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Re: Bird and archosaur genome analysis in Science

I find it odd that the genome of the domestic chicken is the closest to the 
ancestral dinosaur when human breeding has affected the chicken genome. Could 
breeding have caused some kind of regression toward the ancestral form? I note 
with interest that Jack Horner’s book “How to Build a Dinosaur” suggested 
starting with a chicken. 

Jeff Hecht

On Dec 11, 2014, at 8:49 PM, David Černý <david.cerny1@gmail.com> wrote:

> 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:
> http://avian.genomics.cn/en/
> http://www.sciencemag.org/content/346/6215/1308/suppl/DC1
> 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
> Background
> 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.
> Results
> 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.
> Conclusions
> 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