ddRAD-seq data of two Goldeneye species

Delineation of population structure provides valuable information for conservation and management of species. Here, we measure population genetic structure and connectivity across the respective ranges of two sister species of Goldeneye, Barrows and Common Goldeneye. Sampling 3,678 ddRAD-seq loci across 61 samples, we recover strong population structure between these two sister species. Next, although inter-specific brood parasitism was expected to cause some level of gene flow, we only identified a single F1 hybrid with no further evidence of contemporary or historical gene flow. Despite ddRAD-seq demographic analyses which recovered an optimum evolutionary model of split with migration (i.e., secondary contact), estimates of gene flow were <<1 migrant per generation in both directions. Together, we conclude that either strong ecological barriers or assortative mating are likely playing a role in preventing further backcrossing. Finally, demographic analyses estimated a relatively deep divergence time between Barrows Goldeneye and Common Goldeneye of ~1.6 million years before present and that the genomes of both species have been under similar evolutionary constraints.