hoxd11 0.210
Hoxd10 0.107
Hoxd9 0.033
The total number of transcripts (TTc) was derived from the following
regression line, with R2 = 0.93 (Fig. 4B):


The corresponding predicted absolute levels for each gene in the 12
configurations are given in Supplemental Table S7 and compared with observed
values (Figs. 57).



Model in genitals
The same model was used to predict absolute transcripts levels in genitals. As
discussed in the text, internal deletions were ignored when minimizing the sum
of weighted least squares. The optimum model efficiencies, the regression
equation for the total number of transcripts, and the corresponding predicted
absolute levels are given in Supplemental Table S8 and compared with observed
values (Fig. 8).



Acknowledgments


We thank J. Zakany, M. Kmita, and B. Tarchini for sharing mice, and M.
Docquier and P. Descombes, from the NCCR genomic platform, for their help and
advice. This work was supported by funds from the canton de Geneve, the
Louis-Jeantet and Claraz foundations, the Swiss National Research Fund, the
National Center for Competence in Research (NCCR) Frontiers in Genetics, and
the EU programs Cells into Organs and Crescendo to D.D.



Footnotes


Supplemental material is available at http://www.genesdev.org.


Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.1631708

Top
Abstract
Results
Discussion
Materials and methods
References
References


Blackwood, E.M., Kadonaga, J.T. Going the distance: A current view of enhancer
action. Science. 1998;281:6063. [PubMed]

Bulger, M., Groudine, M. Looping versus linking: Toward a model for
long-distance gene activation. Genes & Dev. 1999;13:24652477. [PubMed]

Chen, C.H., Cretekos, C.J., Rasweiler, J.J.T., Behringer, R.R. Hoxd13
expression in the developing limbs of the short-tailed fruit bat, Carollia
perspicillata. Evol. Dev. 2005;7:130141. [PubMed]

Cobb, J., Duboule, D. Comparative analysis of genes downstream of the Hoxd
cluster in developing digits and external genitalia. Development.
2005;132:30553067. [PubMed]

Cohn, M.J. Developmental genetics of the external genitalia. Adv. Exp. Med.
Biol. 2004;545:149157. [PubMed]

Davis, M.C., Dahn, R.D., Shubin, N.H. An autopodial-like pattern of Hox
expression in the fins of a basal actinopterygian fish. Nature.
2007;447:473476. [PubMed]

Deschamps, J., van Nes, J. Developmental regulation of the Hox genes during
axial morphogenesis in the mouse. Development. 2005;132:29312942. [PubMed]

Di-Poi, N., Zakany, J., Duboule, D. Distinct roles and regulations for
posterior and anterior Hoxd genes in metanephric kidney development. PLoS
Genet. 2007;3:e232. doi: 10.1371/journal.pgen.0030232. [PubMed]

Dolle, P., Izpisua-Belmonte, J.C., Brown, J.M., Tickle, C., Duboule, D. HOX-4
genes and the morphogenesis of mammalian genitalia. Genes & Dev.
1991;5:17671776. [PubMed]

Dolle, P., Dierich, A., LeMeur, M., Schimmang, T., Schuhbaur, B., Chambon, P.,
Duboule, D. Disruption of the Hoxd-13 gene induces localized heterochrony
leading to mice with neotenic limbs. Cell. 1993;75:431441. [PubMed]

Drossopoulou, G., Lewis, K.E., Sanz-Ezquerro, J.J., Nikbakht, N., McMahon,
A.P., Hofmann, C., Tickle, C. A model for anteroposterior patterning of the
vertebrate limb based on sequential long- and short-range Shh signalling and
Bmp signalling. Development. 2000;127:13371348. [PubMed]

Freitas, R., Zhang, G., Cohn, M.J. 2007. Biphasic Hoxd gene expression in
shark paired fins reveals an ancient origin of the distal limb domain PLoS ONE
2: :e754 [PubMed].

Fromental-Ramain, C., Warot, X., Messadecq, N., LeMeur, M., Dolle, P.,
Chambon, P. Hoxa-13 and Hoxd-13 play a crucial role in the patterning of the
limb autopod. Development. 1996;122:29973011. [PubMed]

Gonzalez, F., Duboule, D., Spitz, F. Transgenic analysis of Hoxd gene
regulation during digit development. Dev. Biol. 2007;306:847859. [PubMed]

Gould, A., Morrison, A., Sproat, G., White, R.A., Krumlauf, R. Positive
cross-regulation and enghancer sharing: Two mechanisms for specifying
overlapping Hox expression domains. Genes & Dev. 1997;11:900913. [PubMed]

Herault, Y., Rassoulzadegan, M., Cuzin, F., Duboule, D. Engineering
chromosomes in mice through targeted meiotic recombination (TAMERE). Nat.
Genet. 1998;20:381384. [PubMed]

Kmita, M., Duboule, D. Organizing axes in time and space; 25 years of colinear
tinkering. Science. 2003;301:331333. [PubMed]

Kmita, M., Fraudeau, N., Herault, Y., Duboule, D. Serial deletions and
duplications suggest a mechanism for the collinearity of Hoxd genes in limbs.
Nature. 2002a;420:145150.

Kmita, M., Tarchini, B., Duboule, D., Herault, Y. Evolutionary conserved
sequences are required for the insulation of the vertebrate Hoxd complex in
neural cells. Development. 2002b;129:55215528.

Kmita, M., Tarchini, B., Zakany, J., Logan, M., Tabin, C.J., Duboule, D. Early
developmental arrest of mammalian limbs lacking HoxA/HoxD gene function.
Nature. 2005;435:11131116. [PubMed]

Kondo, T., Zakany, J., Innis, J.W., Duboule, D. Of fingers, toes and penises.
Nature. 1997;390:29. [PubMed]

Monge, I., Kondo, T., Duboule, D. An enhancer-titration effect induces
digit-specific regulatory alleles of the HoxD cluster. Dev. Biol.
2003;256:212220. [PubMed]

Morgan, B.A., Izpisua-Belmonte, J.-C., Duboule, D., Tabin, C.J. Targeted
misexpression of Hox4.6 in the avian limb bud causes apparent homeotic
transformations. Nature. 1992;358:236239. [PubMed]

Nelson, C.E., Morgan, B.A., Burke, A.C., Laufer, E., DiMambro, E., Murtaugh,
L.C., Gonzales, E., Tessarollo, L., Parada, L.F., Tabin, C. Analysis of Hox
gene expression in the chick limb bud. Development. 1996;122:14491466. [PubMed]

Reno, P.L., McCollum, M.A., Cohn, M.J., Meindl, R.S., Hamrick, M., Lovejoy,
C.O. Patterns of correlation and covariation of anthropoid distal forelimb
segments correspond to Hoxd expression territories. J. Exp. Zool. Part B: Mol.
Dev. Evol. 2007 doi: 10.1002/jez.b.21207.

Riddle, R.D., Johnson, R.L., Laufer, E., Tabin, C. Sonic hedgehog mediates the
polarizing activity of the ZPA. Cell. 1993;75:14011416. [PubMed]

Sordino, P., van der Hoeven, F., Duboule, D. Hox gene expression in teleost
fins and the origin of vertebrate digits. Nature. 1995;375:678681. [PubMed]

Spitz, F., Gonzalez, F., Duboule, D. A global control region defines a
chromosomal regulatory landscape containing the HoxD cluster. Cell.
2003;113:405417. [PubMed]

Spitz, F., Herkenne, C., Morris, M.A., Duboule, D. Inversion-induced
disruption of the Hoxd cluster leads to the partition of regulatory
landscapes. Nat. Genet. 2005;37:889893. [PubMed]

Suzuki, K., Shiota, K., Zhang, Y., Lei, L., Yamada, G. Development of the
mouse external genitalia: Unique model of organogenesis. Adv. Exp. Med. Biol.
2004;545:159172. [PubMed]

Tarchini, B., Duboule, D. Control of Hoxd genes collinearity during early limb
development. Dev. Cell. 2006;10:93103. [PubMed]

Tarchini, B., Duboule, D., Kmita, M. Regulatory constraints in the evolution
of the tetrapod limb anteriorposterior polarity. Nature. 2006;443:985988.
[PubMed]

Tolhuis, B., Palstra, R.J., Splinter, E., Grosveld, F., de Laat, W. Looping
and interaction between hypersensitive sites in the active b-globin locus.
Mol. Cell. 2002;10:14531465. [PubMed]

Zakany, J., Duboule, D. The role of Hox genes during vertebrate limb
development. Curr. Opin. Genet. Dev. 2007;17:359366. [PubMed]

Zakany, J., Fromental-Ramain, C., Warot, X., Duboule, D. Regulation of number
and size of digits by posterior Hox genes: A dose-dependent mechanism with
potential evolutionary implications. Proc. Natl. Acad. Sci.
1997;94:1369513700. [PubMed]

Zakany, J., Kmita, M., Duboule, D. A dual role for Hox genes in limb
anteriorposterior asymmetry. Science. 2004;304:16691672. [PubMed]
==
Well, dinos & mammals are both amniotes but not
technically reptiles, since the clade Reptilia or
Sauropsida is reserved for diapsids. Its sister clade
is ours, the Synapsida, the mammal-like "reptiles" &
their mammalian descendants. However, if you regard
the anapsid ancestors of both diapsids & synapsids as
reptiles, then, yes we are also phylogenetically
"reptiles" or reptiliomorphs.

The problem with both common & scientific nomenclature
is that "reptile" can mean different things. The
evolutionary history of any lineage can be sliced up
in various ways. Cladistic taxonomy, based upon
shared, derived traits, allows great precision, but
leads to endless multiplication of categories,
compared to the Linnaean system.

By any cladistic analysis, however, birds are
reptiles, being diapsid archosaurs.

To review, the first amniotes, tetrapods capable of
reproducing away from water, & with skins that enabled
life in drier environments, had "anapsid" skulls, ie
lacking fenestrae, holes in their heads. These
creatures could be considered reptiles, in which case,
mammals are reptiles, as Dave says. But now customary
cladistic nomenclature is to reserve the technical
taxonomic term "Reptilia" (preferably Sauropsida) for
diapsids, those amniotes with two postorbital
fenestrae, opening in their skulls behind the eye to
allow for muscle attachment. The Synapsida, like us,
have a single postorbital fenestra, which in mammals
has become the opening through which our single-boned
jaw slides, guarded by our cheekbone.

I know it seems unnecessarily complicated, but
evolution produces gradients along which
categorization is somewhat arbitrary & semantic.

Dealing just with living forms, you can make a simple
cladogram. Draw a diagonal line across a sheet of
paper. Put "Crocodilians" at the upper right end (or
birds, or mammals, it doesn't matter, as long as you
get the branching right). Now a little farther back
down the main line, draw a line at an angle coming off
the base line to the left until it reaches the top of
the paper, at the same level as "Crocs". Write
"Birds" at its end. Repeat the process starting
farther down the main line, but write "Turtles"
instead (actually this position is still a bit
controversial, but genomic analysis seems to confirm
that turtles are more closely related to archosaurs
than lepidosaurs & are only secondarily anapsid).
Repeat it again & write "Lepidosaurs" (or squamates,
or lizards & snakes, & tuataras) at the end of this
branch, or show each of these groups branching off
along the side line. Now go way back down the main
line & draw a long branch at an angle up to the top &
write "Mammals" at the end of it. This is the Amniote
family tree. The tetrapod outgroup is Amphibians.

The mammal line branches off about 320 million years
ago, in the Carboniferous. Lepidosaurs (squamates &
tuataras) split from archosaurs (birds & crocs) in the
Permian, & birds diverged from crocs in the Triassic.
==
Genomic analysis shows that, while their skulls are
secondarily "anapsid", turtles aren't members of the
ancient clade Anapsida, but in fact diapsids more
closely related to Archosaurs than Lepidosaurs.
==
Leaving out a few clades, avian taxonomy goes like
this:

Birds are maniraptoran, coelurosaurian, tetanurian
theropod dinosaurs.

Birds & other dinosaurs are ornithodires.

Birds, other dinosaurs & other ornithodires (like
pterosaurs) are archosaurs.

Birds, other dinosaurs, other ornithodires & other
archosaurs (like crocs) are diapsids.

Birds, other dinosaurs, other ornithodires & other
archosaurs are diapsids (like lepidosaurs, ie lizards,
snakes & tuataras).

Birds, other dinosaurs, other ornithodires, other
archosaurs & other diapsids are members of the clade
Reptilia (also called Sauropsida), so all the above
taxa are equally reptilian in phylogeny.

The sister clade of Sauropsida within clade Amniota is
Synapsida, to which mammals such as ourselves & other
apes, other primates, other placentals, etc. belong.
==
Fossil reveals oldest live birth
A fossil fish uncovered in Australia is the oldest-known example of a mother
giving birth to live young, scientists have reported in the journal Nature.
The 380 million-year-old specimen has been preserved with an embryo still
attached by its umbilical cord.
The find, reported in Nature, pushes back the emergence of this reproductive
strategy by some 200 million years.
Until now, scientists thought creatures from these times were only able to
develop their young inside eggs.

When I looked at it, my jaw dropped. I said we are onto something big here

Before this find, the earliest evidence for this form of reproduction came
from reptile fossils dating to the Mesozoic Era (248 to 65 million years ago)
The team said the latest discovery had a remarkably advanced reproductive
biology, similar to modern sharks and rays.
The extremely well-preserved fossil represents a new species of "placoderm"
fish.
The placoderms were an incredibly diverse group and are thought to be the most
primitive known vertebrates with jaws.
These armoured fish dominated seas, rivers and lakes throughout the Devonian
Period (420-360 million years ago).
This latest placoderm specimen, which measures about 25cm (10in) in length,
was found in the Gogo area of Western Australia in 2005 by a team led by John
Long from Museum Victoria.

The fossil was found in Western Australia

Close examination revealed that the team had unearthed something unusual.
Professor Lane said: "When I looked at it, my jaw dropped. I said: 'we are
onto something big here'."
The team found an embryo and an umbilical cord, which had been exquisitely
preserved along with the female fish.
The scientists have named it Materpiscis attenboroughi, in honour of the
naturalist Sir David Attenborough, who first drew attention to the Gogo fish
fossil sites in the 1970s.
Sir David told the team that he was "very very flattered" to have had his name
given to such an "astonishing creature".
The discovery prompted the researchers to return to another fossil that they
had unearthed in 1986.
Close investigation revealed that this too contained evidence of live births -
it contained three embryos
Professor Lane said: "After we saw this, we realised we had totally nailed it,
everyone was convinced that this creature bore live young."
Until the latest fossil find, scientists thought life forms that existed
during these times had only evolved to reproduce using externally fertilised
eggs - a primitive version of the way fish spawn today.
Now, however, the team believes this ancient species bore live young through
internal fertilisation (viviparity).
Dr Long commented: "This is not only the first time ever that a fossil embryo
has been found with an umbilical cord, but it is also the oldest known example
of any creature giving birth to live young.
"The existence of the embryo and umbilical cord within the specimen provides
scientists with the first ever example of internal fertilisation - or sex -
confirming that some placoderms had remarkably advanced reproductive biology.
He added: "This is a world first fossil find, and it opens up a window into
the developmental biology of an entire extinct class of organisms."
Commenting on the paper, Zerina Johanson, a palaeontologist at London's
Natural History Museum, said: "It is extremely rare to find preservation like
this in the fossil record. This new discovery extends the record of viviparity
back almost 200 million years in the fossil record.
"Placoderms represent the most primitive group of jawed vertebrates, so this
work shows that the capacity for internal fertilisation and giving birth to
live young evolved very early during vertebrate history."
==
DNA rigins
Virtually the only gap that remains to be filled in is the matter of how DNA
arose in a prebiotic environment, and most of the answers are already in
place. Some example scientific papers covering the groundwork include:

A possible prebiotic synthesis of purine, adenine, cytosine, and
4(3H)-pyrimidinone from formamide implications for the origin of life by
Raffaelle Saladino, Claudia Crestini, Giovanna Costanzo, Rodolfo Negri and
Ernesto di Mauro, Bioorganic & Medicinal Chemistry, 9(5): 1249-1253 (May 2001)

A Self-Replicating Ligase Ribozyme by Natasha Paul & Gerald F. Joyce, Proc.
Natl. Acad. Sci. USA., 99(20): 12733-12740, 1st October 2002

A Self Replicating System by T. Tjiviuka, P.Ballester and J. Rebek jr.,
Journal of the American Chemical Society, 112: 1249-1250 (1990)

Carbonyl Sulphide Mediated Prebiotic Formation of Peptides by Luke Leman,
Leslie Orgel and M. Reza Ghadiri, Science, Vol 306, pp 283-286, 8 October 2004

Chemistry for the Synthesis of Nucleobase-Modified Peptide Nucleic Acid by R.
H. E. Hudson, R. D. Viirre, Y. H. Liu, F.Wojciechowski, and A. K. Dambenieks,
Pure Appl. Chem., 76: 1591-1598 (2004)

Nucelotide Synthetase Ribozymes May Have Emerged First In The RNA World by
Wentao Ma, Chunwu Yu, Wentao Zhang and Jiming Hu, The RNA Journal, 13:
2012-2019, 18th September 2007

Peptide Nucleic Acids Rather Than RNA May Have Been The First Genetic Molecule
by Kevin E. Nelson, Matthew Levy and Stanley L. Miller, Proc. Natl. Acad. Sci.
USA., 97: 3868-3871, 2000

Prebiotic Amino Acids As Asymmetric Catalysts by Sandra Pizzarello and Arthur
L. Weber, Science, 303: 1151, 20 February 2004

Racemic Amino Acids from the Ultraviolet Photolysis of Interstellar Ice
Analogues by Max P. Bernstein, Jason P. Dworkin, Scott A. Sandford, George W.
Cooper and Louis. J. Allamandola, Nature, Vol 416, pp 401-403, 28 March 2002

Ribozymes: Building The RNA World by Gerald F. Joyce, Current Biology, 6(8):
965-967, 1996

RNA-Catalysed RNA Polymerisation: Accurate And General RNA-Templated Primer
Extension by Wendy K. Johnston, Peter J. Unrau, Michael S. Lawrence, Margaret
E. Glasner and David P. Bartel, Science 292: 1319-1325 (18 May 2001)

RNA-Directed Amino Acid Homochirality by J. Martyn Bailey, J. Fed. Amer. Socs.
Exp. Biol., 12(6): 503-507

Self Replicating Systems by Volker Patzke and Gunter von Kiedrowski, ARKIVOC
5: 293-310, 2007

Self-Replication of Complementary Nucleotide-Based Oligomers by D. Sievers and
G. von Kiedrowski, Nature, 369: 221-224 (1994)

The Antiquity Of RNA-Based Evolution by Gerald F. Joyce, Nature, 418: 214-221,
11th July 2002
==
Speciation events observed in the laboratory, along with insights into
mechanisms for the origins of multicellularity:

Drosophila paulistorum: A Cluster of Species in Statu Nascendi by Theodosius
Dobzhansky & Boris Spassky, Proc. Natl. Acad. Sci. USA., 45(3): 419-428 (1959)

Evidence for rapid speciation following a founder event in the laboratory by
J.R. Weinberg V. R. Starczak and P. Jora, Evolution vol 46, pp 1214-1220, 1992

Experimentally Created Incipient Species of Drosophila by Theodosius
Dobzhansky & Olga Pavlovsky, Nature 230, pp 289 - 292 (02 April 1971)

Founder-flush speciation in Drosophila pseudoobscura: a large scale experiment
by A. Galiana, A. Moya and F. J. Alaya, Evolution vol 47, pp 432-444, 1993
(Speciation event in Drosophila melanogaster)

Phagotrophy by a flagellate selects for colonial prey: A possible origin of
multicellularity byM.E. Boraas, D.B. Seale and J.E. Boxhorn, Evolutionary
Ecology Vol. 12, no. 2, pp. 153-164. Feb 1998

The phagotrophic origin of eukaryotes and phylogenetic classification of
Protozoa by Tom Cavalier-Smith, International Journal of Systematic and
Evolutionary Microbiology vol 52, pp 297-354, 2002

Evolution of novel cooperative swarming in the bacterium Myxococcus xanthus by
Gregory J. Velicer and Yuen-tsu N. Yu, Nature vol 425, pp 75-78, 2003.

[2] Speciation events in the wild, including supporting evidence from
molecular phylogeny (and this is just in Cichlid fishes, by the way):

Adaptive Evolution And Explosive Speciation: The Cichlid Fish Model by Thomas
D. Kocher, Nature Reviews: Genetics, 5: 288-298 (April 2004)

Cichlid Species Flocks of the Past and Present by A. Meyer, Heredity vol 95,
419-420, 20 July 2005

Fractious Phylogenies by Thomas D Kocher, Nature, Vol 423, pp 489-490, 29 May
2003

Hybridisation and Contemporary Evolution in an introduced Cichlid Fish from
Lake Malawi National Park by J. Todd Streelman, S.L. Gymrek, M.R. Kidd, C.
Kidd, R.L. Robinson, E. Hert, A.J. Ambali and T.D. Kocher, Molecular Ecology,
vol 13, pp 2471-2479, 21 April 2004

Major Histocompatibility Complex Variation In Two Species Of Cichlid Fishes
From Lake Malawi by Hideki Ono, Colm O'hUigin, Herbert Tichy and Jan Klein,
Molecular and Evolutionary Biology, 10(5): 1060-1072 (1993)

Mitochondrial Phylogeny of the Endemic Mouthbrooding Lineages of Cichlid
Fishes from Lake Tanganyika in Eastern Africa by Christian Sturmbauer and Axel
Meyer, Journal of Molecular and Biological Evolution, Vol 10, No. 4, pp
751-768, 1993

Multilocus Phylogeny of Cichlid Fishes (Pisces: Perciformes) : Evolutionary
Comparison of Microsatellite and Single-Copy Nuclear Loci by J. Todd
Streelman, Rafael Zardoya, Axel Meyer and Stephen A Karl, Journal of Molecular
and Biological Evolution, Vol 15, No 7, pp 798-808, 1998

Origin of the Superflock of Cichlid Fishes from Lake Victoria, East Africa by
Erik Verheyen, Walter Salzburger, Jos Snoeks and Axel Meyer, Science, vol 300,
pp 325-329, 11 April 2003

Phylogeny of African Cichlid Fishes as Revealed By Molecular Markers by Werner
E. Mayer, Herbert Tichy and Jan Klein., Heredity, vol 80, pp 702-714, 1998

The Species Flocks of East African Cichlid Fishes: Recent Advances in
Molecular Phylogenetics and Population Genetics by Walter Salzburger and Axel
Mayer, Naturwissenschaft, vol 91, pp 277-290, 20 April 2004

Plus, the following paper contains an experimental test of selection
mechanisms applicable to the above:

Genetics of Natural Populations XII. Experimental Reproduction of Some of the
Changes Caused by Natural Selection by Sewall Wright & Theodosius Dobzkansky,
Genetics, 31(2): 125-156 (1946)
==
Evolution of a new functional gene observed: Apo-AI- Milano is a naturally
occurring genetic mutation that reduces the effects of cholesterol. It was
first observed in a single Italian family, and is currently spreading through
the Italian population. It is so effective drug companies are producing it
artificially as a cholesterol fighting agent.
http://en.wikipedia.org/wiki/Apolipoprotein_A1

Speciation examples: genetic studies show the Cichlid family of fishes has
diverged into dozens of new species in the last few thousand years in the
changing environments of Lake Victoria.
http://en.wikipedia.org/wiki/Cichlid_fish

abiogenesis  http://www.rockefeller.edu/evolution/
==
http://www.talkdesign.org/faqs/flagellum.html

http://www.millerandlevine.com/km/evol/design2/article.html

http://www.pandasthumb.org/archives/2007/07/current_biology.html

From The Origin Of Species To The Origin Of Bacterial Flagella by
Mark J. Pallen and Nick Matzke, Nature Reviews Microbiology, published
online 2006

Incidentally, Matzke published a paper in 2003, in which he predicted that
numerous homologies would be found between the proteins in the bacterial
flagellum and the Type 3 Secretory System, and lo and behold, those homologies
were later found to exist by other scientists working in the field. Score one
for an "imploding" branch of science there methinks.

Another paper on the subject is:

Stepwise Formation Of The Bacterial Flagellar System by Renyi Liu and Howard
Ochman, Proceedings of the National Academy of Sciences of the USA, 104(17):
7116-7121, 24th April 2007
==
Evolution is not something that happens overnight. It would take
generations for even minor changes to become apparent. It would take tens of
thousands of years for any significant changes and much longer for new species
to form. But there is evidence of evolution happening all around us today.
There are 8 different species of bears and many more sub species. There are
over 20,000 species of spiders. These are just 2 examples but nearly every
animal has many different varieties that have evolved differently. Recent
(remember recent in evolution terms is tens of thousands of years) evolution
is also easily seen in humans. Different skin color, facial features and body
structure that came about when pockets of the human population where isolated
for many generations. 
Darwin died in 1889. There has been a lot of research done
since then. I suggest that you dont use a single book written over 150 years
ago as your only source. But to address your comments, for the purpose of this
conversation it really doesnt matter where the original cell of life came from.
Intelligent design totally discredits the claim that species have evolved into
new species (although they do agree that minor changes have occurred). The
facts are that the oldest fossils are of very simple organisms. As time passed
the fossils became much more complex. NO fossils have been found for animals
that exist today. That in itself would lead us to believe that either species
evolved into new species or that new species have magically appeared over time. 
===
Note that phylogenetically, birds are members of
Reptilia.

http://www.pubmedce ntral.nih. gov/articlerende r.fcgi?artid= 1815256

Abstract

We report results of a megabase-scale phylogenomic
analysis of the Reptilia, the sister group of mammals.
Large-scale end-sequence scanning of genomic clones of
a turtle, alligator, and lizard reveals diverse,
mammal-like landscapes of retroelements and simple
sequence repeats (SSRs) not found in the chicken.
Several global genomic traits, including distinctive
phylogenetic lineages of CR1-like long interspersed
elements (LINEs) and a paucity of A-T rich SSRs,
characterize turtles and archosaur genomes, whereas
higher frequencies of tandem repeats and a lower
global GC content reveal mammal-like features in
Anolis. Nonavian reptile genomes also possess a high
frequency of diverse and novel 50-bp unit tandem
duplications not found in chicken or mammals. The
frequency distributions of &#8776;65,000 8-mer
oligonucleotides suggest that rates of DNA-word
frequency change are an order of magnitude slower in
reptiles than in mammals. These results suggest a
diverse array of interspersed and SSRs in the common
ancestor of amniotes and a genomic conservatism and
gradual loss of retroelements in reptiles that
culminated in the minimalist chicken genome.

Program

Comparative genomics is a central focus of modern
biology in part because it facilitates the
understanding of principles of genome evolution (13).
However, it is impractical to expect taxonomically
broad comparative studies to proceed rapidly for
nonmodel organisms on a whole-genome basis. A prime
example of our limited understanding from the present
handful of complete genomes is that we still do not
know the sequence of genomic events that led to the
structural diversity seen in mammalian genomes and
those of their sister group, the Reptilia, which
includes birds (4). The draft chicken genome (5)
substantially increases our understanding of amniote
comparative genomics, but evolutionary interpretation
relying solely on chickenmammal contrasts will remain
difficult without new data for phylogenetically
intermediate lineages. On the one hand, the common
amniote ancestor may have had a small genome as in
extant birds, with mammals and nonavian reptiles
independently acquiring transposable elements that
resulted in genome size increases in these two
lineages. On the other hand, the common amniote
ancestor may have had a large, repeat-rich genome as
in extant mammals, with multiple sequential reductions
in retroelement abundance occurring in the lineages
leading to the smaller genomes of nonavian reptiles
and birds (6). A third scenario might include a
combination of both independent gains and reductions
of specific genomic elements. Here we use a BAC- and
plasmid-end sequencing approach in exemplars of three
major nonavian reptile lineages, American Alligator
(Alligator mississippiensis) , Painted Turtle
(Chrysemys picta), and the Bahamian Green Anole
(Anolis smaragdinus) , to better characterize the
sequence of genomic changes underlying the
diversification of amniote genomes.
Little is known about the large-scale structure of
nonavian reptile genomes at the sequence level.
Alligator and turtle genome sizes are &#8776;30%
smaller than human, &#8776;50% larger than chicken,
and only &#8776;12% larger than Anolis, whose genome
size is close to the mean for nonavian reptiles.
Unlike alligator genomes, the anole, painted turtle,
and chicken contain a significant number of
microchromosomes (7), which we expect would be gene
rich as reported for chickens (8) and the soft-shelled
turtle (9). In general, it is unknown how the
macrochromosomes of reptiles differ from those of
mammals (10) and those of the nonavian reptiles
investigated here. The turtle and alligator species
investigated here have environmental as opposed to
genetic sex determination, and sex determination in
Anolis is inferred to be genetic based on some
karyological evidence (11). Several retroelement
lineages have been characterized in turtles and other
reptiles (1215). Projects in progress will produce
genome sequences for another bird, the Zebra Finch,
Taeniopygia guttata, and a lizard, Anolis
carolinensis. In the meantime, our goal in this
project was to quickly amass a moderate database of
primary sequence distributed throughout the genomes of
genomically understudied lineages, which can reveal
numerous genomewide trends that help characterize the
most fundamental aspects of genome structure. Although
the genomes we have investigated may not reflect
specific changes in subclades of diverse groups such
as squamates, any shortcomings of our limited
taxonomic sampling are overcome by our ability to
present a broad-brush window on genomic trends for
nonavian reptiles, thereby quickly placing the chicken
and mammal genomes in broader context.

(Snip Results & Discussion)

Conclusion

In summary, our analysis suggests that the ancestral
amniote genome featured a relatively low global GC
content as in mammals and a rich repetitive landscape
dominated by CR1 and MIR retroelements and an
abundance of AT-rich SSRs. Our finding of diverse CR1
lineages in nonavian reptiles qualifies a model in
which a chicken-like streamlined ancestral amniote
genome underwent expansion in mammals and nonavian
reptiles independently (6). Rather it implies a
complex scenario in which the diversity of CR1
elements in the ancestral amniote underwent a
wholesale replacement by L1 and related mobile
elements in mammals, and in which multiple sequential
reductions in diversity occurred in the lineages
leading to nonavian reptiles and birds. We expect that
further genomic scans in additional reptile species,
as well as further whole-genome sequencing projects,
will considerably refine the major features in reptile
genome evolution that we have outlined here.
==
http://palaeo.gly.bris.ac.uk/communication/boulton/evolution.html   dinos
==
A great deal is know about these immediate ancestors
to the dinosaurs.

http://en.wikipedia .org/wiki/ Archosaur

Clade Archosauria: Permian or Triassic to Present
(Birds & Crocodilians)

Archosaurs (Greek for 'ruling lizards') are a group of
diapsid reptiles represented by modern birds and
crocodilians. This group also includes extinct
non-avian dinosaurs, pterosaurs and relatives of
crocodiles.

There is some debate about when archosaurs first
appeared. Those who classify the Permian reptiles
Archosaurus rossicus and/or Protorosaurus speneri as
true archosaurs maintain that archosaurs first
appeared in the late Permian. Those who classify both
Archosaurus rossicus and Protorosaurus speneri as
archosauriformes (not true archosaurs but very closely
related) maintain that archosaurs first evolved from
Archosauriform ancestors during the Olenekian (early
Triassic Period).

The simplest and most widely-agreed synapomorphies of
archosaurs are:

* Teeth set in sockets, which makes them less
likely to be torn loose during feeding. This feature
is responsible for the name "thecodonts" ("socket
teeth"), which paleontologists used to apply to all or
most archosaurs.
* Antorbital fenestrae (openings in the skull in
front of the eyes but behind the nostrils), which
reduced the weight of the skull, a useful feature
since most early archosaurs had long, heavy skulls,
rather like those of modern crocodilians. The
preorbital fenestrae (sometimes called anteorbital
fenestrae) are often larger than the orbits (eye
sockets).
* Mandibular fenestrae (small openings in the jaw
bones), which may have reduced the weight of the jaw
slightly.
* A fourth trochanter (ridge for attaching
muscles) on the femur. This seemingly insignificant
detail may have made the evolution of dinosaurs
possible (all early dinosaurs and many later ones were
bipeds), and may also be connected with the ability of
the archosaurs or their immediate ancestors to survive
the catastrophic Permian-Triassic extinction event.

Archosaur takeover in the Triassic

The Synapsida (informally known as "mammal-like
reptiles") were the dominant land vertebrates
throughout the Permian, but most perished in the
Permian-Triassic extinction event. Lystrosaurus (a
herbivorous mammal-like reptile) was the only large
land animal to survive the event, becoming the most
populous land animal on the planet for a time.[1]

But archosaurs quickly became the dominant land
vertebrates in the early Triassic. The two most
commonly-suggested explanations[ citation needed] for
this are:

* Archosaurs made quicker progress than
mammal-like reptiles towards erect limbs, and this
gave them greater stamina by avoiding Carrier's
constraint. This is unconvincing since Archosaurs
became dominant while they still had sprawling or
semi-erect limbs, similar to those of Lystrosaurus and
other mammal-like reptiles.
* The early Triassic was predominantly arid,
because most of the earth's land was concentrated in
the supercontinent Pangaea. Archosaurs were probably
better at conserving water than mammal-like reptiles
because:

* Modern diapsids (lizards, snakes,
crocodilians, birds) excrete uric acid, which can be
excreted as a paste. It is reasonable to suppose that
archosaurs (diapsids and ancestors of crocodilians,
dinosaurs and birds) also excreted uric acid, and
therefore were good at conserving water. The
aglandular (glandless) skins of diapsids would also
have helped to conserve water.
* Modern mammals excrete urea, which requires
a lot of water to keep it dissolved. Their skins also
contain many glands, which also lose water. Assuming
that mammal-like reptiles had similar features, e.g.
as argued in Palaeos [1], they were at a disadvantage
in a mainly arid world. The same well-respected site
points out that "for much of Australia's
Plio-Pleistocene history, where conditions were
probably similar, the largest terrestrial predators
were not mammals but gigantic varanid lizards
(Megalania) and land crocs."

Main types of archosaurs (link has graphics of
anatomical differences)

Since the 1970s scientists have classified archosaurs
mainly on the basis of their ankles.[2] The earliest
archosaurs had "primitive mesotarsal" ankles: the
astragalus and calcaneum were fixed to the tibia and
fibula by sutures and the joint bent about the contact
between these bones and the foot.

The Crurotarsi appeared early in the Triassic. In
their ankles the astragalus was joined to the tibia by
a suture and the joint rotated round a peg on the
astragalus which fitted into a socket in the
calcaneum. Early "crurotarsans" still walked with
sprawling limbs, but some later "crurotarsans"
developed fully erect limbs (most notably the
Rauisuchia). And modern crocodilians are
"crurotarsans" which can walk with their limbs
sprawling or erect depending on how much of a hurry
they are in.

Euparkeria and the Ornithosuchidae had "reversed
crurotarsal" ankles, with a peg on the calcaneum and
socket on the astragalus.

The earliest fossils of Ornithodira ("bird necks")
appear in the Carnian age of the late Triassic, but it
is hard to see how they could have evolved from the
"crurotarsans" - possibly they actually evolved much
earlier, or perhaps they evolved from the last of the
"primitive mesotarsal" archosaurs. Ornithodires'
"advanced mesotarsal" ankle had a very large
astragalus and very small calcaneum, and could only
move in one plane, like a simple hinge. This
arrangement was only suitable for animals with erect
limbs, but provided more stability when the animals
were running. The ornothodires differed from other
archosaurs in other ways: they were lightly-built and
usually small, their necks were long and had an
S-shaped curve, their skulls were much more lightly
built, and many ornothodires were completely bipedal.
The archosaurian fourth trochanter on the femur may
have made it easier for ornothodires to become bipeds,
because it provided more leverage for the thigh
muscles. In the late Triassic the ornithodires
diversified to produce pterosaurs and dinosaurs.[3]

Phylogeny

(Diagram doesn't fit, but not that each of the two
main archosaur groups has living representatives; the
Crurotarsi have crocs & Ornithodira have birds, as the
name implies.)

`--Archosauria [Crown group Archosauria =
Avesuchia]
|--Crurotarsi
| |-?Ctenosauriscidae
| `--Crocodylotarsi
| |--Ornithosuchidae
| `--+--Phytosauria
| `--Suchia
| |--Prestosuchidae
| `--Rauisuchiformes
| |--Aetosauria
| `--Rauisuchia
|
|--Rauisuchidae
|
`--+--Paracrocodylo morpha
|
`--Crocodylomorpha (crocodiles and relatives)
`--Ornithodira
|--Pterosauromorpha
| |--Scleromochlus
| `--Pterosauria
`--Dinosauromorpha
`--Dinosauriformes
`--Dinosauria
|--Ornithischia
`--Saurischia
`--Aves (birds)
==
The modern taxonomic system of cladistics is based on
relatedness between groups of living things, relying
on shared characteristics derived from common
ancestors. It recognizes stem vs. more derived crown
groups, as well as out groups & sister taxons.

Here's a simplified cladistic summary of tyrannosaur
evolution, presented in narrative form, since detailed
cladograms can't be reproduced here, except as links.

Each node in a cladogram marks derived characteristics
distinguishing all the included groups sharing those
traits.

The outgroup to the archosaurs are all those diapsid
reptiles living & extinct more closely related to
lepidosaurs (snakes, lizards & tuataras) & (probably)
turtles than to crocs & birds. Their sister group is
either lepidosaurs or turtles. This node remains
controversial, with morphological & genetic evidence
inconclusive. (To simplify & shorten, I've left out
the extinct marine diapsids like ichthyosaurs,
plesiosaurs & mosasaurs.)

Crocs & their relatives form the sister taxon to the
group dinosaurs (including birds) & pterosaurs, which
are the sister taxon to the two orders of dinosaurs
(saurischians & ornithischians) .

The sister taxon to the saurischians (including birds)
is of course the ornithischians. The sister taxon to
the theropods (including birds) is the sauropods.

Among theropod dinosaurs, the sister taxon to the Late
Triassic Coelophysidae are less derived groups of
early meat-eaters. It now appears that this family
may be ancestral to all later theropods, in sister
groups Ceratosauria (Early Jurassic) & more derived
Tetanurae.

Among Tetanurae, the sister group to Avetheropoda, the
line leading to birds & tyrannosaurs, is now
considered the Megalosauroidea (which includes the
first dinosaur ever recorded, although no one knew in
1676 what the fossil was), alternately called
Spinosauroidea or Torvosauroidea.

Avetheropoda divided into the Carnosauria (including
Jurassic American predator Allosaurus), & the
Coelurosauria, a very large & diverse dinosaur group
that was especially common during the Cretaceous.

From Wiki:

"Thus, during the late Jurassic, there were no fewer
than four distinct lineages of theropods -
ceratosaurs, megalosaurs, carnosaurs, and coelurosaurs
- preying on the abundance of small and large
herbivorous dinosaurs. All four groups survived into
the Cretaceous, although only two - the abelisaurs and
the coelurosaurs - seem to have made it to end of the
period, where they were geographically separate, the
abelisaurs in Gondwana, and the coelurosaurs in
Asiamerica.

"Of all the theropod groups, the coelurosaurs were by
far the most diverse. Some coelurosaur clades that
flourished during the Cretaceous were the
tyrannosaurids (including Tyrannosaurus) the
dromaeosaurids (including Velociraptor and
Deinonychus, which are remarkably similar in form to
the oldest known bird, Archaeopteryx) , the bird-like
troodontids and oviraptorosaurs, the ornithomimosaurs
(or "ostrich dinosaurs"), the strange giant-clawed
herbivorous Therizinosauridae, and the birds, which
are the only dinosaur lineage to survive the end
Cretaceous mass-extinction.

"While the roots of these various groups must have
been in the Late or possibly even the Middle Jurassic,
they only became abundant during the Early Cretaceous.
A few paleontologists, such as Gregory S. Paul, have
suggested that some or all of these advanced theropods
were actually descended from flying dinosaurs or
proto-birds like Archaeopteryx that lost the ability
to fly and returned to a terrestrial habitat.

"Coelurosauria is a diverse group of theropod
dinosaurs that includes tyrannosaurs,
ornithomimosaurs, and maniraptors; Maniraptora
includes birds, the only coelurosaurs alive today. All
feathered dinosaurs discovered so far have been
coelurosaurs; in fact, some scientists believe that
most members of coelurosauria bore some kind of
feathers.

"Most coelurosaurs were bipedal predators. The group
includes some of the largest (Tyrannosaurus) and
smallest (Microraptor, Parvicursor) carnivorous
dinosaurs ever discovered. Characteristics that
distinguish coelurosaurs include:

* a sacrum (series of vertebrae that attach to the
hips) longer than in other dinosaurs
* a tail stiffened towards the tip
* a bowed ulna (lower arm bone).
* a tibia (lower leg bone) that is longer than the
femur (upper leg bone)"

Whatever the case may be, predecessor fossils abound
in the bird & tyrannosaur lineage.

Among Coelurosauria, the sister group to the more
birdy groups is probably the Compsognathidae, although
it may be the stem group or included within
Maniraptora.

http://en.wikipedia .org/wiki/ Compsognathidae

Tyrannosauria is the sister taxon to the group
containing Maniraptora (including birds) & the
Ornithomimosauria, members of which bear a superficial
resemblance to modern ostriches. Obviously, in this
case the sister taxon to Maniraptora (including birds)
is the Ornithomimosauria.

"Maniraptora ("hand snatchers") is a clade of
coelurosaurian dinosaurs which includes the birds and
the dinosaurs that were more closely related to them
than to Ornithomimus velox. It contains the major
subgroups Aves, Deinonychosauria, Oviraptorosauria and
Therizinosauria. Ornitholestes and the Alvarezsauridae
are also often included. Together with the next
closest sister group, the Ornithomimosauria,
Maniraptora comprises the more inclusive clade
Maniraptoriformes. Maniraptors first appear in the
fossil record during the Jurassic Period (see
Eshanosaurus) , and survive today as over 9,000 species
of living birds."

So, the tyrannosaurs would be cousins to the birds,
rather than their sisters. Looking at T. rex as a
big, flightless, carnivorous "bird" gives Thanksgiving
some new meaning!
==
In fact, his formal education was identical to
Newton's, but creationists don't disparage Sir Isaac
based upon his not having earned a PhD in a scientific
discipline. They might if they knew he were a secret
Unitarian.

Newton (BA, 1660) & Darwin (BA, 1830) were both
awarded Bachelor of Arts Degrees from Cambridge, later
upgraded to Master's, as was & is the practice at
Oxford & Cambridge. Newton earned no honors or
distinction, while Darwin finished fairly high overall
in his year. Due to decades of Puritanism, Cambridge
was in a slough of despond when Newton was up. The
education that Darwin received was superior, thanks in
large part to the influence of Newton's achievements
on the university's curriculum.

Darwin also benefited from his earlier medical studies
at Edinburgh. He learned a lot in Edinburgh,
including taxidermy from a black man, which stood him
in good stead later, & some marine biology, but was
ethically opposed to surgery without anesthesia. 
While there & later at Cambridge, he was dedicated to
sporting & nature study, already making scientific
contributions as an undergraduate.

He transferred to Cambridge, but concentrated as much
as possible on subjects that interested him rather
than requirements, taking advantage of all the
university offered. Through pursuits & interests like
collecting beetles, he became a protege of Prof.
Henslow.

Eventually, he graduated with honors, but with highest
marks in "natural theology", derived from the work of
Paley. His friendship & studies with Henslow were
comparable to a modern day college internship. 

After acing his exams, Darwin stayed on studying
geology, for the contemporary equivalent of a master's
degree. He spent a summer tramping Wales with the
Rev. Prof. Sedgwick, namer of the Cambrian Period &
arguably the greatest geologist of the time (certainly
one of the top two or three). Darwin worked in hard
core geology, where he demonstrated great ability, as
evinced in his early publications. 

Cambridge did not offer degrees in specialties; one
graduated in general studies oriented toward the
clergy but in the Anglican Church then, that included
lots of math & science. Darwin was as academically
qualified as anyone else in geology, or any of the
sciences. Doctorates were granted in only a few
professional specialities, unlike the extensive
specialization of today. 

His studies at Cambridge, while designed by the
university to prepare Anglican clergymen, enabled
Darwin to learn what he wanted to about nature, just
as had his ostensibly medical education. As part of
his required curriculum, he studied & enjoyed Paley¹s
"Natural Theology", but of course, it was essentially
a natural science text, or intended to be, when
published in 1802.

There were no undergrad degrees, let alone doctorates,
in scientific subjects in the 15th, 16th, 17th, 18th
or most of the 19th centuries, so Copernicus, Galileo,
Kepler & all the other giants upon whose shoulders
Newton stood should be equally disparaged by lying
creationist goons.

Both Newton & Darwin were both Fellows of the Royal
Society.

Darwin would be remembered today as the outstanding
naturalist of the 19th century even if he hadn't
discovered natural selection. "Naturalist" shouldn't
be considered derogatory, as of course lying
creationist swine try to suggest. It was the common
19th century term for a natural philosopher, ie
scientist, specializing in geology & biology rather
than chemistry, physics or astronomy. 

Many early modern scientific figures were of course
naturalists as well as chemists, physicist &
astronomers. Lavoisier comes to mind. While
primarily remembered today as a pioneering chemist, he
also made important contributions to geology & other
sciences.

As mentioned, putting his career into a 20th or 21st
century framework, his geological field studies with
Prof. Sedgwick in Wales in the summer after graduating
from Cambridge would have merited an MS degree at the
very least, & his biological studies with Henslow
deserved another MS. His first monograph, on the
creation of coral atolls, based upon his Beagle
experience, would easily qualify for a tenure-worthy
PhD. But at that point he was just getting started. 

One difference between Darwin & Newton is that Sir
Isaac remained single & stayed in academia, while
Darwin married his cousin & raised a large family. As
Wedgwoods, they didn't need an academic sinecure to
make ends meet. As a country gentleman, Darwin was
free to conduct research, experiment, collect & write,
which he did prodigiously.

Darwin is the greatest single contributor in history
to the science collections at the British Museum. 
Even before he returned from his five year voyage
around the world on HMS Beagle, he was nominated for
membership in the most prestigious science societies,
which marked professional scientists of his day, years
earlier than most contemporaries, on the basis of his
remarkable work.

But Darwin¹s science recognition came from his voyage.
As noted, he made contributions to the collections at
the British Museum, astounding quantity & scope. His
specimens are still type specimens in ornithology,
mammals, botany & geology. 

This exceptional range of work got him nominated to
the Royal Society, which was then perhaps analogous to
the National Academy of Sciences here. His election
at such an early age is indication of his outstanding
scientific qualifications. 

Nor is it impossible even today for scientists without
PhDs to earn recognition for pioneering work, as Jane
Goodall demonstrates. Most of her great contributions
to ethology & primatology were made well before she
belatedly undertook a formal advanced graduate degree
program.

To quote from a 2007 science blogger: 

"In research, academic qualifications tend to fall by
the way. The question is whether you can devise
original ways to test important questions. People who
can do that tend to get promoted quickly ‹ like
Stanley Miller at the University of Chicago in 1953;
or like (paleontologist) Paul Serrano at Chicago
today...To make it in science, one needs a good,
testable hypothesis.. .

"Among other things, the serious papers propose tests
of the hypothesis that can be done, and they don¹t
claim that a conspiracy keeps the ideas from getting
out ‹ instead explaining how it is that the best
scientists can continue to use as theory an idea that
may be wrong, usually in the form of ³here¹s how we
look at this problem today under the prevailing
theory, and here¹s how this new idea provides better
or more clear observations.² Darwin¹s papers did that,
in coral atoll formation, in evolution theory as a
whole, in climbing plants, in insectivorous plants, in
human evolution, and in the importance of worms.

"Darwin¹s legacy should be much more than just the
theory of evolution. Darwin revolutionized all of
science with his observation methods. He avoided
conjecture about what might happen whenever simple
observation could be devised to provide real data. So,
for example, rather that resort to the philosopher¹s
ramblings on why ivy twines, he spent weeks in his lab
actually watching climbing vines grow, discovering the
methods of their twining. It¹s a stunningly simple
monograph (it¹s available on the web), but no one had
thought, or bothered, to do that before. Darwin¹s work
is still the standard in climbing vines, he covered it
so thoroughly and well."

I'd add his work on barnacles, still the standard, &
on orchids, to mention but a few of his astonishingly
varied contributions to life science. Wallace sent
Darwin his paper on natural selection because of
Darwin's reputation, after all, without knowing of
Darwin's own thoughts on the theory.
Darwin's election to prestigious, elite science
societies based upon even his early work shows
creationist lies about his credentials to be idiotic &
bearing false witness. There is no sin they aren't
willing to commit for their false cult. 
When you win the awards for having done
great work in science, you're a scientist.
In any case, the modern evolutionary synthesis doesn't
depend upon Darwin's work of 150 years ago.
==
Books by Charles Darwin
http://darwin- online.org. uk/contents. html#books

Some examples:

The Structure and Distribution of Coral Reefs [1842]

A monograph on the fossil Lepadidae, or, pedunculated cirripedes of
Great Britain [1851]

A monograph on the fossil Balanidae and Verrucidae of Great Britain [1852]

On the various contrivances by which British and foreign orchids are
fertilised by insects [1862]

On the movements and habits of climbing plants [1864]

Insectivorous plants [1875]

The different forms of flowers on plants of the same species [1877]

The power of movement in plants [1880]

The formation of vegetable mould, through the action of worms [1881]

Articles by Charles Darwin
http://darwin- online.org. uk/contents. html#periodicals
==
The Origins of Life: From the Birth of Life to the Origin of Language by
John Maynard Smith and Eors Szathmary (Paperback -
==
Dinosauria is presently
regarded as a Superorder containing the Orders
Saurischia & Ornithischia. The latter includes
families with "things on their backs", like
Stegosaurus & armored dinos; "things on their heads",
like Triceratops, & the "duck-billed" hadrosaurs.

T. rex' phylogeny:

Division: Archosauria
Subsection: Ornithodira
Superorder: Dinosauria
Order: Saurischia ("lizard hips"; outgroup
Ornithischia)
Taxon: Eusaurischia
Suborder: Theropoda ("beast foot"; outgroup Sauropoda)
Taxon: Neotherapoda
Infraorder: Tetanurae* ("stiff tails"; outgroup
Ceratosauria) 
Taxon: Avetherapoda (outgroup Spinosauroidia)
Taxon: Coelurosauria (feathered tetanurans; outgroup
Carnosauria)
Taxon: Tyrannoraptora (outgroup Compsognathidae)
Superfamily: Tyrannosauroidea (outgroup
Maniraptoriformes)
Family: Tyrannosauridae 
Subfamily: Tyrannosaurinae (outgroup Albertosaurinae)
Genus: Tyrannosaurus
Species: Rex

Other genera presently recognized in the subfamily
Tyrannosaurinae besides Tyrannosaurus are Tarbosaurus,
Daspletosaurus & Nanotyrannus.

*Tetanurae meaning "stiff tails", was named by Jacques
Gauthier on cladistic grounds in 1986 for a large
group of theropod dinosaurs. Gauthier's paper was the
first serious application of the science of cladistics
to vertebrate paleontology.

Tetanurae are defined as all theropods more closely
related to modern birds than to Ceratosaurus (e.g.
Padian et al., 1999). Gauthier considered it to
consist of Carnosauria and Coelurosauria, although
many of what he considered carnosaurs have been
regarded as coelurosaurs or basal tetanurans by
subsequent workers (but see Rauhut, 2003). Paul Sereno
(1999) named Neotetanurae for the node joining
Carnosauria (his Allosauroidea) and Coelurosauria,
excluding other tetanurans such as spinosauroids.
Padian et al. (1999) gave a synonymous definition for
Gregory Paul's (1988) Avetheropoda, but this
definition was published slightly later.

Phylogeny & anatomical details of Tetanurae:

http://www.users. qwest.net/ ~jstweet1/ tetanurae. htm

See the ancestry of other dinosaurs below. Click on
body shape for more different genera:

http://internt. nhm.ac.uk/ jdsml/nature- online/dino- directory/ body.dsml? disp=list& bodytype= 4&sort=Genus

For more on the more distant ancestors of dinosaurs,
please this on the Archosaur pelvic girdle & dinosaur
evolution:

http://www.bioone. org/perlserv/ ?request= get-document& doi=10.1666% 2F0094-8373(2001)027%3C0059% 3ATMOTAR% 3E2.0.CO% 3B2&ct=1

==
Neanderthals were separate species, says new human family tree
A new, simplified family tree of humanity, published on Sunday, has dealt a
blow to those who contend that the enigmatic hominids known as Neanderthals
intermingled with our forebears.
Neanderthals were a separate species to Homo sapiens, as anatomically modern
humans are known, rather than offshoots of the same species, the new
organigram published by the journal Nature declares.
The method, invented by evolutionary analysts in Argentina, marks a break with
the conventional technique by which anthropologists chart the twists and turns
of the human odyssey.
That technique typically divides the the genus Homo into various
classifications according to the shape of key facial features -- "flat-faced,"
"protruding-faced" and so on.
Reconciling these diverse classifications from a tiny number of specimens
spanning millions of years has led to lots of claims and counter-claims, as
well as much confusion in the general public, about how we came to be here.
Various species of Homo have been put up for the crown of being our direct
ancestor, only to find themselves dimissed by critics as failed branches of
the Homo tree.
The authors of the new study, led by Rolando Gonzalez-Jose at the Patagonian
National Centre at Puerto Madryn, Argentina, say the problem with the
conventional method is that, under evolution, facial traits do not appear out
of the blue but result from continuous change.
So the arrival of a specimen that has some relatively minor change of feature
as compared to others should not be automatically held up as representing a
new species, they argue.
The team goes back over the same well-known set of specimens, but uses a
different approach to analyse it, focussing in particular on a set of
fundamental yet long-term changes in skull shape.
They took digital 3D images of the casts of 17 hominid specimens as well as
from a gorilla, chimpanzee and H. sapiens.
The images were then crunched through a computer model to compare four
fundamental variables -- the skull's roundness and base, the protrusion of the
jaw, and facial retraction, which is the position of the face relative to the
cranial base.
When other phylotogenic techniques are used, the outcome is a family tree
whose main lines closely mirror existing ones but offers a clearer view as to
how the evolutionary path unfolded.
The paper suggests that, after evolving from the hominid Australopithecus
afarensis, the first member of Homo, H. habilis, arose between 1.5 and 2.1
million years ago.
We are direct linear descendants of H. habilis. H. sapiens started to show up
around 200,000 years ago.
None of the species currently assigned to Homo are discarded, though.
On the other hand, the Neanderthals are declared "chronological variants
inside a single biological heritage," in other words, evolutionary cousins but
still a separate species from us.
The squat, low-browed Neanderthals lived in parts of Europe, Central Asia and
the Middle East for around 170,000 but traces of them disappear some 28,000
years ago, their last known refuge being Gibraltar.
Why they died out is a matter of furious debate, because they co-existed
alongside anatomically modern man.
Some opinions aver that the Neanderthals were slowly wiped out by the smarter
H. sapiens in the competition for resources.
Other contend that we and the Neanderthals were more than just kissing
cousins. Interbreeding took place, which explains why the Neanderthal line
died out, but implies that we could have Neanderthal inheritage in our genome
today, goes this theory.
http://www.physorg.com/news129132016.html
==
Michael Denton  "Nature's Destiny"
==
Evolutionary history

During the late Triassic, a number of primitive
proto-theropod and theropod dinosaurs existed and
evolved alongside each other.

The earliest and most primitive of the carnivorous
dinosaurs were Eoraptor of Argentina and the
herrerasaurs. The herrerasaurs existed from the early
late Triassic (Late Carnian to Early Norian). They
were found in North America and South America and
possibly also India and Southern Africa. The
herrerasaurs were characterised by a mosaic of
primitive and advanced features. Some paleontologists
have in the past considered the herrerasaurians to be
members of Theropoda, though they are now thought to
be basal saurischians, and may even have evolved prior
to the saurischian- ornithischian split.

The earliest and most primitive unambiguous theropods
(or alternatively, Eutheropoda - 'True Theropods') are
the Coelophysidae. The Coelophysidae (Coelophysis,
Megapnosaurus) were a group of widely distributed,
lightly built and apparently gregarious animals. They
included small hunters like Coelophysis and larger (6
meters) predators like Dilophosaurus. These successful
animals continued from the Late Carnian (early Late
Triassic) through to the Toarcian (late Early
Jurassic). Although in the early cladistic
classifications they were included under the
Ceratosauria and considered a side-branch of more
advanced theropods,[1] they may have been ancestral to
all other theropods (which would make them a
paraphyletic group.[2][3]

The somewhat more advanced true Ceratosauria
(including Ceratosaurus and Carnotaurus) appeared
during the Early Jurassic and continued through to the
Late Jurassic in Laurasia. They competed quite well
alongside their more advanced tetanuran relatives and
- in the form of the abelisaur lineage - lasted to the
end of the Cretaceous in Gondwana.

The Tetanurae are more specialised again than the
Ceratosaurs. They are subdivided into Megalosauroidea
(alternately Spinosauroidea or Torvosauroidea) and the
Avetheropoda. They were most common during the Middle
Jurassic but continued to the Middle Cretaceous. The
latter clade - as their name indicates - were more
closely related to birds and are again divided into
the Carnosauria (including Allosaurus) and the
Coelurosauria, a very large and diverse dinosaur group
that was especially common during the Cretaceous.

Thus, during the late Jurassic, there were no fewer
than four distinct lineages of theropods -
ceratosaurs, megalosaurs, carnosaurs, and coelurosaurs
- preying on the abundance of small and large
herbivorous dinosaurs. All four groups survived into
the Cretaceous, although only two - the abelisaurs and
the coelurosaurs - seem to have made it to end of the
period, where they were geographically separate, the
abelisaurs in Gondwana, and the coelurosaurs in
Asiamerica.

Of all the theropod groups, the coelurosaurs were by
far the most diverse. Some coelurosaur clades that
flourished during the Cretaceous were the
tyrannosaurids (including Tyrannosaurus) the
dromaeosaurids (including Velociraptor and
Deinonychus, which are remarkably similar in form to
the oldest known bird, Archaeopteryx[ 4][5]), the
bird-like troodontids and oviraptorosaurs, the
ornithomimosaurs (or "ostrich dinosaurs"), the strange
giant-clawed herbivorous Therizinosauridae, and the
birds, which are the only dinosaur lineage to survive
the end Cretaceous mass-extinction. [6] While the roots
of these various groups must have been in the Late or
possibly even the Middle Jurassic, they only became
abundant during the Early Cretaceous. A few
paleontologists, such as Gregory S. Paul, have
suggested that some or all of these advanced theropods
were actually descended from flying dinosaurs or
proto-birds like Archaeopteryx that lost the ability
to fly and returned to a terrestrial habitat.[7]

V. Clade Coelurosauria: Triassic Period to Present
(Birds)

Coelurosauria (pronounced
/s&#616;&#716; lj&#650;& #601;r&#601; &#712;s&# 596;ri&#601; /)
is a diverse group of theropod dinosaurs that includes
tyrannosaurs, ornithomimosaurs, and maniraptors;
Maniraptora includes birds, the only coelurosaurs
alive today. All feathered dinosaurs discovered so far
have been coelurosaurs; in fact, some scientists
believe that most members of coelurosauria bore some
kind of feathers.

Description

Most coelurosaurs were bipedal predators. The group
includes some of the largest (Tyrannosaurus) and
smallest (Microraptor, Parvicursor) carnivorous
dinosaurs ever discovered. Characteristics that
distinguish coelurosaurs include:

* a sacrum (series of vertebrae that attach to the
hips) longer than in other dinosaurs
* a tail stiffened towards the tip
* a bowed ulna (lower arm bone).
* a tibia (lower leg bone) that is longer than the
femur (upper leg bone)

Feathers: a coelurosaurian trait

Because fossilized traces of feathers have been
identified (so far) only among coelurosauria, Prum and
Brush hypothesize that feathers "originated in a
lineage of coelurosaurian theropod dinosaurs including
both Sinosauropteryx and birds". Moreover, feathers
probably did not exist in theropod groups outside of
coelurosauria, such as the "allosauroids,
ceratosaurids, and coelophysids. "[1]

In fact, feathers of some type have been found in
fossils of at least one species in almost every
coelurosaur subgroupcompsognath ids, tyrannosauroids,
oviraptorosaurians, therizinosaurians, alvarezsaurids,
troodontids, dromaeosaurids, and birds. (Modern birds
are classified as coelurosaurs by nearly all
palaeontologists[ 2], though not by a few
ornithologists[ 3]) To date, the ornithomimosaurians
are the only group of coelurosaurs without direct
evidence of feathers, and based on phylogenetic
bracketing, most paleontologists agree that they were
feathered as well.

VI. Superfamily Tyrannosauroidea: Jurassic to
Cretaceous Periods

Tyrannosauroidea (meaning 'tyrant lizard forms') is a
superfamily (or clade) of coelurosaurian theropod
dinosaurs that includes the family Tyrannosauridae as
well as more basal relatives. Tyrannosauroids lived on
the Laurasian supercontinent beginning in the Jurassic
Period. By the end of the Cretaceous Period,
tyrannosauroids were the dominant large predators in
the Northern Hemisphere, culminating in the gigantic
Tyrannosaurus itself. Fossils of tyrannosauroids have
been recovered on what are now the continents of North
America, Europe and Asia.

Tyrannosauroids were bipedal carnivores, as were most
theropods, and were characterized by numerous skeletal
features, especially of the skull and pelvis. Early in
their existence, tyrannosauroids were small predators
with long, three-fingered forelimbs. Late Cretaceous
genera became much larger, including some of the
largest land-based predators ever to exist, but most
of these later genera had proportionately small
forelimbs with only two digits. Primitive feathers
have been found on Dilong, an early tyrannosauroid
from China, and may have been present in other
tyrannosauroid genera as well. Prominent bony crests
in a variety of shapes and sizes on the skulls of many
tyrannosauroids may have served display functions.

Description

Tyrannosauroids varied widely in size, although there
was a general trend towards increasing size over time.
Early tyrannosauroids were small animals.[1] One
specimen of Dilong, almost fully grown, measured 1.6
meters (5.3 ft) in length,[2] and a full-grown
Guanlong measured 3 meters (10 ft long).[3] An
immature Eotyrannus was over 4 meters (13 ft) in
length,[4] and a subadult Appalachiosaurus was
estimated at more than 6 meters (20 ft) long,[1]
indicating that both genera reached larger sizes. The
Late Cretaceous tyrannosaurids ranged from the 9 meter
(30 ft) Albertosaurus and Gorgosaurus to
Tyrannosaurus, which exceeded 12 meters (40 ft) in
length and may have weighed more than 6400 kilograms
(7 short tons).[1]

Skulls of early tyrannosauroids were long, low and
lightly constructed, similar to other coelurosaurs,
while later forms had taller and more massive skulls.
Despite the differences in form, certain skull
features are found in all known tyrannosauroids. The
premaxillary bone is very tall, blunting the front of
the snout, a feature which evolved convergently in
abelisaurids. The nasal bones are characteristically
fused together, arched slightly upwards and often very
roughly textured on their upper surface. The
premaxillary teeth at the front of the upper jaw are
shaped differently than the rest of the teeth, smaller
in size and with a D-shaped cross section. In the
lower jaw, a prominent ridge on the surangular bone
extends sideways from just below the jaw joint, except
in the basal Guanlong.[1] [2][3]

Tyrannosauroids had S-shaped necks and long tails, as
did most other theropods. Early genera had long
forelimbs, about 60% the length of the hindlimb in
Guanlong, with the typical three digits of
coelurosaurs. [3] The long forelimb persisted at least
through the Early Cretaceous Eotyrannus,[ 4] but is
unknown in Appalachiosaurus. [5] Derived tyrannosaurids
have forelimbs strongly reduced in size, the most
extreme example being Tarbosaurus from Mongolia, where
the humerus was only one-quarter the length of the
femur.[1] The third digit of the forelimb was also
reduced over time. This digit was unreduced in the
basal Guanlong,[3] but in Dilong it was significantly
more slender than the other two digits.[2] Eotyrannus
still had three functional digits on each hand,[4] but
tyrannosaurids had only two, although the vestigial
remnants of the third are found on some specimens.[6]
As in most coelurosaurs, the second digit of the hand
is the largest, even when the third digit is not
present.

Characteristic features of the tyrannosauroid pelvis
include a concave notch at the upper front end of the
ilium, a sharply defined vertical ridge on the outside
surface of the ilium, extending upwards from the
acetabulum (hip socket), and a huge "boot" on the end
of the pubis, more than half as long as the shaft of
the pubis itself.[1] These features are found in all
known tyrannosauroids, including basal members
Guanlong[3] and Dilong.[2] The pubis is not known in
Aviatyrannis or Stokesosaurus but both show typical
tyrannosauroid characters in the ilium.[7] The
hindlimbs of all tyrannosauroids, like most theropods,
had four toes, although the first toe (the hallux) did
not contact the ground. Tyrannosauroid hindlimbs are
longer relative to body size than almost any other
theropods, and show proportions characteristic of
fast-running animals, including elongated tibiae and
metatarsals. [1] These proportions persist even in the
largest adult Tyrannosaurus, [8] despite its probable
inability to run.[9] The third metatarsal of
tyrannosaurids was pinched at the top between the
second and fourth, forming a structure known as the
arctometatarsus. [1] The arctometatarsus was also
present in Appalachiosaurus[ 5] but it is unclear
whether it was found in Eotyrannus[4] or
Dryptosaurus. [10] This structure was shared by derived
ornithomimids, troodontids and caenagnathids, [11] but
was not present in basal tyrannosauroids like Dilong,
indicating convergent evolution.[2]

VII. Family Tyrannosauridae: Cretaceous Period

Tyrannosauridae (meaning "tyrant lizards") is a family
of coelurosaurian theropod dinosaurs which comprises
two subfamilies containing up to six genera, including
the eponymous Tyrannosaurus. The exact number of
genera is controversial, with some experts recognizing
as few as three. All of these animals lived near the
end of the Cretaceous Period and their fossils have
been found only in North America and Asia.

Although descended from smaller ancestors,
tyrannosaurids were almost always the largest
predators in their respective ecosystems, putting them
at the apex of the food chain. The largest species was
Tyrannosaurus rex, one of the largest known land
predators, which measured up to 13 metres (43 feet) in
length[1] and up to 6.8 metric tons (7.5 short tons)
in weight.[2] Tyrannosaurids were bipedal carnivores
with massive skulls filled with large teeth. Despite
their large size, their legs were long and
proportioned for fast movement. In contrast, their
arms were very small, bearing only two functional
digits.

Unlike most other groups of dinosaurs, most
tyrannosaurids are known from very complete remains.
This has allowed a wide variety of research into their
biology. Scientific studies have focused on their
ontogeny, biomechanics and ecology, among other
subjects. Soft tissue, both fossilized and intact, has
been reported from one specimen of Tyrannosaurus rex.

Description

The known tyrannosaurids were all large animals.[3]
Alioramus is known from the remains of an individual
estimated at between 5 and 6 meters (16.5 to 20 ft)
long,[4] although it is considered by some experts to
be a juvenile.[3] [5] Albertosaurus, Gorgosaurus and
Daspletosaurus all measured between 8 and 10 meters
(26 and 33 ft) long,[6] while Tarbosaurus reached
lengths of 12 meters (40 ft) from snout to tail.[7]
The massive Tyrannosaurus was the largest, approaching
13 meters (43 ft) in the longest specimens.[8]

Tyrannosaurid skull anatomy is well understood as
complete skulls are known for all genera but
Alioramus, which is known only from partial skull
remains. Tyrannosaurus, Tarbosaurus, and
Daspletosaurus had skulls which exceeded 1 meter (3.3
ft) in length, with the largest Tyrannosaurus skull
measuring over 1.5 meters (5 ft) long. Adult
tyrannosaurids had tall, massive skulls, with many
bones fused and reinforced for strength. At the same
time, hollow chambers within many skull bones and
large openings (fenestrae) between those bones helped
to reduce skull weight. Many features of tyrannosaurid
skulls were also found in their immediate ancestors,
including tall premaxillae and fused nasal bones.
Tyrannosaurid skulls had many unique characteristics,
however, including fused parietal bones with a
prominent sagittal crest, which ran longitudinally
along the sagittal suture and separated the two
supratemporal fenestrae on the skull roof. Behind
these fenestrae, tyrannosaurids had a
characteristically tall nuchal crest, which also arose
from the parietals but ran along a transverse plane
rather than longitudinally. The nuchal crest was
especially well-developed in Tyrannosaurus,
Tarbosaurus and Alioramus. Albertosaurus,
Daspletosaurus and Gorgosaurus had tall crests in
front of the eyes on the lacrimal bones, while
Tarbosaurus and Tyrannosaurus had extremely thickened
postorbital bones forming crescent-shaped crests
behind the eyes. Alioramus had a row of six bony
crests on top of its snout, arising from the nasal
bones; lower crests have been reported on some
specimens of Daspletosaurus and Tarbosaurus, as well
as the more basal tyrannosauroid
Appalachiosaurus. [5][9]

Tyrannosaurids, like their tyrannosauroid ancestors,
were heterodont, with premaxillary teeth D-shaped in
cross section and smaller than the rest. Unlike
earlier tyrannosauroids and most other theropods,
however, the maxillary and mandibular teeth of mature
tyrannosaurids are not blade-like but extremely
thickened and often circular in cross-section. [3]
Tooth counts tend to be consistent within species, and
larger species tend to have lower tooth counts than
smaller ones. For example, Alioramus had 76 to 78
teeth in its jaws, while Tyrannosaurus had between 54
and 60.[10]

The skull was perched at the end of a thick, S-shaped
neck, and a long, heavy tail acted as a counterweight
to balance out the head and torso, with the center of
mass over the hips. Tyrannosaurids are known for their
proportionately very small two-fingered forelimbs,
although remnants of a vestigial third digit are
sometimes found.[3][11] Tarbosaurus had the shortest
forelimbs compared to its body size, while
Daspletosaurus had the longest. Tyrannosaurids walked
exclusively on their hindlimbs, so their leg bones
were massive. In contrast to the forelimbs, the
hindlimbs were longer compared to body size than
almost any other theropods. Juveniles and even some
smaller adults, like more basal tyrannosauroids, had
longer tibiae than femora, a characteristic of
fast-running dinosaurs like ornithomimids. Larger
adults had leg proportions characteristic of
slower-moving animals, but not to the extent seen in
other large theropods like abelisaurids or carnosaurs.
The third metatarsals of tyrannosaurids were pinched
between the second and fourth metatarsals, forming a
structure known as the arctometatarsus. [3] It is
unclear when the arctometatarsus first evolved; it was
not present in the earliest tyrannosauroids like
Dilong,[12] but was found in the later
Appalachiosaurus. [9] This structure also characterized
troodontids, ornithomimids and caenagnathids, [13] but
its absence in the earliest tyrannosauroids indicates
that it was acquired by convergent evolution.[12]

Taxonomy and systematics

Tyrannosaurus was named by Henry Fairfield Osborn in
1905, along with the family Tyrannosauridae. [14] The
name is derived from the Ancient Greek words
&#964;&#965; &#961;&#945; &#957;&#957; &#959;&#962; /tyrannos
('tyrant') and
&#963;&#945; &#965;&#961; &#959;&#962; /sauros
('lizard'). The very common suffix -idae is normally
appended to zoological family names and is derived
from the Greek suffix -&#953;&#948; &#945;&#953; /-idai,
which indicates a plural noun.[15] The family name
Deinodontidae was often used by scientists up until
the 1920s,[16] based on the genus Deinodon, which was
named after isolated teeth from Montana.[17] This
taxon, however, is now considered a nomen dubium so
the name Tyrannosauridae is preferred by all modern
experts.[3]

Tyrannosauridae is a family in rank-based Linnaean
taxonomy, within the superfamily Tyrannosauroidea and
the suborder Theropoda. With the advent of
phylogenetic taxonomy in vertebrate paleontology,
Tyrannosauridae has been given several explicit
definitions. The original was produced by Paul Sereno
in 1998, and included all tyrannosauroids closer to
Tyrannosaurus than to either Alectrosaurus, Aublysodon
or Nanotyrannus. [18]. However, Nanotyrannus is often
considered to be a juvenile Tyrannosaurus rex, while
Aublysodon is usually regarded as a nomen dubium
unsuitable for use in the definition of a clade.[3]
Definitions since then have been based on more
well-established genera. A 2003 attempt by Christopher
Brochu included Albertosaurus, Alectrosaurus,
Alioramus, Daspletosaurus, Gorgosaurus, Tarbosaurus
and Tyrannosaurus in the definition.[ 1] Holtz
redefined the family in 2004 to use all of the above
as specifiers except for Alioramus and Alectrosaurus,
which his analysis could not place with certainty.
However, in the same paper, Holtz also provided a
completely different definition, including all
theropods more closely related to Tyrannosaurus than
to Eotyrannus.[ 3] The most recent definition is that
of Sereno in 2005, which defined Tyrannosauridae as
the least inclusive clade containing Albertosaurus,
Gorgosaurus and Tyrannosaurus. [19]

Classification

Carr et al., 2005 [9] regard Gorgosaurus libratus as a
species of Albertosaurus and Tarbosaurus bataar as a
species of Tyrannosaurus. Currie, et al., 2003 [10],
disagree.

FAMILY TYRANNOSAURIDAE

* Subfamily Albertosaurinae
o Albertosaurus
o Gorgosaurus
* Subfamily Tyrannosaurinae
o Alioramus
o Daspletosaurus
o Tarbosaurus
o Tyrannosaurus

Phylogeny

Tyrannosauridae is uncontroversially divided into two
subfamilies. Albertosaurinae comprises the North
American genera Albertosaurus and Gorgosaurus, while
Tyrannosaurinae includes Daspletosaurus, Tarbosaurus
and Tyrannosaurus itself.[3] Some authors include the
species Gorgosaurus libratus in the genus
Albertosaurus and Tarbosaurus bataar in the genus
Tyrannosaurus, [9][20][21] while others prefer to
retain Gorgosaurus and Tarbosaurus as separate
genera.[3][5] Albertosaurines are characterized by
more slender builds, lower skulls, and proportionately
longer tibiae than tyrannosaurines. [3] In
tyrannosaurines, the sagittal crest on the parietals
continues forward onto the frontals.[5]

Cladistic analyses of tyrannosaurid phylogeny often
find Tarbosaurus and Tyrannosaurus to be sister taxa,
with Daspletosaurus more basal than either. A close
relationship between Tarbosaurus and Tyrannosaurus is
supported by numerous skull features, including the
pattern of sutures between certain bones, the presence
of a crescent-shaped crest on the postorbital bone
behind each eye, and a very deep maxilla with a
noticeable downward curve on the lower edge, among
others.[3][9] An alternative hypothesis was presented
in a 2003 study by Phil Currie and colleagues, which
found weak support for Daspletosaurus as a basal
member of a clade also including Tarbosaurus and
Alioramus, both from Asia, based on the absence of a
bony prong connecting the nasal and lacrimal
bones.[10] Alioramus was found to be the closest
relative of Tarbosaurus in this study, based on a
similar pattern of stress distribution in the skull. A
related study also noted a locking mechanism in the
lower jaw shared between the two genera.[22] In a
separate paper, Currie noted the possibility that
Alioramus might represent a juvenile Tarbosaurus, but
stated that the much higher tooth count and more
prominent nasal crests in Alioramus suggest it is a
distinct genus. Similarly, Currie uses the high tooth
count of Nanotyrannus to suggest that it may be a
distinct genus,[5] rather than a juvenile
Tyrannosaurus as most other experts believe.[3][ 23]

Distribution

Tyrannosaurid remains are only found in Asia and
western North America. The exact time and place of
origin of the family remain unknown due to the poor
fossil record in the middle part of the Cretaceous on
both continents, although the earliest confirmed
tyrannosaurids lived in the early Campanian stage in
western North America.[3] Tyrannosaurid remains have
never been recovered from eastern North America, while
more basal tyrannosauroids like Dryptosaurus and
Appalachiosaurus persisted there until the end of the
Cretaceous, indicating that tyrannosaurids must have
evolved in or dispersed into western North America
after the continent was divided in half by the Western
Interior Seaway in the middle of the Cretaceous.[ 9]
Tyrannosaurid fossils have been found in Alaska, which
may have provided a route for dispersal between North
America and Asia.[24] Alioramus and Tarbosaurus are
found to be related in one cladistic analysis, forming
a unique Asian branch of the family.[10]

Of the two subfamilies, tyrannosaurines appear to have
been more widespread. Albertosaurines are unknown in
Asia, which was home to the tyrannosaurines
Tarbosaurus and Alioramus. Both subfamilies were
present in the Campanian and early Maastrichtian
stages of North America, with tyrannosaurines like
Daspletosaurus ranging throughout the Western
Interior, while the albertosaurines Albertosaurus and
Gorgosaurus are currently known only from the
northwestern part of the continent. By the late
Maastrichtian, albertosaurines appear to have gone
extinct, while the tyrannosaurine Tyrannosaurus roamed
from Saskatchewan to Texas. This pattern is mirrored
in other North American dinosaur taxa. During the
Campanian and early Maastrichtian, lambeosaurine
hadrosaurs and centrosaurine ceratopsians are common
in the northwest, while hadrosaurines and
chasmosaurines were more common to the south. By the
end of the Cretaceous, centrosaurines are unknown and
lambeosaurines are rare, while hadrosaurines and
chasmosaurines were common throughout the Western
Interior.[3]

VIII. Genus Tyrannosaurus: Late Cretaceous

Tyrannosaurus (pronounced
/t&#616;&#716; rn&#601;& #712;s&#596; r&#601;s/ or
/ta&#618;&#716; rno&#650; &#712;s&# 596;r&#601; s/,
meaning 'tyrant lizard') is a genus of theropod
dinosaur. The famous species Tyrannosaurus rex ('rex'
meaning 'king' in Latin), commonly abbreviated to T.
rex, is a fixture in popular culture around the world.
It lived throughout what is now western North America,
with a much wider range than other tyrannosaurids.
Fossils of T. rex are found in a variety of rock
formations dating to the last three million years of
the Cretaceous Period, approximately 68 to 65 million
years ago; it was among the last dinosaurs to exist
prior to the CretaceousTertiary extinction event.

Like other tyrannosaurids, Tyrannosaurus was a bipedal
carnivore with a massive skull balanced by a long,
heavy tail. Relative to the large and powerful
hindlimbs, Tyrannosaurus forelimbs were small, though
unusually powerful for their size, and bore two
primary digits, along with a possible third vestigial
digit. Although other theropods rivaled or exceeded T.
rex in size, it was the largest known tyrannosaurid
and one of the largest known land predators, measuring
up to 13 meters (43 ft) in length,[1] up to 4 meters
(13 ft) tall at the hips,[2] and up to 6.8 metric tons
(7.5 short tons) in weight.[3] By far the largest
carnivore in its environment, T. rex may have been an
apex predator, preying upon hadrosaurs and
ceratopsians, although some experts have suggested it
was primarily a scavenger.

More than 30 specimens of T. rex have been identified,
some of which are nearly complete skeletons. Soft
tissue and proteins have been reported in at least one
of these specimens. The abundance of fossil material
has allowed significant research into many aspects of
its biology, including life history and biomechanics.
The feeding habits, physiology and potential speed of
T. rex are a few subjects of debate. Its taxonomy is
also controversial, with some scientists considering
Tarbosaurus bataar from Asia to represent a second
species of Tyrannosaurus and others maintaining
Tarbosaurus as a separate genus. Several other genera
of North American tyrannosaurids have also been
synonymized with Tyrannosaurus.


==
Taxonomy

Subclass Diapsida
o Infraclass ARCHOSAUROMORPHA
Family Euparkeriidae
Family Erythrosuchidae
Family Proterochampsidae
Family Proterosuchidae
Order Choristodera
Order Prolacertiformes
Order Rhynchosauria
Order Trilophosauria
Division Archosauria
Subdivision Crurotarsi
Family Ornithosuchidae
Order Aetosauria
Order Phytosauria
Order Rauisuchia
Superordr
Crocodylomorpha
o Order Crocodilia
Subdivision Avemetatarsalia
Order Pterosauria
Superorder Dinosauria
o Order Ornithischia
o Order Saurischia
==
http://en.wikipedia .org/wiki/ Archosauromorpha

http://en.wikipedia .org/wiki/ Dinosauria

http://en.wikipedia .org/wiki/ Saurischia

http://en.wikipedia .org/wiki/ Theropoda

http://en.wikipedia .org/wiki/ Coelurosauria

http://en.wikipedia .org/wiki/ Tyrannosauroidea

http://en.wikipedia .org/wiki/ Tyrannosauridae

http://en.wikipedia .org/wiki/ Tyrannosaurus

Dinosaur ancestors: Archosaurs

Dinosaurs evolved in the Triassic from archosaur
ancestors. Archosaurs ("ruling reptiles") are so
named since they were the dominant animals of the
Mesozoic Era. They survive today in the birds &
crocodilians. They differ from their diapsid amniote
kin like snakes & lizards in having additional
openings in their skulls besides the two behind the
eye socket that characterize all diapsids &
distinguish them from synapsids, represented today by
mammals like us.

The earliest known dinosaurs are so similar to other
Triassic archosaurs that debate continues over whether
to include them among the dinosaurs at all & if so,
whether they are stem dinosaurs or stem saurischians.
As you apparently don't recall, dinosaurs belong to
two Orders, Saurischia & Ornithischia.

The most closely related archosaur group is the
extinct pterosaurs, Mesozoic flying reptiles. The
next closest related archosaur group is the still
living crocodilians.

Herrerasaurus

Herrerasaurus was discovered in Argentina in 1958 by a
Victorino Herrera, for whom the genus was later named.
The specimen was incomplete, but a skull was found in
1988. At that time, paleontologist Paul Sereno of the
Field Museum of Natural History in Chicago, Illinois,
redescribed the species to incorporate new
information.

Until recently, Herrerasaurus was believed to have
been one of the earliest dinosaurs, living in the late
Triassic Period (230 to 195 million years ago). It
was originally thought to be a theropod, one of the
saurischian dinosaurs. It is now recognized to be an
archosaur.

Originally, Herrerasaurus was considered to be a
dinosaur that was too primitive to be classified as
either a saurischian or ornithischian dinosaur. It
was believed to be a representative of the common
ancestry of both lineages of dinosaurs. The structure
of Herrerasaurus' s skull, which resembled that of
early theropod dinosaurs, resulted in its being
classified as a theropod.

There was a problem with classifying Herrerasaurus as
a theropod, however, since its hip structure did not
really resemble that of a saurischian dinosaur.
Instead, Herrerasaurus' s pelvic structure was more
similar to that of less derived archosaurs. The
pelvic structure was a hotly debated topic: was
Herrerasaurus a theropod with a primitive pelvic
structure, or an archosaur with a theropod-style
skull?

Currently, Herrerasaurus is classified as an
archosaur. Perhaps as more specimens are discovered
and modern paleontological research techniques
improve, we will learn where Herrerasaurus really
belongs on the family tree of ancient animals.

Yet the Wikipedia article suggests a different current
consensus, showing that dinosaurs evolved so gradually
from archosaur stock that it's fairly arbitrary as to
where to place the earliest genera & species, based on
various traits:

http://en.wikipedia .org/wiki/ Herrerasaurus

For many years, the classification of Herrerasaurus
was unclear, as the animal was initially known from
very fragmentary remains; it has been hypothesized to
be a basal theropod, a basal sauropodomorph, a basal
saurischian, or not a dinosaur at all. However, with
the discovery of a mostly-complete skeleton and skull
in 1988,[2][3] Herrerasaurus has been classified as
either an early theropod or an early saurischian in at
least five recent surveys of theropod evolution. This
medium-sized bipedal reptile is a member of the
Herrerasauridae, a group of similar animals which were
among the earliest of the dinosaurian radiation.

Eoraptor

Eoraptor comes from the same formation as
Herrerasaurus & like it, has been assigned to both
archosaur & stem dinosaur positions in dinosaur
evolution.

It appears based on 1993 analysis however now to be
considered a stem dinosaur or saurischian.

http://en.wikipedia .org/wiki/ Eoraptor

The bones of this primitive dinosaur were first
discovered in 1991, by University of Chicago
paleontologist Paul Sereno, in the Ischigualasto Basin
of Argentina. During the Late Triassic Period, this
was a river valley but is now desert badlands.
Eoraptor was found in the Ischigualasto Formation, the
same formation that yielded Herrerasaurus, a very
early theropod. By 1993 it had been determined to be
one of the earliest dinosaurs. Its age was determined
by several factors, not least because it lacked the
specialised features of any of the major groups of
later dinosaurs, including its lack of specialized
predatory features. Unlike later carnivores, it lacked
a sliding joint at the articulation of the lower jaw,
with which to hold large prey. Furthermore, only some
of its teeth were curved and saw-edged, unlike those
in a later predator's mouth.

Eoraptor belonged to a major group of dinosaurs called
saurischians, or lizard-hipped dinosaurs. Their hip
structures are similar to that of the modern lizard.

The fact that it possessed some herbivore teeth and
five fully developed 'fingers' has led scientists to
place Eoraptor at more ancient than even
Herrerasaurus. Only some prosauropods, recently
discovered in Madagascar, are thought to be older.
There is a possibility that Staurikosaurus may be
older, but it is rather large. Staurikosaurus seems to
have features in common with both prosauropods and
theropods, which has led scientists to question how
primitive Eoraptor was in relation to other dinosaurs.

Conclusion

As I showed you before, saurischians split in two
lineages in the Triassic, theropods, mostly carnivores
leading to Jurassic birds (most paleontologists
conclude) & to Cretaceous T. rex, & omnivores &
herbivores leading to the giant sauropods like
Jurassic Diplodocus. Stem ornithischians gave rise to
derived genera like Jurassic Stegosaurus & Cretaceous
Triceratops.

For many lineages, intermediate forms abound. Over
the next 150 years, we'll probably find as many more
genera as have been found since 1842, when the term
"dinosaur" was coined. Fossil dinosaurs had been
found & recorded since 1676, however.
==
Dawkins, Richard. The Blind Watchmaker: 
Why the Evidence of Evolution Reveals a Universe Without Design, 
W.W. Norton & Company, 1996.
==
Whales Evolved Separate Ways to Avoid the Bends
One of the largest studies ever of modern and fossil
whales has
determined that virtually all modern whales appear
to have evolved
safeguards against the bends, a sometimes fatal
condition in which
nitrogen bubbles form in blood and tissues after too
rapid decompression.
[Lead author Brian Beatty, assistant professor of
anatomy at the New
York College of Osteopathic Medicine,] and coauthor
Bruce Rothschild
analyzed vertebrae from 331 modern and 996 ancient
fossil whales
housed at museums and universities across the United
States. They
subjected the whalebones to standard X-rays and
fluoroscopy, a process
that allows for real-time video images, in order to
detect bone damage
linked to the bends.
Beatty explained that pressure changes can "cause a
bit of fat or gas
to form an embolism in a blood vessel" and that, in
turn, can be a
literal bone buster, since the blood vessels "have
little room to
expand within the bone."
The researchers discovered that toothed whales, a
group that includes
killer, sperm and beaked whales, along with
dolphins, likely would
have suffered from the bends some 32 million years
ago, while another
whale group known as the mysticetes would have got
the bends some 22
million years ago.

This isn't surprising to me. Many toothed whales are
deep divers, while even today no baleen whales dive as
deep as the deepest diving toothed whales. Sperm &
beaked whales for instance feed on squid in the
depths, while most baleen whales filter feed on krill,
fish (rorquals & humpbacks) or the continental shelf
(grays) closer to the surface.

The mysticetes include humpback, blue, gray and
other whales that have
baleens, or rows of plates that look like giant
combs. These allow for
filter feeding and are used instead of teeth.

The findings, which have been accepted for
publication in the journal,
Naturwissenschaften , have multiple implications that
could change
current views on whale evolution.

The first is the ancestor to all whales was probably
not a deep-sea
diver, as had been previously proposed. Instead, the
research suggests
it was most likely a crocodile-type shoreline ambush
hunter.

Today's sperm whales can dive for more than one hour
to depths greater
than 4,000 feet below the water's surface. If the
"mother of all
whales" had tried such a dive, its bones probably
would have shattered
to bits.
The study also indicates toothed and baleen whales
independently
evolved anatomical and behavioral abilities to cope
with the bends,
with toothed whales developing the skills long
before baleen whales
did. This provides evidence that the two major
groups of whales split
from their common ancestor early on and went down
their own
evolutionary paths, perhaps explaining the
tremendous amount of
diversity seen among whales today.
Erich Fitzgerald is a noted whale evolution expert
and a
paleontologist at Australia's Museum Victoria.
Fitzgerald described the new research as "quite
important, and it
presents a novel hypothesis on the evolution of one
of the critical
aspects of cetacean biology."
He said that "it seems the odontocetes evolved their
'tool kit' for
deep diving and hunting in the dark using sound,
very early on," while
"the baleen whales were on a different evolutionary
timetable,
'modernizing' much later in their evolutionary
history."
==
The basic adaptation of scallops separating them from other bivalve
mollusks is their generally more active lifestyle. While they may go
through sessile phases in their life cycles & some species have reverted to
largely sessile existence, most don't attach themselves to a substrate most
of the time as adults, unlike their relatives the oysters, for instance.
Scallops are also hermaphroditic. Bivalve shells similar to scallops have
been found from the Carboniferous Period of the Paleozoic Era,
but true members of the family date from the Triassic Period of the
Mesozoic Era, having exploited ecological niches left empty by the "Great
Dying", the biggest of all extinction events of the past 540
million years at the end of the Paleozoic. However, they remained a
relatively minor portion of marine ecosystems throughout the Mesozoic,
after which they underwent an extensive adaptive radiation into the
niches freed up by another large extinction event at the
Cretaceous/Tertiary (K/T) boundary between the Mesozoic & Cenozoic Eras,
when the non-avian dinosaurs died out.
Mammals too evolved in the early to mid-Mesozoic from Paleozoic ancestors,
but underwent adaptive radiation after the K/T mass extinction. Mammalian
evolution has generally proceeded at a more rapid pace than bivalve, since
we live in less stable environments than strictly marine creatures.
==
Chromosomal changes, particularly polyploidy, have played a significant role
in the evolution of plants, and most higher plants are recent polyploids
(DeWit, 1980). Although polyploidy is relatively rare in animals, chromosomal
changes are increasingly recognized as an important force in animal evolution.
It is hypothesized that two rounds of genomic duplication occurred during the
evolution of vertebrates leading to humans (Furlong and Holland, 2002; Spring,
2002). Chromosomal rearrangements may play a role in reproductive isolation and
speciation, by creating barriers to meiotic pairing and reducing the fitness of
hybrids (White, 1978; King, 1993). Genic theories, on the other hand, stress
the importance of accumulation of genic mutations in reproductive isolation.
Recent findings of effects of chromosomal rearrangements on recombination have
bridged the gap between the chromosomal and genic theories of reproductive
isolation, arguing for a major role of chromosomal changes in speciation
(Rieseberg, 2001; Navarro and Barton, 2003). However, the extent of
chromosomal changes and their roles in speciation are poorly understood in
many animal taxa, including marine bivalves. Many marine bivalves are
sympatric broadcast spawners whose mechanisms of reproductive isolation are
particularly interesting but largely unknown. Chromosomal studies may provide
a unique perspective on the evolution of marine bivalves.
==
In this materialist view, people perceive God¹s existence because their brains
have evolved to confabulate belief systems. You put a magnetic helmet around
their heads and they will begin to think they are having a spiritual epiphany.
If they suffer from temporal lobe epilepsy, they will show signs of
hyperreligiosity, an overexcitement of the brain tissue that leads sufferers
to believe they are conversing with God.
==
Excerpt from:
http://www.biotechn ews.com.au/ index.php/ id;283151818

Slimeballs and eyeballs: hagfish and the evolution
of the eye
Hagfish may be ferociously ugly little creatures, but they can teach
us much about the evolution of the vertebrate eye.
"If," Darwin wrote in On the Origin of Species, "numerous gradations
from a perfect and complex eye to one very imperfect
and simple, each grade being useful to its possessor, can be shown to
exist ... and if
any variation or modification in the organ be ever useful to the
animal under changing conditions of life, then the difficulty of
believing that a perfect and complex eye could be formed by natural
selection, though insuperable by our imagination,
can hardly be considered real."
In the Nature Reviews paper, the team of Professors
Trevor Lamb of the John Curtin School of Medical Research at the
Australian National
University, Shaun Collin of the School of Biomedical Sciences at the
University of Queensland and Ed Pugh of the FM Kirby
Centre for Molecular Ophthalmology at the University of
Pennsylvania have taken up Darwin's challenge and set out a proposed
sequence of the evolution of the vertebrate eye which they believe might
satisfy Darwin's prescription. And they have even set homework to
test the hypothesis. The team sets out their view of the sequence of
events in the evolution of opsins, photoreceptors, the retina and
the eye cup in vertebrates. They begin with the separation of
primitive bilateral animals into the super-phyla of the protostomes and
the deuterostomes approximately 580 million years ago. There have been
multiple splits since then, the emergence of the chordates about 550
million years ago being an important one for our purposes.
These little animals, Trevor Lamb says, had developed a notochord and
a dorsal nerve chord. They also had developed photosensitive regions
at the rostral end. "These were just little spots with a few
photoreceptors, " Lamb says, "but their primitive
receptors were remarkably similar to the cones that we have."
The independent development of the remarkably similar
molluscan eye, working with similar elementary animal
genes, shows not only the principle of convergence but
the power of evolutionary processes.
==
When animals hit the big time
Sitting in his sprawling office under the eaves of the Earth sciences building
at the University of Cambridge, Nicholas Butterfield seems a typical denizen of
the ivory tower. A specialist in ancient ecology, Butterfield spends most of
his time pondering the finer points of life in seas that vanished hundreds of
millions of years ago. But perhaps he isn't so far removed from the daily
concerns of the rest of us after all; his biggest problem, it turns out, is
sex.
It's not what you're thinking. His computer screen saver displays radio
telescope data, not earthly delights. But as the discoverer of the earliest
evidence of sexual reproduction--a red alga called Bangiomorpha pubescens
fossilized in the act some 1.2 billion years ago--Butterfield has had to
confront a central mystery of life's history on Earth. Textbooks say that
sexual reproduction should speed up evolution. So why, he asks, did it take
600 million years more for modern animals--active, many-celled creatures like
us--to make their first impression in the fossil record?
Scientists have been posing versions of that question for over a century. And
the puzzle has only deepened with recent discoveries showing that evolution
had laid the groundwork for modern animals tens of millions of years before
their sudden burst of evolutionary exuberance, known as the Cambrian
explosion. New data pouring in from fossil beds, biology labs, and computer
simulations of Earth's history have sparked a matching explosion of new
theories, some invoking a drastic change in the ancient environment and others
a trigger within life itself, such as the first eyes. This week, researchers
are gathering in Seattle to compare notes, promote their pet ideas, and
perhaps plot a strategy to solve the persistent riddle once and for all.
Late starters. For the first 2.5 billion years of life's history, the oceans
were home to little more than bacteria, and what dry land there was remained
lifeless. A few simple animals showed up on the seafloor about 575 million
years ago. But while these soft-bodied "Ediacaran" creatures could grow to
several feet long, they had simple, plantlike body plans and remained rooted
in place on the bottom, filtering food particles out of the seawater.
And then suddenly, 543 million years ago, the shallow coastal seas of the
Cambrian era started to explode into a vibrant bestiary of crawling, swimming,
voraciously snacking animal life. In a geological eye blink--10 million to 20
million years--most Ediacarans died out and were replaced by what would
eventually become everything from animal-rights activists to the creatures
they worry about.
The Burgess Shale fossil beds in eastern British Columbia, discovered in 1909,
gave science its first good look at the Cambrian explosion. Now a steep climb
up the side of Mount Field, the flaky rock was once a coastal seafloor, and it
preserves in intricate detail an otherworldly community of armored trilobites,
spiny worms, and fearsome swimming predators, including the 2-foot monster
Anomalocaris. Yet the Burgess Shale animals aren't quite as bizarre as they
seem. They had the eyes and legs and distinctive left-and-right-hand body
plans that define modern animals. To try to understand where they came from,
scientists are now peering even further back into the geological record. "You
can't understand the Cambrian without looking at the ecology and evolution of
what came before," says Butterfield.

==
There are some 5,400 species of mammals alive today, spread across 
153 families.
==
Here's an updated feminist theory of bipedalism then. Apes and
baboons do not have to actively carry their young, because the infants
cling to their mothers' fur. Now suppose our early ancestors first lost
their fur, for whatever reason. Then bipedalism might have been a useful
adaptation to allow females to carry their infants around. It would in
fact also allow paleolithic metrosexual males to share some of the
carrying work.
The current predominating view is the fur receded around the time we see
the first appearance of modern-like bodily proportions.
==
http://news.nationalgeographic.com/news/2005/02/0216_050216_omo.html

The new findings, published in the February 17 issue of the journal Nature,
establish Omo I and II as the oldest known fossils of modern humans. The prior
record holders were fossils from Herto, Ethiopia, which dated the emergence of
modern humans in Africa to about 160,000 years ago.
"The new dating confirms the place of the Omo fossils as landmark finds in
unraveling our origins," said Chris Stringer, director of the Human Origins
Group at the Natural History Museum in London.
The 195,000-year-old date coincides with findings from genetic studies on
modern human populations. Such studies can be extrapolated to determine when
the earliest modern humans lived.
The findings also add credibility to the widely accepted "Out of Africa"
theory of human origins which holds that modern humans (later versions of Homo
sapiens) first appeared in Africa and then spread out to colonize the rest of
the world.
The new date also widens the gap between when anatomically modern humans
emerged and when "cultural" traitssuch as the creation of art and music,
religious practices, and sophisticated tool-making techniquesseem to have
appeared. Evidence of culture is not extensively documented in the
archaeological record until around 50,000 years ago.
The wider gap could add fuel to a long-term debate swirling around when modern
human behavior, as opposed to modern human anatomy, emerged.
"Those who believe that there is widely scattered evidence of 'modern'
behavior going back 200,000 years in Africa will be delighted that modern
human anatomy also goes back that far," said John Fleagle, a physical
anthropologist at Stony Brook University in New York and one of the co-authors
of the study. "[Scientists] who believe that modern human behavior only
appeared abruptly about 50,000 years ago will see [the new date as] further
expanding the distinction and the temporal gap between modern anatomy and
modern behavior."
Dating Through Geology
Somewhat surprisingly, the first thing the scientific team had to do to come
up with the new dates was to relocate the precise location where the fossil
remains had been excavated in 1967. They were able to do this using National
Geographic Society video footage taken during the first excavation. They also
used photographs taken by Karl Butzer, a geologist currently at the University
of Texas, who did the original geological studies of the site. Also helpful
were hand-drawn maps from the late Paul Abell, another member of the 1967 team.
"So we know where Omo I and Omo II are now, and they're now documented by GPS,
so they won't get lost again. But we didn't have GPS 40 years ago," said Frank
Brown, a geologist at the University of Utah and a co-author of the study.




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NEWS HOMEANIMAL NEWSANCIENT WORLDENVIRONMENT NEWSCULTURES NEWSSCIENCE & SPACE
NEWSWEIRD NEWS




Oldest Human Fossils Identified

<< Back to Page 1 Page 2 of 2



The remains of Omo I and Omo II were buried in the lowest sediment layer,
called Member 1, of the 330-foot-thick (100-meter-thick) Kibish rock formation
near the Omo River.
In addition to GPS, more advanced dating techniques have also been developed.
The researchers sampled the volcanic ash on both sides of the river that lay
above where the fossils were found. The ash was the same on both sides.

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"Then we had to find something to date, and what that takes is a lot of
walking," Brown said. "Most of the ashes are very fine grained, they dont have
pumice [fragments] in them, so you go along and you go along, and eventually
you find a place where there are pumices."
The presence of feldspar crystals from a volcanic eruption inside pumice
fragments is an indication that the crystals have not been contaminated. Such
unadulterated crystals can be dated using a technique called potassium-argon
dating.
"By dating the crystals held in the pumice, you can say with a high level of
confidence that everything in that member [group of sediment layers] is nearly
the same date," Brown said. "We used a dating technique called 40AR/39AR, which
is a variant of potassium-argon dating."
In the same Member 1 sediment layers, the team found additional Omo I bones,
animal fossils, and stone tools.
The work was funded by the National Geographic Society, the National Science
Foundation, the L.S.B. Leakey Foundation, and the Australian National
University.
Widening the Gap
Although both Omo I and Omo II were classified as Homo sapiens in 1967, the
Omo II remains were considered much more primitive. Finding that the two
individuals lived at around the same time in the same location suggests that,
when modern humans first appeared, there were other, less modern populations
also on the scene. The finding may add some new perspective to how we think
about how and when "modern" human anatomy evolved.
"I have previously regarded Omo II as an archaic or primitive H. sapiens and
Omo I as a modern H. sapiens, which would make them the same species,"
Stringer said. "If Omo I and II do belong together, the variation in the
population is greater than I expected, but given what we see in larger fossil
samples from other regions, we may need to accept that African populations
showed large [physical-form] variation at this time."
Everyone agrees that the Omo II cranium is more primitive than the Omo I skull
in many features, Fleagle said.
"Some see the two as part of a continuum, others see them as very distinct
types of hominid," he said. "Whether Omo II gets put in Homo sapiens depends
upon where one draws the boundary between H. sapiens and whatever species
comes beforeH. ergaster, H. erectus, H. heidelbergensis.
"Regardless of how Omo II is classified, " he continued, "I don't consider it
surprising to find two different morphologies existing at the same time. We
know that Homo sapiens and Neandertals existed in Europe at the same time and
that in the early Pleistocene [epoch] there was diversity of early hominid
morphologies [or body forms]. Indeed, virtually every site that has early
modern humans ... seems to show a diversity of morphologies with some more
modern and some less so."
Exactly when modern behavior, as opposed to modern anatomy, emergedindeed even
how to define modern behavioris another area in which the Omo fossils might
contribute some insight. Common elements used to define modern behavior
include planning ahead; innovating technologically; establishing social and
trade networks; adapting to changing conditions and environments; and
exhibiting symbolic behavior like cave painting, beadmaking (used to show
status or group identity), or burying the dead.
The crux of the argument comes down to whether these abilities resulted from a
sudden biological and genetic revolution or from a more gradual evolution of
abilities that culminated around 50,000 years ago.
"I think we are still determining when "modern" behavior started to evolve,
and my guess is that it too will have deeper roots in Africa," Stringer said.
"There is growing evidence that elements of modern behavior were there a
hundred thousand years ago, and I think the gap or mismatch between the
emergence of modern anatomy and modern behavior may well be much less
significant than currently believed."
Spencer Wells is a geneticist and an anthropologist and a National Geographic
Emerging Explorer. From an analysis of DNA of thousands of men around the
world, Wells says he has discovered that all humans alive today can be traced
back to a small tribe of hunter-gatherers who lived in Africa 60,000 years ago.
"Many anthropologists, myself included, believe that what makes us truly human
is our modern behavior, enabled by a modern brain," Wells said. "Modern
behavior starts to show up sporadically around 70,000 to 80,000 years ago but
doesn't really take off until around 50,000 years agothe "Great Leap Forward"
and dawn of the Upper Paleolithic [early Stone Age]."
The human population appears to have crashed to around 2,000 individuals
around 70,000 years ago, at the same time they were headed into the worst part
of the last ice age. The crash was possibly brought on by a massive volcanic
eruption, Wells said.
"The hypothesis is that the survivors of this near-extinction event had to be
smarter in order to survive, and this allowed them to settle the rest of the
world outside of Africa. So, 'human-ness' may not been widespread until around
50,000 to 60,000 years ago, and this could be seen as the real origin of our
species."


==
Experts find jawbone of pre-human great ape in Kenya
NAIROBI Researchers unveiled a 10-million-year-old jaw bone on Tuesday they
believe belonged to a new species of great ape that could be the last common
ancestor of gorillas, chimpanzees and humans.
The Kenyan and Japanese team found the fragment, dating back to between 9.8
and 9.88 million years, in 2005 along with 11 teeth. The fossils were
unearthed in volcanic mud flow deposits in the northern Nakali region of Kenya.
The species somewhere between the size of a female gorilla and a female
orangutan may prove to be the 'missing link', the key step that split the
evolutionary chains of humans and other primates, Kenyan scientists said.
'Based on this particular discovery, we can comfortably say we are approaching
the point at which we can pin down the so-called missing link,' Frederick
Manthi, senior research scientist at the National Museums of Kenya, told
reporters.
'We have to find more fossils from a cross-section of sites to sustain that
particular theory,' he added, speaking at a desk where the approximately
four-inch sliver of bone was displayed alongside human and gorilla skulls.
It was the latest important finding in east Africa's Rift Valley a region
long regarded as the 'cradle of humankind'.
'The teeth were covered in thick enamel and the caps were low and voluminous,
suggesting that the diet of this ape consisted of a considerable amount of
hard objects, like nuts or seeds, and fruit,' Yutaka Kunimatsu at Kyoto
University's Primate Research Institute said in a telephone interview.
'It could be positioned before the split between gorillas, chimps and humans,'
he added.
However, it was hard to determine what the new species, named Nakalipithecus
nakayamai, looked like.
'We only have some jaw fragments and some teeth ... but we hope to find other
body parts in our future research. We plan to go back next year. We will try
to find bones below the neck to tell us how the animal moved,' Kunimatsu said.
Published in the latest issue of the Proceedings of the National Academy of
Sciences, the finding is significant as it gives credence to the theory that
the evolution from ape to man may have taken place entirely in Africa.
Prior to this finding, there had been so little fossil evidence in Africa
dating between 7 to 13 million years ago that some experts began to surmise
that the last common ancestor left Africa for Europe and Asia, and then
returned later.
'Now, we have a good candidate in Africa. We do not need to think the common
ancestor came back from Eurasia to Africa. I think it is more likely the
common ancestor evolved from the apes in the Miocene in Africa,' Kunimatsu
said.
The Miocene is a period extending from 23.03 million to 5.33 million years ago.
'Some apes (then) left Africa and migrated to Eurasia. They then became
orangutans in Southeast Asia. Today's orangutan evolved from the apes that
left Africa,' he said.
==
Exquisitely preserved fossilized body imprints of ancient salamander-like
creatures have been discovered in 330-million-year-old Pennsylvanian rocks.
The foot-long amphibians lived 100 million years before the first dinosaurs.
"Body impressions like this are wholly unheard of," said paleontologist
Spencer Lucas, a curator at the New Mexico Museum of Natural History.
Lucas planned to present the discovery Tuesday at the annual meeting of the
Geological Society of America in Denver.
While lacking bones, the body imprints contain other rare information about
the bones, Lucas said. Without the imprints of the webbed four-toed feet, for
instance, it would be virtually impossible to say they were truly amphibians.
The imprints also provide body proportions data and reveals the creatures'
skin was smooth, not armor plated as might be expected, Lucas said.
The imprints were found in reddish- brown, fine-grained sandstone of the Mauch
Chunk Formation in eastern Pennsylvania. The rocks were collected decades ago
but had been sitting, unexamined, in the Reading Public Museum Collection in
that state. They were rediscovered by college student David Fillmore as part
of his senior thesis at Kutztown State University, also in Pennsylvania
==
Baddest Dinos Breathed Like Birds
Velociraptors, tyrannosaurs and other related carnivorous dinosaurs breathed
like some of todays diving birds and consequently were probably speedy
predators, a new study finds.
In recent years, paleontologists have learned that birds are direct ancestors
of theropod dinosaurs, sharing anatomical features such as hollow bones, three
functional toes on their feet and often even feathers.
"Our findings support this view and show that the similarities also extend to
breathing structures and that these dinosaurs possessed everything they needed
to breathe using an avian-like, air-sac respiratory system," said study leader
Jonathan Codd of the University of Manchester in Great Britain.
Birds, and in particular diving birds, such as pelicans, ospreys and
cormorants, have one of the most efficient respiratory systems of all
vertebrates because they need to supply their bodies with enough oxygen to
sustain them during flight.
Study co-author Phil Manning studied the fossilized remains of maniraptoran
dinosaurs and extinct birds, such as Archaeopteryx, and found that certain
modern birds' breathing structures, known as uncinate processes, were also
present in the dinosaurs.
"The uncinate processes are small bones that act as levers to move the ribs
and sternum during breathing," Codd said. "Interestingly, these structures are
different lengths in different birdsthey are shortest in running birds,
intermediate in flying birds and longest in diving birds."
"The dinosaurs we studied from the fossil record had long uncinate processes
similar in structure to those of diving birds," Codd added. "This suggests
both dinosaurs and diving birds need longer lever arms to help them breathe."
These findings, detailed in the Nov. 7 issue of the journal Royal Society B:
Biological Sciences, also support the theory that these dinosaurs were quick
off the mark when pursuing their prey, Codd said.
"Finding these structures in modern birds and their extinct dinosaur ancestors
suggests that these running dinosaurs had an efficient respiratory system and
supports the theory that they were highly active animals that could run
relatively quickly when pursuing their prey," he said.
==
Many Mammals Came from India, Discovery Suggests
As if hidden from the paleo tooth fairy, a lone molar belonging to a hoofed
mammal stayed tucked beneath a pillow of volcanic rock in central India for
more than 65 million years. Recently uncovered, the tooth predates similar
fossils found across the globe.
The dental discovery sheds light on the evolution of adaptations that allowed
a group of mammals called ungulates to thrive as expert grazers. It also
suggests, according to newly published research on the tooth, that the Indian
subcontinent could be the point of origin of many groups of mammals.
The lower right molar, about half the size of an ant (2.5 millimeters long),
was found embedded in central India's Deccan volcanic flows. The researchers
estimate the tooth dates back to the late Cretaceous period (144 million to 65
million years ago), a time when India was not connected with other continents
and dinosaurs still walked the Earth.
The fossil belonged to a new species of ungulate dubbed Kharmerungulatum
vanvaleni, a hoofed animal related to modern horses, cows, pigs, sheep and
deer. And it represents the oldest known evidence for the so-called archaic
ungulates (small, primitive hoofed mammals), predating by millions of years
the explosion of mammalian life that occurred during Paleocene Epoch, from 65
million to nearly 55 million years ago.
"Until now, the known fossil record of [the] oldest archaic ungulates or
supposed ancestors of living ungulates comes from the Early Paleocene of North
America," Guntupalli Prasad of the University of Jammu in India told
LiveScience. He is the lead author of the tooth study, detailed in the Nov. 9
issue of the journal Science.
The teeth of mammals living during the late Cretaceous, Prasad noted,
generally sported sharp and pointy cusps and, over evolutionary time, dental
modifications led to expert grinders. However, the tooth of the new mammal was
flat and broad, suggesting it was already adapted for munching grass rather
than for tearing through meaty meals.
"We consider Kharmerungulatum to represent an early stage in the evolution of
ungulates," Prasad and his colleagues write.
==
Ancient Spider Guts Revealed in 3-D
Digital wizardry has allowed scientists to see the insides of a
53-million-year-old fossilized spider in 3-D.
The male spider is about the size of a pinhead (or a stack of three salt
grains) and lived during the early Eocene epoch, from about 55 million to
nearly 34 million years ago.
It represents a new genus and species dubbed Cenotextricella simoni. It's also
the earliest fossil species of a family of micro-spiders called
Micropholcommatids from Australia, New Guinea, New Caledonia, New Zealand and
Chile.
The fossil was found preserved in amber in the Paris Basin in France.
Amber provides a unique window into past forest ecosystems," said lead author
David Penney, a paleo-arachnologist at the University of Manchester in
England. "It retains an incredible amount of information, not just about the
spiders themselves, but also about the environment in which they lived."
Normally, observing the minute features of an already tiny specimen would mean
cracking into the amber, potentially destroying the sample.
Instead of physical dissection, Penney and his colleagues used Very High
Resolution X-ray Computed Tomography to scan the bug through its amber grave.
The resulting 3-D reconstructions could be sectioned and viewed from various
angles, essentially allowing for digital dissection of the spider specimen.
This technique essentially generates full 3-D reconstructions of minute
fossils and permits digital dissection of the specimen to reveal the
preservation of internal organs," Penney said.
==
Darwin made important contributions not only to
evolutionary theory but to geology, thanks to his
observations in South America, so helpful to Lyell, &
his theory of atoll formation, & to many areas of
biology. His Beagle samples provided Owen with
invaluable specimens of fossil New World species, as
did his botanical collection for Henslow. He was the
first fully to study & classify barnacles. In botany,
he made fundamental contributions to understanding
orchids & insectivorous plants. His work with worms
was essential in developing behavioral scientists'
knowledge of the evolution of nervous systems &
response to stimuli.
==
Lack of nuclei in our red blood cells is of course a shared, derived
trait of our class of vertebrate, unlike birds, reptiles", amphibians
(except for one genus of.salamanders which independently lost its nuclei) &
fish.
==
http://en.wikipedia.org/wiki/Chimpanzee_genome_project
==
Lifestyle Accounts For Difference In Chimp, Human
Genome
Nearly 99 percent alike in genetic makeup, chimpanzees and
humans might be even more similar were it not for what
researchers call "lifestyle" changes in the 6 million
years that separate us from a common ancestor.
Specifically, two key differences are how humans and
chimps perceive smells and what we eat.
A massive gene-comparison project involving two
Cornell University scientists, and reported in the
latest issue of the journal Science (Dec. 12, 2003),
found these and many other differences in a search for
evidence of accelerated evolution and positive
selection in the genetic history of humans and chimps.
In the most comprehensive comparison to date of the
genetic differences between two primates, the genomic
analysts found evidence of positive selection in genes
involved in olfaction, or the ability to sense and
process information about odors. "Human and chimpanzee
sequences are so similar, we were not sure that this
kind of analysis would be informative, " says
evolutionary geneticist Andrew G. Clark, Cornell
professor of molecular biology and genetics. "But we
found hundreds of genes showing a pattern of sequence
change consistent with adaptive evolution occurring in
human ancestors." Those genes are involved in the
sense of smell, in digestion, in long-bone growth, in
hairiness and in hearing. "It is a treasure-trove of
ideas to test by more careful comparison of human and
chimpanzee development and physiology," Clark says.
The DNA sequencing of the chimpanzee was performed by
Celera Genomics, in Rockville, Md., as part of a
larger study of human variation headed by company
researchers Michele Cargill and Mark Adams.
Celera generated some 18 million DNA sequence "reads,"
or about two-thirds as many as were required for the
first sequencing of the human genome. Statistical
modeling and computation was done by Clark and by
Rasmus Nielsen, a Cornell assistant professor of
biological statistics and computational biology. Some
of the analysis, which also compared the mouse genome,
used the supercomputer cluster at the Cornell Theory
Center. Clark explains, "By lining up the human and
chimpanzee gene sequences with those of the mouse, we
thought we might be able to find genes that are
evolving especially quickly in humans. In a sense,
this method asks: What are the genes that make us
human? Or rather, what genes were selected by natural
selection to result in differences between humans and
chimps?" The study started with almost 23,000 genes,
but this number fell to 7,645 because of the need to
be sure that the right human, chimp and mouse genes
were aligned.

According to Clark, all mammals have an extensive
repertoire of olfactory receptors, genes that allow
specific recognition of the smell of different
substances. "The signature of positive selection is
very strong in both humans and chimps for tuning the
sense of smell, probably because of its importance in
finding food and perhaps mates," says Clark. In
addition to the great departure in smell perception,
differences in amino acid metabolism also seem to
affect chimps' and humans' abilities to digest dietary
protein and could date back to the time when early
humans began eating more meat, Clark speculates.
Anthropologists believe that this occurred around 2
million years ago, in concert with a major climate
change.

"This study also gives tantalizing clues to an even
more complex difference -- the ability to speak and
understand language," Clark says. "Perhaps some of the
genes that enable humans to understand speech work not
only in the brain, but also are involved in hearing."
Evidence for this came from a particularly strong sign
of selection acting on the gene that codes for an
obscure protein in the tectorial membrane of the inner
ear. One form of congenital deafness in humans is
caused by mutations to this gene, called alpha
tectorin.

Mutations in alpha tectorin result in poor frequency
response of the ear, making it hard to understand
speech. "It's something like replacing the soundboard
of a Stradivarius violin with a piece of plywood,"
Clark notes. The large divergence between humans and
chimps in alpha tectorin, he says, could imply that
humans needed to tune the protein for specific
attributes of their sense of hearing. This leads Clark
to wonder whether one of the difficulties in training
chimpanzees to understand human speech is that their
hearing is not quite up to the task. Although studies
of chimpanzee hearing have been done, detailed tests
of their transient response have not been carried out.

Clark emphasizes that a study like this cannot prove
that the biology of humans and chimps differ because
of this or that particular gene. "But it generates
many hypotheses that can be tested to yield insight
into exactly why only 1 percent in DNA sequence
difference makes us such different beasts," he says.

Also collaborating in the study were researchers at
Applied Biosystems (Foster City, Calif.), Celera
Diagnostics (Alameda, Calif.) and Case Western Reserve
University in Cleveland. The Science report is titled,
"Inferring non-neutral evolution from
human-chimp- mouse orthologous gene trios."


Human-Chimp Differences Uncovered With Analysis Of
Rhesus Monkey Genome

ScienceDaily (Apr. 13, 2007) An international
consortium of researchers has published the genome
sequence of the rhesus macaque monkey and aligned it
with the chimpanzee and human genomes. Published April
13 in a special section of the journal Science, the
analysis reveals that the three primate species share
about 93 percent of their DNA, yet have some
significant differences among their genes.

In its paper, the Rhesus Macaque Genome Sequence and
Analysis Consortium, supported in part by the National
Human Genome Research Institute (NHGRI), one of the
National Institutes of Health (NIH), compared the
genome sequences of rhesus macaque (Macaca mulatta)
with that of human (Homo sapiens) and chimp (Pan
troglodytes) , the primate most closely related to
humans. Four companion papers that relied on the
rhesus sequence also appear in the same issue.

The rhesus genome is the second non-human primate,
after the chimp, to have its genome sequenced and is
the first of Old World monkeys to have its DNA
deciphered.

"The sequencing of the rhesus macaque genome, combined
with the availability of the chimp and human genomes,
provides researchers with another powerful tool to
advance our understanding of human biology in health
and disease," said NHGRI Director Francis S. Collins,
M.D., Ph.D. "As we build upon the foundation laid by
the Human Genome Project, it has become clear that
comparing our genome with the genomes of other
organisms is crucial to identifying what makes the
human genome unique."

The rhesus, because of its response to the simian
immunodeficiency virus (SIV), is widely recognized as
the best animal model for human immunodeficiency virus
(HIV) infection. The rhesus genome sequence will also
serve to enhance essential research in neuroscience,
behavioral biology, reproductive physiology,
endocrinology and cardiovascular studies. In addition,
the rhesus serves as a valuable model for studying
other human infectious diseases and for vaccine
research.
The sequencing of the rhesus genome was conducted at
the Baylor College of Medicine Human Genome Sequencing
Center in Houston, the Genome Sequencing Center at
Washington University School of Medicine in St. Louis
and the J. Craig Venter Institute in Rockville, Md.,
which are part of the NHGRI-supported Large-Scale
Sequencing Research Network. The DNA used in the
sequencing was obtained from a female rhesus macaque
at the Southwest National Primate Research Center
(NPRC) in San Antonio, which is supported by the
National Center for Research Resources, part of NIH.
Independent assemblies of the rhesus genome data were
carried out at each of the three sequencing centers
using different and complementary approaches and then
combined into a single "melded assembly." In their
analysis, scientists from 35 institutions compared
this melded assembly to the reference sequence of the
human genome, a newer unpublished draft sequence of
the chimp genome, the sequence of more than a dozen
other more distant species already in the public
databases, the human HapMap, and the Human Gene
Mutation Database that lists known human mutations
that lead to genetic disease.
"This study of the rhesus genome is invaluable because
it gives researchers a perspective to observe what has
been added or deleted in each primate genome during
evolution of rhesus, chimp, and the human from their
common ancestors ," said Richard Gibbs, Ph.D.,
director of Baylor College of Medicine's Human Genome
Sequencing Center in Houston and the project leader.

One of the most useful features of the rhesus genome
is that it is less closely related to the human genome
than to the chimp genome. This means that important
features that have been conserved in primates over
time can be more easily seen by comparing rhesus to
human, than chimp to human.
By adding the rhesus genome to the primate comparison,
researchers identified nearly 200 genes likely to be
key players in determining differences among primate
species. These include genes involved in hair
formation, immune response, membrane proteins and
sperm-egg fusion. Many of these genes are located in
areas of the primate genome that have been subject to
duplication, indicating that having an extra copy of a
gene may enable it to evolve more rapidly and that
small duplications are a key feature of primate
evolution.
The analysis also revealed a few instances in which
whole families of genes were radically different in
the rhesus, containing more copies of certain genes
than in the chimp or human. These gene families
include important immune related genes, as well as
genes with functions not yet fully known.
In addition to comparing the rhesus with the chimp and
human genomes, the group also studied genetic
variation in macaque populations, and developed a set
of 'single nucleotide polymorphisms' or SNPs (single
base DNA differences) that can be used for future
analysis of inheritance of biomedically important
traits in rhesus. The rhesus genomic DNA samples used
for these studies were contributed by the California
NPRC, Oregon NPRC, Southwest NPRC and Yerkes NPRC.
This advance in macaque genetics will enhance the use
of macaques for the study of genetic diseases of man.
The rhesus study is part of an ongoing program to
analyze primate genomes. Other primate genomes
underway include the marmoset, gibbon and gorilla.
Researchers at the Baylor Center and the Washington
University Genome Center completed the raw sequence
for the orangutan and marmoset genomes early this
year. Researchers plan to analyze the orangutan and
marmoset genomes and compare them with the other
primates over the summer.
==
Divergent bird species can hybridize over greater genetic distances
than mammals, but that is probably due to developmental constraints of
having to develop inside an egg instead of a variable womb.
We can still get chicken and quail and chicken and turkey hybrids, and you
don't see mammal hybrids between species that distantly related.
==
What's in Your Genes? Ancient Parasites
You may not know it, but you're part virus.
At least, some of your genes come from viruses that slipped their DNA into the
genes of our primate ancestors millions of years ago.
The DNA remnants of these ancient "retroviruses," distant relatives of today's
HIV, account for an estimated 8 percent of the human genetic code and may have
enabled master genes that account for some of the differences between us and
our chimpanzee relatives.
Master genes
Not all genes are created equal; the master genes can turn the others on and
off, thus gaining control over genes related to cell division, DNA repair and
programmed cell death. (This regulation of genes allows for tighter control of
gene expression (i.e. which genes are turned on or off), which can account for
the wide differences between humans and other apes, despite our very similar
genetic codes.)
One such gene, called p53, has the job of coordinating the surveillance system
that monitors the well-being of cells. It is so important in this job that when
it fails, cancer is often the resultbiologists even call it the "guardian of
the genome."
Scientists had long wondered how genes such as p53 built their powerful empire
over other genes. A new study detailed this week in the online edition of the
journal Proceedings of the National Academy of Sciences implicates the ancient
retroviruses as the force behind p53's rise to power.
Repetitive DNA
Scientists at the University of California, Santa Cruz, analyzed and compared
genetic data from different species and found that certain retroviruses
entered the genome about 40 million years ago and spread rapidly in primates
about 25 million years ago.
Earlier research had shown that the DNA remnants of retroviruses like to jump
around in the genetic code, and it's this movement into new positions
throughout the human genome that spread copies of repetitive DNA sequences,
which in turnallowed p53 to regulate many other genes, the UCSC team said.
(The association between the sequences and gene regulation had been suspected
as far back as 1971.)
"This would have provided a mechanism to quickly establish a gene regulatory
network in a very short evolutionary time frame," said lead researcher Ting
Wang.
The results also call into question previous views that these repetitive
sequences, or so-called junk-DNA, didn't code for anything or serve a
particular purpose.
"We're starting to uncover the treasure in this junk," Wang said.
==
From the
beginning of Chapter 13. This & numerous other parts
of the book explicitly detail Darwin's view that
species evolve from ancestral species, races &
varieties, by means of natural selection acting on the
inherent, heritable variation observable in groups of
organisms:

"From the first dawn of life, all organic beings are
found to resemble each other in descending degrees, so
that they can be classed in groups under groups. This
classification is evidently not arbitrary like the
grouping of the stars in constellations. The existence
of groups would have been of simple signification, if
one group had been exclusively fitted to inhabit the
land, and another the water; one to feed on flesh,
another on vegetable matter, and so on; but the case
is widely different in nature; for it is notorious how
commonly members of even the same subgroup have
different habits. In our second and fourth chapters,
on Variation and on Natural Selection, I have
attempted to show that it is the widely ranging, the
much diffused and common, that is the dominant species
belonging to the larger genera, which vary most. The
varieties, or incipient species, thus produced
ultimately become converted, as I believe, into new
and distinct species; and these, on the principle of
inheritance, tend to produce other new and dominant
species. Consequently the groups which are now large,
and which generally include many dominant species,
tend to go on increasing indefinitely in size. I
further attempted to show that from the varying
descendants of each species trying to occupy as many
and as different places as possible in the economy of
nature, there is a constant tendency in their
characters to diverge. This conclusion was supported
by looking at the great diversity of the forms of life
which, in any small area, come into the closest
competition, and by looking to certain facts in
naturalisation.

"I attempted also to show that there is a constant
tendency in the forms which are increasing in number
and diverging in character, to supplant and
exterminate the less divergent, the less improved, and
preceding forms. I request the reader to turn to the
diagram illustrating the action, as formerly
explained, of these several principles; and he will
see that the inevitable result is that the modified
descendants proceeding from one progenitor become
broken up into groups subordinate to groups. In the
diagram each letter on the uppermost line may
represent a genus including several species; and all
the genera on this line form together one class, for
all have descended from one ancient but unseen parent,
and, consequently, have inherited something in common.
But the three genera on the left hand have, on this
same principle, much in common, and form a sub-family,
distinct from that including the next two genera on
the right hand, which diverged from a common parent at
the fifth stage of descent. These five genera have
also much, though less, in common; and they form a
family distinct from that including the three genera
still further to the right hand, which diverged at a
still earlier period. And all these genera, descended
from (A), form an order distinct from the genera
descended from (I). So that we here have many species
descended from a single progenitor grouped into
genera; and the genera are included in, or subordinate
to, sub-families, families, and orders, all united
into one class. Thus, the grand fact in natural
history of the subordination of group under group,
which, from its familiarity, does not always
sufficiently strike us, is in my judgement fully
explained.

"Naturalists try to arrange the species, genera, and
families in each class, on what is called the Natural
System. But what is meant by this system? Some authors
look at it merely as a scheme for arranging together
those living objects which are most alike, and for
separating those which are most unlike; or as an
artificial means for enunciating, as briefly as
possible, general propositions, that is, by one
sentence to give the characters common, for instance,
to all mammals, by another those common to all
carnivora, by another those common to the dog-genus,
and then by adding a single sentence, a full
description is given of each kind of dog. The
ingenuity and utility of this system are indisputable.
But many naturalists think that something more is
meant by the Natural System; they believe that it
reveals the plan of the Creator; but unless it be
specified whether order in time or space, or what else
is meant by the plan of the Creator, it seems to me
that nothing is thus added to our knowledge. Such
expressions as that famous one of Linnaeus, and which
we often meet with in a more or less concealed form,
that the characters do not make the genus, but that
the genus gives the characters, seem to imply that
something more is included in our classification, than
mere resemblance. I believe that something more is
included; and that propinquity of descent, the only
known cause of the similarity of organic beings, is
the bond, hidden as it is by various degrees of
modification, which is partially revealed to us by our
classifications. "
==
"A few words need to be said about the "theory of evolution," which
most people take to mean the proposition that organisms have evolved
from common ancestors. In everyday speech, "theory" often means a
hypothesis or even a mere speculation. But in science, "theory"
means "a statement of what are held to be the general laws,
principles, or causes of something known or observed." as the Oxford
English Dictionary defines it. The theory of evolution is a body of
interconnected statements about natural selection and the other
processes that are thought to cause evolution, just as the atomic
theory of chemistry and the Newtonian theory of mechanics are bodies
of statements that describe causes of chemical and physical
phenomena. In contrast, the statement that organisms have descended
with modifications from common ancestors--the historical reality of
evolution--is not a theory. It is a fact, as fully as the fact of the
earth's revolution about the sun. Like the heliocentric solar system,
evolution began as a hypothesis, and achieved "facthood" as the
evidence in its favor became so strong that no knowledgeable and
unbiased person could deny its reality. No biologist today would
think of submitting a paper entitled "New evidence for evolution;" it
simply has not been an issue for a century.
- Douglas J. Futuyma, Evolutionary Biology, 2nd ed., 1986, Sinauer
Associates, p. 15
==
The discovery of New World mangrove swamp fish which
can survive for months out of water really doesn't add
much to our understanding of the evolution of land
vertebrates, but is instructive nonetheless.

http://news. yahoo.com/ s/nm/20071114/ sc_nm/belize_ fish_dc

Unlike our tetrapod ancestors, who were blessed with
lungs, these little fish breathe through their skin.
The article mentions the lungfish, who are our closest
relative among primarily aquatic vertebrates. The
South American & African genera of lungfish are
arguably "amphibian" in lifestyle, since they can live
for long periods out of water, although they go into
hibernation when their river, lake or pond habitats
dry out.

Unlike our ancestors, the paired dorsal fins of these
lungfish don't make very good limbs for terrestrial
locomotion. But then neither does the SE Asian
"walking" catfish, although the mudskipper does. The
lobe-finned ancestors of lungfish & tetrapods (like
us) did have fins pre-adapted to become arms & legs,
containing the necessary long bones, but modern
African & American lungfish fins have evolved in one
direction while we land vertebrates have gone in the
other, with the addition of hand, foot & digit bones.

However, the Australian lungfish does show the same
condition as ancestral tetrapods:

http://www.nhm. ac.uk/about- us/news/2007/ october/news_ 12547.html

Land vertebrates are more closely related to
lobe-finned fish, the coelacanths & lungfish, than are
the lobe-fins to the other main group of fish, the
much more numerous ray-fins. We tetrapods are a
specialized group of lobe-finned fish.
==
Dinosaurs are a superorder within an infraclass of the subclass Diapsida,
which includes crocodiles and lizards and snakes, i.e., reptiles.
==
1 species evolve differently under differing environmental pressures
2 members of species will tend to invade new territories that
are similar (for their purposes) to their existing territories.
3 A fluctuating environment will see changes of many and varied
character, but after a fluctuation many existing environments
will have new adjacent environments that are similar to the
old one, but many of the new adjacent (or overlayed)
environments will be similar to the original in different ways.
Thus, in a fluctuating environment different subgroups of an
existing species will find themselves on opposite sides of
differing environments, under differential selective pressures.
I will complete this argument below.
is at least one other known from Northwest Europe. I can look
it up if you're interested, although I cannot imagine it having
any effect on this discussion.
I'm not going to waste time arguing about whether the diet
change in some Rhagoletis is by itself sufficient for
speciation (although I think this to be VERY VERY likely),
rather I will make the obvious point that fruit trees have
various and overlapping/separate ranges, governed by things
like soil conditions, temperature, parasites etc.
Consequently, by a simple process of hopping from host to host
over generations, some Rhagoletis will eventually find
themselves reproductively isolated
==
Double Trouble: What Really Killed the Dinosaurs
Instead of being driven to extinction by death from above, dinosaurs might
have ultimately been doomed by death from below in the form of monumental
volcanic eruptions.
The suggestion is based on new research that is part of a growing body of
evidence indicating a space rock alone did not wipe out the giant reptiles.
The Age of Dinosaurs ended roughly 65 million years ago with the K-T or
Cretaceous-Tertiary extinction event, which killed off all dinosaurs save
those that became birds, as well as roughly half of all species on the planet,
including pterosaurs. The prime suspect in this ancient murder mystery is an
asteroid or comet impact, which left a vast crater at Chicxulub on the coast
of Mexico.
Another leading culprit is a series of colossal volcanic eruptions that
occurred between 63 million to 67 million years ago. These created the
gigantic Deccan Traps lava beds in India, whose original extent may have
covered as much as 580,000 square miles (1.5 million square kilometers), or
more than twice the area of Texas.
Arguments over which disaster killed the dinosaurs often revolve around when
each happened and whether extinctions followed. Previous work had only
narrowed the timing of the Deccan eruptions to within 300,000 to 500,000 years
of the extinction event.
Now research suggests the mass extinction happened at or just after the
biggest phase of the Deccan eruptions, which spewed 80 percent of the lava
found at the Deccan Traps.
"It's the first time we can directly link the main phase of the Deccan Traps
to the mass extinction," said Princeton University paleontologist Gerta Keller.
Clues in other life forms
Keller and colleagues focused on marine fossils excavated at quarries at
Rajahmundry, India, near the Bay of Bengal, about 600 miles (1,000 kilometers)
southeast of the center of the Deccan Traps near Mumbai. Specifically, they
looked at the remains of microscopic shell-forming organisms known as
foraminifera.
"Before the mass extinction, most of the foraminifera species were
comparatively large, very flamboyant, very specialized, very ornate, with many
chambers," Keller explained. These foraminifera were roughly 200 to 350 microns
large, or a fifth to a third of a millimeter long.
These showy foraminifera were very specialized for particular ecological
niches.
"When the environment changed, as it did around K-T, that prompted their
extinction," she added. "The foraminifera that followed were extremely tiny,
one-twentieth the size of the species before, with absolutely no
ornamentation, just a few chambers." As such, these puny foraminifera serve as
very distinct tags of when the K-T extinction event started.
The researchers found these simple foraminifera seem to have popped up right
after the main phase of the Deccan volcanism. This in turn hints these
eruptions came immediately before the mass extinction, and might have caused
it.
Double trouble
Both an impact from space and volcanic eruptions would have injected vast
clouds of dust and other emissions into the sky, dramatically altering global
climate and triggering die-offs. Keller's collaborator, volcanologist Vincent
Courtillot at the Institute of Geophysics in Paris, noted upcoming work from
her collaborators suggests the Deccan eruptions could have quickly released 10
times more climate-altering emissions than the nearly simultaneous Chicxulub
impact.
Keller stressed these findings do not deny that an impact occurred around the
K-T boundary, and noted that one or possibly several impacts may have had a
hand in the mass extinction. "The dinosaurs might have faced an unfortunate
coincidence of a one-two punchof Deccan volcanism and then a hit from space,"
she explained. "We just show the Deccan eruptions might have had a significant
impact no pun intended."
Although paleontologist Kirk Johnson at the Denver Museum of Nature and
Science called these new findings "significant," he noted a great deal of
evidence connected a single massive impact with the K-T extinction event. He
suggested that advances in radioisotope dating could now hone down when the
Deccan eruptions occurred to within 30,000 to 65,000 years. "That could help
put to bed some of the disputes regarding the issue," he said.
==
Observation of evidence they have BEFORE they had the idea of
evolution?
Observation of the similarities among living things.
Observation that living things could be classified into a hierarchy.
Fossils of things that weren't of any existing species. Fossils of
living things in places where they didn't currently exist.
Observation of the historical stratification of the earth's surface.
==
Evidence is accumulating that most phyla began in the Ediacaran, but only
became larger, with more hard body parts, so left more
visible fossil & trace evidence in the Cambrian.
==
Study the 8th chapter of
"Origin", 1st edition, in which Darwin discusses how
his concept of "species, races & varieties" differs
from the creationist idea of immutable forms. But in
fact he does this throughout the book, without that I
know of ever stating a precise definition, which is
precisely his point.
He, like other 19th century biologists, realized that
species weren't immutable, but no one had yet
adequately explained how they changed. In this
preface, he reviews some prior attempts. Similarly,
some 19th century doctors had inklings about the
nature of infection but no one adequately explained
the phenomenon before Pasteur's germ theory of
disease.
To quote from the first paragraph of the preface
(Aristotle on teeth edited out) detailing Darwin's
forebearers in evolution & natural selection:
"I will here give a brief sketch of the progress of
opinion on the Origin of Species. Until recently the
great majority of naturalists believed that species
were immutable productions, and had been separately
created. This view has been ably maintained by many
authors. Some few naturalists, on the other hand, have
believed that species undergo modification, and that
the existing forms of life are the descendants by true
generation of pre existing forms. Passing over
allusions to the subject in the classical writers
(Aristotle, in his "Physicae Auscultationes" ...And in
like manner as to other parts in which there appears
to exist an adaptation to an end. Wheresoever,
therefore, all things together (that is all the parts
of one whole) happened like as if they were made for
the sake of something, these were preserved, having
been appropriately constituted by an internal
spontaneity; and whatsoever things were not thus
constituted, perished and still perish." We here see
the principle of natural selection shadowed forth, but
how little Aristotle fully comprehended the principle,
is shown by his remarks on the formation of the
teeth.), the first author who in modern times has
treated it in a scientific spirit was Buffon. But as
his opinions fluctuated greatly at different periods,
and as he does not enter on the causes or means of the
transformation of species, I need not here enter on
details."
There follows Darwin's citation of numerous
precursors, with some of whose work, such as Lamarck &
his own grandfather, he was familiar. Below, I've
adapted Wiki's article on Buffon.
Buffon is best remembered for his great work "Histoire
naturelle, generale et particuliere" (1749-1778: in 36
volumes, 8 additional volumes published after his
death). It included everything known about the natural
world up until that date. He noted that despite
similar environments, different regions have distinct
plants and animals, a concept later known as Buffon's
Law, widely considered the first principle of
Biogeography. He made the radical conclusion that
species must have both "improved" and "degenerated"
(evolved) after dispersing away from a center of
creation. He also asserted that climate change must
have facilitated the worldwide spread of species from
their center of origin.
Buffon considered the similarities between humans and
apes, and the possibility of a common ancestry. Buffon
debated James Burnett, Lord Monboddo on the question
of ancestry of the primates to man, Monboddo insisting
on the closeness of relationship of man and
apes...Buffon' s work is considered to have greatly
influenced modern ecology (see history of ecology).
His "Histoire" was translated into many different
languages, making him the most widely read scientific
author of the day, equaling Rousseau and Voltaire.
In "Les epoques de la nature" (1778) Buffon...also
suggested that the earth originated much earlier than
the 4004 BC date proclaimed by Archbishop James
Ussher. Based on the cooling rate of iron, he
calculated that the age of the earth was 75,000 years.
For this he was condemned by the Catholic Church in
France and his books were burned. Buffon also denied
that Noah's flood ever occurred and observed that some
animals retain parts that are vestigial and no longer
useful, suggesting that they have evolved rather than
having been spontaneously generated. Despite this,
Buffon insisted that he was not an atheist. (End Wiki)
A later French-German scientist, Cuvier, showed that
extinction was a fact. (Below from Wiki) At the time
(he) presented his 1796 paper on living and fossil
elephants, it was still widely believed that no
species of animal had ever become extinct, because
God's creation had been perfect. Authorities such as
Buffon had claimed that fossils found in Europe of
animals such as the woolly rhinoceros and mammoth were
remains of animals still living in the tropics (ie
rhinoceros and elephants), which had shifted out of
Europe and Asia as the earth became cooler. Cuvier's
early work demonstrated conclusively that this was not
the case.
===
A mutation involves the disabling of a keratin I gene designated hHaA in
humans. The gene remains fully active in chimpanzees and gorillas.
The gene is virtually identical in Man, chimpanzee and gorilla
except that in Man there is a point mutation at base pair 818, changing
the sequence from a C to a T here and completing the TGA "stop"
codon. Production of the protein is stopped at this point and the rest
of the 688 base pairs of the gene are not even read. The fragment of
protein produced is non-functional and is eventually simply
re-digested by the cellular peptide clean up process.
In gorillas and chimpanzees, of course, the whole gene is read and
functional protein is produced by the hHaA gene and incorporated into
the body hair of the animals, giving them their
distinctive thick hairy coat. The gene was sequenced from some 80
human individuals from various ethnic groups, including
representatives of 8 sub-Saharan groups which are some of the oldest human
populations, and all of them were homozygous for the inactivating
point mutation in the hHaA gene. (see H. Winter, January 2001, Human
Genetics (vol.108:37-42).
==
Mutation
Our model bacterium is Esherichia coli the common, and mostly benign,
intestinal bacterium. The entire genome was sequenced in 1997 (Blattner et
al., 1997) and its size is 4,200,000 base pairs (4.2 106 bp). Every time a
bacterium divides this amount of DNA has to be replicated; thats 8,400,000
nucleotides (8.4 106).

The most common source of mutation is due to mistakes made during DNA
replication when an incorrect nucleotide is incorporated into newly
synthesized DNA. The mutation rate due to errors made by the DNA polymerase
III replisome is one error for every one hundred million bases (nucleotides)
that are incorporated into DNA. This is an error rate of 1/100,000,000,
commonly written as 10-8 in exponential notation. Technically, these aren't
mutations; they count as DNA damage until the problem with mismatched bases in
the double-stranded DNA has been resolved. The DNA repair mechanism fixes 99%
of this damage but 1% escapes repair and becomes a mutation. The error rate of
repair is 10-2 so the overall error rate during DNA replication is 10-10
nucleotides per replication (10-8 10-2) (Tago et al., 2005).
Since the overall mutation rate is lower than the size of the E. coli genome,
on average there wont be any mistakes made when the cell divides into two
daughter cells. That is, the DNA will usually be replicated error free.
However, one error will occur for every 10 billion nucleotides (10-10) that
are incorporated into DNA. This means one mutation, on average, every 1200
replications (8.4 106 1200 is about ten billion). This may not seem like
much even if the average generation time of E. coli is 24 hours. It would seem
to take four months for each mutation. But bacteria divide exponentially so the
actual rate of mutation in a growing culture is much faster. Each cell produces
two daughter cells so that after two generations there are four cells and after
three generations there are eight cells. It takes only eleven generations to
get 2048 cells (211 = 2048). At that point you have 2048 cells dividing and
the amount of DNA that is replication in the entire population is enough to
ensure at least one error every generation.
In the laboratory experiment the bacteria divided every half hour so after
only a few hours the culture was accumulating mutations every time the
bacteria divided. This is an unrealistic rate of growth in the real world but
even if bacteria only divide every 24 hours there are still so many of them
that mutations are abundant. For example, in your intestine there are billions
and billions of bacteria. This means that every day these bacteria accumulate
millions of mutations. Thats why theres a great danger of developing drug
resistance in a very short time. Calculating the rate of evolution in terms of
nucleotide substitutions seems to give a value so high that many of the
mutations must be neutral ones.
Motoo Kimura (1968)I based my estimate of mutation rate on what we know about
the properties of the replisome and repair enzymes. Independent measures of
mutation rates in bacteria are consistent with this estimate. For example, the
measured value for E. coli is 5.4 10-10 per nucleotide per replication (Drake
et al., 1998). Many of these mutations are expected to be neutral. The rate of
fixation of neutral mutations is equal to the mutation rate so by measuring the
accumulation of neutral mutations in various lineages of bacteria you can
estimate the mutation rate provided you know the time of divergence and the
generation time. (Ochman et al., 1999) have estimated that the mutation rate
in bacteria is close to 10-10 assuming that bacteria divide infrequently.
The mutation rate in eukaryotes should be about the same since the properties
of the DNA replication machinery are similar to those in eukaryotes. Measured
values of mutation rates in yeast, Caenorhabditis elegans, Drosophila
melanogaster, mouse and humans are all close to 10-10 (Drake et al., 1998).
The haploid human genome is about 3 109 base pairs in size. Every time this
genome is replicated about 0.3 mutations, on average, will be passed on to one
of the daughter cells. We are interested in knowing how many mutations are
passed on to the fertilized egg (zygote) from its parents. In order to
calculate this number we need to know how many DNA replications there are
between the time that one parental zygote was formed and the time that the egg
or sperm cell that unite to form the progeny zygote are produced.
In the case of females, this number is about 30, which means that each of a
females eggs is the product of 30 cell divisions from the time the zygote was
formed (Vogel and Rathenberg, 1975). Human females have about 500 eggs. In
males, the number of cell divisions leading to mature sperm in a 30 year old
male is about 400 (Vogel and Motulsky, 1997). This means that about 9
mutations (0.3 30) accumulate in the egg and about 120 mutations (0.3 400)
accumulate in a sperm cell. Thus, each newly formed human zygote has
approximately 129 new spontaneous mutations. This value is somewhat less than
the number in most textbooks where it's common to see 300-350 mutations per
genome. The updated value reflects a better estimate of the overall rate of
mutation during DNA replication and a better estimate of the number of cell
divisions during gametogenesis.
With a population of 6 billion individuals on the planet, there will be 120
6 109 = 7.2 1011 new mutations in the population every generation. This
means that every single nucleotide in our genome will be mutated in the human
population every 20 years or so.
==
http://www.talkorigins.org/features/whales/
==
The National Human Genome Research Institute of the
NIH has targeted nine chordates for total genomic
sequencing in order to trace the evolution not only of
our genome but of the proteins encoded by our genes.
Understanding on the genetic level evolution of
chordates over the past 550 million years will yield
great practical benefits to medical research,
especially with reference to the proteins encoded by
our genes.
http://www.genome. gov/Pages/ Research/ Sequencing/ SeqProposals/
EvolutionOfProte ome.pdf
The NHGRI wants to sequence characteristic organisms
from each node or major divergence or transition point
in evolution from simple chordates to humans today.
Many significant animals' genomes have already been
fully sequenced, especially among mammals, but certain
key nodes remain to be represented. Below are the
projects the NHGRI wants undertaken. Sorry about the
jargon & abbreviations (Gb refers to genome size):
Summary: We propose the sequencing of 9 chordate
species to complete the coverage of all major nodes of
chordate evolution with at least two sequenced
species. These include;
1. Reptile 1: Alligator mississipiensis (2.5 Gb
genome), the American alligator, for high quality
draft genomic sequence (approx. 6x) plus ESTs.
2. Reptile 2: Chrysemys picta (2.6 Gb genome), the
painted turtle, for high quality draft genomic
sequence (approx. 6x) plus ESTs.
3. Amphibian: Ambystoma mexicanum (>32 Gb genome), the
Mexican axolotl, a urodele, for 100,000 ESTs only.
4. Sarcopterygian fish 1: Latimeria chalumnae (2.75 Gb
genome), the African coelacanth, for high quality
draft genomic sequence (approx. 6x) plus ESTs.
5. Sarcopterygian fish 2: Neoceratodus forsteri (>30
Gb genome), the Australian lungfish, for 100,000 ESTs
only.
6. Basal actinopterygian fish: Lepisosteus oculatus
(1.4 Gb genome), the spotted gar, for high quality
draft genomic sequence (approx. 6x) plus ESTs.
7. Cartliaginous fish: Raja erinacea (3.3 Gb genome),
the little skate, for high quality draft genomic
sequence (approx. 6x) plus ESTs.
8. Jawless fish: Eptatretus burgeri (2.5-3.0 Gb
genome), the Japanese Hagfish, for high quality draft
genomic sequence (approx. 6x) plus ESTs.
9. Basal chordate: Branchiostoma lanceolatum (0.6 Gb
genome), the European lancelet or amphioxus, for high
quality draft genomic sequence (approx. 6x) plus
50,000 ESTs.
On page 19 of the link above, there's an accessible,
simplified cladogram showing the evolutionary
relationships among chordate groups as presently
understood, although a few are still controversial.
Completion of sequences for the species listed above
will help resolve remaining questions.
For instance, the phylogenetic position of turtles has
long been controversial, but genetic evidence has now
fairly firmly nested them as sister group to the
archosaurs (birds & crocs) rather than closer to
lepidosaurs (snakes & lizards) or as out group to both
these diapsid taxa, as once thought. (Turtles are
"anapsid", ie lacking holes in their skulls, but are
now considered not to be Anapsids, ie members of the
early stem group of "reptiles" from which both
Synapsids, the ancestors of mammals, & Diapsids, ie
birds, crocs, snakes, lizards & tuataras, arose. They
are now considered to be secondarily anapsid, ie as
having lost the two openings behind their eyes
characteristic of Diapsids.)
Note the smaller genome size for basal chordates.
Recent research has found two instances of gene
duplication in vertebrate evolution, particularly in
the Hox complex. Duplications appear to have occurred
both before & after the jawless fish node. (The
precise status of hagfish & lampreys as vertebrates
remains somewhat controversial & partly merely
definitional. ) We are polyploid for a number of
genes. Certain amphibians & African lungfish have
gigantic genomes.
==
The first monsters: long before sharks, Anomalocaris ruled the seas.
The doomed trilobite trilobite(tri`l?bit'), subphylum of the phylum
Arthropodathat includes a large group of extinct marine animals that were
abundant in the Paleozoic era. They represent more than half of the known
fossils from the Cambrian period.scuttled across the floor of some prehistoric
ocean, oblivious to a pair of bulbous eyes projecting up out of the muck like
twin periscopes. As the unsuspecting animal passed, the camouflaged predator
bolted from its lair, raising a cloud of obscuring silt.
The trilobite rolled into an armored ball, its hardened shell forming a nearly
impenetrable shield. But against this opponent, the defensive gesture provided
little protection. Two grasping limbs pucked the trilobite off the seafloor
and popped it into a circular mouth unlike any known on the planet today. A
ghastly ring of teeth crushed the shell as if it were a nut.
Just as it terrorized the seas of Earth's Cambrian period Cambrian period[Lat.
Cambria=Wales], first period of the Paleozoic geologic era (see Geologic
Timescale, table) extending from approximately 570 to 505 million years ago.
It was named by the 19th-century English geologist Adam Sedgwick, who first
studied the great sequence of rocks characteristic of the period near Cambria,
Wales. During the Cambrian, the continents and seas differed from present day
configurations.a half billion years ago, this nightmarish creature called
Anomalocaris has plagued paleontologists since the 1880s, when parts of the
strange beast first surfaced. A century passed before researchers could
finally piece together the different parts of this anatomical oddity Today,
Anomalocaris and its kin are yielding new secrets, thanks to specimens
recently uncovered in southwest China and other regions.
"We have found the earliest monsters," declares Jun-yuan Chen of the Nanjing
Institute of Geology and Paleontology, referring to the extreme antiquity of
the Chinese animals. These anomalocaridids are the oldest-known large
predators in the fossil record, and their presence in the Cambrian seas
reveals that an elaborate ecosystem had developed far earlier than
paleontologists previously thought.
The anomalocaridids appeared at a turning point in the history of life. Prior
to the start of the Cambrian period 544 million years ago, animals had
extremely simple bodies capable of limited motion. A zoo at the close of
Precambrian time would have displayed a relatively mundane array of creatures
related to jellyfish and coral; the star attractions would have been wormlike
animals, which distinguished themselves with their ability to slither across
the seafloor.
At the beginning of the Cambrian, however, life took a sudden turn toward the
complex. In a few million years - the equivalent of a geological instant - an
ark's worth of sophisticated body types filled the seas. This biological
burst, dubbed the Cambrian explosion, produced the first skeletons and hard
shells, antennae and legs, joints and jaws. It set the evolutionary stage for
all that followed by giving rise to most of the major phyla known on Earth
today. Even our own chordate
1. an animal of the Chordata.
2. having a notochord.
------------------------------------------------------------------------
chordate(kordtancestors got their start during this long-past era.
Yet alongside the familiar arthropods arthropod(arthr-pd)
n., echinoderms, mollusks, and other phyla, this frenzy of innovation produced
many creatures that defy imagination. The history of Anomalocaris research,
littered with errors, demonstrates the difficulty paleontologists have
experienced in trying to crack some of these conundrums.
"The unfolding story of the anomalocaridids (the group including Anomalocaris
and its near relatives) is almost as unlikely as the animal itself," declares
paleontologist Derek E.G. Briggs of the University of Bristol in England in
the May 27 Science.
Through the years, researchers have misidentified almost all major parts of
Anomalocaris, sticking them on a variety of other animals almost like a game
of pin the tail on the donkey. Even the creature's name, which means "odd
shrimp," has its origins in a mistake. When Canadian paleontologist J. E
Whiteaves found the front appendages
epiploic appendages see under appendix .
------------------------------------------------------------------------
appendage(-pndof Anomalocaris in 1886, he identified them as the body of a
shrimplike crustacean with an unknown type of head, recounts Stephen J. Gould
in his book Wonderful Life: The Burgess Shale and the Nature of History (1989,
Norton).
Charles Doolittle Walcott made the next set of errors after discovering the
rich deposit of Cambrian fossils in Canada's Burgess Shale in 1909. He
classified the broad Anomalocaris body as the squashed remains of a sea
cucumber sea cucumber,any of the flexible, elongated echinoderms belonging to
the class Holothuroidea. Although sea cucumbers have the basic echinoderm
radial symmetry, they do not have arms like starfish. Instead the oral-anal
distance is greatly increased, resulting in the typical cucumber-shaped body.
Sea cucumbers live with one side facing permanently down.. At the same time,
he put an Anomalocaris appendage on the head of a different creature called
Sidneyia. As for the peculiar ring-shaped mouth, Walcott identified this as a
flattened jellyfish with a hole in the middle.
For over 70 years, the giant predator lay disassembled and unknown, until
Harry B. Whittington of the University of Cambridge in England and his
then-student Briggs finally put the pieces of the puzzle together. During
careful study of fossils from the Burgess Shale, they discovered the feeding
appendages, mouth, and body of Anomalocaris in their bizarre but true-to-life
positions.
In their reconstruction, Whittington and Briggs envisioned a
60-centimeter-long animal that raised and lowered its side flaps as a form of
underwater wings. The resulting undulating motion would have resembled the way
modern manta rays swim. Compared to most other Cambrian animals, which measured
no longer than a finger, this flounder-sized predator qualified as a giant.
Whittington and Briggs noted that the jointed front appendages had just the
right reach and flexibility to capture prey and pass it back to the strange
circular mouth. Unlike most maws, this ring of 32 teeth could not close
completely Rather, it worked by crunching food and pushing the pieces to
additional rings of teeth inside. Some specimens from the Burgess Shale showed
three circles of teeth stacked one atop the other.
While the animal made sense anatomically the researchers could not fit it into
any existing taxonomical category With its jointed feeding appendages and
segmented body, Anomalocaris looked somewhat like an arthropod - the great
phylum
phyla (-l)
A taxonomic category that is a primary division of a kingdom and ranks above a
class in size.that includes insects and crustaceans. But the resemblance ended
there. Neither the mouth nor the body of the animal showed a connection with
arthropods or any other phylum. The only group in which Anomalocaris seemed to
belong was a grab bag of misfits with the self-explanatory title of
"problematica."
A decade later, paleontologists know that Anomalocaris was not alone.
Excavations from 1990 through 1992 outside the city of Chengjiang in southwest
China have turned up three similar, but distinct, creatures belonging to the
anomalocaridids, report Chen and Nanjing colleague Gui-qing Zhou, who
collaborated with Lars Ramskold of the University of Uppsala in Sweden. They
describe the Chinese finds in the May 27 Science.
Chen and his colleagues have added more parts to the body of Anomalocaris. The
Chinese specimens reveal that the animal had a broad tail with a pair of long,
trailing spines - elements missing from the creatures described by Whittington
and Briggs. The tail and spines are also preserved on a complete specimen
collected in 1991 by Desmond Collins of Toronto's Royal Ontario Museum, who is
working near Walcott's original quarry in the Burgess Shale.
The second type of giant predator from Chengjiang resembles Anomalocaris, but
it had a wider body and shorter front grasping limbs, each armed with
daggerlike pincers.
A third type is known only by its imposing jaws: Chen and coworkers found a
large ring of teeth measuring 25 cm across, which apparently belonged to
another anomalocaridid. Judging from the dimensions of complete Anomalocaris
specimens, the researchers estimate that this beast would have reached 2
meters in length, making it bigger than most people.
Unlike Whittington and Briggs, Chen's group believes that Anomalocaris
propelled itself with fishlike movements of its body and tail instead of its
side flaps. "Side-flap swimming is very energy-consuming. I don't think they
would get any speed that way," Chen says.
Because the predators had flat bodies, Chen and his colleagues suggest that
"anomalocaridids may have spent much time partly buried or camouflaged in the
bottom sediment, with the stalked eyes protruding over the bottom and scanning
the surroundings for swimming prey."
Taken together, the range of new fossils points to a wide variety of eating
habits. The two new Chinese forms as well as the original Anomalocaris have
front limbs well designed for grasping large animals, says Briggs. In the case
of the gaping jaws from Chengjiang, this anomalocaridid could easily have
consumed something the size of a human head.
A new type of Anomalocaris from Australia, however, went for more delicate
fare. It had front limbs suited for straining small animals from the water.
Another relative, called Peytoia, bore long, rakelike appendages apparently
adapted for combing through seafloor sediments, Briggs says. He was the first
to recognize the use of this limb back in 1979, although he did not know to
what creature it belonged until 2 years later.
The anomalocaridid discoveries have forced paleontologists to redraw their
earlier, simplistic image of life in the ancient oceans. Not only did the
Cambrian explosion produce a diversity of different body types, it also gave
birth to a remarkably complex ecology
"Originally," says Briggs, "people regarded the Cambrian as a rather early
stage in the development of ecosystems. The assumption was that predation
wouldn't have been a very well developed strategy."
According to this theory, the earliest predators would have started off as
relatively simple creatures that then evolved more specialized features over
many millions of years. As the predators added to their offensive weaponry,
prey would evolve sophisticated defense systems.
But the fossils show that the arms race accelerated almost overnight during
the Cambrian explosion. Creatures with hard shells and long spines abound in
the Chengjiang fauna, displaying a broad sweep of protective armor. Likewise,
Anomalocaris appeared on the scene with an array of formidable feeding tools.
"Things like Anomalocaris indicate that there were very highly evolved, large,
well-adapted predators even in the lower Cambrian. It indicates that the
Cambrian ecosystems were not that dissimilar to the types of things that you
see today. There were different organisms occupying the niches, but it was the
same sort of setup," says Briggs.
Chen agrees that the early Cambrian ecology blossomed quickly "There was a
highly developed ecosystem. The food chain was as complicated as it is today,"
he says.
When they described Anomalocaris a decade ago, Whittington and Briggs regarded
the creature as an evolutionary dead end, without a home in any existing
phylum. But new interpretations, driven by fossil discoveries, are starting to
make sense of these peculiar predators.
Chen and his colleagues see a distinct resemblance between anomalocaridids and
two other Cambrian oddballs: a creature from Greenland called Kerygmachela (SN:
7/11/92, p.22) and another called Opabinia from the Burgess Shale. By Chen's
analysis, the Greenland creature was the closest relative of the
anomalocaridids because both possessed a pair of movable front appendages, 11
body segments, side flaps and two long rear spines.
Opabinia - which looked somewhat like a swimming vacuum cleaner because of its
long , hoselike front appendage - also resembled the anomalocaridids in having
large eyes on stalks, side flaps, two rear spines and a similar tail. Chen's
team therefore folds anomalocaridids, Kerygmachela, and Opabinia together in a
taxonomic category closely related to arthropods, perhaps even with the phylum
Arthropoda Arthropoda/Arthropoda/ (ahr-thropo-dah) the largest phylum of
animals, composed of bilaterally symmetrical organisms with hard, segmented
bodies bearing jointed legs, including, among other related forms, arachnids,
crustaceans, and insects, many species of which are parasites or are vectors
of disease-causing organisms..
A once unclassifiable patchwork of body parts, Anomalocaris is finally
revealing its kinship with the more familiar phyla of animal life. "We no
longer need to think of anomalocaridids as something really strange or
bizarre. It's beginning to look like quite an important group, one pretty
close to the arthropods," says Briggs.
With that, paleontologists are finding the early Cambrian seas an easier place
in which to navigate.
==
Yes, it is easy literally to see what has happened
over 545 million years, because all you have to do is
split open rocks of Paleozoic, Mesozoic or Cenozoic
age. For billions of years, it's harder to detect the
fossils, as they're smaller or lack hard body parts,
but the tracks & traces they left in hardened
sediments & their chemical signatures have been
discovered.
Fossils & the geologic column are
scientific facts, ie observations of how nature
actually is, not suppositions. You can ignore the
plain message that they tell about God's work, but to
lie about it puts your soul at peril.
The men who long before Darwin worked out the
development (their word) of life through time did so
based on what they actually found in the layers of
rocks they studied. If you went to Scotland, England,
Wales, France, Germany, Russia or any of the places
where these pioneering 18th & 19th century geologists
studied the earth & looked at their rock formations,
you would not be able to deny certain facts, just as
they, largely clerics who believed in creation, could
not. Now we've studied all the continents &
everywhere, the stratigraphic order is the same.

From these facts, they derived certain unavoidable,
irrefutable conclusions, not suppositions, but
conclusions forced upon them by applying their
God-given reason to the evidence presented them by the
physical world, Creation itself.
Here are just a few of the facts that geologists noted
before & during Darwin's lifetime.
1) Everywhere we look on earth, we see the same layers
of rocks in the same order. If they're out of order,
there are obvious reasons for it, such as folding or
faulting, which only reinforce the conclusion that the
earth is very, very old. Before & independent of
Darwin, this order was worked out, although he made
important contributions to knowledge of South American
geology. Today we can precisely date the age of rocks
in absolute terms, as well as relative to each other,
although the ages worked out by 19th century
geologists weren't far off.
2) One of the most important ways in which rocks can
be dated is by looking at the fossils within them.
Permian rocks from Russia, Texas & South Africa, for
instance, contain fossils of the same genera, families
& orders of organisms, indeed often even the same
species. The same is true globally for rocks from
the preceding Paleozoic periods, the Cambrian,
Ordovician, Silurian, Devonian & Carboniferous, & for
all the periods of the Mesozic & Cenozoic Eras, named
for the varieties of fossil organisms found within
their rocks (Old Life, Middle Life & Recent Life).
3) Fossils within rocks from these eras show
development in ways confirmed by other sciences, such
as comparative anatomy, embryology, biochemistry &
genetics. As I've posted before, taking just one
phylum, our own, the Chordates, it's plain, indeed
easy, as Randy said, to follow its evolution in rocks
of succeeding ages. These fossils are facts, Gabor,
not suppositions. They exist.
http://tolweb. org/tree? group=Chordata& contgroup= Deuterostomia
In the Cambrian, for instance, you find chordates
smaller & simpler, ie less "derived", but similar to,
sharing heritable characteristics with, jawless fish
still living today, like the hagfish & lampreys.
While early vertebrates exist in Cambrian rocks, they
become common & more derived in the Ordovician. For
example, fish developed jaws during this period,
co-opting the first gill arch for this purpose.
In the Silurian, if not before, cartilaginous fish
like today's sharks, skates & rays diverged from bony
fish like those from whom we're descended. By the
late Silurian, fossils show that the ancestors of the
vast majority of bony fish alive today, the ray-fins,
had separated from those ancestral to us, the lobe-fins.
During the Devonian, ever more abundant fossils from
discoveries old & new allow us to study the evolution
of lobe-fin fish towards tetrapods, ie the ancestors
of land vertebrates. In Late Devonian rocks from
various places around the world, but particularly
Arctic Canada, Greenland, Scotland & the Baltic region
(which were then united in the same "Old Red
Sandstone" continent) we in fact can see the first
still mainly aquatic tetrapods, ie lobe-finned fish
with digits at the end of their four paired dorsal
fins, which already contained arm & leg bones.
In the Carboniferous, you find, in Pennsylvania among
other locales, more terrestrial tetrapods, ie large
amphibians with hand & foot bones & other skeletal
features better adapted to life on land, followed in
younger rocks (such as Nova Scotia, Canada) the first
reptiles, ie tetrapods even more adapted to life on
land, including the ability to lay shelled eggs,
enabling breeding away from water. Rapidly, in
geologic time, the reptiles separate into the lines
leading to mammals & on the other hand to turtles,
lizards, snakes, crocodiles & birds. The
proto-mammalian line of "reptiles" has a single
opening in their skulls behind their eyes, while the
other line has two.
The further development of all these different sorts
of fish & land vertebrates can be tracked via their
fossils in the Permian, which ended with the most
spectacular extinction event of the past 545 million
years, at least. The break in continuity, with so
many groups dying off, that some 19th century
geologists & biologists thought there might have been
a second creation. But happily, some mammal-like
reptiles, our ancestors, survived into the Mesozoic
along with the ancestors of dinosaurs & birds. I'll
skip a description of Mesozoic & Cenozoic fossils that
show these facts.
==
Study suggests how DNA building block might have formed
Many experiments have shown it: simple molecules can combine
chemicallyout side of living thingsto form the building blocks
of DNA, the key component of life. But just how this combination
occurs is unknown. Scientists want to find out, since that might
explain how DNA originated.
Now, chemists have proposed what they call the first detailed,
feasible account of how one of DNA's major building blocks could
have arisen on an early, lifeless Earth. The necessary
ingredients: five cyanide molecules, they said.
Where "biomolecules, " such as DNA's components, originated
isn't known, said University of Georgia chemist Paul von Rague
Schleyer, one of the researchers.
"One can only speculate. They could have formed from smaller
molecules present on primitive Earth, either very slowly over
millions of years or rapidly before the Earth cooled down.
Asteroids may have brought them from outer space," he added,
thought this doesn't explain how they would have formed there.
DNA is life's molecular blueprint, passed from generation to
generation. First isolated in 1869 by a Swiss doctor from pus
in discarded bandages, DNA's structure was discovered in 1953.
It's shaped somewhat like a twisted ladder with rungs anchored by
interlocking pairs of two out of four molecules, known as
nucleic acid bases. The four are adenine, guanine, cytosine
and thymine.
Schleyer's team focused on adenine because of its prevalence
and ability to form from simple components in the dark. Along with
other building blocks of life, adenine has even been detected in
outer space, though there, the great distances among its smaller
molecular ingredients make its emergence trickier to explain.
But many experiments have shown that simulated primitive Earth
conditions can lead to the formation of essential compounds of
life including amino acids, nucleotides and carbohydrates, the
researchers wrote in their study. The work was published Oct. 30
in the scientific journal Proceedings of the National
Academies of Science.
Remarkably, they said, adenine has been found to arise from highly
poisonous cyanide dissolved in ammonia and frozen in a
refrigerator for 25 years. A hightempera ture experiment
designed to simulate early volcanolike environments also
produced adenine. But the question is how.
Schleyer's team devised an answer by solving a series of key
riddles. They worked out processes in which five cyanide
molecules might combine to make adenine under terrestrial
conditions. The proposal was based on computerassisted studies
that involved quantum mechanics, the sometimes illogicalseeming
rules that govern atomic interactions.
The researchers said the report provides a more detailed
understanding of some of the processes of "chemical evolution,"
and a partial answer to the basic question of how life's chemistry
emerged. The investigation should trigger similar probes into
the origins of the three remaining bases and of other
biologically relevant molecules, they added.
==
Bones of Contention: Controversies in the Search for Human Origins
by Roger Lewin (Paperback - Aug 16, 1997)
==
Oldest Known Jellyfish Fossils Found
The oldest known fossils of jellyfish have been found in rocks in Utah that
are more than 500 million years old, a new study reports.
The fossils are an unusual discovery because soft-bodied creatures, such as
jellyfish, rarely survive in the fossil record, unlike animals with hard
shells or bones.
"The fossil record is biased against soft-bodied life forms such as jellyfish,
because they leave little behind when they die," said study member Bruce
Lieberman of the University of Kansas.
These jellyfish left their lasting imprint because they were deposited in fine
sediment, rather than coarse sand. The film that the jellyfish left behind
shows a clear picture, or "fossil snapshot," of the animals.
"You can see a distinct bell-shape, tentacles, muscle scars and possibly even
the gonads," said study team member Paulyn Cartwright, also of KU.
The rich detail of the fossils allowed the team to compare the cnidarian (the
phylum to which jellyfish, coral and sea anemones belong) fossils to modern
jellyfish. The comparison confirmed that the fossils were, in fact, jellyfish
and pushed the earliest known occurrence of definitive jellyfish back from 300
million to 505 million years ago.
The fossils also offer insights into the rapid species diversification that
occurred during the Cambrian radiation, which began around 540 million years
ago and when most animal groups start to show up in the fossil record,
Lieberman said.
The complexity of these early jellyfish seems to suggest that either the
complexity of modern jellyfish developed rapidly about 500 million years ago,
or that jellyfish are even older and developed long before that time.
==
They didn't even live at the same time! Y-chromosome
Adam lived about 60,000 years ago. Mitochondrial
Eve lived about 140,000 years ago.
==
Consider stoneflies (Plecoptera) . The adults die
within a week or two of laying their eggs, and the nymphs spend one or more
aquatic years before they come up and emerge as terrestrial adults. Normally
they walk around and eat etc for a week while the internal biochemistry is
realigned from an aquatic environment to an airial one, and then they start
drumming for a partner or five to mate with. They never saw their parents,
or even adult behaviour, so everything has to be hardwired. Apart from
adapting to new water temperature regimes (something they do in a few
generations) they haven't changed very much in 200 million years.
==
Plant genomes frequently double (or occasionally even triple) in a single
polyploid event, which can lead to full speciation with a single mutant
individual.
"Various estimates suggests that as many as 30-70% of flowering plants are of
polyploid origin (Grant, 1971; Goldblatt, 1980). For example, the plants in
the
rosaceous subfamily maloideae (Malus, Pyrus, Photinia, Chaenomeles, etc.) are
believed to have originated from an ancient allopolyploids since they have
n=17 base chromosomes whereas plants in other rosaceous subfamilies have n=8
or 9 (Rowley, 1993).
==
Genetic Entropy & the Mystery of the Genome by John C. Sanford
===
There are 394 primate species.
==
Every human has multiple mutations. The majority of them are neutral.
The scientific paper: Nachman, M. W. and S. L. Crowell.
2000. "Estimate of the mutation rate per nucleotide in humans".
Genetics 156(1): 297-304, estimates around that 172 neutral mutations occur
out of 175 total mutations per generation in humans .
==
The origin of speakies
More evidence that Neanderthals could talk to each other
IF YOU found yourself in a cocktail bar with a Neanderthal man, what would he
say? A good conversation is one of the great joys of being human, but it is
not clear just how far back in the hominid lineage the ability to use language
stretches. The question of when grunts and yelps turned into words and phrases
is a tricky one. One way of trying to answer it is to look in the fossil
record for evidence about what modern humanity's closest relatives could do.
Svante Paabo, of the Max Planck Institute for Evolutionary Anthropology in
Leipzig, and his colleagues have done just that. Dr Paabo is an expert in
extracting and interpreting the DNA of fossils. As he reports in the latest
issue of Current Biology, he and his team have worked their magic on a gene
called FOXP2 found in Neanderthal remains from northern Spain.
The reason for picking this particular gene is that it is the only one known
so far to have a direct connection with speech. In 1990, a family with an
inherited speech disorder known as verbal dyspraxia drew the attention of
genetics researchers. Those researchers identified a mutation in FOXP2 as the
cause of the dyspraxia.
Since then FOXP2 has been the subject of intensive study. It has been linked
to the production of birdsong and the ultrasonic musings of mice. It is a
conservative type, not changing much from species to species. But it has
undergone two changes since humans split from chimpanzees 6m years ago, and
some researchers believe these changes played a crucial role in the
development of speech and language.
If these changes are common to modern humans and Neanderthals, they must
predate the separation of the line leading to Homo sapiens from the one
leading to Homo neanderthalensis. Dr Paabo's research suggests precisely that:
the FOXP2 genes from modern humans and Neanderthals are essentially the same.
To the extent that the gene enables language, it enables (or enabled) it in
both species.
There has been much speculation about Neanderthals' ability to speak. They
were endowed with a hyoid bone, which anchors the tongue and allows a wide
variety of movements of the larynx. Neanderthal skulls also show evidence of a
large hypoglossal canal. This is the route taken by the nerves that supply the
tongue. As such, it is a requisite for the exquisitely complex movements of
speech. Moreover, the inner-ear structure of Homo heidelbergensis, an ancestor
of Neanderthals, shows that this species was highly sensitive to the
frequencies of sound that are associated with speech.
That Neanderthals also shared with moderns the single known genetic component
of speech is another clue that they possessed the necessary apparatus for
having a good natter. But suggestive as that is, the question remains open.
FOXP2 is almost certainly not the language gene. Without doubt, it is involved
in the control and regulation of the motions of speech, but whether it plays a
role in the cognitive processes that must precede talking remains unclearjokes
about engaging brain before putting mouth in gear notwithstanding.
The idea that the forebears of modern humans could talk would scupper the
notion that language was the force that created modern human cultureotherwise,
why would they not have built civilisations? But it would make that chat with a
Neanderthal much more interesting.


==
Crocodilians & birds are both archosaurs, members of
the same diapsid group containing extinct pterosaurs &
non-avian dinosaurs.
Unlike snakes, lizards, tuataras & turtles, whose
three-chambered hearts are adapted to low-energy
lifestyles, crocs, like birds, have complicated
four-chambered hearts, which don't jibe with the
crocs' "reptilian" metabolism. This is compelling
evidence that the archosaurian ancestor of crocs &
birds was warm-blooded to some extent, so that the
non-avian dinosaurs & pterosaurs may well have been,
too, as hypothesized by some specialists.

http://pharyngula. org/index/ science/comments /hot_blooded_ crocodiles/
==
The missing link
Scientist discovers that evolution is missing from Arkansas classrooms.

In the fall of 2004, I received an e-mail from an old friend back in Arkansas,
where I was raised. She was concerned about a problem her father was having at
work. Bob is a geologist and a teacher at a science education institution
that serves several Arkansas public school districts. My friend did not know
the details of Bobs problem, only that it had to do with geology education.
This was enough to arouse my interest, so I invited Bob to tell me about what
was going on.
He responded with an e-mail. Teachers at his facility are forbidden to use the
e-word (evolution) with the kids. They are permitted to use the word
adaptation but only to refer to a current characteristic of an organism, not
as a product of evolutionary change via natural selection. They cannot even use
the term natural selection. Bob feared that not being able to use
evolutionary terms and ideas to answer his students questions would lead to
reinforcement of their misconceptions.
But Bobs personal issue was more specific, and the prohibition more
insidious. In his words, I am instructed NOT to use hard numbers when telling
kids how old rocks are. I am supposed to say that these rocks are VERY VERY OLD
... but I am NOT to say that these rocks are thought to be about 300 million
years old.
As a person with a geology background, Bob found this restriction hard to
justify, especially since the new Arkansas educational benchmarks for 5th
grade include introduction of the concept of the 4.5-billion-year age of the
earth. Bobs facility is supposed to be meeting or exceeding those benchmarks.
The explanation that had been given to Bob by his supervisors was that their
science facility is in a delicate position and must avoid irritating some
religious fundamentalists who may have their fingers on the purse strings of
various school districts. Apparently his supervisors feared that teachers or
parents might be offended if Bob taught their children about the age of rocks
and that it would result in another school district pulling out of their
program. He closed his explanatory message with these lines:
So my situation here is tenuous. I am under censure for mentioning numbers.
I find that my fire for this place is fading if were going to dissemble
about such a basic factor of modern science. I mean ... the Scopes trial was
how long ago now??? I thought we had fought this battle ... and still it goes
on.
I immediately referred Bob to the National Center for Science Education
(NCSE). They responded with excellent advice. Bob was able to use their
suggestions along with some of the position statements of numerous scientific
societies and science teacher organizations listed by the NCSEs Voices for
Evolution Project in defense of his continued push to teach the science he
felt obligated to present to his students. Nevertheless, his supervisors
remained firm in their policy of steering clear of specifically mentioning
evolution or deep time chronology.
I was going to be in Arkansas in that December anyway, so I decided to
investigate Bobs issue in person. He was happy for the support, but even more
excited to show me around the facility. Bob is infectiously enthusiastic about
nature and science education. He is just the kind of person we want to see
working with students. He had arranged for me to meet with the directors of
the facility, but he wanted to give me a guided tour of the place first.
Self-censorship in defense of science?
I would like to describe the grounds of the facility in more detail, but I
must honor the request of all parties involved to not be identified. It was,
however, a beautiful place, and the students, fifth-graders that day, seemed
more engaged in their learning than most I had ever seen. To be sure, the
facility does a fantastic job of teaching science, but I was there to find out
about what it was not teaching. Bob and I toured the grounds for quite some
time, including a hike to a cave he had recently discovered nearby, and when
we returned I was shown to my interview with the program director and
executive director.
Both of the directors welcomed me warmly and were very forthcoming in their
answers to my questions. They were, however, quite firm in their insistence
that they and their facility be kept strictly anonymous if I was to write a
story about Bobs issue. We talked for over an hour about the sites mission,
their classes, and Bobs situation specifically. Both directors agreed that
in a perfect world they could, and would, teach evolution and deep time.
However, back in the real world, they defended their stance on the prohibition
of the e-word, reasoning that it would take too long to teach the concept of
evolution effectively (especially if they had to defuse any objections) and
expressing concern for the well-being of their facility. Their program depends
upon public support and continued patronage of the regions school districts,
which they felt could be threatened by any political blowback from an unwanted
evolution controversy.
With regard to Bobs geologic time scale issue, the program director likened
it to a game of Russian roulette. He admitted that probably very few students
would have a real problem with a discussion about time on the order of
millions of years, but that it might only take one childs parents to cause
major problems. He spun a scenario of a students returning home with stories
beginning with Millions of years ago that could set a fundamentalist
parent on a veritable witch hunt, first gathering support of like-minded
parents and then showing up at school board meetings until the district pulled
out of the science program to avoid conflict. He added that this might cause a
ripple effect, other districts following suit, leading to the demise of the
program.
Essentially, they are not allowing Bob to teach a certain set of scientific
data in order to protect their ability to provide students the good science
curriculum they do teach. The directors are not alone in their opinion that
discussions of deep time and the e-word could be detrimental to the
programs existence. They have polled teachers in the districts they serve and
have heard from them more than enough times that teaching evolution would be
political suicide.
Bobs last communication indicated that he had signed up with NCSE and was
leaning towards the grin and bear it approach, which, given his position and
the position of the institution, may be the best option. I was a bit
disheartened, but still impressed with all the good that is going on at Bobs
facility. I was also curious about other educational institutions, so I
decided to ask some questions where I could.
The first place I happened to find, purely by accident, was a privately run
science museum for kids. As with Bobs facility, the museum requested not to
be referred to by name. I was only there for a short time, but Im not quite
sure what to make of what happened there. I looked around the museum and found
a few biological exhibits, but nothing dealing with evolution. I introduced
myself to one of the museums employees as a science educator (I am indeed a
science educator) and asked her if they had any exhibits on evolution. She
said that they used to, but several parents some of whom home-schooled their
children, some of whom are associated with Christian schools had been
offended by the exhibit and complained. They had said either that they would
not be back until it was removed or that they would not be using that part of
the museum if they returned. It was right over there, she said, pointing to
an area that was being used at that time for a kind of holiday display.
Later that evening, I had a visit with the coordinator of gifted and talented
education at one of Arkansass larger public school districts. As before, she
has requested that she and her school system be kept anonymous, so I will call
her Susan. Susan told me she had overheard a teacher explaining the balanced
treatment given to creationism in her classroom. This was not just any
classroom, but an Advanced Placement biology classroom. This was important to
Susan, not only because of the subject and level of the class, but also
because it fell under her supervision. Was she obliged to do something about
this? She knew quite well that the balanced treatment being taught had been
found by a federal court to violate the Constitutions establishment clause
perhaps there is no greater irony than that two of the most significant cases
decided by federal courts against teaching creationism were Epperson v.
Arkansas and McLean v. Arkansas Board of Education.
Susan sincerely wanted to do something about it, but she decided to let it go.
Her reasoning was that this particular teacher is probably in her final year of
service. To Susan, making an issue out of this just was not worth the strife it
would have caused in the school and in the community.
As the discussion progressed that evening, I learned that omission was the
method of dealing with evolution in another of Arkansass largest, most
quickly growing, and wealthiest school districts an omission that was
apparently strongly suggested by the administration. I tried to check on this,
but made little progress, receiving the cold shoulder from the administration
and the science department at that school. However, I spoke with a person who
works for a private science education facility that does contract work for
this district: Helen she, like the other people I had visited, requested
that she and her employers not be identified. I asked Helen about her
experiences with the districts teachers. Her story was that in preparation
for teaching the students from that district, she had asked some of the
teachers how they approached the state benchmarks for those items dealing with
evolution. She said, Oh, I later got in trouble for even asking, but went on
to describe their answers. Most teachers said that they did not know enough
about evolution to teach it themselves, but one of them, after looking around
to make sure they were safely out of anyones earshot, explained that the
teachers are told by school administrators that it would be good for their
careers not to mention such topics in their classes.
Inadequate science education
How often does this kind of thing happen? How many teachers are deleting the
most fundamental principle of the biological sciences from their classes due
to school and community pressure or due to lack of knowledge? How many are
disregarding Supreme Court decisions and state curriculum guidelines? These
are good questions, and I have been given relevant data from a person
currently working in Arkansas. We will call this science teacher Randy. I was
introduced to him through the NCSE. He made it clear that his identity must be
protected.
Randy runs professional development science education workshops for public
school teachers. Hes been doing it for a while now, and he has been taking
information on the teachers in his workshops via a survey. He shared some data
with me.
According to his survey, about 20 percent are trying to teach evolution and
think they are doing a good job; 10 percent are teaching creationism, even
though during the workshop he discusses the legally shaky ground on which they
stand. Another 20 percent attempt to teach something but feel they just do not
understand evolution. The remaining 50 percent avoid it because of community
pressure. On an e-mail to members of a list he keeps of people interested in
evolution, Randy reported that the latter 50 percent do not cover evolution
because they felt intimidated, saw no need to teach it, or might lose their
jobs.
By their own description of their classroom practices, 80 percent of the
teachers surveyed are not adequately teaching evolutionary science. Remember
that these are just the teachers who are in a professional development
workshop in science education! What is more disturbing is what Randy went on
to say about the aftermath of these workshops. After one of my workshops at a
[state] education cooperative, it was asked that I not come back because I
spent too much time on evolution. One of the teachers sent a letter to the
governor stating that I was mandating that teachers had to teach evolution,
and that I have to be an atheist, and would he do something.
Of course its false to suggest youre either an anti-evolutionist or youre
an atheist. Many scientists who understand and accept evolution are also
quite religious, and many people of faith also understand and accept
evolution. But here was a public school teacher appealing to the governor to
do something about this guy teaching teachers to teach evolution. Given that
evolutionary science is prescribed in the state curriculum guidelines, and
given that two of the most important legal cases regarding evolution education
originated in Arkansas, how exactly would we expect the governor to respond? I
am not sure whether Gov. Mike Huckabee responded to this letter, but I have
seen him address the subject on Arkansans Ask, his regular show on the
Arkansas Educational Television Network. Ive seen two episodes on which
students expressed their frustration about the lack of evolution education in
their public schools. Both times, Huckabee advocated the teaching of
creationism in public schools. Here is an excerpt from one of these
broadcasts, from July 2004:
Student: Many schools in Arkansas are failing to teach students about
evolution according to the educational standards of our state. Since it is
against these standards to teach creationism, how would you go about helping
our state educate students more sufficiently for this?
Huckabee: Are you saying some students are not getting exposure to the various
theories of creation?
Student (stunned): No, of evol well, of evolution specifically. Its a
biological study that should be educated [taught], but is generally not.
Moderator: Schools are dodging Darwinism? Is that what you ?
Student: Yes.
Huckabee: Im not familiar that theyre dodging it. Maybe they are. But I
think schools also ought to be fair to all views. Because, frankly, Darwinism
is not an established scientific fact. It is a theory of evolution, thats why
its called the theory of evolution. And I think that what Id be concerned
with is that it should be taught as one of the views thats held by people.
But its not the only view thats held. And any time you teach one thing as
that its the only thing, then I think that has a real problem to it.
Huckabees answer was laced with important misconceptions about science.
Perhaps the most insidious problem with his response is that it plays on our
sense of democracy and free expression. But several court decisions have
concluded that fairness and free expression are not violated when public
school teachers are required to teach the approved curriculum. These decisions
recognized that teaching creationism is little more than thinly veiled
religious advocacy.
Furthermore, Huckabee claimed not to be aware of the omission of evolution
from Arkansas classrooms. From my limited visit, it is clear that this
omission is widespread. But its certain Huckabee had heard about the omission
before. This is from the July 2003 broadcast of Arkansans Ask:
Student: Goal 2.04 of the Biology Benchmark Goals published by the Arkansas
Department of Education in May of 2002 indicates that students should examine
the development of the theory of biological evolution. Yet many students in
Arkansas that I have met have not been exposed to this idea. What do you
believe is the appropriate role of the state in mandating the curriculum of a
given course?
Huckabee: I think that the state ought to give students exposure to all points
of view. And I would hope that that would be all points of view and not only
evolution. I think that they also should be given exposure to the theories not
only of evolution but to the basis of those who believe in creationism
The governor goes on for a bit and finishes his sentiment, but the moderator
keeps the conversation going:
Moderator (to student): Youve encountered a number of students who have not
received evolutionary biology?
Student: Yes, Ive found that quite a few peoples high schools simply prefer
to ignore the topic. I think that theyre a bit afraid of the controversy.
Huckabee: I think its something kids ought to be exposed to. I do not
necessarily buy into the traditional Darwinian theory, personally. But that
does not mean that Im afraid that somebody might find out what it is
Sisyphean Challenges
How are teachers like Bob, administrators like Susan, and teacher trainers
like Randy supposed to ensure proper science education if politicians like
the governor consistently advocate the teaching of non-science?
It is telling that none of the people I spoke with were willing to be
identified or to allow me to reveal their respective institutions. In the case
of Bob and his facilitys directors, they were concerned about criticism from
both sides. They did not want to lose students by offending fundamentalists or
lose credibility in the eyes of the scientific community for omitting
evolution.
The shortcomings of evolution instruction in Arkansas dont end at the states
borders. But we seldom realize the wider influence our local politicians might
have. For instance, the Educational Commission of the States is an important
and powerful organization that shapes educational policy in all 50 states.
Forty state governors have served as the chair of the ECS, and Governor
Huckabee currently holds this position.
Because anti-evolutionists have been quite successful in placing members of
their ranks and sympathizers in local legislatures and school boards, it is
imperative that we point out the danger that these people pose to adequate
science education. The science literacy of our future leaders may depend on
it. Although each school, each museum, or each science center may seem to be
an isolated case, answering to and, perhaps trying to keep peace with its
local constituency, the examples suggest that evolution is being squeezed out
of education systematically and broadly. Anti-evolutionists have been
successful by keeping the struggle focused on the local level. The fallout is
widespread ignorance of the tools and methods of science for generations to
come.

==
A single domestication for maize shown by multilocus microsatellite genotyping
Yoshihiro Matsuoka*,, Yves Vigouroux*, Major M. Goodman, Jesus Sanchez G.,
Edward Buckler, and John Doebley*,

There exists extraordinary morphological and genetic diversity among the maize
landraces that have been developed by pre-Columbian cultivators. To explain
this high level of diversity in maize, several authors have proposed that
maize landraces were the products of multiple independent domestications from
their wild relative (teosinte). We present phylogenetic analyses based on
264individual plants, each genotyped at 99microsatellites, that challenge
the multiple-origins hypothesis. Instead, our results indicate that all maize
arose from a single domestication in southern Mexico about 9,000years ago.
Our analyses also indicate that the oldest surviving maize types are those of
the Mexican highlands with maize spreading from this region over the Americas
along two major paths. Our phylogenetic work is consistent with a model based
on the archaeological record suggesting that maize diversified in the
highlands of Mexico before spreading to the lowlands. We also found only
modest evidence for postdomestication gene flow from teosinte into maize.

Most domesticated plant and animal species originated during a brief period in
human history between 5,000and 10,000years ago. During this time, many crops
and animals were domesticated multiple times independently, including rice
(1), common bean (2), millet (3), cotton (4), squash (5), cattle, sheep, and
goats (6). Like these, maize (Zea mays ssp. mays) has been considered to be
the product of multiple independent domestications from its wild progenitor
(teosinte) because of the remarkable morphological and genetic diversity that
exists within it. For example, based in part on the diversity of ear shapes in
maize, Galinat (7) concluded that distinct ancestral types of annual teosinte
in different regions of Mexico were the starting points for at least two
independent domestications of maize. Similarly, based on the diversity of
chromosome knob patterns among annual teosinte and maize races, Kato (8)
inferred that multiple domestications had occurred independently in several
regions of Mexico.

Although the remarkable diversity found within maize is consistent with
multiple domestications, it is equally consistent with a single domestication
and subsequent diversification. Distinguishing between these two models
requires phylogenetic analyses that incorporate comprehensive samples of maize
and its progenitor, teosinte. In this article, we report the first such
comprehensive phylogenetic analyses for maize and teosinte by using
99microsatellite loci that provide broad coverage of the maize genome and a
sample of 264maize and teosinte plants.
Plant Materials.
We sampled 193maize accessions (one plant each) representing the entire
pre-Columbian range of maize from eastern Canada to northern Chile (Fig. 1).
This sample includes maize adapted to the short growing season of eastern
North America, the deserts of Arizona, the highlands and lowlands of Mexico
and Guatemala, the Caribbean Islands, the rainforest of the Amazon Basin, and
regions of the Andes Mountains that exceed 3,500m in elevation. We also
sampled 67Mexican annual teosinte (Z.mays ssp. parviglumis and ssp.
mexicana) accessions (one plant each) that represent the full geographic range
of ssp. mexicana (33accessions) and ssp. parviglumis (34accessions) (Fig. 1).
We included four plants of a more distantly related teosinte (Z.mays ssp.
huehuetenangensis) from Guatemala as an outgroup for rooting the phylogenies.
Three other forms of teosinte (Zea diploperennis, Zea perennis, and Zea
luxurians) were not included in this study because they are all separate
species and it is well-established that they were not involved in the origins
of maize (9). The complete passport data for the plant materials, including
landrace designations, germplasm bank accession numbers, and geographical
coordinates, have been published as supporting information on the PNAS web
site, www.pnas.org.

Geographic distribution of maize and teosinte used in this study.
Core Andean maize characterized by hand-grenade-shaped ears (22samples), other
South American maize (47), Guatemalan and southern Mexican maize (31),
Caribbean maize (6), lowland western and northern Mexican maize (15), highland
Mexican maize (20), eastern and central U.S. maize (24), southwestern U.S.
maize (22), northern Mexican maize (6), ssp. parviglumis (34), and ssp.
mexicana (33). Inset shows the distribution of the 34populations of ssp.
parviglumis in southern Mexico with the populations that are basal to maize in
Fig. 2 (represented as asterisks). The blue line is the Balsas River and its
major tributaries.
Simple Sequence Repeat Genotyping.
The plants were genotyped at Celera AgGen (Davis, CA). The details of the
genotyping have been published elsewhere (10). Briefly, DNA was extracted from
individual plants by the cTAB method, and the microsatellite regions were
amplified by PCR with florescent-labeled primers. PCR products were
size-separated on Applied Biosystems automated sequencers equipped with
GENESCAN software and then classified to specific alleles or bins by GENESCAN
and GENOTYPER software programs (10). We used 99microsatellite loci that are
evenly distributed throughout the genome. A list of the microsatellite loci
with their chromosomal locations has been published as supporting information.
Primer sequences are available at the MaizeDB
(www.agron.missouri.edu/ssr.html).

Phylogenetic Analysis.

Obtaining a reliable phylogeny for outcrossing taxa requires one to construct
an average tree of the genome by using a large number of loci. For this
reason, we used large-scale microsatellite genotyping with 99microsatellite
loci and a genetic distance measure that fits the pattern of mutation
displayed by the microsatellites. This approach has been successfully applied
in humans (11) and horses (12) by using many fewer microsatellite loci (30and
15,respectively). Because many microsatellites of maize and other species do
not evolve in a stepwise manner (13), they violate the assumptions for the
genetic distance measures that are based on the stepwise mutation model. This
feature makes the use of these distance measures inappropriate. Therefore, we
used the proportion of shared alleles distance that is free of the stepwise
assumption, enjoys low variance (14), and is widely used with multilocus
microsatellite data (11, 12, 15). We used the FITCH program in the PHYLIP
package (16) with the log-transformed proportion of shared alleles distance as
implemented in the computer program MICROSAT (17) to construct phylogenetic
trees. In FITCH, the J option was used to randomize the input order of
samples. To determine the degree of statistical support for different branch
points in the phylogenies, we evaluated 1,000bootstrap samples of the data
(16).

Principal Component Analysis (PCA).

PCA was performed with the among sample variance-covariance matrix of allele
frequencies with SAS software version 6.12(SAS Institute, Cary, NC). The
principal component scores for each plant have been published as supporting
information.

Dating the Domestication Event.

To estimate the time of divergence of maize and its ancestral teosinte, we
used 33loci with dinucleotide repeats for which fewer than 10% of the alleles
did not fit a stepwise distribution. Nonstepwise alleles were treated as
missing data. We calculated the mean ()2 distance (18) over the 33loci
between Mexican maize and ssp. parviglumis. The number of generations () after
a population splits into two fully isolated populations was estimated with the
following equation:
[1] where is the effective mutation rate, that is, the product of the
mutation rate () and the second moment of mutational change in the number of
repeats () (19). We estimated and by using 86recombinant inbreds. The
details will be published elsewhere. In short, the recombinant inbreds were
selfed for 11generations on average and then genotyped with their parents as
described above. Thirteen novel alleles were found for the 33loci and
confirmed by sequencing. The estimates of and were 4.28104 and
2.08,respectively. The estimated number of generations () was converted into
years by assuming 1year equals 1generation. Ten thousand bootstrap samples
for ()2 were computed to estimate 95% confidence limits for the time of
divergence.

Population Structure Analysis.

To assess gene flow and population structure, we used a model-based clustering
method that infers the number of clusters (populations) and the frequency of
each allele in different clusters (20). For each individual plant, the method
estimates the proportion of its genome derived from the different clusters.
The analyses were preformed with the computer program STRUCTURE
(www.pritch.bsd.uchicago.edu/software.html), using 106 iterations and a
burn-in period of 30,000.In the different simulations, no prior information
was used to define the clusters. Because these analyses require codominant
alleles and are sensitive to missing data, only 78microsatellites with fewer
than 11% missing data or null alleles were used. When assessing the population
structure for maize, a plant was assigned to a cluster if an arbitrary value of
75% of its genome is estimated to belong to that cluster.

Single Domestication for Maize.
The microsatellite-based phylogeny for our sample of 264maize and teosinte
plants shows all maize in a single monophyletic lineage that is derived from
within ssp. parviglumis, thus supporting a single domestication for maize
(Fig. 2a). We pooled the individual plant samples into 95ecogeographically
defined groups. Each ecogeographic group consists of two to four plants of
similar latitude, longitude, and altitude as well as neighboring positions in
Fig. 2a. The composition of these groups can be found in the supporting
information. With this smaller number of taxonomic units, it was possible to
perform statistical testing via bootstrap resampling. The phylogeny for the
pooled samples shows maize to be monophyletic in 930of 1,000bootstrap
samples (Fig. 2b), indicating that a single origin for maize is far more
likely than multiple independent origins as proposed (7, 8). Our results stand
in contrast to those for crops such as rice (1), beans (2), and cotton (4) in
which different cultivated forms cluster with distinct wild relatives in
phylogenetic trees, supporting multiple origins for these crops. For maize,
our data clearly favor a single domestication event.

Phylogenies of maize and teosinte rooted with ssp.
huehuetenangensis based on 99microsatellites. Dashed gray line circumscribes
the monophyletic maize lineage. Asterisks identify those populations of ssp.
parviglumis basal to maize, all of which are from the central Balsas River
drainage. (a) Individual plant tree based on 193maize and 71teosinte. (b)
Tree based on 95ecogeographically defined groups. The numbers on the branches
indicate the number of times a clade appeared among 1,000bootstrap samples.
Only bootstrap values greater than 900are shown. The arrow indicates the
position of Oaxacan highland maize that is basal to all of the other maize.

To explore further the relationship between maize and teosinte with the
microsatellite data, we performed a PCA that was free of the assumption of
tree-based methods that evolution has been predominantly divergent (Fig. 3).
The pattern of relationships revealed by the PCA closely corresponds to that
seen in Fig. 2. Subspecies mexicana is separated from all maize samples,
whereas samples of ssp. parviglumis overlap those of maize, documenting the
close relationship between ssp. parviglumis and maize and supporting the
phylogenetic result that the latter subspecies was the sole progenitor of
maize.

Graph of the first two axes from a principal component analysis
of 193maize and 71teosinte individual plants. The first component explains
3.5% and the second 2.6% of the total variation.

Available isozyme and chromosome knob data could also be used in theory to
infer the number of domestications for maize. However, the available isozyme
data have principally been used to examine relationships among maize races and
only two studies (9, 21) have used isozyme data to make inferences about the
origin of maize. Like our simple sequence repeat (SSR) phylogeny, the results
of the two isozyme studies suggest a single domestication for maize; however,
these two studies did not include a comprehensive sample of maize germplasm
and thus could not authoritatively differentiate between the single and
multiple domestication hypotheses. The chromosome knob data (8) has never been
examined by formal phylogenetic analyses with respect to the origin of maize,
and thus cannot be directly compared with our SSR phylogeny. Most importantly,
chromosome knob data may not be appropriate for phylogenetic studies because
chromosome knob frequencies can change in a concerted and nonneutral fashion
as a result of meiotic drive (22).

Cradle of Maize Domestication.

If maize is the product of a single domestication event as our results
indicate, then its origin can be pinpointed to a specific geographic locality.
The region harboring those teosinte populations that are phylogenetically most
closely allied with maize can be considered a candidate for the region in
which maize was domesticated. Previously, populations of ssp. parviglumis from
the central region of the Balsas River drainage were identified as those most
similar to maize by using allozyme data (9). In our microsatellite-based
phylogenies, these same populations are basal to maize (populations with
asterisks in Fig. 2), supporting this earlier report and identifying the
central Balsas River drainage (Fig. 1 Inset) as a candidate for the cradle of
maize domestication. This region should be considered only a candidate because
new teosinte populations that are even more closely related to maize may yet be
discovered and the modern distribution of teosinte populations may differ from
their distribution during the domestication period. One example is teosinte
recovered from a archaeological site in Tamaulipas where teosinte is unknown
today (23).

Date of the Domestication Event.

Because our phylogenies reveal the origin of maize as a single event, it is
possible to estimate the date of this event with the microsatellite data. When
microsatellites adhere to the stepwise mutation model, they can provide an
estimate of the time of separation of two populations. Of the
99microsatellites, 33follow a stepwise model and have a known mutation rate.
With this set of microsatellites, ssp. parviglumis and Mexican maize have a
divergence time of 9,188B.P. (95% confidence limits of 5,689-13,093 B.P.).
This date represents an upper limit on the time of maize domestication because
our sample of ssp. parviglumis may not contain descendants of the exact
population that was ancestral to maize. For this reason, the time of
divergence between maize and the specific ancestral population of ssp.
parviglumis will likely have a somewhat younger date. Our molecular date is
consistent with the date of 6,250B.P. for the oldest known fossil maize (24)
and with archaeological estimates that crop domestication in Mexico did not
likely precede 10,000B.P. (25).

Impact of Gene Flow from Teosinte.

Our phylogenetic analyses (Fig. 2) provide an estimate of the
ancestral-descendent relationships averaged over the entire genome and they
indicate that all types of maize were derived from within ssp. parviglumis via
a single domestication event. After this initial event, introgression from
other teosinte types may have contributed to the maize gene pool and thereby
helps explain the remarkable phenotypic and genetic diversity in maize. Our
data allow us to make an assessment of the importance of gene flow from ssp.
mexicana as a factor contributing to maize diversity. This subspecies grows as
a weed in many maize fields of the highlands (above 1,700m) of central and
northern Mexico where it forms frequent hybrids with maize, whereas ssp.
parviglumis often grows as part of native vegetation at lower elevations
(below 1,800m) and rarely hybridizes with maize (26). We performed population
structure analysis (20) with ssp. mexicana and Mexican maize to estimate the
proportion of the Mexican maize gene pool that can be attributed to gene flow
from ssp. mexicana. Estimates from this analysis indicated that the genomes of
our sample of Mexican maize from elevations at which ssp. mexicana grows are
composed of about 2.3% ssp. mexicana germplasm (range 0.2-12%), whereas
Mexican maize from lower elevations contains only 0.4% ssp. mexicana (range
0.2-2%). These numbers suggest a measurable but modest overall contribution of
gene flow from ssp. mexicana into highland maize. However, the ssp. mexicana
contribution to some highland maize races is apparently larger. Our samples of
maize races Cacahuacintle, Palomero de Jalisco, and Palomero Toluqueno are
estimated to have 11,9,and 12%, respectively, of ssp. mexicana germplasm.
Thus, gene flow from ssp. mexicana may have contributed appreciably to some
races of the Mexican highlands as suggested by field observations (26).

Early Diversification.

In addition to the single maize domestication from ssp. parviglumis, the
phylogenies and PCA reveal the geographic diversification of the native
landraces of maize. The basal maize types in both phylogenies (Fig. 2) are
those from the Mexican highlands, and it is these types that overlap with ssp.
parviglumis in the PCA (Fig. 3). This result places the early diversification
of maize in the highlands between the states of Oaxaca and Jalisco. In this
regard, it is striking that the oldest known archaeological maize is from the
highlands of Oaxaca (24) and remarkably the basal-most maize in Fig. 2b is
from Oaxaca. This result presents an enticing correspondence between genetic
and archaeological evidence, and calls for further botanical and
archaeological exploration in this region. Among archaeologists, there have
been two models for the early diversification of maize. According to one,
because the oldest directly dated fossil maize comes from the Mexican
highlands, then the early diversification of maize occurred in the highlands
with maize spreading to the lowlands at a later date (25, 27). The second
model interprets maize phytoliths from the lowlands as the oldest maize, and
accordingly places the early diversification of maize in the lowlands (28).
Our data suggest that maize diversified in the highlands before it spread to
the lowlands.

Spread of Maize over the Americas.

From an early diversification in the Mexican highlands, the phylogenies and
PCA suggest two lineages or paths of dispersal. One path traces through
western and northern Mexico into the southwestern U.S. and then into the
eastern U.S. and Canada. A second path leads out of the highlands to the
western and southern lowlands of Mexico into Guatemala, the Caribbean Islands,
the lowlands of South America, and finally the Andes Mountains.

These relationships offer several phylogenetic hypotheses: maize of the
eastern U.S. with its long, slender ears was derived from that of the
southwestern U.S., which in turn came from northern Mexico. A scenario much
like this has been proposed based on morphology and archaeology (29). The
maize of the Andes Mountains with its distinctive hand-grenade-shaped ears was
derived from the maize of lowland South America, which in turn came from maize
of the lowlands of Guatemala and southern Mexico. Consistent with a dispersal
out of Mexico along two paths, population structure analysis (20) divides our
sample of the maize gene pool into three clusters: (i) an Andean group that
includes the hand-grenade-shaped ear types and some other Andean maize
(35plants); (ii) all other South American and Mexican maize (80plants); and
(iii) U.S. maize (40plants), plus 38plants whose genomes are intermediate
between or admixtures of two of these three clusters.

Although a high degree of ecogeographic patterning is seen in the phylogenies
and PCA, there are several exceptions, some of which have clear explanations.
For example, the Amazonian race Coroico (C in Fig. 2a), which clusters with
Andean maize, was thought to be related to Andean maize (30). The northern
Mexican race Tuxpeno Norteno (T in Fig. 2a), which clusters with southern
Mexican maize, was thought to be closely related to race Tuxpeno of southern
Mexico (31). The Venezuelan race Puya Grande (P in Fig. 2a), which groups with
southern Mexican races, is thought to have some parentage from race Tuxpeno of
southern Mexico (32). These exceptions present examples of recent movement of
maize races. There are also two "misplaced" samples of ssp. parviglumis that
group with ssp. mexicana. Our results from population structure analysis and
morphological observations suggest that one of these (J.Sanchez G.374) is a
parviglumis-mexicana hybrid and that the other (J.Sanchez G.159) was
misclassified in the germplasm collections (data not shown).

There remains an untold chapter in the origin and early diversification of
maize. Microsatellite data identify ssp. parviglumis of the Balsas River
drainage below 1,800m in elevation as the ancestor of maize. However, the
microsatellite data and some archaeological evidence suggest maize from the
highlands (above 1,800m) as the basal or most primitive form of maize. Thus,
there is a geographic gap between the present-day location of the progenitor
and the location of the basal maize and earliest fossil maize cobs (27). This
paradox raises several questions. Was ssp. parviglumis first transported to
the highlands where it was then domesticated? Did the distribution of ssp.
parviglumis 9,000years ago differ from that today? Do even older
archaeological maize fossils remain to be discovered at lower elevations in
the Balsas Valley? To answer these questions will require additional
archaeological and botanical exploration, more powerful molecular analyses,
and perhaps DNA analysis of archaeological materials, which could place
archaeological specimens in phylogenetic trees such as those presented here.

ReferencesTop

1. 	Second, G. (1982) Jpn. J.Genet. 57, 25-57.
2. 	Sonnante, G. , Stockton, T. , Nodari, R. O. , Becerra Velasquez, V. L. &
Gepts, P. (1994) Theor. Appl. Genet. 89, 629-635[ISI].
3. 	Yabuno, T. (1962) Cytologia 27, 296-305[ISI].
4. 	Wendel, J. F. (1995) in Evolution of Crop Plants, eds. Smartt, J. &
Simmonds, N. W. (Longman, Essex, U.K.), pp. 358-366.
5. 	Decker, D. S. (1988) Econ. Bot. 42, 4-15[ISI].
6. 	MacHugh, D. E. & Bradley, D. G. (2001) Proc. Natl. Acad. Sci. USA 98,
5382-5384[FreeFullText].
7. 	Galinat, W. C. (1988) in Corn and Corn Improvement, eds. Sprague, G. F. &
Dudley, J. W. (Am. Soc. Agron./Crop Sci. Soc. Am./Soil Sci. Soc. Am., Madison,
WI), pp. 1-31.
8. 	Kato, Y., T.A. (1984) Evol. Biol. 17, 219-253[ISI].
9. 	Doebley, J. F. (1990) Econ. Bot. 44,Suppl., 6-27[ISI].
10. 	Romero-Severson, J. , Smith, J. S.C. , Zeigle, J. , Hauser, J. , Joe, L.
& Hookstra, G. (2001) Theor. Appl. Genet. 103, 567-574[ISI].
11. 	Bowcock, A. M. , Ruiz-Linares, A. , Tomfohrde, J. , Minch, E. , Kidd, J.
R. & Cavalli-Sforza, L. L. (1994) Nature (London) 368,
455-457[CrossRef][ISI][Medline] [OrderarticleviaInfotrieve].
12. 	Vila, C. , Leonard, J. A. , Gotherstrom, A. , Marklund, S. , Sandberg, K.
, Liden, K. , Wayne, R. K. & Ellegren, H. (2001) Science 291,
474-477[Abstract/FreeFullText].
13. 	Matsuoka, Y. , Mitchell, S. E. , Kresovich, S. , Goodman, M. & Doebley,
J. (2001) Theor. Appl. Genet. 104, 436-450[ISI].
14. 	Goldstein, D. B. , Ruiz Linares, A. , Cavalli-Sforza, L. L. & Feldman, M.
W. (1995) Genetics 139,463-471[Abstract/FreeFullText].
15. 	Rosenberg, N. A. , Woolf, E. , Pritchard, J. K. , Schaap, T. , Gefel, D.
, Shpirer, I. , Lavi, U. , Bonne-Tamir, B. , Hillel, J. & Feldman, M. W.
(2001) Proc. Natl. Acad. Sci. USA 98, 858-863[Abstract/FreeFullText].
16. 	Felsenstein, J. (1993) PHYLIP, Phylogeny Inference Package (Univ. of
Washington, Seattle), Version 3.5c.
17. 	Minch, E. , Ruiz-Linares, A. , Goldstein, D. B. , Feldman, M. W. &
Cavalli-Sforza, L. L. (1997) MICROSAT: A Computer Program for Calculating
Various Statistics on Microsatellite Allele Data (Stanford Univ., Palo Alto,
CA), Version 1.5c.
18. 	Goldstein, D. B. , Ruiz Linares, A. , Cavalli-Sforza, L. L. & Feldman, M.
W. (1995) Proc. Natl. Acad. Sci. USA 92, 6723-6727[Abstract].
19. 	Zhivotovsky, L. A. & Feldman, M. W. (1995) Proc. Natl. Acad. Sci. USA 92,
11549-11552[Abstract].
20. 	Pritchard, J. K. , Stephens, M. & Donnelly, P. (2000) Genetics 155,
945-959[Abstract/FreeFullText].
21. 	Doebley, J. F. , Goodman, M. M. & Stuber, C. W. (1987) Econ. Bot. 41,
234-246[ISI].
22. 	Buckler, E. S. , Phelps-Durr, T. , Keith Buckler, C. , Dawe, R. K. ,
Doebley, J. & Holtsford, T. (1999) Genetics 153,
415-426[Abstract/FreeFullText].
23. 	Wilkes, H. G. (1967) Teosinte: The Closest Relative of Maize (Harvard
Univ., Cambridge, MA).
24. 	Piperno, D. R. & Flannery, K. V. (2001) Proc. Natl. Acad. Sci. USA 98,
2101-2103[Abstract/FreeFullText].
25. 	Smith, B. D. (1998) The Emergence of Agriculture (Sci. Am. Library, New
York).
26. 	Wilkes, H. G. (1977) Econ. Bot. 31, 254-293[ISI].
27. 	Smith, B. D. (2001) Proc. Natl. Acad. Sci. USA 98,
1324-1326[FreeFullText].
28. 	Piperno, D. R. & Pearsall, D. M. (1998) The Origins of Agriculture in the
Lowland Neotropics (Academic, San Diego).
29. 	Galinat, W. C. & Campbell, R. G. (1967) Mass. Agric. Exp. Station Monogr.
Ser. 1, 1-16.
30. 	Ramirez, E., R. , Timothy, D. H. , Diaz, B. E. & Grant, U. J. (1960)
Races of Maize in Bolivia (Natl. Acad. Sci./Natl. Res. Council, Washington,
DC).
31. 	Goodman, M. M. & Brown, W. L. (1988) in Corn and Corn Improvement, eds.
Sprague, G. F. & Dudley, J. W. (Am. Soc. Agron./Crop Sci. Soc. Am./Soil Sci.
Soc. Am., Madison, WI), pp. 33-79.
32. 	Grant, U. J. , Hatheway, W. H. , Timothy, D. H. , Cassalett, C. &
Roberts, L. M. (1963) Races of Maize in Venezuela (Natl. Acad. Sci./Natl. Res.
Council, Washington, DC). www.pnas.org/cgi/doi/10.1073/pnas.052125199

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==
Little Girl, 3 Million Years Old, Offers New Hints on Evolution
If the fossil Lucy, the most famous woman from out of the deep human past, had
a child, it might have looked a lot like the bundle of skull and bones
uncovered by scientists digging in the badlands of Ethiopia.
The paleontologists who are announcing the discovery in the journal Nature
today said the 3.3-million-year-old fossils were of the earliest
well-preserved child ever found in the human lineage. It was estimated to be
about 3 years old at death, probably female and a member of the
Australopithecus afarensis species, the same as Lucys.
An analysis of the skeleton revealed evidence of a species in transition, the
scientists said in interviews yesterday.
The lower limbs supported earlier findings that afarensis walked upright, like
modern humans. But gorillalike arms and shoulders suggested that it possibly
retained an ancestral ability to climb and swing through the trees.
Her completeness, antiquity and age at death make this find unprecedented in
the history of paleoanthropology, said Zeresenay Alemseged, the Ethiopian
leader of the discovery team and a researcher at the Max Planck Institute for
Evolutionary Anthropology in Leipzig, Germany.
Two reports of the findings are being published in Nature. The National
Geographic Society, a supporter of the research, will run a popular article on
the fossil child in the November issue of its magazine.
At a news conference in Addis Ababa, Ethiopia, the scientists gave the fossil
the name Selam, which means peace in Ethiopias official Amharic language.
Scientists not involved in the research said the fossils were a significant
find that should provide new insights about the afarensis species and a
little-known period of early human origins.
The child really confirms that afarensis was walking upright, said Tim D.
White, a paleoanthropologist at the University of California, Berkeley. It has
the potential to answer old questions and raises some new ones including their
behavior in trees. Dr. White, who has found even earlier human ancestors in
Ethiopia, participated in the analysis of the 3.2-million-year-old Lucy
fossils. They were uncovered not far away in Ethiopia in 1974 by Donald C.
Johanson, who is now director of the Institute of Human Origins at Arizona
State University.
Other discoveries show that the afarensis species, a major branch of the human
family tree, lived in Africa from earlier than 3.7 million to 3 million years
ago.
In an accompanying commentary in the journal, Bernard Wood of George
Washington University, who had no part in the discovery, said the specimen was
a veritable mine of information about a crucial stage in human evolutionary
history.
Dr. Wood, a paleoanthropologist, also noted how rare it was for the fragile
bones of infants to survive long enough to fossilize. But if they do, they
provide precious evidence about the growth and development of the individual
and the species, he wrote.
Until now, Dr. Wood said, the earliest comparably complete specimen of a
human-related child was that of a Neanderthal who lived less than 300,000
years ago in Syria.
The discovery team said the largely intact condition of the fossils indicated
that the child was presumably buried in sand and rocks shortly after death
during a flood in a desert region known today as Dikika, in northeastern
Ethiopia.
Then, in December 2000, along came a team of fossil hunters led by Dr.
Alemseged. On a steep hillside, one of the men, Tilahun Gebreselassie of the
Ethiopia Ministry of Culture and Tourism, was the first to see the childs tiny
face looking up from a block of sandstone. It was a long and projecting face
with a flat nose.
The face and skull were clearly that of a young afarensis, the scientists
concluded almost immediately.
Dr. Alemsegeds team spent much of the last five years extracting the rest of
the specimen from the surrounding stone with dentists drills and picks. The
tedious work exposed the full cranium and jaws, the torso and spinal column,
limbs and the left foot. The childs one complete finger was curled in a tiny
grasp, much like a young chimpanzees. The skeleton is much more complete than
Lucys.
Although the fossils are still being studied, Dr. Alemseged and his colleagues
noted several important findings and areas for further research. The Dikika
girls brain size, for example, was about the same as that of a similarly aged
chimpanzee, but a comparison with adult afarensis skulls indicates a
relatively slow brain growth slightly closer to that of humans.
The presence of a hyoid bone was a surprise. It is a rarely preserved bone in
the larynx, or voice box, that supports muscles of the throat and tongue. The
bone in the infant appeared to be primitive and more similar to those found in
apes than in humans, the scientists said, but is the first hyoid found in such
an early human-related species and thus important in research about the
origins of human speech.
The first relatively complete shoulder blades to be found in an
australopithecine individual was one of the most puzzling aspects of the
discovery, several scientists said. The lower body appeared to be adapted for
upright walking by afarensis. But the shoulders and long arms were more
apelike.
In the journal report, Dr. Alemseged and his team wrote that the functional
interpretation of these features is highly debated, with some arguing that the
upper limb features are nonfunctional retentions from a common ancestor only,
whereas others proposed that they were preserved because A. afarensis
maintained, to some degree, an arboreal component in its locomotor repertoire.
===
http://www.associatedcontent.com/article/53752/human_evolution_step_by_
step.html
-------------
Human Evolution, Step by Step
Our ancestors--the original hominids--diverged from the ancestors of modern
chimpanzees. Over millions of years, multiple bipedal and more or less
"apelike" hominid species evolved. Scientists say that arrival of modern human
beings happened less than 200K years ago.

Some say the awe-inspiring complexity of the human body reveals an
"intelligent design." Others say it reveals billions of years of genetic
mutation and natural selection - eons of evolution. Whatever you believe, it's
worth knowing what most scientists say. They disagree on plenty. But most agree
that humans evolved in something like these four steps.
Step 1: Monkeys, Gorillas, and the Third Chimpanzee
Based on genetic evidence, scientists say the ancestors of contemporary apes -
including humans, chimpanzees, gorillas, orangutans, and gibbons - diverged
from the ancestors of contemporary "Old World" monkeys around 30 million years
ago. Then, during the next 20 million years, our ancestors split off from the
ancestors of the gibbons, orangutans, and gorillas. Finally, sometime between
6 and 8 million years ago, our ancestors - the original hominids - diverged
from the ancestors of modern chimpanzees.
The DNA structures of humans and chimps still look alike. Of the 3 billion
base units of DNA in each of the species' genomes, more than 98 percent are
the same. Such similarity has led at least one influential writer to call us
the "third chimpanzee," along with bonobos and common chimps. By some genetic
measures, we're more similar to chimpanzees than chimpanzees are to gorillas.
We're also closer to chimpanzees than two species of gibbon are to each other.
Step 2: Bipedal Apes and Adaptive Radiation
Evolution works very slowly, so the original hominid species would have looked
a lot like the other ape species hanging around Africa at the time - except
that, unlike some of them, it stood up and walked on two feet. Over millions
of years, multiple bipedal and more or less "apelike" hominid species evolved
from this progenitor in a process that biologists call "adaptive radiation."
Adaptive radiation produces "bushes" of related species within the larger tree
of life, each adapted to a different ecological niche. Natural selection then
"prunes" the bushes back, leaving alive only the species best adapted to
current conditions in the competitive environment. In the case of our
ancestors, scientists say, the radiating species were basically adaptive
variations on the theme "bipedal ape."
Step 3: The First Humans?
About 2.5 million years ago, the adaptive radiation of hominid species led to
the evolution of a larger-brained hominid, Homo habilis ("man the handyman").
Importantly, the evolution of Homo habilis coincides with the appearance of
the earliest stone tools yet discovered. Most experts agree that by the time
we're dealing with larger-brained tool users, we're dealing with a "human," or
Homo, species. Still, Homo habilis wasn't human in the same way we are. While
his handyman brain was much larger than the brains of earlier hominids, it was
only half as large as yours or mine.
Two more Homo species then arrived on the scene: Homo rudolfensis, a species
like Homo habilis but with a bigger body, and Homo ergaster, a species with a
bigger brain and better tools. All three Homo species likely lived in Africa
at this time, along with two or more other hominid species. Crowds like that
suggest that older, more linear models of human evolution are way too
simplistic. Rather than one hominid species replacing another, many likely
existed at the same time - and even competed for scarce resources.
Step 4: World Conquerors
About 1.8 to 1.5 million years ago, scientists say another new Homo species
evolved, probably from Homo ergaster. Called Homo erectus, the big-brained
brutes left the confines of Africa and spread across Asia - and thrived liked
no Homo species had ever thrived before. Some fossils suggest that Homo
erectus still lived in Asia as recently as 30,000 years ago. Another probable
Homo ergaster offshoot, Homo heidelbergensis, which some scientists lump
together with Homo erectus, later left Africa for Europe.
Scientists argue over whether modern Homo sapiens evolved from these early
conquerors or whether we evolved from a species that remained in Africa - and
then fanned out and conquered the earlier conquerors. Little is certain here.
Experts argue about whether particular fossils belong to Homo erectus, Homo
heidelbergensis, or even Homo neanderthalensis, the Neanderthal Man, who
appeared about 230,000 years ago and lasted until about 30,000 years ago, long
after the arrival of modern Homo sapiens.
Scientists say that arrival - the arrival of fully modern human beings -
happened less than 200,000 years ago. Apparently well adapted, Homo sapiens
spread across the globe and rapidly replaced all similar species. By around
30,000 years ago, Homo sapiens were the sole remaining human species (except
for maybe Homo floresiensis, the hobbit-like hominids whose bones were
recently found on the Indonesian island of Flores). Before long, humans were
growing crops, building civilizations, and writing down questions about where
we came from - questions we argue over still.
===
People have been measuring mutation rates since Alan
Robertson's work on moths (not peppered) back in 1956. And all
such measures have proven that the rates are fast enough to
support both observed and theorized evolution.
==
How evolution cooks up life's endless variety
Minute changes in proteins affect genes, theory says

Dueling chefs are given a featured ingredient and then race to create dishes.
They both start with, say, lobster meat, but one might produce a seaweed salad
while the other would make corn and lobster dumplings.

Substitute genes for ingredients, and it explains how humans can be so similar
to chimpanzees -- sharing more than 98 percent of our genetic code -- and yet
so different. In becoming human, people didn't evolve a lot of new genes,
scientists believe; they made different use of the ones they had.

In December, researchers at Duke University announced some of the first
concrete evidence for this idea. They focused on a gene that makes a protein
involved in memory and perception. Although the protein is exactly the same in
human and chimpanzee brains, the team found that humans have evolved minute
genetic changes that cause brain cells to make, or "express," more of the
crucial protein, perhaps helping the human brain to work better. A little more
of these proteins here, a little less of those proteins there, and -- voila --
a chimp becomes a human.

The chimpanzee research is part of a profound conceptual shift. Biologists
have long suspected that "gene expression" -- the way cells make more of some
proteins and less of others -- could be important in answering many biological
questions. But now some biologists believe that this process could play a vital
role in explaining the way one species evolves into another with sometimes
shocking speed.

"What we used to think of as big, complex changes are in fact remarkably easy
to achieve" through changes in gene expression, said Gregory A. Wray, a
professor of biology at Duke University who led the chimpanzee research. "This
is changing the way that we think about evolution."

The new research on gene expression could provide an answer to a puzzle that
has confounded biologists since Darwin and that has recently been seized on by
proponents of intelligent design: the idea that life is too complex to have
happened without the help of a higher being. With the "survival of the
fittest," it is easy to see that a lion that runs a little faster will be a
better hunter and thus be more likely to survive and pass on this attribute to
its offspring. Over time, these improvements accumulate, and lions evolve.

But where do these changes come from in the first place? In other words, how
could it be that a single, random genetic change would be able to improve on
something so complex as, say, the legs of a lion, with all of their
interconnected joints, tendons, nerves, and muscles.

"We need to understand how you get the various kinds of novelty -- the first
hand, the first eye, the first brain," said Marc Kirschner at a recent talk at
Harvard Medical School, where he is a professor. "It is the variety of life
that needs explaining." Kirschner is co-author of a new book, "The
Plausibility of Life," about the biological sources of evolutionary change.

The research on gene expression, and particularly an active field called
"evolutionary developmental biology," or "evo devo," is now addressing this
question, according to Sean B. Carroll, a scientist at the University of
Wisconsin-Madison and the Howard Hughes Medical Institute.

In every cell, there are genes that create the proteins that are the building
blocks of life. But these proteins can also work as signals, turning on or off
other genes. The proteins from these genes may affect still more genes. So a
protein from a single gene can set off a cascade of other changes. A study
published in Nature last week by scientists at Yale University found that as
humans evolved from their ape ancestors, the regulatory genes were more likely
to have changed than genes that don't switch other genes.

Changes in gene expression are particularly important during embryonic
development. One small, accidental genetic change, Carroll and others say, can
cause changes in the expression of many genes, which change how the body of an
animal develops before it is born. For example, changing a single gene in the
fruit fly will cause it to grow a leg on its head instead of an antenna. In a
sense, the mutation has changed the biological signal that means "grow an
antenna here" to "grow a leg here." Sometimes, such a genetic change -- and
all the physical changes it causes -- will leave the animal better adapted to
its surroundings, and evolution takes off.

Biologists widely agree that gene expression is important, but its role in
evolution is still very much an open question because researchers only
recently began finding clear examples.

One of their more remarkable discoveries is research published on what have
come to be called "Darwin's finches." When Charles Darwin's ship, the Beagle,
came upon the Galapagos Islands off the coast of Ecuador in 1835, the young
naturalist was particularly amazed by the finches. Across the islands, the
brown-feathered birds looked similar, but their beaks were different.

In some of the species, the finches had beaks that were broad and stout, ideal
for cracking through tough seeds, while in others the beaks were more pointed,
ideal for reaching the pollen in flowers or piercing fruits. The finches,
Darwin surmised, had begun as one species but then separated into the species
he saw, each with a beak adapted to take advantage of particular foods in its
environment. The finches helped inspire Darwin's theory of evolution.

In 2004, a team led by Harvard Medical School Professor Cliff Tabin showed
that many of the complex changes in the beak -- a stouter structure that must
meet reshaped bones of the skull -- could be explained by a single genetic
switch. When a particular gene, called Bmp4, turned on earlier in the
development of the beak, the finches ended up with the stouter beaks,
according to a paper in the journal Science. His team, which included Arhat
Abzhanov of Harvard Medical School, verified the finding by artificially
activating the gene earlier in a developing chicken. The chicken's beak looked
more like one of Darwin's seed-cracking finches.

Tabin's team did not identify what caused the gene to come on earlier in some
finches, but the gene is known to signal other genes to become more or less
active. Such genes, known as regulatory genes, act like the choreographers of
a developing animal. In a sense, the gene can be thought of like a dial: Turn
it up, and the entire beak structure morphs one way; turn it down, and the
beak morphs another way.

This, then, explains how small random genetic changes could create a
coordinated set of changes that might make for a better adapted animal. It is
just a twist of a dial, triggered by an accidental genetic change.

Other scientists have discovered similar systems at work in the evolution of
other forms of life. Carroll, author of a recent book on evo devo, "Endless
Forms Most Beautiful," has documented shifts in regulatory genes that change
the patterns of spots on fruit flies. John Doebley, another scientist at the
University of Wisconsin-Madison, has identified small changes that helped the
teosinte, a plant that looks like a large grass, develop into maize, the plant
with dramatic ears that was a key source of food for Native Americans.

Another example is the increase in the size of human brains compared with the
brains of their ape cousins, according to Dr. Christopher A. Walsh, chief of
genetics at Children's Hospital Boston. He helped identify a gene that, when
mutated, causes children to be born with brains less than half the normal size
-- comparable, in fact, to the size of a chimpanzee brain. What is remarkable
about the disease, called microcephaly, is that it is not deadly. It is
debilitating, but patients can learn to walk on their own and sometimes even
speak a few words.

It seems likely, Walsh suggested, that changes in this one gene, long ago, may
have helped humans develop larger brains. The gene does not appear to be
involved in regulating other genes, but it shows how a relatively small change
can have a dramatic effect.

==
Life would be the same if all chiral centers were
inverted, right? That the energy difference due to nonconservation
of parity is nil, and that leads to racemic mixtures when they are
synthesized. Homochirality is a result of one stereoisomer becoming
dominant for kinetic reasons, and was the luck of the draw.

http://arxiv.org/ftp/physics/papers/0209/0209069.pdf

Salam's papers on this subject are well enough
known. They're also widely considered to be crazy.
Salam is not by any means the first person to want to tie
the problem of homochirality in living systems to parity
violation in weak interactions. The problem is not whether
parity violation in weak interactions exists. It does. The
problem is in providing any believable mechanism for such a
tiny violation as exists to make any difference at all in
production rates for different enantiomers in a macroscopic
system.
Look, Salam starts from the fact that there is a parity
violating interaction, mediated by Z_0 exchange, acting
between neutrons and electrons. That's perfectly fine so
far as it goes; we know it to be the case from high energy
experiments on weak interactions.
But due to the extremely large Z_0 mass, these parity
violating interactions are very short range in their
effects. The relevant length scale is far, far less than the
size of an atom, never mind the size of an amino acid.
So it does not follow at all that this interaction can form
Cooper pairs out of electrons and neutrons in an amino acid,
as Salam proposes, or produce a phase transition to a
`superconducting state' in the context of a mixture of amino
acids, say, dissolved in a liquid at ordinary temperatures.
This is a highly questionable step in his argument, and his
whole argument rises or falls on the validity of this step,
namely the use of BCS, Landau-Ginzburg, or mean field theory
to model the transition.
For an example where a pairing interaction does produce a
phase transition, just consider how pairing works in a
normal superconductor. In a superconductor, one has
negatively charged and effectively light electrons moving
around inside an atomic lattice, having characteristic
spacing between the positively charged nuclei on the order
of a few angstroms, and with characteristic effective
electron energies being less than an eV. The massive atomic
nuclei are free to execute small oscillations around their
equilibrium positions, with the energy scale for such
oscillations being also considerably smaller than an eV.
An electron moving through the lattice can collide with the
an oscillating nucleus, and transfer some of its momentum to
the nucleus. That nucleus can in turn collide with a second
electron and transfer some momentum to it. For the right
combination of relative momentum and spin of the two
electrons, this interaction produces an attractive force
between the two electrons, with an interaction energy
considerably less than an eV. The attraction can produce
bound pairs of electrons, with a finite binding energy. If
the temperature is then made low enough so that there is not
enough thermal energy to break up the pairs, then they form,
and there is a phase transition to a superconducting state.
The key thing, though, is that the range of this pairing
interaction is a lot larger than the spacing between atoms
in the lattice. The pairs are also larger than this
spacing. That is what makes the Landau-Ginzburg theory, or
the BCS theory, applicable to the interactions of the
electron gas in the lattice of a superconductor. The basic
length scales allow for an application of the mean field
theory.
These conditions are not satisfied for electrons and
neutrons in an amino acid, interacting via Z_0
exchange. Salam's theory seems to be dead in the water based
on basic considerations of the length scales involved.
But never mind, lets consider the experimental evidence that
exists for and against such a thing anyway ...

the authors say is very interesting. I quote:
It seems a contradiction to accept the existence of Salam
phase transition but deny the configuration change D- to
L-. All these experimental evidence suggest a revision of
Salam hypothesis. We may divide the Salam hypothesis into
two parts: 1. Theoretical deduction of a specific phase
transition based on quantum mechanics and BCS theory. 2.
His prediction of a configuration change of D- to L- during
the transition. All the experiments that refute Salam
hypothesis are actually against the second part of his
hypothesis not the first part. A better definition of Salam
phase transition should be: a phase transition in which D-
and L- enantiomers exhibit different transition behaviour.
My comment on this is:
Yes indeedy, it sure is a contradiction, and a very glaring
contradiction at that, to accept the existence of the `Salam
phase transition' but deny the `configuration change D- to
L-'.
We may not divide the Salam hypothesis into two parts,
because, that the configuration change occurs is the whole
and entire point of the Salam hypothesis. If it doesn't
occur, then it's of no interest at all in the context of
explaining homochirality.
A further comment is: the results that these authors claim
to have observed would be absolutely stunning in and of
themselves if true.
They claim to observe a phase transition in racemic
(D/L)-valine,alanine, D-alanine,valine and L-alanine,valine
single crystals at a temperature of about 250 K. That's
fine, there could be all sorts of reasons for such a
transition having to do with the crystal structure. It
wouldn't be at all surprising to me to find such a thing
happening.
What is stunning is that there is *any* observed difference
in temperature dependent heat susceptibilities or magnetic
susceptibilities between the D- and L- form crystals, given
the extremely tiny energy differences expected to exist
between the enantiomers. In crystals, electromagnetic forces
are completely dominant, and they *do not violate parity*:
no such long range effects of the weak interactions are
expected in crystals. You'ld expect the different forms to
rotate polarized light in opposite directions and so on, but
bulk properties like susceptibility should behave the same
within the bounds of measurability.
So I smell a rat here. I strongly suspect that there are
problems with these experiments. I'm no condensed matter
theorist or chemist, but the first thing that I would
question is the purity of the crystals in question. Suppose
the D form crystal is more impure than the L form crystal,
or possibly the D and L form crystals are actually somewhat
racemic mixtures, but the fraction of L vs D is actually
different in the `D' crystals than is the fraction of D vs L
in the `L' crystals.
Then the observed experimental effect would be spurious.
I know it's claimed by the authors that these were `single
crystals', but the masses quoted are pretty large (about 100
mg), so how can this be known?
That would be my hypothesis, and until I see this experiment
being duplicated, I'm strongly inclined not to believe it.
Nonsense: the mechanism is not established. There are many
other, and much more likely possibilities than this one.
Tracy's statement is certainly the default hypothesis. It's
not speculative, far from it.
Yeah, yeah, yeah.
I certainly don't buy all of this quantum crap you're
talking, but who cares, suppose you were even right about
it.
There's still a big problem with all of it: even if there is
a tiny energy difference between L- and D- forms of the
molecules, and even if there were a measurable difference
between L- and D- form crystals, that still doesn't get you
to the point of explaining homochirality.
To do that, you'ld need to transform D- form into L- form at
a significant rate, and that just is not observed to
explicitly.
It isn't too surprising that it isn't observed. It's
probably a helluva lot harder to do via the weak
interactions than it is to tranform diamond into graphite at
room temperature. The barrier to doing so is likely similar
in the D-crystal, and the energy difference is a lot
smaller.

Tracy has it right, many natural mechanisms known for
producing the basic molecules produce racemic mixtures
period, weak interactions or no weak interactions. That's
the fact which has to be somehow gotten around to explain
homo-chirality
==
Primate fossils.
- A post-orbital bar. This is an extension of the skull that forms
part of the eye socket, resulting in the eye being completely
encircled by bone.
- Reliance on stereoscopic vision rather than smell. This can be
determined from the shape and size of the brain, which can be
ascertained from the interior of the skull.
- Opposable thumb and toe (in all but hominids, e.g., humans).
- A flat nail, as opposed to a claw, on the big toe.
- A large brain for animals of corresponding size.
(Martin 1990:639-640; Shipman 1990)
Primates of modern aspect are also sometimes referred to as
euprimates. But since adapids and omomyids are euprimates, and since
euprimates are considered to be more advanced than the plesiadapiformes,
a primative and extinct branch of the primate family tree, we can see
For instance,
Palaeocene dermopterans and the Eocene primates continue to attest to a
common ancestry. The Beard and Kay papers merely advocate the idea that
_Phenacolemur_, _Ignacius_, and _Plesiadapis_ were more closely related to
calugos than they were to
primates. So rather than being used as evidence for primate evolution,
these authors now use them as evidence for calugo evolution.

For instance, Beard (1990) bases his claim for a close relationship with
calugos on the relative lengths of newly discovered finger bones of
_Phenacolemur_, stating that only calugos have such proportions among
living tree-dwelling mammals. Based on these proportions, Beard
concludes that _Phenacolemur_ was a glider.
However, Krause (1991) points out that the finger bones that Beard
studied were not found in the relationship with each other that they
were in life, but were instead isolated from each other in a rock
roughly two cubic meters in volume. Beard identified these bones and
their relationships within the hand of _Phenacolemur_ based on
comparisons with other known, but incomplete, specimens. Also, the
remains of another, larger animal (_Ignacius_) were apparently found in
the same rock, and so while some of these bones were attributed to
_Phenacolemur_ and some to _Ignacius_, it is possible that some were
misassigned, or from the feet of either animal. Krause throws further
doubts on Beard's identification of individual bones by noting that some
do not articulate with each other as they would be expected to if they
were adjacent to each other while the animal was alive.
say that early primate evolution as we know it has just glided out the
window.' But considering that the paleontologist quoted is Richard Kay,
the senior author of the paper
Kay et al. (1990) state that the floor of middle ear (also known as the
auditory bulla) of _Ignacius_ is formed by the entotympanic bone,
rather than the petrosal bone as it is in all euprimates. The authors
also state that there is a similarity in the way the entotympanic
contacts the basioccipital bone to the situation in the calugo. In
addition, they claim that the blood supply to the brains of
_Phenacolemur_, _Ignacius_, and _Plesiadapis_ was similar to that of
calugos based on the anatomy of the base of the skull. Based on these
points, the authors state that the plesiadapiformes, the group that
these three animals are members of, were not archaic primates at all,
but were instead members of the order Dermoptera.

But Fox (1993) points out that the teeth of plesiadapiformes are
significantly different from those of calugos. As well, Martin (1993)
reveals that the auditory bulla of calugos formed from the ectotympanic
bone, and not the entotympanic. Martin also points out that the ear drum
of calugos is almost horizontal, the primitive state of early mammals,
where as the ear drum of euprimates, plesiadapiformes, and virtually all
other mammals is closer to the vertical. Martin also observes that the
skeletons of _Plesiadapis_ show no adaptations for gliding. In addition,
he states that not all the plesiadapiformes have the arterial pattern of
blood supply for the brain as is found in the specimens that Kay et al,
studied, and such a condition could easily have developed independently
in the two groups, as it has in other placental mammals (Martin 1993;
Wible & Martin 1993)
Based on these points, Martin points out that the plesiadapiformes may
not be monophyletic (that is, a natural grouping). Regarding the
plesiadapiformes, Shipman (1990) states that not everyone agrees on
exactly which families are primates and which are simply their close
relatives...
However, recent papers support the idea that plesiadapiformes are the
closest relatives of euprimates (Bloch & Boyer 2002).
Moving right along,
Biologists have a similar problem when classifying life. Is a creature a
reptile, or a bird? Is it a reptile, or a mammal? Is it an insectivore,
or a primate? What is a primate anyway? Should only euprimates to be
considered to be primates, or should the definition be more encompassing
to include the plesiadapiformes? Creationists take advantage of the fact
that creatures are classified as either one type or another, and will
argue that there are no transitional forms, just as one could claim that
there are no colors between red and orange.
He quotes Elwyn Simons, who states that In
spite of recent finds, the time and place of origin of order Primates
remains shrouded in mystery (Simons 1969). Simons believes that there
are transitional forms between primates and insectivores, but he was
commenting on the *origin* of primates, and not the transition to modern
Present evidence indicates that the primates belong among the
oldest documented divisions of placental mammals. _Purgatorius_
species from the late Cretaceous and early Tertiary of Montana
may represent the earliest occurrence of members of this order,
but until better specimens than isolated individual teeth are
found, the character, adaptations, and even definite
identification of them as the earliest primates will remain
uncertain. [Simons 1969]
(It should be noted that more complete specimens of _Purgatorius_ have
questions as to whether it was actually present in the Cretaceous. See
Buckley (1997).)
After obscure beginnings in the late Mesozoic, primates are
better documented in the fossil record of earliest Tertiary
Paleocene faunas. Specifically, paleontologists have named the
following Middle Paleocene North America genera of primates:
(1) _Elphidotarsius_, (2) _Pronothodectes_, (3) _Paromomys_,
(4) _Palechthon_, (5) _Palenochtha_, (6) Plesiolestes, and
(7) _Picrodus_. These mammals have generally been assigned to
four different families of Primates: the first to Carpolestidae,
the second to Plesiadapidae, 3-6 to Paromomyidae and 7 to
Picrodontidae. [Simons 1969]
The families named by Simons are all members of the plesiadapiformes, so
even if one accepts the idea that plesiadapiformes are not closely
related to euprimates, Simons believes that they are, and so would
qualify as transitional forms in his eyes. To claim that he believes
otherwise is a misrepresentation.
Romer states that
lemurs first arrive apparently as immigrants from some unknown area
(Romer 1966). But Romer has other things to say about lemurs as well:
Forms which most would agree are definitely on the primate side
of the ordinal boundary appear in the Middle Paleocene. They
pertain to three families, of which _Plesiadapis_,
_Carpolestes_, and _Phenacolemur_ are typical; the three are
confined to the Paleocene and Lower Eocene and are principally
known from the American West. For the most part, they are
represented by fragmentary remains, mainly of the dentition. The
molar teeth seem to agree with those of early lemurs, and in
_Plesiadapis_, in which alone the skull is preserved, the ear
region has the structure seen in typical lemuroids.
[Romer 1966:217]
So we see that some features of lemurs were present in earlier
creatures. In addition, Romer points out that the earliest lemurs were
not exactly like the modern variety:
_Notharctus_ was a small mammal with a skull about two inches
long, which probably resembled the ordinary lemurs of today in
general appearance. It was probably quite lemur-like in its
proportions and many structural features. The dentition,
however, is more primitive in a number of respects. Although
some members of the group had but three premolars, _Notharctus_
still had the full complement of four. Further, the upper
incisors were comparatively normal; the canines were of
primitive type, and the lower incisors were little, if at all,
procumbent. [Romer 1966:218]
So while certain stages of lemur evolution may be currently unknown, the
claim that there are no known transitional forms is incorrect.
... the transition from insectivore to primate is not documented
by fossils. The basis of knowledge about the transition is by
inference from living forms.
But here is a more complete sample:
The important features of the emergence and evolution of the
early pre-primate insectivores can be summarized briefly as
follows: 1) They are possibly the oldest placental mammalian
order. 2) The evolved and diversified rapidly during the latter
part of the Mesozoic, and, by early Cenozoic times, had given
rise to three more mammalian orders, the rodents, the
multituberculates, and the primates. 3) The subsequent evolution
of the insectivores is characterized by a decline in their
diversity and habitat range. 4) While the fossil record of
insectivore evolution is reasonably good in some lines, the
transition from insectivore to primate is not documented by
fossils. The basis of knowledge about the transition is by
inference from living forms. 5) There is sufficient reason to
suspect, however, that the major factor which served to
distinguish the primates as a separate order was an arboreal
adaptation. The adjustment made by the early primates to living
in the trees is by far the most important event in the evolution
of the primates, and there is a reasonable amount of direct
fossil evidence bearing on the early stages of the evolution of
the prosimians, which were the first primates to show the
effects of this adaptation. [Kelso 1974:142]
So we see that, like Simons above, Kelso was commenting on the *origin*
of primates, and not their subsequent evolution into modern forms. But
just in case there's any doubt as to Kelso's position on the matter:
_Plesiadapis_ does, however, represent one of the lines that lay
along the transitional pathway from insectivore to primate, or,
in other words, it represents a morphological transition of the
early effects of an arboreal adaptation on the primates.
[Kelso 1974:148]
Robert Carroll:
The specific origin of primates among the more primitive
eutherians has not been established, although they could have
evolved from animals with a molar pattern like that of
_Cimolestes_. No specific derived characters have been
demonstrated as being uniquely shared between early primates and
the early members of any other order. [Carroll 1988:464,467]
A single lower molar from the late Cretaceous of Montana
provides the oldest fossil evidence of the primates. This tooth
is distinguished from those of other primitive eutherians by the
relative blunt cusps and its squarish outline. It is almost
identical to the molars of the genus _Purgatorius_ from the
Lower Paleocene, which is known from a nearly complete dentition
with a formula of
3 1 4 3
-
3 1 4 3
The digits represent the numbers of incisors, canines, premolars, and
molars respectively on either side of the mouth. The first row is the
count of each tooth type in the upper jaw, and the second row the count
in the lower jaw. After a few sentences Carroll continues:
We recognize four or five quite distinct families, all of which
are grouped within the suborder Plesiadapiformes. This
assemblage may include the ancestors of all higher primates. The
most primitive genus in which a skull can be reconstructed is
_Palaechthon_, a member of the superfamily Paromomyoidea from
the middle Paleocene. It is approximately 4 centimeters long.
The posterior margin of the orbit is constricted, but there is
not a complete postorbital bar. The tooth row is continuous,
without a diastema [gap], but the third incisor and the first
premolar are lost, giving a dental formula of
2 1 3 3
-
2 1 3 3
The particular
insectivore that paleontologists have suggested as the ancestor of the
primates is the tree shrew. But only one of the sources places tree shrews
with the insectivores, and with an interesting qualification:
As we use the term here, the order Insectivora will serve as a
category for several types of animals. We shall include
primative early placental types found in the Cretaceous and
early Tertiary, the more modern groups of insectivores which
have surviving members, and, in addition, a number of twigs of
the placental evolutionary tree which have departed from the
insectivore pattern but are hardly worthy of characterization as
distinct orders. [Romer 1966:208]
One of these 'twigs' are the tree shrews, and another are the
aforementioned calugos. However, Carroll (1988:477) classifies them as
the only members of the order Scandentia, while Kelso (1974:37) places
them in the primates, although he does mention that there are other
opinions on the matter.
There's obviously some controversy regarding the classification of tree
shrews, and we'll see more momentarily.
I have attempted to indicate the large number of recent studies
whose results indicate that a close relationship between
tupaiids and primates is unlikely. [Campbell 1966]
R. D.
Martin, who supposedly states that The tree shrew is not on the roster
hint at it. Martin *does* feel that there are significant differences
between tree shrews and primates, and that the gulf between them is to
that:
Nevertheless, it does seem likely that tree shrews still have a
special significance for future evolutionary studies, not as
models for the earliest primates, but as models for the
ancestral placental mammals, by virtue of their retention of so
many primitive mammalian features. Whatever else they may be,
tree shrews are exceedingly primitive mammals. [Martin 1982]
Although in some quarters the view persists that tree-shrews may
be the closest relatives of primates among placental mammals,
there is no convincing evidence that this is the case. It
therefore seems appropriate to exclude tree-shrews from the
order Primates and to allocate them to their own order
Scandentia, to reflect their wide degree of separation from
primates. Even if reliable evidence of an early specific
relationship between tree-shrews and primates were to emerge,
there would still be no convincing case for including tree-
shrews in the order Primates. The order Primates can be most
satisfactorily defined to the exclusion of tree-shrews,
regardless of the relationships of the latter, and the
separation between tree-shrews and primates must be very
ancient. [Martin 1990:710]
...the question of inclusion or exclusion of the tree-shrews in
the definition of the order Primates is only a matter of
classificatory convention _provided that it has been
demonstrated that tree shrews are indeed more closely related to
primates than to any other group of placental mammals_.
[emphasis in original] [Martin 1990:203]
And finally:
If it is accepted that tree-shrews share any specific ancestry
with primates among placental mammals, inclusion of tree-shrews
in the order Primates once more boils down to the arbitrary
recognition of taxonomic boundaries. [Martin 1990:650]
primates had a specific relationship, but his position seems to have
that:
If euprimates share a special relationship with any archontans
[a superorder of mammals], it is with scandentians based on
the basicranial evidence. Both have an enlarged tegmen tympani
that roofs the entire middle-ear ossicular chain and there are
further unique resemblances in the tegmen tympani of lemuriforms
and scandentians. [Wible & Martin 1993:144]
Ironically, a recent review of primate origins indicates that tree
shrews may be the closest living relatives of euprimates after all (see
Rasmussen 2002).
There was a recent fossil find that preserves several
The teeth of _T. eocaenus_ resemble teeth of modern
_Tarsius_, but not any more than those of _Afrotarsius_, long considered
a probably tarsiid from north Africa.
In addition, Martin explicitly stated that the
adapids and omomyids were not ancestral to tarsiers based on fossil
evidence, and that tarsiers were an old group (Martin 1990, 1993). So
the discovery of such an ancient specimen is hardly a problem for
evolution, but in fact fulfills a prediction based upon it.
Beard et al. write:
Although the retention of several primitive feature
distinguishes these animals from more advance simian taxa, such
a combination of primitive and derived traits is not unexpected
in basal simians. [Beard et al. 1994]
at the beginning of this essay. It should be obvious by now that there
is indeed fossil evidence linking primates of modern aspect to earlier
forms.
It's true that there are gaps in our knowledge, but new fossils are
being discovered all the time, and those gaps are slowly being filled.
For instance, the discovery of a new specimen of _Carpolestes_ was
announced in 2002. It lacked a postorbital bar and stereoscopic vision,
but did possess opposable thumbs and toes (Bloch & Boyer 2002). An
excellent example of a transitional form.

REFERENCES
Beard, K. C. 1990. Gliding behaviour and palaeoecology of the alleged
primate family Paromomyidae (Mammalia, Dermoptera). Nature 345:340-341.
Beard, K. C., Tao, Q., Dawson, M. R., Wang, B., & Li, C. 1994. A diverse
new primate fauna from middle Eocene fissure-fillings in southeastern
China. Nature 368:604-609.
Bloch, J. I., & Boyer, D. M. 2002. Grasping Primate Origins. Science
298:1606-1610.
Buckley, G. A. 1997. A New Species of _Purgatorius_ (Mammalia;
Primatomorpha) from the Lower Paleocene Bear Formation, Crazy Mountain
Basin, South-Central Montana. Journal of Paleontology 71(1):149-155.
Campbell, C. B. G. 1966. Taxonomic Status of Tree Shrews. Science
153:436.
Carroll, R. L. 1988. Vertebrate Paleontology and Evolution. New York: W.
H. Freeman and Company.
Fox, R. C. 1993. The Primitive Dental Formula of the Carpolestidae
(Plesiadapiformes, Mammalia) and Its Phylogenetic Implications. Journal
of Vertebrate Paleontology 13(4):516-524.

Kay, R. F., Thorington, R. W., & Houde, P. 1990. Eocene plesiadapiform
shows affinities with flying lemurs not primates. Nature 345:342-344.
Kelso, A. J. 1974. Physical Anthropology: An Introduction, 2nd Edition.
Philadelphia: J. B. Lippincott Company.
Krause, D. W. 1991. Were paromomyids gliders? Maybe, maybe not. Journal
of Human Evolution 21:177-188.
Martin, R. D. 1982. Et tu, Tree Shrew? Natural History 91(8):26-33.
Martin, R. D. 1990. Primate origins and evolution: a phylogenetic
reconstruction. Princeton, New Jersey: Princeton University Press.
Martin, R. D. 1993. Primate origins: plugging the gaps. Nature
363:223-234.
Rasmussen, D. T. 2002. The origin of primates. In The Primate Fossil
Record edited by Walter Carl Hartwig, pp. 5-9. Cambridge, United
Kingdom: Cambridge University Press.
Romer, A. S. 1966. Vertebrate Paleontology, 3rd Edition. Chicago:
University of Chicago Press.
Shipman, P. 1990. Primate origins up in the air again. New Scientist
126(June 23, 1990):57-60.
Simons, E. L. 1969. The Origin and Radiation of the Primates. Annals of
the New York Academy of Sciences 167:319-331.
Tarsiers: Past Present, and Future edited by Patricia C. Wright, Elwyn
L. Simons, and Sharon Gursky, pp. 9-34. New Brunswick, New Jersey, and
London: Rutgers University Press.
Wible, J. R., & Martin, J. R. 1993. Ontogeny of the Tympanic Floor and
Roof in Archontans. In Primates and Their Relatives in Phylogenetic
Perspective, edited by Ross. D. E. MacPhee, pp. 111-148. New York:
Plenum Press.
==
Bell, Graham, The Masterpiece of Nature: The Evolution and Genetics of
Sexuality, University of California Press, Berkeley, CA, 1982.

Ridley, Mark, The Cooperative Gene, The Free Press, New York, 2001.

Schecter, Julie, How Did Sex Come About?, Bioscience, 34:680, December 1984.

Crow, J.F., The Importance of Recombination, The Evolution of Sex:
An Examination of Current Ideas, ed. Michod and Levin, Sinauer Associates,
Sunderland, MA, 1988.

Eldredgen Niles and Joel. Cracraft, Phylogenetic Patterns and the Evolutionary
Process: Method and Theory in Comparative Biology, Columbia Universiy Press,
New York, 1980.

Maddox, John, What Remains to be Discovered, The Free Press, New York, 1998.

Dobzhansky, Theodosius, Francisco J. Ayala, G. Ledyard Stebbins, and James W.
Valentine, Evolution, W.H. Freeman, San Francisco, CA, 1977.

Williams, George C., Sex and Evolution: in the Monographs in Population
Biology series, Princeton University Press, Princeton, NJ, 1975.

Zimmer, Carl, Parasite Rex, The Free Press, New York, 2000.

Ridley, Matt, The Red Queen Viking, London, 1993.

Cartwright, John, Evolution and Human Behavior, Macmillan, London,
Grasse, Pierre-Paul, Evolution of Living Organisms, Academic Press, New York,
1977.

Van Valen, Leigh, A New Evolutionary Law, Evolutionary Theory, 1:1-30, 1973.

Bernstein, H., F.A. Hopf, and R.E. Michod, The Evolution of Sex: DNA Repair
Hypothesis, The Sociobiology of Sexual and Reproductive Strategies, ed.
C. Rasa and E. Voland, Chapman and Hall, London, 1989.

Zimmer, Carl, Evolution: The Triumph of an Idea, HarperCollins, New York,
231, 2001.

Ward, Peter, Future Evolution, Henry Holt, New York, 2001.

Mayr, Ernst, What Evolution Is, Basic Books, New York, 2001.

Crow, J.F., The High Spontaneous Mutation Rate: Is it a Health Risk?,
Proceedings of the National Academy of Sciences, U.S.A., 94:8380-8386, 1997.

Cavalli-Sforza, Luigi Luca, Genes, Peoples, and Languages, North Point
Press, New York, 2000.

Gould, Stephen Jay, Is a New and General Theory of Evolution Emerging?,
speech presented at Hobart College, February 14, 1980; as quoted in Luther
D. Sunderland, Darwins Enigma, Master Books, San Diego, CA, 1984.

Margulis, Lynn and Dorion Sagan, Slanted Truths: Essays on Gaia, Symbiosis,
and Evolution, Springer-Verlag, New York, 1997.

Ackerman, Jennifer, Chance in the House of Fate, Houghton Mifflin,
Boston, MA, 2001.

Thomas, Lewis, The Medusa and the Snail, Viking, New York, 1979.

==
www.frombearcreek.com
http://biocrs.biomed.brown.edu/Darwin/DI/Parts-is-Parts.html

Hall, B.G. \Evolution on a Petri Dish. The Evolved beta=Galactosidase
system as a Model for Studying Acquisitive Evolution in the Laboratory.
_Evolutionary Biology_ 15 (1982): 85-150

There are true snakes with much better-developed legs than are
found in some legless lizards.

This is an important point. One of the chief problems with using
paraphyletic groups in classifications is the \grade inflation\ it
tends to impose on groups. A sub-group is given much higher taxonomic
rank than its sister group, and may be given a rank equivalent to that
of a much larger clade-equivalent. The traditional Aves is given a rank
equal to the traditional Reptilia. The tomato and its closest wild
relatives are often recognized as a separate genus Lycopersicon, and
not as just a small species group within one section of one subgenus
of the giant genus Solanum [thus getting assigned equal taxonomic rank
to the whole group of which it's really just one small part].
But traditionally, many would want to give Serpentes a rank
equal to a group \Lacertilia\ or \Sauria\ consisting of all the [other]
lizards. Therefore, they'd have Serpentes ranked high above any other
squamate clade like Iguanidae. But then again they aren't lizards
But you're agreeing to some extent that this common understanding
doesn't mean that Serpentes need be ranked above Iguania or Varanoidea
or whatever. To a cladist, the problem isn't in recognizing the
specialized groups like Serpentes, or Aves or Tetrapoda. Those are
clades, they're fine. The problem is in formally recognizing the
everything else groups like Lacertilia or non-avian whatever, or
Pisces as being groups equivalent to them.
And that's fine. Cladistic terminology and methods are good for
technical discussions where saying something clear and precise about
relationships and its evidence is required. It's also a lot tougher
standard. For most of our discussions much vaguer statements about
phylogeny are plenty clear enough. Australopithecines are a
perfectly good transitional grade between other apes and other
near-humans even if their monophyly is unlikely and their precise
phylogeny of their species with regard to the origin of the genus
Homo is unclear. That degree of precision isn't really required here.
Still, when talking about the origin of snakes I'll continue to enjoy
pointing out that some lizards like varanids are thought to actually
be closer relatives to the snakes than they are to the other lizards.
I remember talks with groups who found that sort of thing very interesting.
Okay then. It's likely because of frequent arguements with traditional
taxonomists who saw nothing wrong with having a group Serpentes equal in
rank to a group Lacertilia [or a genus Lycopersicon equal to Solanum, or
a class Aves equal to a class Reptilia]. You seemed to be taking a very
familiar position. If you weren't, good for you.
But young as reptile groups go.
dinosaurs as older than snakes and scorpions older than
Good. Another way to get the age and relatedness angles in is to use
those quasi-cladistic explanations. I'll say that snakes are really
one specialized group of the \lizards\ [meaning squamata], and that
they're understood to be closer to some particular groups of living
lizards and that their ancestors were lizards with four legs just
like other reptiles' [then I might show them the boa's spurs]. Ever
see legs on a snake?
We can show that even those extinct Mesozoic reptiles included some
extremely birdlike forms with feathers. The differences are getting
pretty small.
That sounds like just the sort of evidence needed to sort out
the detailed relationships among eurypterids and scorpions.
Well, the usual dictionary definitions may specifically exclude humans.
Actually \ape\ just the common word for hominid\
But cladists need no word for fish. They can say vertebrates other than
tetrapods. The interesting \fish\ grades are those sarcopterygians
closest to the point of tetrapod origin. I hope that someday we may
find complete skeletons [especially limbs] of ones in the narrowing
gap between Panderichthys and Acanthostega.
1 & 2 don't put them within the clade. If scorpions
just shared features like 1 & 2 with all eurypterids, they might still
just be the sister group to the eurypterids. It's sharing 3-6 that

Title: The arthropod Offacolus kingi (Chelicerata) from the Silurian
of Herefordshire, England: Computer based morphological reconstructions
and phylogenetic affinities.
Author, Editor, Inventor: Sutton-Mark-D; Briggs-Derek-E-G;
Siveter-David-J; Siveter-Derek-J {a}; Orr-Patrick-J
Source: Proceedings-of-the-Royal-Society-Biological-Sciences-Series-B.
[print] 22 June, 2002; 269 (1497): 1195-1203.
Abstract: The small, non-biomineralized, three-dimensionally preserved
arthropod Offacolus kingi Orr et al. from the Wenlock Series (Silurian)
of Herefordshire, England, is re-evaluated, and the new family
Offacolidae erected. This new study is based on specimens which have
been serially ground, reconstructed by computer and rendered in the
round as coloured models. Offacolus possesses a prosomal appendage
array similar to that of Limulus, but also bears robust and setose
exopods on appendages II-V which are unlike those found in any other
arthropods. Opisthosomal appendages are similar in number and
morphology to the book-gills of Limulus. Cladistic analysis places
Offacolus basally within the Chelicerata, as a sister taxon to the
eurypterids and extant chelicerates, but more derived than the Devonian
Weinbergina.
Title: On the Emsian (Early Devonian) arthropods of the Rhenish Slate
Mountains: 3. The chasmataspidid Diploaspis.
Author, Editor, Inventor: Dunlop-Jason-A {a}; Poschmann-Markus;
Anderson-Lyall-I
Source: Palaeontologische-Zeitschrift. [print] Dezember, 2001; 75 (2):
253-269.
Abstract: New specimens of the chasmataspid Diploaspis casteri STORMER,
1972 (Chelicerata: Chasmataspidida) are described from the late Lower
Emsian of Alken an der Mosel, Germany. Chasmataspidids represent a
distinct clade within Chelicerata, sharing characters with both
xiphosurans and eurypterids. Diploaspis is significant in having the
most complete appendage series of any known chasmataspidid, while we
question previous interpretations of the ventral preabdominal plate.
Diploaspis has unmineralized cuticle and is therefore preserved with a
number of different morphologies. Study of both our new fossils and
STORMER'S type material suggests that the co-occurring Alken fossil
Heteroaspis novojilovi STORMER, 1972 is a preservational variant, which
is regarded here as a junior synonym, of D. casteri.
Title: Fossil evidence, terrestrialization and arachnid phylogeny.
Author, Editor, Inventor: Dunlop-Jason-A {a}; Webster-Mark
Source: Journal-of-Arachnology. 1999; 27 (1): 86-93.
Abstract: Geological and morphological evidence suggests that the
earliest scorpions were at least partially aquatic and that
terrestrialization occurred within the scorpion clade. Scorpions and
one or more other arachnid lineages are therefore likely to have come
onto land independently. The phylogenetic position of scorpions
remains controversial and we question Dromopoda, in which scorpions
are placed derived within Arachnida, as this is not supported by
scorpions' lateral eye rhabdomes, embryology and sperm morphology. We
propose a synapomorphy for scorpions + eurypterids, a postabdomen of
five segments as part of an opisthosoma of 13 segments. Scorpions and
tetrapulmonates must have evolved their book lungs convergently while
fossil evidence indicates that a stomotheca, synapomorphic for
Dromopoda, is probably convergent too. 'Arachnid' characters such as
Malpighian tubules, the absence of a carapace pleural margin, and an
anteriorly directed mouth may also be convergent, although their status
as synapomorphies can be defended using parsimony. Convergence is
difficult to prove unequivocally, but when there are strong grounds for
suspecting it, such characters are questionable evidence for arachnid
monophyly.
Title: The phylogeny of the extant chelicerate orders.
Author, Editor, Inventor: Wheeler-Ward-C {a}; Hayashi-Cheryl-Y
Source: Cladistics-. June, 1998; 14 (2) 173-192.
Abstract: The phylogeny of the extant chelicerate orders is examined in
the light of morphological and molecular evidence. Representatives from
each of the chelicerate \orders\ and mandibulate and onychophoran
outgroups are examined. Molecular (small and large ribosomal subunit
DNA) and morphological information is combined in a total evidence
regime to determine the most consistent picture of extant chelicerate
relationships for these data. Multiple phylogenetic analyses are
performed with variable analysis parameters yielding largely consistent
results. A normalized incongruence length metric is used to assay the
relative merit of the multiple analyses. The combined analysis with
lowest character incongruence yields the scheme of relationships
(Pycnogonida+(Xiphosura+((Opiliones+((Solifugae+Pseudoscorpiones)
+Scorpiones))+((Ricinulei+Acari)+(Palpigradi+((Thelyphonida+Schizomida
=Uropygi)+(Amblypygi+Araneae))))))). This result is fairly robust to
variation in analysis parameters, with the placement of solifugids and
the status of the pedipalps responsible for most disagreement.
Title: EVOLUTIONARY MORPHOLOGY AND PHYLOGENY OF ARACHNIDA.
Author, Editor, Inventor: SHULTZ-J-W {a}
Source: Cladistics-. 1990; 6 (1): 1-38.
Abstract: This paper reports results from a cladistic analysis of the
11 Recent arachnid orders. The polarities of 64 newly discovered and
traditional characters were determined through outgroup comparisons
that included Eurypterida, Xiphosura, Trilobita and Crustacea. A
branch-and-bound algorithm was used to discover a single tree
(consistency index 0.59). The relationships suggested by this analysis
differ substantially from previous interpretations of arachnid
phylogeny, and a new taxonomic system is introduced to accommodate
these results. This analysis suggests that Arachnida is monophyletic
and two principal lineages, Micrura and Dromopoda. Possible
synapomorphies of Micrura include a pygidium, tritosternum, six
principal lateral eyes, poorly schlerotized postgenital appendages,
coxal gland orifices near leg 1, an array of microtubules associated
with the spermatozoan nucleus, and absence of coxal endites on the
walking legs. The micruran orders appear to have the following
relationships: (Palpigradi (Araneae (Amblypygi (Thelyphonida,
Schizomida)))) (Ricinulei, Acari). Possible synapomorphies of Dromopoda
include transverse carapacal furrows, greatly reduced prosomal sternum,
prosomal endosternite with two segmental components, stomotheca,
bicondylar femoropatellar and patellotibial joints and extensor muscles.
The dromopodan orders appear to have the following relationships:
Opiliones (Scorpiones (Pseudoscorpiones, Solifungae)).

The Finnish tree, but not
http://tolweb.org/tree?group=Carnivora&contgroup=Eutheria
which leaves both Feliformia and Caniformia unresolved.
[previous snips in 2nd abstract restored]
Title: Genets and 'Genet-like' taxa (Carnivora, Viverrinae):
Phylogenetic analysis, systematics and biogeographic implications.
Author, Editor, Inventor: Gaubert-Philippe {a}; Veron-Geraldine;
Tranier-Michel
Source: Zoological-Journal-of-the-Linnean-Society. [print] March,
2002; 134 (3): 317-334.
Abstract: The subfamily Viverrinae is a taxon of uncertain systematic
status. This study consists of cladistic analyses based on morphological
characters of specimens belonging to the genera Genetta, Osbornictis,
Poiana and Prionodon. Two levels of analysis are carried out, one
concerning generic relationships (intergeneric analysis) and one dealing
with the interrelationships of species within the genus Genetta
(intrageneric analysis). In the first analysis, different outgroups were
used in order to test the ingroup topology. With regard to the
intergeneric analysis, Osbornictis, Poiana and Prionodon, together with
Genetta johnstoni, constitute a monophyletic group (including Nandinia),
which is the sister-group of a clade formed by the other species of
genets. Thus, the genus Genetta is regarded as paraphyletic. Prionodon
appears to be a derived taxon. The Poiana-Prionodon clade is well
supported, especially by ultrastructural hair characters. The cladogram
topology in the intrageneric analysis indicates an ecological transition
from the rain forest genets to the savanna genets. Thissupports a rain
forest origin of the genus Genetta, a conclusion which may be generalized
to the entire study group.
But see below
It was one of the genera studied in the second paper I cited above [see
above]. Apparently there's a related African genus:
Title: Basicranial anatomy of the living linsangs Prionodon and Poiana
(Mammalia, Carnivora, Viverridae), with comments on the early evolution
of Aeluroid carnivorans. Author, Editor, Inventor: Hunt-Robert-M-Jr {a}
Source: American-Museum-Novitates. [print] April 26, 2001; (3330): 1-24.
Abstract: The living Asian linsang Prionodon pardicolor, shares marked
anatomical similarities in basicranium and dentition with the extinct
Oligocene aeluroid, Palaeoprionodon lamandini, from the Quercy fissures,
France. The living African linsang, Poiana richardsoni, is similar yet
slightly more derived in basicranial traits relative to Prionodon
pardicolor, and also has basicranial and dental features indicating a
relationship to the living genets (Genetta). The basicranial and
auditory anatomy of a series Palaeoprionodon-Prionodon-Poiana can be
interpreted as a morphocline showing the progressive alteration of the
form of the petrosal and auditory bulla from the plesiomorohic aeluroid
state in the Quercy fossils to a derived condition typical of the
linsangs (Prionodon, Poiana) and living genets (Genetta). The
basicranial anatomy of Genetta, including the structure of the petrosal
and auditory bulla, is typical of other species of the Viverridae. The
other lineages of living viverrids are believed to have undergone a
similar transformation in their basicranial anatomical pattern from the
plesiomorphic state present in Oligocene aeluroids, exemplified by
Palaeoprionodon, to the modern patterns typical of the living subfamilies
(including the endemic Malagasy viverrid genera).
a

Title: Single origin of Malagasy Carnivora from an African ancestor.
Author, Editor, Inventor: Yoder-Anne-D {a}; Burns-Melissa-M; Zehr-Sarah;
Delefosse-Thomas; Veron-Geraldine; Goodman-Steven-M; Flynn-John-J
734-737.
Abstract: The Carnivora are one of only four orders of terrestrial
mammals living in Madagascar today. All four (carnivorans, primates,
rodents and lipotyphlan insectivores) are placental mammals with
limited means for dispersal, yet they occur on a large island that has
been surrounded by a formidable oceanic barrier for at least 88 million
years, predating the age of origin for any of these groups. Even so, as
many as four colonizations of Madagascar have been proposed for the
Carnivora alone. The mystery of the island's mammalian origins is
confounded by its poor Tertiary fossil record, which leaves us with no
direct means for estimating dates of initial diversification. Here we
use a multi-gene phylogenetic analysis to show that Malagasy
carnivorans are monophyletic and thus the product of a single
colonization of Madagascar by an African ancestor. Furthermore, a
bayesian analysis of divergence ages for Malagasy carnivorans and
lemuriforms indicates that their respective colonizations were
temporally separated by tens of millions of years. We therefore
conclude that a single event, such as vicariance or common dispersal,
cannot explain the presence of both groups in Madagascar.
The above abstract doesn't detail their phylogeny, so its nice to
have a library key.
Their maximum-likelihood tree has all Malagasy carnivora as a single
clade [including the large, misleadingly catlike fossa Cryptoprocta*].
This group is sister to a clade consisting of African and Asian
mongooses and allies. Sister to that [Malagasy carnivore/mongoose]
group is their hyenid representative. Sister to that whole clade is
clade of several civets and genets, then the Felidae. Sister to all
the above Feliformia on their tree is Nandinia, the African palm
\civet\ [their quotes].
* Amusingly, the well-known pumalike fossa [_Cryptoprocta ferox_]
doesn't belong to the genus _Fossa_, which includes an entirely
different Malagasy carnivore.
They argue that lemurs reached Madagascar long before the mongooselike
ancestor of the carnivores reached the island.
So, perhaps this little critter is sister to all the other living
catlike Carnivora:
http://www.kostich.com/two_spotted_palm_civet.htm
[nice skull pics at
http://1kai.dokkyomed.ac.jp/mammal/en/species_all/nandinia_binotata.html
==
Any attempt to use \interfertile, and produces fertile F1 offspring\
as the main criterion for \kind\ recognition will run into many
serious problems throughout the real biological world.
You'll find examples illustrating every degree in between
\interfertile, with fully viable, fully fertile offspring\ and \not
at all interfertile\. You'll find \ring species\ cases where form A
can cross with B, and B with C, but A can't cross with C. You'll
find cases where only the female or only the male F1 hybrids are
fertile. There are cases where all the F1 hybrids are nearly, but
not quite, completely sterile, but subsequent backcrosses and
inbreeding eventually restores hybrid fertility. There are plenty
of cases where very different looking species never form hybrids in
the wild, but do form fully fertile hybrids in captivity
[intergeneric hybrids in orchids, colubrid snakes, etc.]. Conversely,
there are many cases of very low or nonexistent fertility among some
closely-similar species that creationists will likely consider one
\kind\ [such as say, horses, donkeys and zebras (genus Equus)].
There's the difficulty of actually applying the criterion. Nobody
can use it for any extinct species. Even for living species, there
are little or no experimental data for most \possibly the same kind\
species pairs. Nobody even really knows for sure if humans and any
of the nonhuman great apes could produce any viable hybrid offspring,
and nobody can even be sure whether any such F1 offspring [if they
did form and did survive] would be fertile or not.
Nowhere does it say that full interfertility can't be lost among
the different groups of descendants of formerly interfertile
ancestors. Biologists know full well that interfertility can be
lost and often is lost [i.e., \speciation\ occurs].
Further, I really don't see why even demonstrated interfertility
would necessarily require creationists to classify two species as
being in the same kind. Surely any omnipotent creator could have
made different separately-created kinds that were fully interfertile
with one another if it pleased it to do so. If so, then even full
interfertility wouldn't necessarily prove \same-kind-hood\. [I
suspect creationists might take this tack if some unscrupulous
experimenter ever did come up with viable, fertile human/chimp
hybrids].
And there are plenty of other plant and animal examples of \observed
speciations\. Thus, the inability to breed can't alone be a sufficient
single criterion for identifying separately-created kinds.
They were in my view one kind, but they have
Again, in nature we do see every gray zone between \clearly different
local forms of one species\ and \clearly two related but separate
species\. Just as we'd expect to see if speciation is a gradual,
ongoing process.
But they can still exchange genes by matings of both with the various
intermediate-sized dogs. Still, if an experimental island was set up
and populated by wild packs of just chihuahuas [eating mice and
insects?] and great danes [eating deer?], we'd most likely see them
behaving as two fully separate species.
At any rate, the diversity of domesticated dogs is pretty dramatic
morphological \macro\ evolution, especially when we compare them with
the wild gray wolves that the first human dog breeders had to start
with. [Would a timber wolf recognize the horny chihuahua as something
to breed with, or just a light snack?]
This clearly shows that interbreeding vs. unable-to-interbreed can't
be the sole criterion for \kind\ recognition. So, what else is needed?
Many creationists will claim that functional, adaptive features like
mimicry, symbiosis, etc. can't possibly have evolved naturally [part
of the whole \microevolution is just the loss of information\
business], so we may infer that differences in any such \can't evolve\
features could be another way to recognize \separate kinds\. But then,
the ones without the special features might have lost that information.
Would the original \Corydoras kind\ have had all of the special
features now found throughout the genus?
You mean, how many _known_ fossil species have been found and named
_so far_?
Actually, that web page doesn't say that only this one fossil
Corydoras species is known. I question that it really is the only one,
but I'll accept that that's the case for now for the sake of argument.
Maybe there are many more, but they've not been found as yet. [Or,
maybe there are more known Corydoras fossils, but you and I haven't
heard about them.] How many suitable strata are exposed and have been
thoroughly studied by catfish paleontologists? Or, maybe there are
some very good reasons why Corydoras catfish rarely form fossils [this
last seems unlikely, since they're so well provided with bony armor].
I note that it sounds like this fossil species may be known from just
this one specimen. Presumably, you don't think this means that it's
the only individual of that species that ever lived. Where are all
the fossils of all the others that must have lived and died?
For that matter, the same fallacy [the false expectation that the
currently-known fossil record should be very complete] also cuts
against any creationist viewpoint that all Corydoras are one \kind\:
where are all the fossil intermediates documenting in detail the
\micro\ evolution of the modern diversity of Corydoras from their
single original ancestral type?
The explanation thus must be the same for the creationist view as
for the evolutionary view: the intermediate forms existed, but
either they weren't preserved as fossils, or the fossils haven't
yet been found and studied.
Good for them and good for you. It's great that you have an interest
in ichthyology; but it's pretty rare for creationists to be
knowledgeable in any area of systematic biology.
Really? How long ago was that? Tens of millions of years or a
few thousand?
The
So you think the whole genus Corydoras is the \kind\ here. But how
do we tell if this is the case? How can we know that the family
Callichthyidae isn't the relevant \kind\ instead, or some larger
group of families of catfishes [such as their superfamily
Loricarioidea], or the whole catfish group Siluriformes? How do we
know that some much smaller groups within Corydoras, perhaps the
individual species, aren't the separately-created kinds?
http://personal.www.umich.edu/~rreis/tree/corydoras.htm
http://personal.www.umich.edu/~rreis/tree/callichthyidae.htm
http://tolweb.org/tree?group=Siluriformes&contgroup=Ostariophysi
http://tolweb.org/tree?group=Ostariophysi&contgroup=Teleostei
For that matter, why are there any clearly recognizable above-\kind\
groups at all? If Corydoras was separately created, why does it seem
so clearly related to other Callichthyidae and to other Siluriformes?
What do the groups \ Callichthyidae\ and \Siluriformes\ or
\Ostariophysi\ or \Teleostei\ even mean, if their members aren't
actually related to one another by descent? Why are there apparently
no clear breaks in the nested hierarchy of groups within groups,
within groups, within groups, that would correspond to the \kinds\
level? If separately-created kinds really existed, one might expect
that their boundaries would be qualitatively different [different in
\kind\ as it were] from those of any below-kind groups [ones due to
common descent] and the above-kind groups [due to what? Accidental or
imaginary resemblances?]
Do
Right, that's the definition. My question remains, how can we
recognize the separately-created kinds and their boundaries? How can
we even tell that different separately-created kinds exist at all?
Biologists might argue that there seems to be just one kind according
to your definition of \kind\: \all life on earth\
No, but the fact that essentially all known life happens to use a
common genetic code [which enables us to do that splicing you mention]
is part of the evidence that all life shares a common origin. If
seemingly related organisms had had completely different codes [there's
no reason why they shouldn't, if they were created separately], it
would have been very hard to explain evolutionarily.
==
Common descent and descent with modification are factual observations
that we observe today. The fossil record and the genetic and
morphological evidence do not give us any indication that things were
different in the past. Species arise from existing species, and
allele frequencies change from one generation to another. There is no
evidence that these things are going to change in the future for most
of the life on earth. We have evidence that life has changed in a
long history and we don't have any really good evidence that tells us
that things are any different today or will be tomorrow.
==
Rhynchocephalia or Sphenodonta.
I have an order or two of birds to add for you. Hoatzins (Opisthocomus
hoazin) are often put into their own order, Opisthocomiformes. Likewise,
ostriches (Struthio camelus) are often put into their own order
Struthioniformes (but which name is also often used for all the
ratites). There are no other single-species bird orders (at least that
are often used -- there have been eccentric classifications with other
monotypic orders, since after all there is no real criterion for judging).
===
A highly corroborated, stable phylogeny remains, which is largely consistent
with the temporal distributions of taxa recorded in the fossil record.
Similarly, Gingerich has stated (1977) "While living mammals are well
separated from other groups of animals today, the fossil record clearly
shows their origin from a reptilian stock and permits one to trace the
origin and radiation of mammals in considerable detail." For more details,
see Kermack's superb and readable little book (1984), Kemp's more detailed
but older book (1982), and read Szalay et al.'s recent collection of review
This list starts with pelycosaurs (early synapsid reptiles) and continues
with therapsids and cynodonts up to the first unarguable "mammal". Most of
the changes in this transition involved elaborate repackaging of an expanded
brain and special sense organs, remodeling of the jaws & teeth for more
efficient eating, and changes in the limbs & vertebrae related to active,
legs-under-the-body locomotion. Here are some differences to keep an eye " on:

# Early Reptiles Mammals
----------------------------------------------------------------------------"

1 No fenestrae in skull Massive fenestra exposes all of
braincase
2 Braincase attached loosely Braincase attached firmly to skull
3 No secondary palate Complete bony secondary palate
4 Undifferentiated dentition Incisors, canines, premolars,
molars
5 Cheek teeth uncrowned points Cheek teeth (PM & M) crowned & cusped
6 Teeth replaced continuously Teeth replaced once at most
7 Teeth with single root Molars double-rooted
8 Jaw joint quadrate-articular Jaw joint dentary-squamosal (*)
9 Lower jaw of several bones Lower jaw of dentary bone only
10 Single ear bone (stapes) Three ear bones (stapes, incus,
malleus)
11 Joined external nares Separate external nares
12 Single occipital condyle Double occipital condyle
13 Long cervical ribs Cervical ribs tiny, fused to
vertebrae
14 Lumbar region with ribs Lumbar region rib-free
15 No diaphragm Diaphragm
16 Limbs sprawled out from body Limbs under body
17 Scapula simple Scapula with big spine for
muscles
18 Pelvic bones unfused Pelvis fused
19 Two sacral (hip) vertebrae Three or more sacral vertebrae
20 Toe bone #'s 2-3-4-5-4 Toe bones 2-3-3-3-3
21 Body temperature variable Body temperature constant
----------------------------------------------------------------------------"

----
(*) The presence of a dentary-squamosal jaw joint has been arbitrarily
selected as the defining trait of a mammal.
Paleothyris (early Pennsylvanian) -- An early captorhinomorph reptile, with
no temporal fenestrae at all.
Protoclepsydrops haplous (early Pennsylvanian) -- The earliest known
synapsid reptile. Little temporal fenestra, with all surrounding bones
intact. Fragmentary. Had amphibian-type vertebrae with tiny neural
processes. (reptiles had only just separated from the amphibians)
Clepsydrops (early Pennsylvanian) -- The second earliest known synapsid.
These early, very primitive synapsids are a primitive group of pelycosaurs
collectively called "ophiacodonts".
Archaeothyris (early-mid Pennsylvanian) -- A slightly later ophiacodont.
Small temporal fenestra, now with some reduced bones (supratemporal).
Braincase still just loosely attached to skull. Slight hint of different
tooth types. Still has some extremely primitive, amphibian/captorhinid
features in the jaw, foot, and skull. Limbs, posture, etc. typically
reptilian, though the ilium (major hip bone) was slightly enlarged.
Varanops (early Permian) -- Temporal fenestra further enlarged. Braincase
floor shows first mammalian tendencies & first signs of stronger attachment
to rest of skull (occiput more strongly attached). Lower jaw shows first
changes in jaw musculature (slight coronoid eminence). Body narrower,
deeper: vertebral column more strongly constructed. Ilium further enlarged,
lower-limb musculature starts to change (prominent fourth trochanter on
femur). This animal was more mobile and active. Too late to be a true
ancestor, and must be a "cousin".
Haptodus (late Pennsylvanian) -- One of the first known sphenacodonts,
showing the initiation of sphenacodont features while retaining many
primitive features of the ophiacodonts. Occiput still more strongly "
attached
to the braincase. Teeth become size-differentiated, with biggest teeth in
canine region and fewer teeth overall. Stronger jaw muscles. Vertebrae "
parts
by fusing to three sacral vertebrae instead of just two. Limbs very well
developed.
Dimetrodon, Sphenacodon or a similar sphenacodont (late Pennsylvanian to
early Permian, 270 Ma) -- More advanced pelycosaurs, clearly closely "
related
to the first therapsids (next). Dimetrodon is almost definitely a "
"cousin"
and not a direct ancestor, but as it is known from very complete fossils,
it's a good model for sphenacodont anatomy. Medium-sized fenestra. Teeth
further differentiated, with small incisors, two huge deep- rooted upper
canines on each side, followed by smaller cheek teeth, all replaced
continuously. Fully reptilian jaw hinge. Lower jaw bone made of multiple
bones & with first signs of a bony prong later involved in the eardrum, but
there was no eardrum yet, so these reptiles could only hear ground-borne
vibrations (they did have a reptilian middle ear). Vertebrae had still
longer neural spines (spectacularly so in Dimetrodon, which had a sail), "
and
longer transverse spines for stronger locomotion muscles.
Biarmosuchia (late Permian) -- A therocephalian -- one of the earliest, "
most
primitive therapsids. Several primitive, sphenacodontid features retained:
jaw muscles inside the skull, platelike occiput, palatal teeth. New
features: Temporal fenestra further enlarged, occupying virtually all of "
the
cheek, with the supratemporal bone completely gone. Occipital plate slanted
slightly backwards rather than forwards as in pelycosaurs, and attached
still more strongly to the braincase. Upper jaw bone (maxillary) expanded "
to
separate lacrymal from nasal bones, intermediate between early reptiles and
later mammals. Still no secondary palate, but the vomer bones of the palate
developed a backward extension below the palatine bones. This is the first
step toward a secondary palate, and with exactly the same pattern seen in
cynodonts. Canine teeth larger, dominating the dentition. Variable tooth
replacement: some therocephalians (e.g Scylacosaurus) had just one canine,
like mammals, and stopped replacing the canine after reaching adult size.
Jaw hinge more mammalian in position and shape, jaw musculature stronger
(especially the mammalian jaw muscle). The amphibian-like hinged upper jaw
finally became immovable. Vertebrae still sphenacodontid-like. Radical
alteration in the method of locomotion, with a much more mobile forelimb,
more upright hindlimb, & more mammalian femur & pelvis. Primitive
sphenacodontid humerus. The toes were approaching equal length, as in
mammals, with #toe bones varying from reptilian to mammalian. The neck &
tail vertebrae became distinctly different from trunk vertebrae. Probably
had an eardrum in the lower jaw, by the jaw hinge.
Procynosuchus (latest Permian) -- The first known cynodont -- a famous "
group
of very mammal-like therapsid reptiles, sometimes considered to be the "
first
mammals. Probably arose from the therocephalians, judging from the
distinctive secondary palate and numerous other skull characters. Enormous
temporal fossae for very strong jaw muscles, formed by just one of the
reptilian jaw muscles, which has now become the mammalian masseter. The
large fossae is now bounded only by the thin zygomatic arch (cheekbone to
you & me). Secondary palate now composed mainly of palatine bones
(mammalian), rather than vomers and maxilla as in older forms; it's still
only a partial bony palate (completed in life with soft tissue). Lower
incisor teeth was reduced to four (per side), instead of the previous six
(early mammals had three). Dentary now is 3/4 of lower jaw; the other bones
are now a small complex near the jaw hinge. Jaw hinge still reptilian.
Vertebral column starts to look mammalian: first two vertebrae modified for
head movements, and lumbar vertebrae start to lose ribs, the first sign of
functional division into thoracic and lumbar regions. Scapula beginning to
change shape. Further enlargement of the ilium and reduction of the pubis "
in
the hip. A diaphragm may have been present.
Dvinia [also "Permocynodon"] (latest Permian) -- Another early cynodont.
First signs of teeth that are more than simple stabbing points -- cheek
teeth develop a tiny cusp. The temporal fenestra increased still further.
Various changes in the floor of the braincase; enlarged brain. The dentary
bone was now the major bone of the lower jaw. The other jaw bones that had
been present in early reptiles were reduced to a complex of smaller bones
near the jaw hinge. Single occipital condyle splitting into two surfaces.
The postcranial skeleton of Dvinia is virtually unknown and it is not
therefore certain whether the typical features found at the next level had
already evolved by this one. Metabolic rate was probably increased, at "
least
approaching homeothermy.
Thrinaxodon (early Triassic) -- A more advanced "galesaurid" cynodont.
Further development of several of the cynodont features seen already.
Temporal fenestra still larger, larger jaw muscle attachments. Bony
secondary palate almost complete. Functional division of teeth: incisors
(four uppers and three lowers), canines, and then 7-9 cheek teeth with "
cusps
for chewing. The cheek teeth were all alike, though (no premolars & "
molars),
did not occlude together, were all single- rooted, and were replaced
throughout life in alternate waves. Dentary still larger, with the little
quadrate and articular bones were loosely attached. The stapes now touched
the inner side of the quadrate. First sign of the mammalian jaw hinge, a
ligamentous connection between the lower jaw and the squamosal bone of the
skull. The occipital condyle is now two slightly separated surfaces, though
not separated as far as the mammalian double condyles. Vertebral "
connections
more mammalian, and lumbar ribs reduced. Scapula shows development of a new
mammalian shoulder muscle. Ilium increased again, and all four legs fully
upright, not sprawling. Tail short, as is necessary for agile quadrupedal
locomotion. The whole locomotion was more agile. Number of toe bones is
2.3.4.4.3, intermediate between reptile number (2.3.4.5.4) and mammalian
(2.3.3.3.3), and the "extra" toe bones were tiny. Nearly complete "
skeletons
of these animals have been found curled up - a possible reaction to "
conserve
heat, indicating possible endothermy? Adults and juveniles have been found
together, possibly a sign of parental care. The specialization of the "
lumbar
area (e.g. reduction of ribs) is indicative of the presence of a diaphragm,
needed for higher O2 intake and homeothermy. NOTE on hearing: The eardrum
had developed in the only place available for it -- the lower jaw, right
near the jaw hinge, supported by a wide prong (reflected lamina) of the
angular bone. These animals could now hear airborne sound, transmitted
through the eardrum to two small lower jaw bones, the articular and the
quadrate, which contacted the stapes in the skull, which contacted the
cochlea. Rather a roundabout system and sensitive to low-frequency sound
only, but better than no eardrum at all! Cynodonts developed quite loose
quadrates and articulars that could vibrate freely for sound transmittal
while still functioning as a jaw joint, strengthened by the mammalian jaw
joint right next to it. All early mammals from the Lower Jurassic have this
low-frequency ear and a double jaw joint. By the middle Jurassic, mammals
lost the reptilian joint (though it still occurs briefly in embryos) and "
the
two bones moved into the nearby middle ear, became smaller, and became much
more sensitive to high-frequency sounds.
Cynognathus (early Triassic, 240 Ma; suspected to have existed even
earlier) -- We're now at advanced cynodont level. Temporal fenestra larger.
Teeth differentiating further; cheek teeth with cusps met in true occlusion
for slicing up food, rate of replacement reduced, with mammalian-style "
tooth
roots (though single roots). Dentary still larger, forming 90% of the
muscle-bearing part of the lower jaw. TWO JAW JOINTS in place, mammalian "
and
reptilian: A new bony jaw joint existed between the squamosal (skull) and
the surangular bone (lower jaw), while the other jaw joint bones were
reduced to a compound rod lying in a trough in the dentary, close to the
middle ear. Ribs more mammalian. Scapula halfway to the mammalian "
condition.
Limbs were held under body. There is possible evidence for fur in fossil
pawprints.
Diademodon (early Triassic, 240 Ma; same strata as Cynognathus) -- Temporal
fenestra larger still, for still stronger jaw muscles. True bony secondary
palate formed exactly as in mammals, but didn't extend quite as far back.
Turbinate bones possibly present in the nose (warm-blooded?). Dental "
changes
continue: rate of tooth replacement had decreased, cheek teeth have better
cusps & consistent wear facets (better occlusion). Lower jaw almost "
entirely
dentary, with tiny articular at the hinge. Still a double jaw joint. Ribs
shorten suddenly in lumbar region, probably improving diaphragm function &
locomotion. Mammalian toe bones (2.3.3.3.3), with closely related species
still showing variable numbers.
Probelesodon (mid-Triassic; South America) -- Fenestra very large, still
separate from eyesocket (with postorbital bar). Secondary palate longer, "
but
still not complete. Teeth double-rooted, as in mammals. Nares separated.
Second jaw joint stronger. Lumbar ribs totally lost; thoracic ribs more
Probainognathus (mid-Triassic, 239-235 Ma, Argentina) -- Larger brain with
various skull changes: pineal foramen ("third eye") closes, fusion of "
some
skull plates. Cheekbone slender, low down on the side of the eye socket.
Postorbital bar still there. Additional cusps on cheek teeth. Still two jaw
joints. Still had cervical ribs & lumbar ribs, but they were very short.
Reptilian "costal plates" on thoracic ribs mostly lost. Mammalian #toe
bones.
Exaeretodon (mid-late Triassic, 239Ma, South America) -- (Formerly lumped
with the herbivorous gomphodont cynodonts.) Mammalian jaw prong forms,
related to eardrum support. Three incisors only (mammalian). Costal plates
completely lost. More mammalian hip related to having limbs under the body.
Possibly the first steps toward coupling of locomotion & breathing. This is
probably a "cousin" fossil not directly ancestral, as it has several new "
but
non-mammalian teeth traits.
GAP of about 30 my in the late Triassic, from about 239-208 Ma. Only one
early mammal fossil is known from this time. The next time fossils are "
found
in any abundance, tritylodontids and trithelodontids had already appeared,
leading to some very heated controversy about their relative placement in
the chain to mammals. Recent discoveries seem to show trithelodontids to be
more mammal- like, with tritylodontids possibly being an offshoot group "
(see
Hopson 1991, Rowe 1988, Wible 1991, and Shubin et al. 1991). Bear in mind
that both these groups were almost fully mammalian in every feature, "
lacking
only the final changes in the jaw joint and middle ear.
Oligokyphus, Kayentatherium (early Jurassic, 208 Ma) -- These are
tritylodontids, an advanced cynodont group. Face more mammalian, with
changes around eyesocket and cheekbone. Full bony secondary palate.
Alternate tooth replacement with double-rooted cheek teeth, but without
mammalian-style tooth occlusion (which some earlier cynodonts already had).
Skeleton strikingly like egg- laying mammals (monotremes). Double jaw "
joint.
More flexible neck, with mammalian atlas & axis and double occipital
condyle. Tail vertebrae simpler, like mammals. Scapula is now substantially
mammalian, and the forelimb is carried directly under the body. Various
changes in the pelvis bones and hind limb muscles; this animal's limb
musculature and locomotion were virtually fully mammalian. Probably cousin
fossils (?), with Oligokyphus being more primitive than Kayentatherium.
Thought to have diverged from the trithelodontids during that gap in the
late Triassic. There is disagreement about whether the tritylodontids were
ancestral to mammals (presumably during the late Triassic gap) or whether
they are a specialized offshoot group not directly ancestral to mammals.
Pachygenelus, Diarthrognathus (earliest Jurassic, 209 Ma) -- These are
trithelodontids, a slightly different advanced cynodont group. New
discoveries (Shubin et al., 1991) show that these animals are very close to
the ancestry of mammals. Inflation of nasal cavity, establishment of
Eustachian tubes between ear and pharynx, loss of postorbital bar. "
Alternate
replacement of mostly single- rooted teeth. This group also began to "
develop
double tooth roots -- in Pachygenelus the single root of the cheek teeth
begins to split in two at the base. Pachygenelus also has mammalian tooth
enamel, and mammalian tooth occlusion. Double jaw joint, with the second
joint now a dentary-squamosal (instead of surangular), fully mammalian.
Incipient dentary condyle. Reptilian jaw joint still present but "
functioning
almost entirely in hearing; postdentary bones further reduced to tiny rod "
of
bones in jaw near middle ear; probably could hear high frequencies now. "
More
Probably had coupled locomotion & breathing. These are probably "cousin"
fossils, not directly ancestral (the true ancestor is thought to have
occurred during that late Triassic gap). Pachygenelus is pretty close,
though.
Adelobasileus cromptoni (late Triassic; 225 Ma, west Texas) -- A recently
discovered fossil proto-mammal from right in the middle of that late
Triassic gap! Currently the oldest known "mammal." Only the skull was "
found.
"Some cranial features of
Adelobasileus, such as the incipient promontorium housing the cochlea,
represent an intermediate stage of the character transformation from
non-mammalian cynodonts to Liassic mammals" (Lucas & Luo, 1993). This "
fossil
was found from a band of strata in the western U.S. that had not previously
been studied for early mammals. Also note that this fossil dates from
slightly before the known tritylodonts and trithelodonts, though it has "
long
been suspected that tritilodonts and trithelodonts were already around by
then. Adelobasileus is thought to have split off from either a trityl. or a
trithel., and is either identical to or closely related to the common
ancestor of all mammals.
Sinoconodon (early Jurassic, 208 Ma) -- The next known very ancient
expanded. Permanent cheekteeth, like mammals, but the other teeth were "
still
replaced several times. Mammalian jaw joint stronger, with large dentary
condyle fitting into a distinct fossa on the squamosal. This final
refinement of the joint automatically makes this animal a true "mammal".
Reptilian jaw joint still present, though tiny.
Kuehneotherium (early Jurassic, about 205 Ma) -- A slightly later
proto-mammal, sometimes considered the first known pantothere (primitive
placental-type mammal). Teeth and skull like a placental mammal. The three
major cusps on the upper & lower molars were rotated to form interlocking
shearing triangles as in the more advanced placental mammals & marsupials.
Still has a double jaw joint, though.
Eozostrodon, Morganucodon, Haldanodon (early Jurassic, ~205 Ma) -- A group
of early proto-mammals called "morganucodonts". The restructuring of the
secondary palate and the floor of the braincase had continued, and was now
very mammalian. Truly mammalian teeth: the cheek teeth were finally
differentiated into simple premolars and more complex molars, and teeth "
were
replaced only once. Triangular- cusped molars. Reversal of the previous
trend toward reduced incisors, with lower incisors increasing to four. Tiny
remnant of the reptilian jaw joint. Once thought to be ancestral to
monotremes only, but now thought to be ancestral to all three groups of
modern mammals -- monotremes, marsupials, and placentals.
Peramus (late Jurassic, about 155 Ma) -- A "eupantothere" (more advanced
placental-type mammal). The closest known relative of the placentals &
marsupials. Triconodont molar has with more defined cusps. This fossil is
known only from teeth, but judging from closely related eupantotheres (e.g.
Amphitherium) it had finally lost the reptilian jaw joint, attaing a fully
mammalian three-boned middle ear with excellent high-frequency hearing. Has
only 8 cheek teeth, less than other eupantotheres and close to the 7 of the
first placental mammals. Also has a large talonid on its "tribosphenic"
molars, almost as large as that of the first placentals -- the first
development of grinding capability.
Endotherium (very latest Jurassic, 147 Ma) -- An advanced eupantothere.
Fully tribosphenic molars with a well- developed talonid. Known only from
tribosphenic molar evolved there.
Kielantherium and Aegialodon (early Cretaceous) -- More advanced
eupantotheres known only from teeth. Kielantherium is from Asia and is "
known
from slightly older strata than the European Aegialodon. Both have the
talonid on the lower molars. The wear on it indicates that a major new "
cusp,
the protocone, had evolved on the upper molars. By the Middle Cretaceous,
animals with the new tribosphenic molar had spread into North America too
(North America was still connected to Europe.)
Steropodon galmani (early Cretaceous) -- The first known definite "
monotreme,
discovered in 1985.
Vincelestes neuquenianus (early Cretaceous, 135 Ma) -- A probably-placental
mammal with some marsupial traits, known from some nice skulls.
Placental-type braincase and coiled cochlea. Its intracranial arteries &
veins ran in a composite monotreme/placental pattern derived from "
homologous
extracranial vessels in the cynodonts. (Rougier et al., 1992)
Pariadens kirklandi (late Cretaceous, about 95 Ma) -- The first definite
marsupial. Known only from teeth.
Kennalestes and Asioryctes (late Cretaceous, Mongolia) -- Small, slender
animals; eyesocket open behind; simple ring to support eardrum; primitive
placental-type brain with large olfactory bulbs; basic primitive
tribosphenic tooth pattern. Canine now double rooted. Still just a trace of
a non-dentary bone, the coronoid, on the otherwise all-dentary jaw. "Could
have given rise to nearly all subsequent placentals." says Carroll (1988).
Cimolestes, Procerberus, Gypsonictops (very late Cretaceous) -- Primitive
North American placentals with same basic tooth pattern.
So, by the late Cretaceous the three groups of modern mammals were in "
place:
monotremes, marsupials, and placentals. Placentals appear to have arisen in
East Asia and spread to the Americas by the end of the Cretaceous. In the
latest Cretaceous, placentals and marsupials had started to diversify a "
bit,
and after the dinosaurs died out, in the Paleocene, this diversification
accelerated. For instance, in the mid- Paleocene the placental fossils
include a very primitive primate-like animal (Purgatorius - known only from
a tooth, though, and may actually be an early ungulate), a herbivore-like
jaw with molars that have flatter tops for better grinding (Protungulatum,
probably an early ungulate), and an insectivore (Paranyctoides).
The decision as to which was the first mammal is somewhat subjective. We "
are
placing an inflexible classification system on a gradational series. What
happened was that an intermediate group evolved from the 'true' reptiles,
which gradually acquired mammalian characters until a point was reached
where we have artificially drawn a line between reptiles and mammals. For
instance, Pachygenulus and Kayentatherium are both far more mammal-like "
than
reptile-like, but they are both called "reptiles".
===
Taxonomy, Transitional Forms, and the Fossil Record

Keith B. Miller Department of Geology
Kansas State University, Manhattan, KS 66506

http://asa.calvin.edu/ASA/index.html
The recognition and interpretation of patterns in the fossil record require an
awareness of the limitations of that record. Only a very small fraction of the
species that have lived during past geologic history is preserved in the rock
record. Most marine species are soft-bodied, or have thin organic cuticles,
and are essentially unpreservable except under the most extraordinary
conditions. Furthermore, the destructive processes active in most marine
environments prevent the preservation of even shelled organisms under normal
conditions. Preservational opportunities are even more limited in the
terrestrial environment. Most fossil vertebrate species are represented by
no more than a few fragmentary remains. Because of the preservational biases
of the fossil record, paleontologists must reconstruct evolutionary
relationships from isolated branches of an originally very bushy tree.
The process of describing and classifying organisms introduces its own
patterns into the taxonomic hierarchy. First, because organisms must be
placed in one group or another, taxonomy gives the impression of discontinuity.
Secondly, the placement of species into higher taxa is done retrospectively;
that is, bylooking backward through time. The evolutionary significance of
particular morphologic transitions is only recognized because of the subsequent
success of particular lineages. The defining characters of higher taxa are
thus a consequence of history, and do not represent some objective scale of
the magnitude of morphologic divergence. Closely-related species from two
different distantly-related species belonging to the same group. Because
new character states are added over geologic time, the morphology of species
within a higher taxonomic group becomes less divergent toward the point of
origin of that group. In addition, species appearing early in the history of
a taxon approach more closely the morphology of species from other closely
related higher taxa, often to the extent that their taxonomic assignment is
uncertain. Transitional forms between higher taxa are thus a common feature
of the fossil record, although continuous fossil lineages are rarely if
ever preserved. Evidence from the fossil record is consistent with a wide
range of proposed evolutionary mechanisms.

Introduction

The fossil record provides persuasive evidence for macroevolutionary change
and common descent. The pattern of appearance of fossil species through
geologic time is critical for reconstructing evolutionary relationships. In
addition, the fossil record may also contribute to our understanding of the
tempo and mode of evolution, and help select between competing
macroevolutionary theories.

However, before the fossil record can be applied to these questions, two
critically important topics need to be addressed. The first concerns the
completeness and resolution of the fossil record, and the second concerns
taxonomic procedures. Taxonomy refers to the methods by which species are
defined and grouped into a hierarchy of categories.

Nature of the Fossil Record

There are two opposite errors which need to be countered about the fossil
record: (1) that it is so incomplete as to be of no value in interpreting
patterns and trends in the history of life, and (2) that it is so good that
we should expect a relatively complete record of the details of evolutionary
transitions within most lineages.

What then is the nature of the fossil record? It can be confidently stated
that only a very small fraction of the species that once lived on Earth has
been preserved in the rock record and subsequently discovered and described
by science. Our knowledge of the history of life can be put into perspective
by a comparison with our knowledge of living organisms. About 1.5 million
living species have been described by biologists, while paleontologists have
catalogued only about 250,000 fossil species representing over 540 million
years of Earth history (Erwin, 1993)! Why such a poor record?

Limits of the Fossil Record

Soft-bodied or thin-shelled organisms have little or no chance of
preservation, and the majority of species in living marine communities are
soft-bodied. Consider that there are living today about 14 phyla of worms
comprising nearly half of all animal phyla, yet only one, the Annelida, has
a significant fossil record. The inadequacy of the fossil record to preserve
with any completeness the evolutionary history of soft-bodied organisms can
be illustrated by the Conodonta. Originally assigned to their own phylum,
they are now believed to belong to the cordates. These soft-bodied animals
are represented by tiny tooth-like phosphatic fossils which are very
abundant in sedimentary rocks extending over about 300 million years of
Earth history, and have a worldwide distribution. Conodonts are a very
important group of marine fossils for paleontologists, yet until only very
recently the organism to which they belonged was completely unknown.
Specimens of the worm-like conodont animal have now been discovered in
Carboniferous, Ordovician, and Silurian rocks (Briggs et al., 1983; Mikulic
et al., 1985; Aldridge & Purnell, 1996). Only a handful of specimens is now
known from a very large and diverse group of marine animals known to be
extremely abundant and widespread over a tremendous length of time!

The discovery of new soft-bodied fossil localities is always met with great
enthusiasm. These localities typically turn up new species with unusual
morphologies, and new higher taxa are built from a few specimens! Such
localities are also erratically and widely spaced in geologic time between
which essentially no soft-bodied fossil record exists.

Even those organisms with preservable hard parts are unlikely to be
preserved under normal conditions. Recent studies of the fate of clam
shells in shallow coastal waters reveal that shells are rapidly destroyed by
scavenging, boring, chemical dissolution, and breakage. Rare events such as
major storms appear to be required to incorporate shells into the
sedimentary record. Getting terrestrial vertebrate material into the fossil
record is even more difficult.

The limitations of the vertebrate fossil record can be easily illustrated.
The famous fossil Archaeopteryx, occurring in a rock unit renowned for its
fossil preservation, is represented by only seven known specimens, of which
only two are essentially complete. Considering how many individuals of this
genus probably lived and died over the thousands or millions of years of its
existence, these few known specimens give some feeling for how few
individuals are actually preserved as fossils and subsequently discovered.
Yet this example actually represents an unusual wealth of material. The
great majority of fossil vertebrate species are represented by only very
fragmentary remains, and many are described on the basis of single specimens
or from single localities. Complete skeletons are exceptionally rare. For
many fossil taxa, particularly small mammals, the only fossils are teeth and
jaw fragments. If so many fossil vertebrate species are represented by
single specimens, the number of completely unknown species must be enormous!

In addition to these preservational biases, the erosion, deformation, and
metamorphism of originally fossiliferous sedimentary rocks have eliminated
significant portions of the fossil record over geologic time. Furthermore,
much of the fossil-bearing sedimentary record is hidden in the subsurface,
or located in poorly accessible or little studied geographic areas. For
these reasons, of those once living species actually preserved in the fossil
record, only a small portion has been discovered and described by science.

Because of the biases of the fossil record, the most abundant and
geographically widespread species of hard part-bearing organisms would tend
to be best represented. Also, because evolutionary change is probably most
rapid within small isolated populations, species within rapidly evolving
lineages are less likely to be preserved in the fossil record. In addition,
the completeness of the fossil record improves up the taxonomic hierarchy
(Erwin, 1993). A smaller proportion of once-living species is preserved than
genera, of genera than families, of families than orders, etc. As a result
we can better discern the general patterns of evolutionary change than the
population-by-population or species-by-species transitions.

Potential of Fossil Record for Understanding Evolutionary Change

Given the limitations and biases discussed above, what should be expected
from the fossil record? The situation is not as bleak as it may appear from
my previous comments. Exceptional deposits, such as the Burgess Shale,
Solnhofen Limestone, and Green River Shale, do provide surprisingly detailed
glimpses of once living communities. These rare cases of exceptional
preservation (fossil lagerstatten) are essentially snapshots in the history
of life and are invaluable in gaining a more comprehensive picture of
ancient communities. They also provide some of the most detailed anatomical
data.

More commonly, thick sequences of fossiliferous rocks can enable selected
skeleton or shell-bearing taxa to be examined at closely-spaced intervals.
These localities provide opportunities to study patterns of evolutionary
change within isolated lineages. Important information can be gained on
morphologic change within species populations, and transitions between
species and, rarely, even genera can be examined (Fig. 1). However, the time
interval recorded by continuous series of closely-spaced fossil populations
is limited because of changing environmental, depositional, and
preservational conditions.

Fig 1 Changes in the shape of molar teeth of the Early Eocene mammal Hypsodus,
showing evolutionary transitions from species to species within a genus.
(From Gingerich [1976]
Speciation events appear to take place primarily in small isolated
peripheral populations. Therefore to catch a population in the act
requires the fortuitous sampling of the particular geographic locality where
the changes occurred. Even within well-preserved fossil series it is usually
difficult to distinguish the record of speciation occurring within a
particular depositional basin (or environment) from the effects of
immigration of new species from outside that basin. For this and other
reasons, well-documented and widely-accepted examples of speciation in the
fossil record are few (for an example, see Gingerich, 1976).
The expectation, therefore, is for the preservation of isolated branches on
an originally very bushy, evolutionary tree. A few of these branches
(lineages) would be fairly complete, while most are reconstructed with only
very fragmentary evidence (Fig. 2). While the details are missing, a general
understanding of the large-scale patterns and trends in evolutionary history
should be discernible. Evolutionary trends over longer periods of time and
across greater morphologic transitions can be followed by reconstructing
morphological sequences. Morphological transitions can be recognized in the
fossil record that cross all levels of the taxonomic hierarchy.
Fig. 2 The effects of an incomplete fossil record on the reconstruction of
evolutionary relationships. (A) This branching tree (phylogeny) represents
the actual pattern of evolutionary relationships. (B) The actual preserved
record of species in the fossil record might look something like this. (C)
This branching tree represents a possible
reconstruction of the evolutionary tree based on the fossil evidence. Note
that the general pattern of relationships is preserved, but that errors
have been made with regard to specific ancestor-descendant relationships.
Taxonomy and Transitional Forms
Taxonomy, the process of classifying living and fossil organisms, produces
its own patterns which order the diversity of life. It is thus important to
recognize that names do much more than describe nature: they also interpret
it. There is considerable ferment now within the field of taxonomy because
of conflicting philosophies of classification, and different perceptions of
which patterns in the history of life should be reflected in the taxonomic
hierarchy (Eldredge & Cracraft, 1980; Schoch, 1986). Higher taxa can be
either artificial groupings of species with similar morphologies
(evolutionary grades), or natural groups sharing derived characteristics
inherited from a common ancestor (monophyletic taxa or clades).

The Linnean classification system is hierarchical, with species grouped into
genera, genera into families, families into orders, etc. This system
reflects the discontinuity and hierarchy observed among living organisms.
However, this system leads to the impression that species in different
categories differ from one another in proportion to differences in taxonomic
rank (Carroll, 1988, p. 578). This impression is false. Higher taxa are
distinct and easily recognizable groups only when we ignore the time
dimension of the history of life. When the fossil record is included, the
boundaries between higher taxa become blurred during the major morphological
radiations associated with the appearance of new higher taxa. Even in the
modern world, discontinuity is not as great as it may appear superficially.
In practice, species are often not easily recognized, and accepted species
definitions cannot always be applied.
Another common misperception is that the origin of higher taxa does not take
place at the level of populations and species. If the concept of common
descent is accepted, then transitions between higher level taxonomic
categories must also be species transitions (Fig. 3). This is recognized by
all evolutionary paleobiologists, even those who stress the significance of
the origin of phyla and classes (Valentine, 1992). Therefore, the more
complete the fossil record of the origin and early radiation of higher taxa
the more similar the transitional species, and the more difficult it is to
determine their taxonomic assignments. Species placed into two different
higher taxa may thus have very similar morphologies.
Fig. 3. Pattern of phylogeny in which one clade (or higher taxon) emerges
from another. In retrospect (time T2), the two clades are seen as being
distinct, and the phylogeny is divided at the position of the heavy, dashed
bar into taxa A and B. A taxonomist living at time T1, however, would have
recognized only a single clade and would have grouped the entire phylogeny
that had developed by that time into a single taxon (A). (From
Macroevolution: Pattern and Process by Stanley 1979 by W.H. Freeman and
Company,

The character states used to define higher taxa are determined
retrospectively. That is, they are chosen based on a knowledge of the
subsequent history of the lineages possessing those traits. They do not
reflect the attainment of some objective higher level of morphologic
innovation at the time of their appearance. Also, all the features
subsequently identified with a particular higher taxon do not appear in a
coordinated and simultaneous manner but as character mosaics within numerous
closely-related species lineages, many of which are not included in the new
higher taxon. In addition, as discussed above, the species associated with
the origin and initial radiation of a new taxon are usually not very
divergent in morphology. Were it not for the subsequent evolutionary history
of the lineages, species spanning the transitions between families, orders,
classes, and phyla would be placed in the same lower taxon (Fig. 3).

Based on the above discussion, a transitional form is simply a fossil
species that possesses a morphology intermediate between that of two others
belonging to different higher taxa. Such transitional forms commonly possess
a mixture of traits considered characteristic of these different higher
taxa. They may also possess particular characters that are themselves in an
intermediate state. During the time of origin of a new higher taxon, there
are often many described species with transitional morphologies representing
many independent lineages. It is usually very difficult if not impossible to
determine which, if any, of the known transitional forms actually lay on the
lineage directly ancestral to the new taxon. For this reason, taxonomists
commonly have difficulty defining higher taxa, and assigning transitional
fossil species to one or the other taxon. But, although the details may
elude us, the patterns of evolutionary change are in many cases well
recorded in the fossil record.

Examples from the Fossil Record

As stated above, the diversity of life appears much more discontinuous when
viewed at any given point in time, than it does when viewed through time.
For a given time slice through the tree of life, transitions between taxa
are seen only where the slice intersects the branching points of lineages.
Once a lineage is split, its branches continue to evolve and diverge such
that their morphological (and genetic) distance increases and they become
more readily distinguished taxonomic entities. When looking backward through
time using the fossil record, it is found that representatives of different
higher level taxa become more primitive, that is have fewer derived
characters, and appear more like the primitive members of other closely
related taxa. As a result, for lineages with a good fossil record, the
appearance of a new higher taxon is associated with the occurrence of
species whose taxonomic identities are uncertain or whose morphologies
converge closely on that of the new higher taxon. Such patterns are found
repeatedly by paleontologists.

A longstanding misperception of the fossil record of evolution is that
fossil species form single lines of descent with unidirectional trends. Such
a simple linear view of evolution is called orthogenesis, and has been
rejected by paleontologists as a model of evolutionary change (MacFadden,
1992). The reality is much more complex than that, with numerous branching
lines of descent and multiple morphologic trends (Fig. 4). The fossil record
reveals that the history of life can be understood as a densely branching
bush with many short branches (short-lived lineages). The well-known fossil
horse series, for example, does not represent a single continuous evolving
lineage (MacFadden, 1992). Rather it records more or less isolated parts of
an adapting and diversifying limb of the tree of life. While incomplete,
this record provides important insights into the patterns of morphological
divergence and the modes of evolutionary change.
Figure 4. Comparison of a single direct line of descent
(orthogenesis) with a branching phylogeny. Diversification is such
an important feature of the history of life that orthogenesis is
probably very rare. Fossils from a chronological series thus do
not represent direct ancestor-descendant relationships, but
individual branches. (From MacFadden [1992], reprinted with
permission of Cambridge University Press).
Interestingly, some critics of evolution view the record of fossil horses
from Eohippus (Hyracotherium) to Equus as trivial (Denton, 1985). However,
that is only because the intermediate forms are known (Fig. 5, 6). Without
them, the morphologic distance would appear great. Eohippus was a very
small (some species only 18 inches long) and generalized herbivore (probably
a browser). Besides the well-known difference in toe number (four toes at
front, three at back), Eohippus had a narrow elongate skull with a
relatively small brain and eyes forward in the skull. It possessed small
canine teeth, premolars, and low-crowned simple molars. Over geologic time
and within several lineages, the skull became much deeper, the eyes moved
back, and the brain became larger. The incisors were widened, premolars were
altered to molars, and the molars became very high-crowned with a highly
complex folding of the enamel (Evander, 1989; McFadden, 1988).

Fossil horse series from Hyracotherium (Eohippus) to Equus showing changes
in skull proportions associated with an adaptive shift from browsing to
grazing. This sequence shows a chronological sequence of genera within the
perissodactyl family Equidae from the Eocene to the Recent. (From MacFadden
[1992] Stages in horse evolution showing the reduction in the number of toes
and foot bones. Forefeet above, hind feet below. (A) Hyracotherium, a
primitive early Eocene horse with four toes in front and three behind,
(B) Miohippus, an Oligocene three-toed horse, (C) Merychippus, a late Miocene
form with reduced lateral toes, and (D) Equus. (From
Vertebrate Paleontology by Alfred Sherwood Romer published by The University of
Chicago Press.
The significance of the fossil record of horses becomes clearer when it is
compared with that of the other members of the order Perissodactyla
(odd-toed ungulates). The fossil record of the extinct titanotheres is
quite good (Fig. 7), and the earliest representatives of this group are very
similar to Eohippus (Stanley, 1974; Mader, 1989). Likewise, the earliest
members of the tapirs and rhinos were very Eohippus-like. Thus, the
different perissodactyl groups can be traced back to a group of very similar
small generalized ungulates (Radinsky, 1979; Prothero, et al., 1989;
Prothero & Schoch, 1989) (Fig. 8). But this is not all; the most primitive
ungulates (hoofed mammals) are the condylarths, which are assemblages of
forms transitional in character between the insectivores and true ungulates
(Fig. 9). Some genera and families of the condylarths had been previously
assigned to the Insectivora, Carnivora, and even Primates (Romer, 1966).
Thus, the farther you go back in the fossil record, the more difficult it is
to place species in their correct higher taxonomic group. The boundaries
of taxa become blurred.

Stages in the evolution of the extinct perissodactyl family of the
titanotheres. (A) Eotitanops (early Eocene), (B) Limnohyops (middle Eocene),
(C) Manteoceras (middle Eocene), (D) Protitanotherium (late Eocene),
(E) Brontotherium (early Oligocene), and (F) Brontotherium. (From Stanley
[1974], reprinted with permission of the journal Evolution.)
Comparison of the early members of four perissodactyl families.
(A) Hyracotherium (Equoidea), (B) Hyrachyus (Rhinoceratoidea), (C) Heptodon
(Tapiroids), (D) Eotitanops (Titanotheriomorpha). (A and B from Vertebrate
Paleontology by Alfred Sherwood Romer published by The University of
Chicago Press.
Figure 9. (A) The Eocene horse (Hyracotherium) and representatives of the
condylarths, (B) Phenacodus (early Eocene) and (C) Mesonyx (middle Eocene).
Note how very carnivore-like Mesonyx is although it possessed small hooves
rather than claws and is classified with the ungulates. (From Vertebrate
Paleontology by Alfred Sherwood Romer published by The University of Chicago
Press.
Moving further up the taxonomic hierarchy, the condylarths and primitive
carnivores (creodonts, miacids) are very similar to each other in morphology
(Fig. 9, 10), and some taxa have had their assignments to these orders
changed. The Miacids in turn are very similar to the earliest
representatives of the Families Canidae (dogs) and Mustelidae (weasels),
both of Superfamily Arctoidea, and the Family Viverridae (civets) of the
Superfamily Aeluroidea. As Romer (1966) states in Vertebrate Paleontology
(p. 232), Were we living at the beginning of the Oligocene, we should
probably consider all these small carnivores as members of a single family.
This statement also illustrates the point that the erection of a higher
taxon is done in retrospect, after sufficient divergence has occurred to
give particular traits significance.
Figure 10. Comparison of skulls of the early ungulates (condylarths) and
carnivores. (A) The condylarth Phenacodus possessed large canines as well as
cheek teeth partially adapted for herbivory. (B) The carnivore-like condylarth
Mesonyx. The early Eocene creodonts (C) Oxyaena and (D) Sinopa were primitive
carnivores apparently unrelated to any modern forms. (E) The Eocene Vulpavus
is a representative of the miacids which probably was ancestral to all living
carnivore groups. (From Vertebrate Paleontology
by Alfred Sherwood Romer published by The University of Chicago Press.
At the level of the class, the reptile/mammal transition is particularly
well documented. Near the appearance of unquestioned mammals in the fossil
record, a group of mammal-like reptiles called cynodonts included species
that were exceptionally mammal-like in appearance (Hopson, 1994). In
skeletal features the approach to the mammalian condition was almost
complete (Fig. 11, 12). The following mammalian characteristics were
possessed by advanced cynodonts: (1) enlarged temporal openings with the
loss of the post-orbital bar, (2) absence of the pineal eye, (3)
differentiation of teeth, with front nipping teeth, canines, and molar-like
back teeth, (4) a secondary palate permitting respiration while chewing, (5)
a double occipital condyle which enlarges the hole for the spinal cord, (6)
absence of lumbar ribs (possibly related to the presence of a diaphragm),
(7) a nearly erect stance, and (8) an enlarged dentary bone in the lower jaw
with an extremely close approach to the mammalian jaw articulation.
Furthermore, some workers argue persuasively that some mammal-like reptiles
were endothermic (deRicqles, 1974; Bakker, R.T., 1975; McNab, 1978). And a
few exceptional fossils show evidence of glandular skin and horn (Hotton,
1991), features associated with the presence of hair.

Figure 11. Reconstructed skeletons of cynodont (advanced mammal-like reptiles)
and early mammals. (A) The early Triassic cynodont Thrinaxodon and (B) the
advanced cynodont Probelesodon from the middle Triassic. Note the very
mammal-like erect posture of these skeletons. (C) The early mammal
Megazostrodon from the early Jurassic., Museum of Comparative Zoology,
Harvard University, Figure 12. Comparison of the skulls of cynodonts and
early mammals. Thecynodont skulls are (A) the late Permian Procynosuchus;
(B) the early Triassic Thrinaxodon; (C) the middle Triassic Probainognathus;
and (D) the early Jurassic Pachygenelus. Note the differentiation of the
teeth and the
reduction in the bones at the back of the lower jaw. The early mammal skulls
are (E) the early Jurassic Sinoconodon; and (F) the early Jurassic
Morganucodon. (A through D from Systematics of the nonmammalian Synapsida
and implications for patterns of evolution in synapsids by J.A. Hopson
[1991], published in Origins of the Higher Groups of Tetrapods: Controversy
and Consensus edited by H.-P. Schultze and L. Trueb.
The complex of transitional fossil forms has created significant problems
for the definition of the class Mammalia (Desui, 1991). For most workers,
the establishment of a squamosal-dentary jaw articulation is considered one
of the primary defining characters. The transition in jaw articulation from
reptiles to mammals is particularly illustrative of the appearance of a
class level morphologic character (Fig. 12). In reptiles, the lower jaw
contains several bones, and the articular bone at the back of the jaw
articulates with the quadrate bone of the skull. In mammals, the lower jaw
has only one bone, the dentary, and it articulates with the squamosal bone
of the skull. Within the cynodont lineage, the dentary bone becomes
progressively larger and the other bones are reduced to nubs at the back. In
one group of advanced cynodonts, the dentary bone has been brought nearly
into contact with the squamosal, and in another, a secondary articulation
exists between the surangular (another small bone at the back of the jaw)
and squamosal (Hopson, 1991). The earliest known mammals, the
morganucodonts, retain the vestigial lower jaw bones of the reptiles. These
small bones still form a reduced, but functional, reptilian jaw joint medial
to the new dentary-squamosal mammalian articulation. These reptilian jaw
elements were subsequently detached completely from the jaw to become the
mammalian middle ear (Crompton & Parker, 1978). Better intermediate
character states could hardly be imagined!
As with most transitions between higher taxonomic categories, there is more
than one lineage that possesses intermediate morphologies. Again, this is
consistent with both the expectations of evolutionary theory, and the nature
of the fossil record. The prediction would be for a bush of many lineages,
many of which would be dead ends. Because of their objective to erect only
monophyletic taxa (an ancestor is grouped with all of its descendants), some
paleontologists have advocated including mammals with the advanced
cynodonts, or even with the whole group of mammal-like reptiles, in a single
higher taxon (Desui, 1991).
As in the case of the reptile-mammal transition, the distinctiveness of the
classes also becomes blurred during the amphibian-reptile transition. The
oldest known reptiles (Fig. 13) have been collected within the fossilized
stumps of lycopod trees from the late Pennsylvanian in Nova Scotia (Carroll,
1970, 1991). Several groups of reptiliomorph amphibians occur near the
appearance of these unquestioned reptiles. Some of these (the
seymouriamorphs and diadectomorphs) were in fact previously regarded as
reptiles (Carroll, 1988; Benton, 1991).

Figure 13. Skeleton and skull of the earliest known reptile Hylonomus from the
early Pennsylvanian. Reptiliomorph amphibians placed in a group called the
anthracosaurs converge closely on the reptiles in skeletal morphology (see
reconstructions of the anthracosaur amphibians Bruktererpeton and
Proterogyrinus in Carroll [1991]). (From Vertebrate Paleontology by
Alfred Sherwood Romer published by The University of Chicago Press,
Fossil Transitions Associated with Major Adaptive Shifts
Of special interest in the history of life are the morphological transitions
associated with the major adaptive shifts from water to land, land to water,
and land to air. These major changes in mode of life opened up tremendous
new adaptive opportunities for animal life. While the fossil evidence for
some of these transitions is minimal, for others exciting parts of the
puzzle have been uncovered.

The transition from water to land was one of the most significant events in
animal evolution. Recent paleontological and systematic work has shed new
light on this transition (Fig. 14). The most primitive amphibian yet known
is the late Devonian Ichthyostega, a tetrapod with a flattened skull and
bearing a tail fin. The limbs were until recently poorly known, but new
fossil evidence has come to light. The hand, previously unknown, shows that
these amphibians possessed seven to eight digits. The limbs also had a very
limited range of movement and the animal was not as well adapted to
terrestrial locomotion as previously thought (Ahlberg & Milner, 1994). The
rhipidistian fishes are widely considered to have given rise to the
amphibians. One small group of late Devonian rhipidistians, the
panderichthyids, appears to be closely related to the ichthyostegids
(Schultze, 1991). These fishes have flattened skulls very similar to that of
the early amphibians. In addition, the anal and dorsal fins are absent, and
the tail is very similar to that of Ichthyostega (Vorobyeva & Schultze,
1991). The lobed pectoral and pelvic fins have bones that homologize with
the limb bones of the tetrapods. Whether part of a single direct lineage or
not, ichthyostegid amphibians and panderichthyid fishes are clearly
transitional forms between class level taxa. The first known skull of a
panderichthyid was in fact initially considered to be an amphibian
(Vorobyeva & Schultze, 1991), again illustrating the taxonomic problems
encountered during the appearance and early radiation of a new taxon.
Figure 14. The transition from fish to amphibian illustrated by body form and
skeletons, with details of skulls and vertebrae. (A) Osteolepiform fish
Eusthenopteron; (B) panderichthyid fish Panderichthys; and (C) labyrinthodont
amphibian Ichthyostega. (From Ahlberg & Milner [1994],
Probably one of the most celebrated and mysterious transitions has been that
of the origin of whales from a primitive condylarth (ungulate) ancestor. The
earliest whales possessed skulls similar in many ways to those of a group of
Eocene carnivorous condylarths called mesonycids. Until 1993 the earliest
fossil whales were only known from partial skulls with no postcranial
material. However, several very important transitional fossils from Pakistan
have been described over the last several years (Gingerich, et al., 1993)
and more discoveries are certain to follow. The geologically oldest included
enough of the skeleton to reveal that this otter-sized whale had short front
limbs and longer hind legs with large feet apparently used in swimming
(Berta, 1994; Thewissen, et al., 1994). The second, somewhat younger species
had shorter hind limbs indicating a trend toward reduction in limb size
(Gingerich, et al., 1994). Whales apparently evolved in what is now Pakistan
since all the known fossil material for earliest whales has been found in
that geographic area. Because the evolution of new body plans is likely to
occur in an isolated geographic area, the discovery of the fossil record of
such transitions is dependent on the serendipitous sampling of the right
locality.
http://www.talkorigins.org/features/whales/
The most famous of transitional fossils is the earliest known bird,
Archeopteryx. Ostrum has described over 20 shared characteristics between
Archeopteryx and coelurosaur theropods. Among these are: a theropod-like
pelvis, the close similarities of the bones of the forelimbs including a
swivel wrist joint, and the similarity of the hind limbs and feet with the
presence of a reversed first toe (Hecht, et al., 1985; Dodson, 1985; Ostrom,
1994). The similarities of Archeopteryx to theropod dinosaurs such as
Velociraptor and Deinonychus are especially strong, and a newly discovered
dinosaur called Unenlagia has features of the limbs and pelvis that are the
most bird-like yet known (Novas & Puerta, 1997). As interesting as the
similarities with the theropods are, the differences between Archeopteryx
and modern birds are also significant: it has a long bony tail, a sternum is
absent, its vertebrae are not fused together over the pelvis to form a
synsacrum, and air ducts are absent in its long bones. In most respects,
Archeopteryx is more of a flying feathered dinosaur than a bird. In the last
several years the discovery of new fossil birds from the Cretaceous has led
to the erection of a whole new subclass of primitive birds called the
enantiornithes (Chiappe, 1995). This new group includes several fossil
species previously identified as theropod dinosaurs (e.g., Ornithomimus)!
There are also some newly discovered fossils whose classification as
theropod or bird is in dispute (Chiappe, 1995). The recent discovery in
China of a theropod dinosaur with the possible preservation of fine
feathers, even suggests that feathers may not be exclusively characteristic
of birds (Morell, 1997). This again illustrates the taxonomic uncertainties
that surround transitional forms.

Conclusions

From this brief survey of fossil vertebrates, it is clear that transitional
forms between higher taxa are common features of the fossil record. The
morphology of species within a higher taxonomic group becomes less divergent
toward the point of origin of that group. Morphological diversity and
disparity increase with time. In addition, transitional species possess
mixtures of morphologic characters from different higher taxa often to the
extent that their taxonomic assignment is uncertain. This pattern is
obscured by taxonomy which gives a false impression of discontinuity.

The fossil record thus provides good evidence for the large-scale patterns
and trends in evolutionary history. Recognizing its limitations, the fossil
record appears to be consistent with the wide range of evolutionary
mechanisms already proposed. Any wholesale abandonment of present paradigms
would be very premature. Many critical gaps in our knowledge remain, but as
evident from this review important discoveries are continually being made
that intrigue, surprise, and enrich our understanding of the evolutionary
history of life.

Bibliography

Ahlberg, P.E. and Milner, A.R., 1994, The origin and early diversification
of tetrapods: Nature, vol. 368, p. 507-14.

Aldridge, R.J. and Purnell, M.A., 1996, The conodont controversies: Trends
in Ecology and Evolution, vol. 11, p. 463-8.

Bakker, R.T., 1975, Dinosaur renaissance: Scientific American, vol. 232, p.
5878.

Benton, M.J., 1991, Amniote phylogeny: IN, H.-P. Schultze and L. Trueb,
(eds.), Origins of the Higher Groups of Tetrapods: Controversy and
Consensus, Comstock Publishing Associates, Ithaca, p. 317-30.

Berta, A., 1994, What is a whale?: Science, vol. 263, p. 180-1.

Briggs, D.E.G., Clarkson, E.N.K., and Aldridge, R.J., 1983, The conodont
animal: Lethaia, vol. 16, p. 1-14.

Carroll, R.L., 1970, The earliest known reptiles: Yale Scientific Magazine,
October issue, p. 16-23.

Carroll, R.L., 1988, Vertebrate Paleontology and Evolution: W.H. Freeman &
Co., New York, 698 p.

Carroll, R.L., 1991, The origin of reptiles. IN, H.-P. Schultze and L. Trueb
(eds.), Origins of the Higher Groups of Tetrapods: Controversy and
Consensus, Comstock Publishing Associates, Ithaca, p. 331-53.

Chiappe, L.M., 1995, The first 85 million years of avian evolution: Nature,
vol. 378, p. 349-55.

Crompton, A.W. and Parker, P., 1978, Evolution of the mammalian masticatory
apparatus: American Scientist, vol. 66, p. 192-201.

Denton, M, 1985, Evolution: A Theory in Crisis: Adler & Adler, Bethesda, MD,
368 p.

deRicqles, A.J., 1974, Evolution of endothermy: histological evidence:
Evolutionary Theory, vol. 1, p. 51-80.

Desui, M., 1991, On the origins of mammals. IN, H.-P. Schultze and L. Trueb
(eds.), Origins of the Higher Groups of Tetrapods: Controversy and
Consensus, Comstock Publishing Associates, Ithaca, p. 570-97.

Dodson, P., 1985, International Archaeopteryx Conference: Journal of
Vertebrate Paleontology, vol. 5, p. 177-9.

Eldredge, N. and Cracraft, J., 1980, Phylogenetic Patterns and the
Evolutionary Process: Columbia University Press, New York, 349 p.

Erwin, D.H., 1993, The Great Paleozoic Crisis: Life and Death in the
Permian: Columbia University Press, New York, 327 p.

Evander, R.L., 1989, Phylogeny of the family Equidae. IN, D.R. Prothero and
R.M. Schoch (eds.), The Evolution of the Perissodactyls: Oxford University
Press, New York, p. 109-27.

Gingerich, P.D., 1976, Paleontology and phylogeny: Patterns of evolution at
the species level in early Tertiary mammals: American Journal of Science,
vol. 276, p. 1-28.

Gingerich, P.D., Raza, S.M., Arif, M., Anwar, M., and Zhou, X., 1993,
Partial skeletons of Indocetus ramani (Mammalia, Cetacea) from the lower
middle Eocene Domanda Shale in the Sulaiman Range of Punjab (Pakistan):
Contributions from the Museum of Paleontology, University of Michigan, vol.
28, p. 393-416.

Gingerich, P.D., Raza, S.M., Arif, M., Anwar, M., and Zhou, X., 1994, New
whale from the Eocene of Pakistan and the origin of cetacean swimming:
Nature, vol. 368, p. 844-7.

Hecht, M.K., Ostrom, J.H., Viohl, G., and Wellnhofer, P. (eds.), 1985, The
Beginnings of Birds: Proceeding of the International Archaeopteryx
Conference, Eichstatt, 1984: Bronner & Daentler, Eichstatt.

Hopson, J.A., 1991, Systematics of the nonmammalian Synapsida and
implications for patterns of evolution in synapsids. IN, H.-P. Schultze and
L. Trueb (eds.), Origins of the Higher Groups of Tetrapods: Controversy and
Consensus, Comstock Publishing Associates, Ithaca, p. 635-93.

Hopson, J.A., 1994, Synapsid evolution and the radiation of non-eutherian
mammals. IN, D.R. Prothero and R.M. Schoch (eds.), Major Features of
Vertebrate Evolution, Short Courses in Paleontology, No. 7: Paleontological
Society, Knoxville, p.190-219.

Hotton, N, III, 1991, The nature and diversity of synapsids: Prologue to the
origin of mammals. IN, H.-P. Schultze and L. Trueb (eds.), Origins of the
Higher Groups of Tetrapods: Controversy and Consensus, Comstock Publishing
Associates, Ithaca, p.598-634.

Mader, B.J., 1989, The Brontotheriidae: A systematic revision and
preliminary phylogeny of North American genera. IN, D.R. Prothero and R.M.
Schoch (eds.), The Evolution of the Perissodactyls: Oxford University Press,
New York, p. 109-27.

McFadden, B.J., 1988, Horses, the fossil record, and evolution: Evolutionary
Biology, vol. 22, p. 131-58.

McFadden, B.J., 1992, Fossil Horses: Systematics, Paleobiology, and
Evolution of the Family Equidae: Cambridge University Press, Cambridge, 369
p.

McNab, B.K., 1978, The evolution of endothermy in the phylogeny of mammals:
American Naturalist, vol. 112, p. 1-21.

Mikulic, D.G., Briggs, D.E.G., and Kluessendorf, J., 1985, A Silurian
soft-bodied fauna: Science, vol. 228, p. 715-7.

Morell, V., 1997, The origin of birds: the dinosaur debate: Audubon, vol.
99, no. 2, p. 36-45.

Norman, D., 1985, The Illustrated Encyclopedia of Dinosaurs: Crescent Books,
New York, 208 p.

Norman, D., 1994, Prehistoric Life: The Rise of the Vertebrates: Macmillan,
New York, 246 p.

Novas, F.E. and Puerta, P.F., 1997, New evidence concerning avian origins
from the Late Cretaceous of Patagonia: Nature, vol. 387, p. 390-2.

Ostrum, J.H., 1979, Bird flight: How did it begin?: American Scientist, vol.
67, p. 46-56.

Ostrum, J.H., 1994, On the origin of birds and of avian flight. IN, D.R.
Prothero and R.M. Schoch (eds.), Major Features of Vertebrate Evolution,
Short Courses in Paleontology, No. 7: Paleontological Society, Knoxville,
p.160-77.

Prothero, D.R., Guerin, C., and Manning E., 1989, The history of the
Rhinocerotoidea. IN, D.R. Prothero and R.M. Schoch (eds.), The Evolution of
the Perissodactyls: Oxford University Press, New York, p.321-40.

Prothero, D.R. and Schoch, R.M., 1989, Origin and evolution of the
Perissodactyla: Summary and synthesis: IN, D.R. Prothero and R.M. Schoch
(eds.), The Evolution of the Perissodactyls: Oxford University Press, New
York, p.504-29.

Radinsky, L.B., 1979, The early evolution of the Perissodactyla: Evolution,
vol. 23, p. 308-28.

Romer, A.S., 1966, Vertebrate Paleontology: University of Chicago Press,
Chicago,
468 p.

Schoch, R.M., 1986, Phylogeny Reconstruction in Paleontology: Van Nostrand
Reinhold Company, New York, 351p.

Schultze, H.-P., 1991, A comparison of controversial hypotheses on the
origin of tetrapods. IN, H.-P. Schultze and L. Trueb (eds.), Origins of the
Higher Groups of Tetrapods: Controversy and Consensus, Comstock Publishing
Associates, Ithaca, p. 29-67.

Stanley, S.M., 1974, Relative growth of the titanothere horn: a new approach
to an old problem: Evolution, vol. 28, p. 447-57.

Stanley, S.M., 1979, Macroevolution: Pattern and Process: WH. Freeman &
Company, San Francisco, 332 p.

Thewissen, J.G.M., Hussain, S.T., and Arif, M., 1994, Fossil evidence for
the origin of aquatic locomotion in archaeocete whales: Science, vol. 263,
p. 210-2.

Valentine, J.W., 1992, The macroevolution of phyla. IN, J.H. Lipps and P.W.
Signor (eds.), Origin and Early Evolution of the Metazoa: Plenum Press, New
York, p. 525-53.

Vorobyeva, E. and Schultze, H.-P., 1991, Description and systematics of
panderichthyid fishes with comments on their relationship to tetrapods. IN,
H.-P. Schultze and L. Trueb (eds.), Origins of the Higher Groups of
Tetrapods: Controversy and Consensus, Comstock Publishing Associates,
Ithaca, p. 68-109.
==
The fossil genus _Hyracotherium_ [Eohippus] included several
species and was supposed to be very near the base of the radiation
of the entire order Perissodactyla. MacFadden [1992] starts his
section on _Hyracotherium_s relationships with a quote from
Matthew [1926, p. 153] that clearly expressed this view.:

It is quite possible that certain species of Eohippus, when more
intensively studied, will appear to be more directly in the line of
ancestry of the horse, others of the tapir or rhinoceros or of
some of the extinct phyla of Perissodactyls.

Further on, MacFadden writes [p.90]:
It may seem that too much time is being devoted to _Hyracotherium_ or
eohippus. On the contrary, being at or near [depending upon phylogenetic
interpretations] the base of both the perissodactyl and equid radiations, it
is central to an understanding of the higher-level interrelationships of the
Perissodactyla and the definition of the family Equidae. A recent detailed
cladistic analysis [Hooker 1989] of critical new and previously studied
specimens resulted in a radical rethinking of the concept of the
genus_Hyracotherium_and the base of the perissodactyl radiation[Figure5.10].

[The cladogram in fig. 5.10 shows that some named species of Hyracotherium
are related to different named families: H. leporinum is sister to the
Palaeotheridae, H. vasacciense is sister to the other Equidae, H. aff.
vulpiceps and H. tapirinum are successive outgroups to the equid/palaeothere
clade and H. sp., Rians is related to the Pachynolophidae in the sister
group to the Equoidea.]

... Regardless of the exact details of all the new hypotheses that have
been or will be generated from his work, the following conclusions from
Hookers studies are important here: (1) In contrast to previous dogma, there
are several fossil perissodactyl taxa such as _Cymbalophus_ that are
dentally more primitive than _Hyracotherium_. (2) _Hyracotherium_ is a
horizontal, paraphyletic wastebasket taxon, with different species
currently allocated to this genus giving rise to different perissodactyl
clades [not unlike what is described in the foregoing quotation from
Matthew].
Thus the traditional genus _Hyracotherium_ includes different
species that are related to different more-derived families.
Still, the species are all phenetically similar enough to one
another to have been classified as one genus.

Refs:
MacFadden, B. J. 1992. Fossil horses. Systematics, paleobiology,
and evolution of the family Equidae. Cambridge University Press,
Cambridge.

Hooker, J.J. 1989. Character polarities in early perissodactyls
and their significance for _Hyracotherium_ and infraordinal
relationships. pp. 79-101 _In_ D. R. Prothero & R. M. Schoch,
[eds.] The Evoluton of Perissodactyls Clarendon Press, Oxford.

Matthew, W. D. 1926. The evolution of the horse: a record and its
interpretation. Quart. Rev. Biol. 1:139-185.

A similarly relevant quote:
In effect, there was no family Equidae when eohippus lived. The
family and all of its distinctive characters developed gradually
as time went on. Eohippus is referred to the Equidae because we
happen to have more nearly complete lines back to it from later
members of this family than from other families. There is no
particular time at which the Equidae became a family rather than a
genus or a species; the whole process is gradual and we assign the
categorical rank after the result is before us.
-- Simpson, G. G. 1953. The Major Features
of Evolution. Columbia University Press, NY. p. 345. [as quoted
in: MacFadden, B. J. 1992. Fossil horses...]

An additional, more recent reference:
TI The beginning of the equoid radiation.
AU Hooker-J-J
SO Zoological Journal of the Linnean Society 112(1-2): 29-63.
PY 1994
AB With the benefit of newly collected material primitive equoids
are analysed cladistically to determine the detailed relationships
of the families Equidae and Palaeotheriidae. The most primitive
equid is shown to be Pliolophus. Cymbalophus cuniculus and
Hyracotherium sandrae are closely related stem equoids. The
Pachynolophidae are not equoids, but most closely related to the
primitive tapiromorph family Isectolophidae. Hallensia is sister
to these two and therefore also not an equoid. Hyracotherium is
restricted to the type species H. leporinum Owen, part of whose
lower dentition is made known for the first time. It is closest to
a restricted genus Propachynolophus within the family
Palaeotheriidae. The original concept of Propachynolophus is
polyphyletic. Using the cladogram, newly extended stratigraphic
ranges and paleogeography, an attempt is made to reconstruct the
very early speciation and biogeographical history of the group.
The fossil genus Diacodexis is evidently very close to the common ancestry
of several later artiodactyl families. See:

Krishtalka, L., and Stucky, R.K. 1985. Revision of the Wind River
Faunas. Early Eocene of Central Wyoming. Part 7. Revision of
Diacodexis (Mammalia, Artiodactyla). Am. Carnegie Mus. 54:413-486.
==
Instead of one universal evolutionary tree, picture a three-trunk stand sharing
a communal root system. A new theory of cellular evolution published in the
2002 of the Proceedings of the National Academy of Sciences rejects
Charles Darwins Doctrine of Common Descentthe idea that all organism
University of Illinois-Champaign proposes that the three cell types that
comprise life on earth arose from three forms of proto cells that swam together
in a dense genetic soup, freely sharing their DNA.

Indeed, such DNA swapping was the driving force in the evolution of unicellular
organisms, Woese argues. Biologists have traditionally credited this so-called
horizontal gene transfer with just a minor role in cellular evolution. But
Woese asserts that only by sharing their genesor evolutionary inventions, as
he calls themcould simple cellular organizations have given rise to more
complex cell designs. In the beginning, he says, primitive cells "did not have
stable genealogical records." But eventually, these linesincluding the three
that spawned all extant life formsreached what Woese terms the "Darwinian
threshold," the point at which a lineage matures to genetic stability. Here the
cellular organization became fixed, leading to a traceable cell line via
reproduction. "Crossing a Darwinian threshold leads to a more solidified,
organized cellular design," he explains.
The idea could overturn conventional cell evolution wisdom. Instead of the
individual, "it is the community as a whole, the ecosystem which evolves,"
Woese remarks. "We cant expect to explain cellular evolution if we stay
locked in the classical Darwinian mode of thinking," he adds. "The time has
come for biology to go beyond the Doctrine of Common Descent."
==
Dromaeosaurids, despite their notoriety, are poorly characterized meat-eating
dinosaurs, and were previously known only from disarticulated or fragmentary
specimens. Many studies have denied their close relationship to birds. Here we
report the best represented and probably the earliest dromaeosaurid yet
discovered, Sinornithosaurus millenii gen. et sp. nov., from Sihetun, the
famous Mesozoic fish-dinosaur-bird locality in China. Sinornithosaurus not only
greatly increases our knowledge of Dromaeosauridae but also provides evidence
for a filamentous integument in this group. It is remarkably similar to early
birds postcranially. The shoulder girdle shows that terrestrial dromaeosaurids
had attained the prerequisites for powered, flapping flight, supporting the
idea that bird flight originated from the ground up. The discovery of
Sinornithosaurus widens the distribution of integumentary filaments among
non-avian theropods. Phylogenetic analysis indicates that, among known
theropods with integumentary filaments or feathers, Dromaeosauridae is the
most bird-like, and is more closely related to birds than is Troodontidae.
==
It astonished most people of Darwin's time to suggest that one species
could change into another species, even of the same general kind. And
nothing scientists have learned of evolution suggests that there are
barriers to the degree of change which mutation and selection can
produce. A series of known types of mutation, one after the other,
can change the genome of any species into that of any other species,
along a multitude of different routes. Now, along most of these
routes, one will likely pass through a number of genomes that don't
code for a viable life form in any plausible environment. But you
only need one path that contains a sequence of species, each viable in
some environment which it can encounter. Do not confuse what can be
accomplished in a few generations, or even a few thousand, with what
can be done over scores of millions of years -- it is like watching
someone take ten steps, and saying that obviously he can never cover
ten miles that way.
Actually, all humans are of the same race; the so-called "racial"
differences among humans all vary on a continuum, with intermediate
populations between populations of those we arbitrarily choose to call
the "pure" races. In addition, there is less genetic variation --
fewer and smaller differences in genes -- among humans than among most
other animals. There is less genetic variation between, say, the
Masai and the Koreans than one might find between two bands of
chimpanzees living ten miles apart.
As I noted in my previous post, the hominid fossil record consists of
humans (not all very much like us -- consider the Neanderthals), and
apes (e.g. the australopiths), and various fossils that don't seem to
be clearly one or the other (e.g. the Dmanisi hominids variously
placed in _Homo ergaster_, _H. habilis_, and _H. georgicus_ -- but
which seem rather neatly intermediate between humans and apes -- or,
if you don't like them, _Homo habilis_). If you can never produce, no
matter how long you keep at it, anything but a human from human stock,
or anything but an ape from ape stock, these \\hard cases\\ would not
exist.
Strictly speaking, horses and camels shared a common ancestor,
probably some 65 million years ago; they're not very closely related
for mammals (although they seem to be slightly more closely related to
each other than either is to us). Horses and camels both possess
specializations that would have to be lost, and replaced by other
specializations, for one to directly become the other. Rather, you
start with a less specialized, small, rather shrew-like common
ancestor and progressively modify it -- increase the size, change
nails to hooves by degrees, etc.
The fossil record shows some of the intermediates. Their genes and
proteins show traces of this history -- genes that are not identical,
yet are more similar than required by their similarity of function.
There are weirder and more wonderful things in the fossil record as
well -- species with the distinctive ankle bones of artiodactyls
(cows, camels, giraffes, pigs, hippos, etc.), but the distinctive ear
bones of whales, or whales which still have hind legs (now present
only as embryonic vestiges). Whales and living artiodactyls share
other signs of common ancestry -- bits of DNA, like pseudogenes and
endogenous retroviruses -- that seem to serve no purpose, and are not
present in most mamals, but are shared by these unexpectedly close
relatives.
You can interbreed horses and donkeys, and produce (usually, but not
always) sterile hybrids. You can interbreed wolves and coyotes, and
produce hybrids that are often fertile. There is no sharp dividing
line between perfectly interfertile separate populations (races or
subspecies), and perfectly intersterile separate populations
(clear-cut different species or genera). You can find cases where one
population, of one species, gave rise to another which could not
interbreed with the parent species -- in plants, this happens all the
time through polyploidy (duplication of the entire genome).
Piltdown man does not count as evidence against Lucy, or the Turkana Boy,
or the Dmanisi hominids.
He thought that they were the bones of a sort of giant gibbon (he
felt, rather eccentrically, that gibbons were closer to humans than
the great apes), but definitely intermediate between nohuman apes and
humans. Note that, from a biological point of view, even modern
humans are a sort of ape, so logically all our hominid ancestors would
be apes of some sort.
Note also that what Dubois said about _Homo erectus_
(_Pithecanthropus_, or Java Man) does not establish the fact of the
matter. Evolutionary theory is not a religion; it does not have
prophets or holy texts regarded as inerrant. Modern paleontologists
who have studied Dubois's finds for themselves are quite convinced
that they, and other specimens of _H. erectus_, are primitive humans,
intermediate between ourselves and clearly nonhuman apes, although
almost surely not our direct ancestors.
Actually, that was two teeth. And "Nebraska man" was an invention of
the popular press; the paleontologists merely misidentified them as
some sort of ape, not a human ancestor. And the scientist who made
the mistake later, after discovering more evidence, corrected it.
Again, there bits of bad evidence can be found for any theory; the
existence of mistakes or frauds does not make all evidence mistaken or
fraudulent, or eliminate the value of the evidence which is not false.
Darwin once noted that if any structure could be found,
which could not be produced by incremental modifications of some
predecessor structure, it would be fatal to his theory. Behe takes
this to mean that \\irreducibly complex\\ biochemical structures, which
cannot perform their *present* function *by themselves* if you remove
a single component, cannot evolve by mutation and natural selection,
because in their evolutionary history, they would have been missing
those parts until a mutation added them.
Behe overlooks some points (aside from the question of whether any of
the structures or systems he identifies are really IC). A system may
start off performing a different function, in a species that doesn't
need the function of the later system. Just as the theropods from
which birds evolved didn't originally need wings at all, so the early
precursors of an IC system may have belonged to a species that didn't
need the abilities of the IC system at all. Function may increase
incrementally along with the need for that function.
In addition, an IC system may not function with any component removed,
because the current components are too specialized. The ancestral
systems may have been less specialized, able to work without all the
present components, even if they worked less well. And, in addition,
some components of current IC systems may do the work of components
possessed by ancestors, but then lost because they were no longer
needed.
==
Horse phylogeny
_Pliohippis_, in a way, is still is ancestral to _Equus_. According to
MacFadden (p.110), _Pliohippus_ was once broader in concept, but two
lineages were recognized in the 1950s, one which (of course) retained the
name _Pliohippus_ (i.e. the one with the type species), and one which didnt.
The latter concept needed a new name (_Dinohippus_), because they cant be
naked species without a genus, and the new concept happened to include
the species considered ancestral to _Equus_. How, exactly, the species
played out in all this, I dont know, but there is a distinct possibility
that the same species as ever is just as basal to _Equus_ as before -- in
other words, the species position in the phylogeny may not have changed
-- despite the name change (a new combination) from the genus _Pilohippus_
(old concept) to _Dinohippus_. This species seems to be the one once
known as _Pliohippus_mexacanus_, now _Dinohippus_mexacanus_, which
MacFadden mentions. The question, therefore, is whether it actually
moved, phylogenetically speaking, when the name changed? It sure didnt
go as far as the dethroning of the genus _Pliohippus_ for _Dinohippus_
would suggest, by my reading.
Andrew MacRae
macrae@agc.bio.ns.ca
==
talk.origins message by mturner@acpub.duke.edu
Id thought that the fossil genus _Hyracotherium_ [Eohippus] was
a likely candidate to meet a challenge, since it included
several species and was supposed to be very near the base of the
radiation of the entire order Perissodactyla. MacFadden [1992]
starts his section on _Hyracotherium_s relationships with a quote
from Matthew [1926, p. 153] that clearly expressed this view.:

It is quite possible that certain species of Eohippus, when more
intensively studied, will appear to be more directly inthe line of
ancestry of the horse, others of the tapir or rhinoceros or of some of the
extinct phyla of Perissodactyls.

Further on, MacFadded writes [p.90]:
It may seem that too much time is being devoted to _Hyracotherium_ or
eohippus. On the contrary, being at or near [depending upon phylogenetic
interpretations] the base of both the perissodactyl and equid radiations,
it is central to an understanding of the higher-level interrelationships of
the Perissodactyla and the definition of the family Equidae. A recent
detailed cladistic analysis [Hooker 1989] of critical new and previously
studied specimens resulted in a radical rethinking of the concept of the
genus_Hyracotherium_ and the base of the perissodactyl radiation
[Figure 5.10].
[The cladogram in fig. 5.10 shows that some named species of
Hyracotherium are related to different named families:
H. leporinum is sister to the Palaeotheridae, H. vasacciense is sister
to the other Equidae, H. aff. vulpiceps and H. tapirinum are successive
outgroups to the equid/palaeothere clade and H. sp., Rians is related
to the Pachynolophidae in the sister group to the Equoidea.]

... Regardless of the exact details of all the new hypotheses that have
been or will be generated from his work, the following conclusions from
Hookers studies are important here: (1) In contrast to previous dogma,
there are several fossil perissodactyl taxa such as _Cymbalophus_ that
are dentally more primitive than _Hyracotherium_.
(2) _Hyracotherium_ is a horizontal, paraphyletic wastebasket taxon,
with different species currently allocated to
this genus giving rise to different perissodactyl clades [not unlike what is
described in the foregoing quotation from Matthew].

Thus the traditional non-cladistic genus _Hyracotherium_ includes
different species that are related to different more-derived families.

The genus _Hyracotherium_ now is being broken up and redefined by cladists,
restricting it to the monophyletic basal lineage of the Equidae. The species
are all phenetically similar enough to one another to have been classified
as one genus, therefore its all merely MICRO-evolution.
Refs:
MacFadden, B. J. 1992. Fossil horses. Systematics, paleobiology, and
evolution of the family Equidae. Cambridge University Press, Cambridge.
Hooker, J.J. 1989. Character polarities in early perissodactyls
and their significance for _Hyracotherium_ and infraordinal relationships.
pp. 79-101 _In_ D. R. Prothero & R. M. Schoch, [eds.] The Evoluton of
Perissodactyls Clarendon Press, Oxford.
Matthew, W. D. 1926. The evolution of the horse: a record and its
interpretation.
Quart. Rev. Biol. 1:139-185.
additional, more recent reference:
The beginning of the equoid radiation. Hooker-J-J
Zoological Journal of the Linnean Society 112(1-2): 29-63.
PY 1994 AB With the benefit of newly collected material primitive equoids are
analysed
cladistically to determine the detailed relationships of the families Equidae
and Palaeotheriidae. The most primitive equid is shown to be Pliolophus.
Cymbalophus cuniculus and Hyracotherium sandrae are closely related stem
equoids. The Pachynolophidae are not equoids, but most closely related to
the primitive tapiromorph family Isectolophidae. Hallensia is sister to these
two and therefore also not an equoid. Hyracotherium is restricted to the
type species H. leporinum Owen,part of whose lower dentition is made known
for the first time. It is closest to a restricted genus Propachynolophus
within the family Palaeotheriidae. The original concept of Propachynolophus
is polyphyletic. Using the cladogram, newly extended stratigraphic ranges
and paleogeography, an attempt is made to reconstruct the very early
speciation and biogeographical history of the group. Cymbalophus hookeri
Godinot is recombined in the genus Pachynolophus and H. pernix in
Pliolophus. Hallensia louisi sp. nov. and Propachynolophus levei sp. nov.
are described.
===
DNA doesnt evolve into a cellular stucture directly in the formation of
life, RNA ocupies an intermeidiate stage where it is both genome and
metabolic cycle. then polypetides develope from cofactors attached to
cataltic RNA, finally DNA take s over as the genetic material. Not
eveybody agrees with this scenario, but in _rough_ outline it is the
major theory of development of life on this planet.
------
This is a reference to autocatalytic cycles (or hypercycles, see 3),
where molecule A can synthesize molecule B, B makes C, C makes D and D
makes A. There is an extensive theoretical treatment of this (see for
example Kaufmann) as well as some wet chemistry examples (4,5).
Molecule A is envisaged to arise abiotically (1,2). Note that these
molecules do not have to be very large, the Ghadiri peptides are only
24 amino acids long, well within the size range that can be produced
abioticaly (althought the Ghadiri peptides are unlikely to be
plausible ancestor molecules). Similar considerations apply to RNA
ribozymes.

1. Ferris JP, Hill AR Jr, Liu R, and Orgel LE. (1996 May 2).
Synthesis of long prebiotic oligomers on mineral surfaces [see comments]
Nature , 381, 59-61.
2. Saetia S, Liedl KR, Eder AH, and Rode BM. (1993 Jun). Evaporation cycle
experiments--a simulation of salt-induced peptide synthesis under possible
prebiotic conditions. Orig Life Evol Biosph , 23, 167-76.
3. Orgel LE. (1992 Jul 16). Molecular replication. Nature , 358, 203-9.
4. Lee DH, Severin K, Yokobayashi Y, and Ghadiri MR. (1997 Dec 11).
Emergence of symbiosis in peptide self-replication through a hypercyclic
network. Nature , 390, 591-4.
5. Doudna JA, Couture S, and Szostak JW. (1991 Mar 29). A multisubunit
ribozyme that is a catalyst of and template for complementary strand RNA
synthesis. Science , 251, 1605-8.

_Origins of Order_ by Kauffman
==
Reznick, D N (1997) Life history evolution in guppies (Poecilia
reticulata): guppies as a model for studying the evolutionary biology of
aging Exp.
Gerontol 32(3)245-258 Mueller, L D (1988) Evolution of competitive
ability in Drosophila by density-dependent natural selection Proc Nat
Acad Sci USA 85(12)4383-4386 Townsend JM, Wasserman T (1997)
The perception of sexual attractiveness: sex differences in variability.
Arch Sex Behav 1997 Jun;26(3):243-268
==
Science, 25 July 1997, titled Evidence for a Large-Scale Reorganization
of Early Cambrian Continental Masses .

Julian Huxley, _Evolution: The Modern Synthesis_ (1963),
==
It is not only possible but highly probable that among these [large
numbers of gene-differences with extremely small effects] and that it is
by means of small mutations, notably in the form of series of multiple
allelic steps, each adjusted for viability and efficiency by recombinations
and further small mutations, that progressive and adaptive evolution has
occurred.[cited in Orr & Coyne, The Genetics of Adaptation: A Reassessment
_The American Naturalist_ 140: 725-42 (1992).]
==
The paleontologic deposits in the litographic limestone of Cerin (France),
for example, display fossils which had kept the flesh, fish have kept their
scales even their viscera. Those fossils lay flat and are not bent which
shows that the surrouding (the hydrodynamism) was very quiet. Unlike
other similar fossils like those found at Canjuers (france), Solnhofen
(Germany) or Lerida (Spain), those fossils always lay on top of the strata.
In the model, the organisms fall on the very fine substratum, they are not
burried but quickly covered by a protecting microbial sheet
(cyanobacteria).
--------
Burgessochaeta, Pikaia,Anomalocaris, Hallucigenia, Opabinia, Marrella,Odaraia
are Cambrian sea life
==
The difference in chromosome number between chimpanzees (24 pairs) and
humans (23 pairs).
==
The Annelida, which includes the polychaetes and the clitellates, has
long held the taxonomic rank of phylum. The unsegmented, mud-dwelling
echiuran spoon worms and the gutless, deep-sea pogonophoran tube worms
(including vestimentiferans) share several embryological and morphological
features with annelids, but each group also has been considered as a
separate metazoan phylum based on the unique characters each group
displays. Phylogenetic analyses of DNA sequences from the nuclear gene
elongation factor-1-alpha place echiurans and pogonophorans within the
Annelida. This result, indicating the derived loss of segmentation in
echiurans, has profound implications for our understanding of the evolution
of metazoan body plans and challenges the traditional view of the
phylum-level diversity and evolutionary relationships of protostome worms.
----
Life is a self-sustained chemical system capable of undergoing Darwinian
evolution.
==
Compare apples with wild crab apples, carrots with Queen Annes Lace,
turnips cabbages and broccoli with wild weedy mustards, corn with teosinte.
==
Alternative to phyletic gradualism, in T.J.M. Schopf (ed.),_Models In
Paleobiology_).
==
Michael J. Benton, Amniote Phylogeny, in: _Origins of the Higher Groups of
Tetrapods: Controversy and Consensus_,ed. by Hans-Peter Schultze and Linda
Trueb, co. 1991, Cornell University Press, pp. 317-330Frontiers of
Complexity

Paul Ehrlich and L.C. Birch, Evolutionary History and Population
Biology, Nature, Vol.214 (1967)

CHORDATE MORPHOLOGY author Malcolm Jollie.

D. Dwight Davis, Comparative Anatomy and the Evolution of Vertebrates,
in Genetics, Paleontology and Evolution, (ed.by Jepsen, Mayr and Simpson,
Princeton University Press, 1949)

Today, the theory of evolution is an accepted fact for everyone but a
fundamentalist minority, whose objections are based not on reasoning but on
doctrinaire adherence to religious principles. (James D. Watson)
==
Herbert Spencer was much intrigued by the size of a whales femur. Buried
deep in the huge carcass of the whale is a tiny bone weighing about two
ounces. It is the exact homologue of the femur, the largest bone in the
mammalian skeleton. We know nothing about the process by which certain
mammals reverted to a purely marine existence. The earliest skeletons of
whales are found in the Oligocene formations, and differ little from
our present species. Before this period the geological record is completely
silent. But suppose they are descended from animals that at one time has
legs, and that as the legs became an encumbrance in their new aquatic
environment, they gradually atrophied. It could surely make no difference
to the survival of the whale if its femur weighted twenty ounces instead
of two. The atrophy has proceeded far beyond the point where natural
selection could apply. Exactly the same line of argument applies to the
atrophy of the wings of flightless birds. On isolated oceanic islands
flightless birds are found which belong unmistakably to species which
elsewhere have to power to fly. If a bare incapacity to fly was what natural
selection favoured (and it is difficult to see how such an incapacity could
be an advantage) natural selection cannot explain an atrophy which has
proceeded far beyond the capability to fly.
==
The echolocating toothed whales have about 67 species and the filter-feeding
baleen whales, 10 species) .
=
G. A. Mchedlidze, General Features of the Paleobiological Evolution of
Cetacea, trans. from Russian (Rotterdam: A. A. Balkema, 1986), 91
==
When Whales Walked the Earth: The Oldest Known Whale Fossils
The oldest known fossil whale has been reported from Eocene rocks in the
Subathu Formation in the Himalaya Mountains of northern India. A whale jawbone
and three teeth were found in a layer of rock that is 53.5 million years old.
This fossil discovery is about 3.5 million years older than the oldest
previously-known whale fossils. Named Himalayacetus subathuensis, the fossil
represents a new species, according to the Indian and American scientists,
Sunil Bajpai and Philip D. Gingerich, who described the findings in the
Proceedings of the National Academy of Sciences of the U.S.
Although it may sound surprising, whales had four legs in the past. They are
thought to have originally been land mammals, inhabiting the land around the
Tethys Sea, an ancient sea that separated India from Asia in the past. The
first direct fossil bone evidence that whales once had hind legs and feet was
found in 1990 in fossils excavated by Gingerich in Egypt. The Egyptian whales
retained smaller, but functional versions of the hind legs and feet for more
than 10 million years after they left the land for a sea-dwelling life. The
flippers in modern whales are remnants of the forelimbs. The only remnants of
former hind limbs in living whales are a vestigial pelvis and femur imbedded
in the body wall. In addition, one whale in 100,000 is estimated to have a
protruding stub of a hind limb.
Oxygen isotopes in the tooth-enamel of Himalayacetus have a composition that is
in between that of freshwater and marine forms, indicating that the whale
probably spent some time both on land and in the sea. This suggests that early
whales were amphibious, feeding on both freshwater and saltwater fish.
==
Ambulocetus's skull was quite cetacean (Novacek 1994). It had a long muzzle,
teeth that were very similar to later archaeocetes, a reduced zygomatic arch,
and a tympanic bulla (which supports the eardrum) that was poorly attached to
the skull. Although Ambulocetus apparently lacked a blowhole, the other skull
features qualify Ambulocetus as a cetacean. The post-cranial features are
clearly in transitional adaptation to the aquatic
environment, they gradually atrophied. It could surely make no difference
to the survival of the whale if its femur weighted twenty ounces instead
of two. The atrophy has proceeded far beyond the point where natural
selection could apply. Exactly the same line of argument applies to the
atrophy of the wings of flightless birds. On isolated oceanic islands
flightless birds are found which belong unmistakably to species which
elsewhere have to power to fly. If a bare incapacity to fly was what natural
selection favoured (and it is difficult to see how such an incapacity could
be an advantage) natural selection cannot explain an atrophy which has
proceeded far beyond the capability to fly.
==
Basilosaurus and Dorudon were fully aquatic whales (like Basilosaurus,
Dorudon had
very small hind limbs that may have projected slightly beyond the body wall).
They were no longer tied to the land; in fact, they would not have been able to
move around on land at all. Their size and their lack of limbs that could
support
their weight made them obligate aquatic mammals, a trend that is elaborated and
reinforced by subsequent whale ta
==
Atoms require a specific activation energy to reach a reactive state,
and the reaction is associated with a probability factor (not all
collisions result in products). The magnitude of the activation energy
changes by huge amounts, changing the rare, depending on composition and
catalysis. Once two atoms have reacted, the molecule will affect the rate
of subsequent reactions:
Some reactions are extremely autocatalytic. At some point, different phases
condense, and rates change at phase boundaries and in different phases.
Rates in liquid phases are not the same as in a gas phase or a solid.
Surfaces can provide templates for the synthesis of complex molecules,
and polarized light can direct the formation of specific optically active
forms. All of these influences affect the process
which could lead the formation of a genetic chemical system.

Ekland EH, and Bartel DP. (1996 Jul 25). RNA-catalysed RNA
polymerization using nucleoside triphosphates. Nature , 382, 373-6.

McMenamin, M.A.S., 1987. The emergence of animals. Scientific American,
v.257, no.4,

Chia-Wei Li; Jun-Yuan Chen; Tzu-En Hua, 1998 (Feb. 6). Precambrian
sponges with cellular structures. Science, v.279, p.879-882.

Shuhai Xiao; Yun Zhang and Knoll, A.H., 1998 (Feb. 5). Three-dimensional
preservation of algae and animal embryos in a Neoproterozoic phosphorite.
Nature, v.391, p.553-558. (See also the comment on p.529-530.)

Budd, G.E., 1998. Arthropod body-plan evolution in the Cambrian with an
example from anomalocaridid muscle. Lethaia, v.31, p.197-210.

Gerhart and Kirschner _Cells, Embryos and Evolution_
Werner Muller in _Developmental Biology_

There are no definite gastropods known from the Early Cambrian. They
arrive later. What is found in the Early Cambrian is a whole host of other
strange shells with transitional morphologies between several molluscan
classes. What is also found are organisms that combine features of other
phyla, like annelids and brachiopods.The trace fossils, for example, show a
nifty progression from fairly simplified, shallow burrows that imply simple
behaviours to ones that show more elaborate feeding and burrowing strategies
and eventually ones that penetrate deeper into the sediment. It is hard
to know exactly what organisms were responsible for the traces, but that
pattern of increasingly elaborate behaviour certainly fits the pattern
expected of an evolutionary change, even if it is still a relatively rapid
change. I mention the halkieriids, _Wiwaxia_, and cite Conway-Morris
and Peel. They and some related groups are transitional between the
molluscs, annelids, and brachipods. I also mentioned, and keep on mentioning,
_Kimberella_ from the Precambrian Ediacaran fauna, which is a probable
mollusc-like, entirely soft-bodied animal. I also mentioned the armored
lobopods, like _Microdictyon_ and _Xenusion_, and the strange
lobopod-arthropod transitional animals like _Opabinia_, _Anomalocaris_, and
_Kerygmachela_ (Budd, 1993). There is plenty missing from the story, but
the phyla are clearly not as distinct and unique as they appeared a decade
ago when interest in the Precambrian-Cambrian interval increased greatly,
and many the ones that seemed totally unique and different from all known
phyla turn out to occupy transitional states, or not be so weird after all,
once more specimens have been discovered.

Read WONDERFUL LIFE by Gould for descriptions of these organisms.
==
Triticale is a new genus of grain.
The cereal crop Triticale (X Triticosecale Wittmack) is well-suited to growing
conditions. Triticale is a man-made crop, developed by crossing wheat (Triticum
aestivum ) with rye (Secale cereale). Early attempts to cross wheat and rye
produced only sterile off-spring. It was not until the 1930s that techniques
were available to produce fertile hybrids. Once this was accomplished, it was
possible to develop new combinations between wheat and rye as well as direct
combinations between triticales with differing wheat and rye parents.
Consequently, new varieties of winter or spring triticale can be developed with
the same methods used for breeding other cereal crops.
==
Kirschner and Gerharts Evolvability (Proc. Natl.Acad. Sci. USA 95:8420-8427,
July 1998) on body plans characteristic of phyla.

Within each of the 30-35 phyla, all members share a characteristic body plan
that is first evident in development at an intermediate stage called the
phylotypic stage. Although it has been suggested that the common body plan
within a phylum may just be artifact of random phylogeny, in which
taxonomists endow the residue of common characteristics with exaggerated
significance, modern molecular studies have given the conserved body plan
and the phylotypic stage much more meaning. In arthropods for example, the
conserved stage, called the segmented germ band, is much more than a
morphological composite of distinguishable parts. It is a spatially
arranged collection of 50-60 self-sustaining compartments of developmental
processes of great versatility. Each compartment has an identifying set of
expressed selector genes for transcription factors (such as ems, otd, and
Hox genes) and for secreted signals. The compartments include multiple
segmented domains, each with an anterior and posterior portion, the
nonsegmental terminal domains (acron and telson), and several dorsal-
ventral subregions including the three germ layers. Each is largely
independent from other compartments in the subsequent development occurring
within it, and in its evolution.
The body plan is easily observed in long germ band insects in which it is
generated nearly synchronously in the embryo. In short germ band insects
where thoracic and abdominal segments arise later and successively from a
proliferating zone of cells, there is a temporal lag from the anterior
to the posterior ends. Yet the basic pattern is very similar in all
arthropods. Chordates also have a phylotypic body plan and stage, the
pharyngula, with a segmented mesoderm (the somites), an anteriorposterior
series of regions distinguished by emx, otx, and Hox selector gene
expression, and a dorsal-ventral organization strikingly similar to the
arthropods. The inverse orientation of this dimension in chordates compared
with arthropods reflects merely the organisms preferred orientation with
respect to gravity, not a basic difference in this aspect of the body
plans. Beyond these similarities, the pharyngula differs of course from the
segmented germ band in terms of gill slits, a post-anal tail, a notochord,
and a dorsal hollow nerve cord. Because representatives of virtually all
30-35 modern phyla were present 530 million years ago in the mid-Cambrian
period, body plans and phylotypic stages must have been fixed by that time.
For a period 10-100 million years before then, a great radiation of large,
forcefully moving metazoa took place into new niches and then stopped.
Since then, there has been extensive diversification of the larval and
adult stages of members of each phylum as in the great diversity of
classes and orders of modern phyla. These diversifications occur at
developmental stages after the phylotypic stage has formed, and they are
built upon the body plan. They were absent in the
pre-Cambrian founders of the phylum. Also, there have been extensive
diversifications of the egg and early stages of development before the
phylotypic stage is formed. Thus, evolution since the mid-Cambrian has
involved modifications before and after the phylotypic stage but not of the
stage itself.
---
Macroevolution, as defined in American Heritage Dictionary, 3rd ed.,
is Large scale evolution occurring over geologic time that results in the
formation of new taxonomic groups.
----
Although RNA can serve as an adequate but relatively short-lived and
mutation-prone carrier for a limited amount of genetic information, as seen
in RNA viruses, the development of autonomously replicating cells probably
depended on the reduction of the ribose moiety in nucleotides to the unusal
sugar, deoxyribose.T. Lindahl, 1993, Instability and decay of the primary
structure of DNA. Nature 362:709-714.
---
Data implies that annelid intracellular hemoglobins and molluscan
hemocyanins existed either in annelids and molluscs or in their immediate
ancestors, from which they were inherited with little or no modification.
Of the two the first alternative is the more probable, and it means that
the original metazoans evolved far earlier still.
C. Mangum, 1991, Precambrian oxygen levels, the sulfide biosystem, and the
origin of metazoa. The Jour. Exp. Zool. 260: 33-42.
==
Evolution, like the tinker, does not produce innovations from scratch.
it works on what already exists, transforming a system to give it a new
function or combining several systems to produce a more complex one.
-- F. Jacob
==
A recently discovered primate that lived about 30 million years ago is
thought to be an ancestor of the primate link. Named Aegyptopithecus
(the principle fossil remains were first found in Egypt) this primate lived
during the Oligocene period had a skull capacity of about 30 cubic
centimeters and was no bigger than a house cat, but was the most advanced
life form on Earth at the time. Scientists belive that Aegyptopithecus had
a strong social behavior that was conducive to the development of larger
brains. Considering brain size, social behavior, and physical
characteristics, puts Aegyptopitecus in the direct line of mans ancestors.
==
The polychaete worm, N Acuminata was OBSERVED to
speciate between 2 populations raised at WHOI and UCLA between 1962 and 1992.
==
All mammals have three bones in the ear (and the Organ of Corti) and a
single bone on each side of the lower jaw. All reptiles have a single bone
in the ear and on average six bones on each side of the lower jaw.
==
A butterfly that shows a rather unique adaption is the Kallima who lives
in Asia. The top of his wings are very colorful, but, when he lands and
folds his wings he looks just like a dead leaf.
==
Evolution, Science, and Society: a white paper on behalf of the field of
evolutionary biology
http:www-rci.rutgers.edu~ecolevolexecsumm.html

An interview with Miller:
http:www.gene.comaeWNNMmiller.html
==
Werner Mullers text (1997. _Developmental Biology_.
Springer. New York_) has this pertinent quote:...all vertebrates pass
through a highly conserved common stage that displays a uniform basic body
architecture characteristic of all vertebrates. Therefore, the biogenetic
law is valid if it is modified by stating that all vertebrates recapitulate
certain embryonic traits of their ancestors- in particular, a common
phylotypic stage.
==
There is no newly invented complex of genes that codes for all the parts of
legs rather that differs from some set of genes that encode all the parts of
antennae. Antennae and legs are composed of the same material structures
encoded by the same genes. The differential expression of those genes is
*modified* in certain specified segments of the insect to produce antennae or
legs (and modified to produce mouthparts in others). Only a few genes are
involved in the specification of the segment. That simple specification event
results in the *modified* expression of genes. The antennae is a *modified*
leg, not a novel structure. Evolution *modifies* structures more often than it
invents new ones. The haltere is not a degenerate wing. It is a clublike
vibrating dual structure in some insects, used for orientation. It is an
evolved organ that is derived from original wings, which serves a different
function from wings.
==
How many generations of animals can I observe during a single lifetime?
How many years has humanity been able to scientifically observe animals at
all- a few hundred? It takes tens of thousands of years for anything
significant to happen in evolution. Therfore demanding that someone
observe it happening; in front of their face, poof is totally dishonest
and pointless. Science does not expect to ever witness large-scale
evolutionary changes firsthand, so the fact that it has not does not
disprove anything. Science has many other ways of indirectly observing
evolution, observing the products of evolution and observing natural
selection on a small scale. Artificial selection and simulations of
evolution has a solid theory basis with great predictive power, the
ultimate test of any science model.
==
Charles Darwin,Charles Darwin, The Origin of Species, 1859.
Here is a quote:

To suppose that the eye, with all its inimitable contrivances for
adjusting the focus to different distances, for admitting different
amounts of light, and for the correction of spherical and chromatic
aberration, could have been formed by natural selection, seems,
I freely confess, absurd in the highest possible degree. Yet
reason tells me, that if numerous gradations from a perfect and
complex eye to one very imperfect and simple, each grade being
useful to its possessor, can be shown to exist; if further, the eye
does vary ever so slightly, and the variations be inherited, which
is certainly the case; and if any variation or modification in the
organ be ever useful to an animal under changing conditions of
life, then the difficulty of believing that a perfect and complex
eye could be formed by natural selection, though insuperable by our
imagination, can hardly be considered real....

In the Articulata we can commence a series with an optic nerve
merely coated with pigment, and without any other mechanism; and
from this low stage, numerous gradations of structure, branching
off in two fundamentally different lines, can be shown to exist,
until we reach a moderately high stage of perfection. In certain
crustaceans, for instance, there is a double cornea, the inner one
divided into facets, within each of which there is a lens shaped
swelling. In other crustaceans the transparent cones which are
coated by pigment, and which properly act only by excluding lateral
pencils of light, are convex at their upper ends and must act by
convergence; and at their lower ends there seems to be an imperfect
vitreous substance. With these facts, here far too briefly and
imperfectly given, which show that there is much graduated
diversity in the eyes of living crustaceans, and bearing in mind
how small the number of living animals is in proportion to those
which have become extinct, I can see no very great difficulty (not
more than in the case of many other structures) in believing that
natural selection has converted the simple apparatus of an optic
nerve merely coated with pigment and invested by transparent
membrane, into an optical instrument as perfect as is possessed by
any member of the great Articulate class.
--
Investigation of this problem of eye origins by Nilsson and Pelger indicates
that a fish-like eye could evolve from a light-senstive spot in less than
400,000,000 generations, using conservative estimates. (_River out of Eden_,
Dawkins, 1995, citing Nilsson & Pegler A Pessimistic Estimate of the time
Required for an Eye to Evolve, Proceedings of the Royal Society of London,
B[1994]) The first fossils of chordates have no eyes and neither do
primitive chordates today.
Since the various types of eyes found in the animal kingdom are
morphologically very different and also develop differently, it has been
proposed that photoreceptors have originated independently in at least 40,
but possibly up to 65 or more different phyletic lines (Salvini-Plawen and
Mayr, 1961)...There is at least one key gene that is shared by the
photoreceptors of all the phyla -...rhodopsin...The finding that eye (pax-6)
is the master control gene for eye morphogenesis in Drosophila and that a
homologous gene is found in mammals raises the possibility that it is a
universal master control gene for eye morphogenesis and evolution of the
eye. Than he describes the testing of this hypothesis by induction of
ectopic eyes in drosophila by mouse and squid genes - both quite functional
in Drosophila and concludes with:
...Since Pax-6 homologs have been now found in vertebrates, tunicates,
echinoderms, arthropods, nematodes, nemertines and flatworms, the
hypothesis that Pax-6 is a universal master control gene has gained
considerable support. This suggests that the prototypic eye originated only
once in evolution and various eye types arose from the same origin, which
is much more compatible with Darwins theory. After all, Darwin was right
again. - here he refers to a specific proposal by Darwin of a hypothetic
simple protoeye.
I know that Pax-6 isnt an eye gene, it plays a role in the development
of other organs like the brain and olfactory bulbs and that it is even
expressed in some animals that dont have eyes (Though the speculation that
Pax-6 is intimately associated