Re: Two new archosaur papers

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

Stephan Pickering (stefanpickering2002@yahoo.com) wrote:

<Truls Moum, Ulfur Arnason, Einar Arnason, 2002. Mitochondrial DNA
sequence evolution  and phylogeny of the Atlantic Alcidae, including the
extinct great auk (Pinguinus impennis). Molecular Biology & Evolution
19(9):1434-1439.

Belinda S.W. Chang, Karolina Jonsson, M.A. Kazmi, M.J. Donoghue, T.P.
Sakmar, 2002. Recreating a functional archosaur visual pigment. Molecular
Biology & Evolution 19(9):1483-1489.>

There's also, not to be missed:

Escriva, H.; Manzon, L.; Youson, J.; & Laudet, V. 2002. Analysis of
lamprey and hagfish genes reveals a complex history of gene duplications
during early vertebrate evolution. _Molecular Biology & Evolution_ 19 (9):
1440-1450.

Abstract: "It has been proposed that two events of duplication of the
entire genome occurred early in vertebrate history (2R hypothesis).
Several phylogenetic studies with a few gene families (mostly Hox genes
and proteins from the MHC) have tried to confirm these polyploidization
events. However, data from a single locus cannot explain the evolutionary
history of a complete genome. To study this 2R hypothesis, we have taken
advantage of the phylogenetic position of the lamprey to study the history
of gene duplications in vertebrates. We selected most gene families that
contain several paralogous genes in vertebrates and for which lamprey
genes and an out-group are known in databases. In addition, we isolated
members of the nuclear receptor superfamily in lamprey. Hagfish genes were
also analyzed and found to confirm the lamprey gene analysis. Consistent
with the 2R hypothesis, the phylogenetic analysis of 33 selected gene
families, dispersed through the whole genome, revealed that one period of
gene duplication arose before the lamprey-gnathostome split and this was
followed by a second period of gene duplication after the
lamprey-gnathostome split. Nevertheless, our analysis suggests that
numerous gene losses and other gene-genome duplications occurred during
the evolution of the vertebrate genomes. Thus, the complexity of all the
paralogy groups present in vertebrates should be explained by the
contribution of genome duplications (2R hypothesis), extra gene
duplications, and gene losses."

  For the others:

Moum et al., 2002:

Abstract: "The Atlantic auk assemblage includes four extant species,
razorbill (*Alca torda*), dovekie (*Alle alle*), common murre (*Uria
aalge*), and thick-billed murre (*U. lomvia*), and one recently extinct
species, the flightless great auk (*Pinguinus impennis*). To determine the
phylogenetic relationships among the species, a contiguous 4.2-kb region
of the mitochondrial genome from the extant species was amplified using
PCR. This region included one ribosomal RNA gene, four transfer RNA genes,
two protein-coding genes, the control region, and intergenic spacers. Sets
of PCR primers for amplifying the same region from great auk were designed
from sequences of the extant species. The authenticity of the great auk
sequence was ascertained by alternative amplifications, cloning, and
separate analyses in an independent laboratory. Phylogenetic analyses of
the entire assemblage, made possible by the great auk sequence, fully
resolved the phylogenetic relationships and split it into two primary
lineages, *Uria* versus *Alle,* *Alca,* and *Pinguinus.* A sister group
relationship was identified between *Alca* and *Pinguinus* to the
exclusion of *Alle.* Phylogenetically, the flightless great auk originated
late relative to other divergences within the assemblage. This suggests
that three highly divergent species in terms of adaptive specializations,
*Alca,* *Alle,* and *Pinguinus,* evolved from a single lineage in the
Atlantic Ocean, in a process similar to the initial adaptive radiation of
alcids in the Pacific Ocean."

Chang et al., 2002:

Abstract: "The ancestors of the archosaurs, a major branch of the diapsid
reptiles, originated more than 240 MYA near the dawn of the Triassic
Period. We used maximum likelihood phylogenetic ancestral reconstruction
methods and explored different models of evolution for inferring the amino
acid sequence of a putative ancestral archosaur visual pigment. Three
different types of maximum likelihood models were used: nucleotide-based,
amino acid?based, and codon-based models. Where possible, within each type
of model, likelihood ratio tests were used to determine which model best
fit the data. Ancestral reconstructions of the ancestral archosaur node
using the best-fitting models of each type were found to be in agreement,
except for three amino acid residues at which one reconstruction differed
from the other two. To determine if these ancestral pigments would be
functionally active, the corresponding genes were chemically synthesized
and then expressed in a mammalian cell line in tissue culture. The
expressed artificial genes were all found to bind to 11-cis-retinal to
yield stable photoactive pigments with max values of about 508 nm, which
is slightly redshifted relative to that of extant vertebrate pigments. The
ancestral archosaur pigments also activated the retinal G protein
transducin, as measured in a fluorescence assay. Our results show that
ancestral genes from ancient organisms can be reconstructed de novo and
tested for function using a combination of phylogenetic and biochemical
methods."

  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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