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

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.