Raw ddRAD-seq data for Chinese Spotbilled ducks and Mallards

Using double-digest restriction-associated DNA sequencing (ddRAD-seq) we examined genomic divergence of two closely related ducks, the Mallard (Anas platyrhynchos) and Chinese Spot-billed Duck (A. zonorhyncha). While these taxa were distinguishable based on small allele frequency differences across autoromal ddRAD-seq loci, the Z-chromosome was elevated in divergence, included three fixed differences. These SNPs are the first species-specific molecular markers revealed among mallard-group species.