UC Riverside

When divergent populations come into contact and interbreed, incompatible genotypes can result in decreased hybrid fitness and partial reproductive isolation. By studying patterns of gene flow between populations, we can identify the genetic, phenotypic, and ecological components of partial reproductive isolation. Using whole-genome sequence data generated from 1201 yellow-rumped warblers (Setophaga coronata coronata, S. c. auduboni, and their hybrids), we measure variation of a hybrid zone’s position in space and over time, identify genomic regions where gene flow is restricted, and compare the genetic basis of reproductive barriers to the genetic basis of plumage traits. We find that reproductive isolation is generated by the effects of many loci throughout the genome, with a large influence of the sex-chromosomes, that “barrier loci” cluster in some highly differentiated regions, and that gene flow and introgression are broadly asymmetric. Barrier loci show strong linkage disequilibrium, which augments the strength of the barrier to gene flow and may indicate the presence of genetic incompatibilities. Clines in plumage traits and their associated SNPs suggest strong selection against some hybrid phenotypes, although loci with the strongest associations with plumage color traits do not exhibit the strongest barrier to gene flow.