Z-chromosome outliers as diagnostic markers to discriminate Mallard and Chinese Spot-billed Duck (Anatidae)

Closely related bird species often exhibit elevated differentiation in the Z-chromosome. Genetic differentiation is repeatedly found in so-called 'islands of differentiation' that might contain loci under selection that contribute to reproductive isolation. Using double-digest restriction-associated DNA sequencing (ddRAD-seq), we examined genomic divergence of Mallard (Anas platyrhynchos) and Chinese Spot-billed Duck (A. zonorhyncha), two closely related species of ducks that occasionally hybridize. The taxa were distinguishable based on overall ddRAD-seq allele frequency differences. However, differentiation on the Z-chromosome was about 4.5 times greater than observed for autosomal DNA and included three fixed differences in SNPs. These SNPs are the first species-specific molecular markers revealed among mallard group species. The causes of elevated Z-chromosome divergence are discussed, including the possibility that Z-linked loci are resistant to introgression and potentially linked to phenotypic differences between the species.