Re: Two new archosaur papers

["Jaime A. Headden" <qilongia@yahoo.com>]

And I missed these two, general evolution. Seems the issue is rife with
interesting stories. BTW, like PNAS, MB&E has a moving wall and these
issues will eventually be freely available. Check in the back issues form
last year and earlier and there are very many interesting articles for the
evolution process-minded.

O'hUigin, C.; Satta Y.; Takahata N.; & Klein, J. 2002. Contribution of
homoplasy and of ancestral polymorphism to the evolution of genes in
anthropoid primates. _Molecular Biology & Evolution_ 19 (9): 1501-1513.

Abstract: "Molecular phylogenies of lineages that split from one another
in short succession are often difficult to resolve because different loci
and different sites within the same locus yield incongruent relationships.
The incongruity is commonly attributed to two causes: differential
assortment of ancestral polymorphisms and homoplasy. To assess the
relative contribution of these two causes, sequences of 57 segments from
51 loci in six primate lineages (human, chimpanzee, gorilla, orangutan,
macaque, and tamarin, abbreviated as H, C, G, O, M, and T, respectively)
were subjected to "partitioning" analysis, in which phylogenetically
informative sites were identified in all 15 pairwise comparisons of each
of the 57 segments and tallied for their support or lack thereof for each
of the theoretically possible phylogenies. The six lineages include one of
the best known cases of a difficult-to-resolve phylogeny: the trichotomy
(H, C, G), in which the three lineages may have diverged from each other
within a short period of time. In this period many of the ancestral
polymorphisms apparently persisted and yielded phylogenetically
incongruent signals. By contrast, no ancestral polymorphism is expected to
have survived during the interval separating the divergences of the O, M,
and T lineages from the ancestor of the (H, C, G) group. Any phylogenetic
incompatibilities at sites in the O, M, and T lineages relative to the (H,
C, G) group are therefore presumably the result of homoplasy. The
frequency of homoplasy estimated in this manner is unexpectedly high: 12%
for the (H, C, G) clade and 19% for the (H, C, G, O) clade. At least
three-quarters of the 48% incompatibility observed in the (H, C) clade is
attributable to the sorting out of ancestral polymorphisms coupled with
intragenic recombination. Possible reasons for this high level of
homoplasy in the O, M, and T lineages are discussed, and a computer
simulation has been carried out to produce a model explaining the observed
data."

  And what a gorgeous Irish name ... I beleive the modern version is
"O'Haegin" and I think the origin of "Higgins" and "Hoagan" may be
wrong...

Jow, H.; Hudelot, C.; Rattray, M.; & Higgs, P.G. 2002. Bayesian
phylogenetics using an RNA substitution model applied to early mammalian
evolution. _Molecular Biology & Evolution_ 19 (9): 1591-1601.

Abstract: "We study the phylogeny of the placental mammals using molecular
data from all mitochondrial tRNAs and rRNAs of 54 species. We use
probabilistic substitution models specific to evolution in base paired
regions of RNA. A number of these models have been implemented in a new
phylogenetic inference software package for carrying out maximum
likelihood and Bayesian phylogenetic inferences. We describe our Bayesian
phylogenetic method which uses a Markov chain Monte Carlo algorithm to
provide samples from the posterior distribution of tree topologies. Our
results show support for four primary mammalian clades, in agreement with
recent studies of much larger data sets mainly comprising nuclear DNA. We
discuss some issues arising when using Bayesian techniques on RNA sequence
data."

  Cheers,

=====
Jaime A. Headden

  Little steps are often the hardest to take.  We are too used to making leaps 
in the face of adversity, that a simple skip is so hard to do.  We should all 
learn to walk soft, walk small, see the world around us rather than zoom by it.

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