Abstract
Eurasian wigeon (Mareca penelope) and American wigeon (Mareca americana) are sister species with diagnosable differences mostly in male plumage. They breed in the Palearctic and Nearctic, respectively, but due to transoceanic migrations come in contact in North America, Western Europe, and north-eastern Asia, where they occasionally hybridize. To estimate genomic divergence and study their population structure we sequenced mitochondrial (mt) DNA control region and obtained 3092 autosomal and 189 Z chromosome loci from double-digest restriction associated DNA sequencing (ddRAD-seq). Consistent with previous work with few nuclear loci, we observed discordant patterns between mtDNA and nuclear DNA divergence. Deeply divergent species-specific mtDNA haplogroups contrasted with low autosomal differentiation and moderate Z-sex chromosome divergence. Meanwhile, Z-linked differentiation (ФST = 0.192) between taxa was five times higher than differentiation of autosomal loci (ФST = 0.0386), with four fixed and eight nearly fixed differences in SNPs discovered in three and six Z-linked outlier loci, respectively. No species-specific SNP variants were found among 83 autosomal outlier loci. This elevated Z-chromosome differentiation is most likely the result of selection that has been important in speciation. The lack of population genetic structure within Eurasian wigeon and American wigeon supports the common notion that migratory waterfowl have high dispersal ability that contributes to strong genetic connectivity between geographic populations.