Molecular evolution of genes in avian genomes

Background

Obtaining a draft genome sequence of the zebra finch (Taeniopygia guttata), the second bird genome to be sequenced, provides the necessary resource for whole-genome comparative analysis of gene sequence evolution in a non-mammalian vertebrate lineage. To analyze basic molecular evolutionary processes during avian evolution, and to contrast these with the situation in mammals, we aligned the protein-coding sequences of 8,384 1:1 orthologs of chicken, zebra finch, a lizard and three mammalian species.

Results

We found clear differences in the substitution rate at fourfold degenerate sites, being lowest in the ancestral bird lineage, intermediate in the chicken lineage and highest in the zebra finch lineage, possibly reflecting differences in generation time. We identified positively selected and/or rapidly evolving genes in avian lineages and found an over-representation of several functional classes, including anion transporter activity, calcium ion binding, cell adhesion and microtubule cytoskeleton.

Conclusions

Focusing specifically on genes of neurological interest and genes differentially expressed in the unique vocal control nuclei of the songbird brain, we find a number of positively selected genes, including synaptic receptors. We found no evidence that selection for beneficial alleles is more efficient in regions of high recombination; in fact, there was a weak yet significant negative correlation between ω and recombination rate, which is in the direction predicted by the Hill-Robertson effect if slightly deleterious mutations contribute to protein evolution. These findings set the stage for studies of functional genetics of avian genes.     

High fidelity does not preclude colonization: range expansion of molting Black Brant on the Arctic coast of Alaska

High rates of site fidelity have been assumed to infer static distributions of molting geese in some cases. To test this assumption, we examined movements of individually marked birds to understand the underlying mechanisms of range expansion of molting Black Brant (Branta bernicla nigricans) on the Arctic Coastal Plain (ACP) of Alaska. The Teshekpuk Lake Special Area (TLSA) on the ACP was created to protect the primary molting area of Brant. When established in 1977, the TLSA was thought to include most, if not all, wetlands used by molting Brant on the ACP. From 2010 to 2013, we surveyed areas outside the TLSA and counted an average of 9800 Brant per year, representing 29–37% of all molting Brant counted on the ACP. We captured and banded molting Brant in 2011 and 2012 both within the TLSA and outside the TLSA at the Piasuk River Delta and Cape Simpson to assess movements of birds among areas across years. Estimates of movement rates out of the TLSA exceeded those into the TLSA, demonstrating overall directional dispersal. We found differences in sex and age ratios and proportions of adult females with brood patches, but no differences in mass dynamics for birds captured within and outside the TLSA. Overall fidelity rates to specific lakes (0.81, range = 0.49–0.92) were unchanged from comparable estimates obtained in the early 1990s. We conclude that Brant are dispersing from the TLSA into new molting areas while simultaneously redistributing within the TLSA, likely as a consequence of changes in relative habitat quality. Shifts in distribution resulted from colonization of new areas by young birds as well as low levels of directional dispersal of birds that previously molted in the TLSA. Based on combined counts, the overall number of molting Brant across the ACP has increased substantially.