Molecular evolutionary genomics of birds

Abstract

Insight into the molecular evolution of birds has been offered by the steady accumulation of avian DNA sequence data, recently culminating in the first draft sequence of an avian genome, that of chicken. By studying avian molecular evolution we can learn about adaptations and phenotypic evolution in birds, and also gain an understanding of the similarities and differences between mammalian and avian genomes. In both these lineages, there is pronounced isochore structure with highly variable GC content. However, while mammalian isochores are decaying, they are maintained in the chicken lineage, which is consistent with a biased gene conversion model where the high and variable recombination rate of birds reinforces heterogeneity in GC. In Galliformes, GC is positively correlated with the rate of nucleotide substitution; the mean neutral mutation rate is 0.12–0.15% at each site per million years but this estimate comes with significant local variation in the rate of mutation. Comparative genomics reveals lower d_N/d_S ratios on micro- compared to macrochromosomes, possibly due to population genetic effects or a non-random distribution of genes with respect to chromosome size. A non-random genomic distribution is shown by genes with sex-biased expression, with male-biased genes over-represented and female-biased genes under-represented on the Z chromosome. A strong effect of selection is evident on the non-recombining W chromosome with high d_N/d_S ratios and limited polymorphism. Nucleotide diversity in chicken is estimated at 4–5 × 10^–3 which might be seen as surprisingly high given presumed bottlenecks during domestication, but is lower than that recently observed in several natural populations of other species. Several important aspects of the molecular evolutionary process of birds remain to be understood and it can be anticipated that the upcoming genome sequence of a second bird species, the zebra finch, as well as the integration of data on gene expression, shall further advance our knowledge of avian evolution.

Nucleotide Variation, Linkage Disequilibrium and Founder-Facilitated Speciation in Wild Populations of the Zebra Finch (Taeniopygia guttata)

“…This calibration and the harmonic mean of the estimated rate for each locus results in an average rate of 7.38 3 10 À7 substitutions/locus per year. Given the lengths of the loci in our study, our per-locus estimate translates into a rate of 2.95 3 10 À9 substitutions/site/ year, similar to a previous estimate of 1.5 3 10 À9 substitutions/site/year on the basis of the divergence of galliformes chicken and turkey in autosomal introns (Ellegren 2007).…”

“…With the production of bacterial artificial chromosome (BAC) libraries, cDNA microarrays (Naurin et al 2008;Replogle et al 2008), and the forthcoming complete genome sequence (Clayton et al 2005), the zebra finch is now also a model system for genomics (Clayton 2004). Indeed, the first large-scale comparisons of orthologous genes in birds have been made possible through analysis of the chicken and zebra finch genomes (Ellegren 2007;Mank et al 2007;Axelsson et al 2008). The zebra finch genome will provide valuable insights into whether patterns observed in the chicken can be generalized across all birds or whether there are important differences among avian lineages, such as those that learn songs and those that do not.…”

Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent inFicedulaFlycatcher Genome Sequences

“…We simulated constant N e = 100,000 (Nadachowska-Brzyska et al 2016), and mutation rate (m) = 5 3 10 29 per base pair per generation (Ellegren 2007;Smeds et al 2016) on a single 50-Mb chromosome with variable recombination rate along its length. We set recombination rates that were representative of the spectrum of recombination rates in the collared flycatcher genome, ranging from 1 to 20 cM/Mb in 10-Mb blocks along the length of the simulated chromosome.…”

Is Continued Genetic Improvement of Livestock Sustainable?

“…Polymorphism at the nucleotide level in poultry is 4-5 3 10 23 and does not stand out as particularly high or low among species of birds, although it is much higher than in humans (Ellegren 2007). Modern commercial poultry stocks have lost about half the molecular variation of their native Jungle Fowl source, but most of this loss occurred before the current populations, including fanciers' strains, were bred (Muir et al 2008).…”