Mosaic genome evolution in a recent and rapid avian radiation

Abstract

Recent genomic analyses of evolutionary radiations suggest that ancestral or standing genetic variation may facilitate rapid diversification, particularly in cases involving convergence in ecological traits. Likewise, lateral transfer of alleles via hybridization may also facilitate adaptive convergence, but little is known about the role of ancestral variation in examples of explosive diversification that primarily involve the evolution of species recognition traits. Here, we show that genomic regions distinguishing sympatric species in an extraordinary radiation of small finches called munias (genus Lonchura) have phylogenetic histories that are discordant with each other, with the overall pattern of autosomal differentiation among species, and with sex-linked and mitochondrial components of the genome. Genome-wide data for 11 species sampled in Australia and Papua New Guinea indicate substantial autosomal introgression between sympatric species, but also identify a limited number of divergent autosomal regions, several of which overlap known colour genes (ASIP, EDN3, IGSF11, KITLG, MC1R and SOX10). Phylogenetic analysis of these outlier regions shows that different munia species have acquired unique combinations of alleles across a relatively small set of phenotypically relevant genes. Our results demonstrate that the recombination of ancestral genetic variation across multiple loci may be an important mechanism for generating phenotypic novelty and diversity.

Evolutionary dynamics of hybridization and introgression following the recent colonization of Glossy Ibis (Aves: Plegadis falcinellus) into the New World

“…Divergence between the species was widely distributed across the genome based on the distribution of fixed SNPs and d XY and F ST values. This contrasts with many recent studies in birds that have found isolated regions of elevated divergence, and often support for the importance of those regions in reproductive isolation (e.g., Poelstra et al, 2014;Küpper et al, 2016;Tuttle et al, 2016;Campagna, Gronau, Silveira, Siepel, & Lovette, 2015;Toews et al, 2016;Oswald et al, 2016;Stryjewski & Sorenson, 2017). Many of those studies, however, involved taxa that likely experienced episodes of contact and introgression during the history of species formation.…”

ddRAD‐seq data reveal significant genome‐wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America

“…Loci with <20% missing genotypes were retained for downstream analyses, and final output files (e.g., fasta, NEXUS, ADMIXTURE) were generated with custom python scripts (Lavretsky et al, ). Input files for fineRADstructure analyses were created using a custom python script from Stryjewski and Sorenson ().…”

“…Arrows highlight two samples consistently identified as admixed across PCA, admixture, and fineRADstructure (see Figure 3) analyses python scripts . Input files for fineRADstructure analyses were created using a custom python script from Stryjewski and Sorenson (2017).…”

Parallel plumage colour evolution and introgressive hybridization in wheatears

“…Increasing evidence from genomewide studies suggests that ancestral and heterospecific genetic variation plays an important role in the evolution of phenotypic diversity (Abbott et al., ; Cui et al., ; Racimo, Sankararaman, Nielsen, & Huerta‐Sánchez, ; Stryjewski & Sorenson, ; The Heliconius Genome Consortium, ). Different phenotypes and different regions within the same genome often show discordant patterns of divergence, suggesting that they followed different evolutionary trajectories, most of which do not follow the species tree.…”

“…Such adaptive introgression may be restricted to single genome regions and single components of phenotypes. However, plumage phenotypes in Munia finches and wing‐colour patterns in Heliconius butterflies, for instance, suggest that repeated, multidirectional introgression of entire toolkits of genomic regions may constitute an important pathway towards the rapid evolution of mosaic phenotypes (Stryjewski & Sorenson, ; Van Belleghem et al., ). Regardless of the proportion of the genome involved, introgression upon hybridization is increasingly proving to be an important contributor to evolutionary novelty (Abbott et al., ; Rheindt & Edwards, ) and may fuel entire adaptive radiations, such as the one of east African cichlid fish (Meier et al., ).…”