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

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.

Usage notes

Catharus_ustulatus_draft_assembly_annotation_Feb13_2015.tar Folder containing draft genome assembly and annotation. Assembly generated using a reference-based approach and three paired-end 100bp Illumina libraries (one fragment, two mate pair). Annotation generated using the MAKER pipeline.

SNP table SNP table generated using snp-frequency-diff.pl in Popoolation2. Includes statistics on the major and minor alleles for all SNPs in coastal (_1) and inland (_2) populations of Swainson's thrushes. snp_table_coastal_inland.txt