Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation

Abstract

Differential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns of genomic differentiation during the process of speciation. Possible sources of reproductive isolation are well studied between coastal and inland subspecies groups of Swainson's thrushes, with differences in seasonal migratory behaviour likely playing a key role in reducing hybrid fitness. We assembled and annotated a draft reference genome for this species and generated whole-genome shotgun sequence data for populations adjacent to the hybrid zone between these groups. We documented substantial genomewide heterogeneity in relative estimates of genetic differentiation between the groups. Within population diversity was lower in areas of high relative differentiation, supporting a role for selective sweeps in generating this pattern. Absolute genetic differentiation was reduced in these areas, further suggesting that recurrent selective sweeps in the ancestral population and/or between divergent populations following secondary contact likely occurred. Relative genetic differentiation was also higher near centromeres and on the Z chromosome, suggesting that features of the genome also contribute to genomewide heterogeneity. Genes linked to migratory traits were concentrated in islands of differentiation, supporting previous suggestions that seasonal migration is under divergent selection between Swainson's thrushes. Differences in migratory behaviour likely play a central role in the speciation of many taxa; we developed the infrastructure here to permit future investigations into the role several candidate genes play in reducing gene flow between not only Swainson's thrushes but other species as well.

Genomic insights into adaptive divergence and speciation among malaria vectors of theAnopheles niligroup

“…Highly divergent genomic regions do not necessarily coincide with regions of reduced gene flow among established or emerging species. Several alternative interpretations exist for the numerous high-F ST regions we detected in all pairwise comparisons (Cruickshank & Hahn, 2014;Delmore et al, 2015;Nachman & Payseur, 2012;Noor & Bennett, 2009). Nevertheless, careful examination of these outliers of differentiation may reveal significant insights into the wide range of genes and traits that contribute to ecological divergence and/or reproductive isolation between subgroups of An.…”

Avian introgression in the genomic era

“…Genomic analyses of contact zones between other Corvus subspecies (cornix, corone, orientalis and pectoralis) revealed clustering of certain pigmentation genes, albeit in different genomic islands (Vijay et al 2016). Other studies, however, have shown that genes potentially involved in reproductive isolation do not always cluster together, instead they are scattered across the genome (Parchman et al 2013;Ruegg et al 2014; but see Delmore et al 2015). These contrasting findingscandidate 'speciation genes' clustered in genomic islands versus scattered throughout the genome-suggests that the genetic basis of speciation is highly species-specific and context-dependent.…”

“…Cathartus ustulatus (subspecies) GBS Migration, plumage, and song (−) Ruegg et al (2014) WGS Migration (+) Delmore et al (2015) Anas platyrhynchos GBS Lavretsky et al (2015) Anas diazi 4 species of Ficedula WGS Burri et al (2015) Corvus corone WGS Plumage coloration (+) Poelstra et al (2014) (subspecies) WGS Plumage coloration (+) Vijay et al (2016) 16 species of Darwin's finches WGS Bill morphology (+) Lamichhaney et al (2015) Sphyrapicus nuchalis GBS Grossen et al (2016) Sphyrapicus ruber…”

Patterns of genetic, phenotypic, and acoustic variation across a chiffchaff (Phylloscopus collybita abietinus/tristis) hybrid zone

“…By studying the secondary contact hybrid zones closely, we may investigate if there are any barriers to gene flow between the taxa involved and combine that with information about potential forces behind divergence, that is if taxa have diverged because of random acquisition of incompatibility alleles (observed trait differences not related to ecology) or if adaptation has played a major role in the divergence process (potential trait differences clearly associated with ecology) (Toews & Irwin, 2008). In addition, studying secondary contact zones can give information about the designation of lineages with unclear taxonomic status by allowing for quantification of genetic differentiation and potential introgression between involved taxa (Abbott et al., 2016; Delmore et al., 2015; Payseur & Rieseberg, 2016). …”