Willet be one species or two?: A genomic view of the evolutionary history of Tringa semipalmata

The Willet (Tringa semipalmata; Scolopacidae) is composed of two morphologically and vocally distinct subspecies with broadly disjunct breeding distributions in North America. Nominate T. s. semipalmata breeds in coastal salt and brackish marshes along the Atlantic and Gulf coasts of eastern North America and the West Indies, and T. s. inornata breeds in wet grasslands and prairies in the northwestern interior of North America. To assess divergence and test for hybridization between the two subspecies, we sampled breeding and wintering populations and collected morphological data, mitochondrial DNA sequences from the ND2 locus, and nuclear DNA sequences from genomic libraries enriched for ultraconserved elements (UCEs). Mitochondrial haplotypes were reciprocally monophyletic between the two subspecies and divergence dating indicated a divergence time of roughly 730,000 years ago. The UCE dataset included 4,635 UCE loci containing 19,322 (single nucleotide polymorphisms; SNPs); based on these data individuals clustered by subspecies with no evidence of admixture, and no sub-structure within subspecies. Despite the apparent recent divergence based on mitochondrial data, we identified 42 nuclear loci that contained SNPs fixed for alternate alleles between the two subspecies, many more than expected by chance. Seventeen of the 42 loci with fixed differences were on the Z chromosome, which is a sex chromosome in birds. This suggests a role for sexual selection in the divergence of the two subspecies. Genetic, morphological, ecological, and behavioral differences suggest the two Willet subspecies merit treatment as separate species. Our study demonstrates that a genome-wide perspective is important for assessing taxon rank when the impacts of processes responsible for divergence vary across the genome.