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The evolution of avian feathers has recently been illuminated by fossils and the identification of genes involved in feather patterning and morphogenesis. However, molecular studies have focused mainly on protein-coding genes. Using comparative genomics and more than 600,000 conserved regulatory elements, we show that patterns of genome evolution in the vicinity of feather genes are consistent with a major role for regulatory innovation in the evolution of feathers. Rates of innovation at feather regulatory elements exhibit an extended period of innovation with peaks in the ancestors of amniotes and archosaurs. We estimate that 86% of such regulatory elements and 100% of the nonkeratin feather gene set were present prior to the origin of Dinosauria. On the branch leading to modern birds, we detect a strong signal of regulatory innovation near insulin-like growth factor binding protein (IGFBP) 2 and IGFBP5, which have roles in body size reduction, and may represent a genomic signature for the miniaturization of dinosaurian body size preceding the origin of flight.

We used mitochondrial DNA (mtDNA) gene sequences and nuclear microsatellite loci to investigate the extent and outcome of hybridization between the Black‐billed Gull Chroicocephalus bulleri and the Red‐billed Gull Chroicocephalus novaehollandiae scopulinus in New Zealand. Six of 26 sampled Black‐billed Gulls possessed mtDNA typical of Red‐billed Gulls, but allele frequencies at six polymorphic microsatellites provided little evidence of mixed ancestry expected in very recent hybrids. None of the Red‐billed Gulls sampled from different colonies possessed Black‐billed Gull mtDNA expected in the reciprocal cross, suggesting that hybridization in the two species typically occurs between female Red‐billed Gulls and Black‐billed Gull males. The lack of any hybrid signal in the nuclear loci indicates that there has been extensive backcrossing with Black‐billed Gulls, effectively diluting the Red‐billed Gull nuclear DNA contribution. Divergence of Red‐billed Gulls and Black‐billed Gulls occurred approximately 250 000 years ago, indicating that unsorted ancestral polymorphism is an unlikely alternative to hybridization. Comparing demographic models within an approximate Bayesian computation (ABC) framework, we confirm that the observed patterns cannot result from incomplete lineage sorting. Using an ABC random forest approach, we determined that the most likely model explaining the data is a recent introgression scenario, whereby unidirectional gene flow is re‐established following a period of strict isolation. The ability of Black‐billed and Red‐billed Gulls to successfully interbreed shows that despite significant differentiation (FST > 0.3), there has been insufficient time for the two species to develop complete reproductive isolation. The apparent one‐way transfer of Red‐billed Gull mtDNA into Black‐billed Gulls and extensive backcrossing argues against cytoplasmic–nuclear genome incompatibilities between the two species. We hypothesize that the specific mate recognition system cued on colours of soft parts normally functions to prevent hybridization, but that it can break down under demographic conditions where there is a shortage of available mates and a surplus of females in the Red‐billed Gull population. The high incidence of introgression in Black‐billed Gulls conflicts with field observations that interbreeding is extremely rare. [ABSTRACT FROM AUTHOR]

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The relative importance of gene flow, genetic drift, and natural selection in driving genetic divergence of local populations, as well as the factors that disrupt gene flow in natural populations, are uncertain. Comparative analyses enable us to test explicit hypotheses regarding the roles of these factors. Gannets (Morus spp.) include three morphologically and ecologically similar seabird species: the Cape Gannet M. capensis, which breeds in southern Africa; the Australasian Gannet M. serrator, which breeds in southeastern Australia and New Zealand; and the Northern Gannet M. bassanus, which breeds in the North Atlantic. We assessed the extent of differentiation in mitochondrial control region sequences and morphometrics among colonies of each species to test mechanisms of divergence. No evidence was found for introgression of mitochondrial DNA between Cape and Australasian gannets, despite the existence of mixed-species pairs, consistent with their taxonomic status as biological species. Significant population differentiation, both in control region sequences and in morphology, was found within both Australasian and Northern gannets. Analyses based on coalescent theory indicated that little to no female-mediated gene flow occurs either between Australasian Gannets in Australia versus New Zealand, or between Northern Gannets in Canada versus Europe. Divergence of these regional populations, as well as Cape versus Australasian gannets, appears to pre-date the Pleistocene glaciations and corresponds to differences in non-breeding distributions. Northern and Australasian gannets may each represent at least two management units for conservation, but additional data are needed on nuclear DNA variation in individuals sampled from more colonies to confirm this result. [ABSTRACT FROM AUTHOR]

Identifying genomic signatures of natural selection can be challenging against a background of demographic changes such as bottlenecks and population expansions. Here, we disentangle the effects of demography from selection in the House Finch ( Haemorhous mexicanus) using samples collected before and after a pathogen-induced selection event. Using dd RADseq, we genotyped over 18,000 SNPs across the genome in native pre-epizootic western US birds, introduced birds from Hawaii and the eastern United States, post-epizootic eastern birds, and western birds sampled across a similar time span. We found 14% and 7% reductions in nucleotide diversity, respectively, in Hawaiian and pre-epizootic eastern birds relative to pre-epizootic western birds, as well as elevated levels of linkage disequilibrium and other signatures of founder events. Despite finding numerous significant frequency shifts (outlier loci) between pre-epizootic native and introduced populations, we found no signal of reduced genetic diversity, elevated linkage disequilibrium, or outlier loci as a result of the epizootic. Simulations demonstrate that the proportion of outliers associated with founder events could be explained by genetic drift. This rare view of genetic evolution across time in an invasive species provides direct evidence that demographic shifts like founder events have genetic consequences more widespread across the genome than natural selection. [ABSTRACT FROM AUTHOR]