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Re: Bird and archosaur genome analysis in Science

As the news stories make clear, all the Science papers are just part
of the results of the Avian Phylogenomics Project, which have been
published almost simultaneously in a number of journals. The full list
is available at the following links:


Some of the links and DOIs don't work; perhaps the papers will be
published later today.

This paper might be of particular interest to the list:

Romanov MN, Farré M, Lithgow PE, Fowler KE, Skinner BM, O'Connor R,
Fonseka G, Backström N, Matsuda Y, Nishida C, Houde P, Jarvis ED,
Ellegren H, Burt DW, Larkin DM, Griffin DK 2014 Reconstruction of
gross avian genome structure, organization and evolution suggests that
the chicken lineage most closely resembles the dinosaur avian
ancestor. BMC Genom 15: 1060
Free PDF: http://www.biomedcentral.com/1471-2164/15/1060/abstract


The availability of multiple avian genome sequence assemblies greatly
improves our ability to define overall genome organization and
reconstruct evolutionary changes. In birds, this has previously been
impeded by a near intractable karyotype and relied almost exclusively
on comparative molecular cytogenetics of only the largest chromosomes.
Here, novel whole genome sequence information from 21 avian genome
sequences (most newly assembled) made available on an interactive
browser (Evolution Highway) was analyzed.


Focusing on the six best-assembled genomes allowed us to assemble a
putative karyotype of the dinosaur ancestor for each chromosome.
Reconstructing evolutionary events that led to each species' genome
organization, we determined that the fastest rate of change occurred
in the zebra finch and budgerigar, consistent with rapid speciation
events in the Passeriformes and Psittaciformes. Intra- and
interchromosomal changes were explained most parsimoniously by a
series of inversions and translocations respectively, with breakpoint
reuse being commonplace. Analyzing chicken and zebra finch, we found
little evidence to support the hypothesis of an association of
evolutionary breakpoint regions with recombination hotspots but some
evidence to support the hypothesis that microchromosomes largely
represent conserved blocks of synteny in the majority of the 21
species analyzed. All but one species showed the expected number of
microchromosomal rearrangements predicted by the haploid chromosome
count. Ostrich, however, appeared to retain an overall karyotype
structure of 2n = 80 despite undergoing a large number (26) of
hitherto un-described interchromosomal changes.


Results suggest that mechanisms exist to preserve a static overall
avian karyotype/genomic structure, including the microchromosomes,
with widespread interchromosomal change occurring rarely (e.g. in
ostrich and budgerigar lineages). Of the species analyzed, the chicken
lineage appeared to have undergone the fewest changes compared to the
dinosaur ancestor.

David Černý