Swainson's thrush hybrid zone WGS

Hybrid zones create natural tests of genetic incompatibilities by combining loci from two species in the same genetic background in the wild, making them useful for identifying both intrinsic and ecological (extrinsic) incompatibilities. Two Swainson's thrush subspecies form a hybrid zone in western North America. These coastal and inland subspecies exhibit dramatic differences in migration routes; their hybrids exhibit poor migratory survival, suggesting that ecological incompatibilities maintain this zone. We used a panel of ancestry informative markers to identify repeated patterns of selection and introgression across four hybrid populations that span the entire length of the Swainson's thrush hybrid zone. Two repeatable patterns consistent with selection against incompatibilities - steep genomic clines and few transitions between ancestry states - were found in large genetic blocks on chromosomes 1 and 5. The block on chromosome 1 showed evidence for inland subspecies introgression while the block on chromosome 5 exhibited coastal subspecies introgression. Some regions previously associated with migratory phenotypes, including migratory orientation, or exhibiting misexpression between the subspecies were under selection in the hybrid zone. Selection and introgression across the genome were shaped by genomic structural features and evolutionary history, with stronger selection and reduced introgression in regions of low recombination, high subspecies differentiation, positive selection within the subspecies, and on macrochromosomes. Cumulatively, these results suggest that linkage among loci interacts with divergent selection and evolution between species to strength barriers to gene flow within hybrid zones.