Delineation of population structure provides valuable information for conservation and management of species, as levels of demographic and genetic connectivity not only affect population dynamics but also have important implications for adaptability and resiliency of populations and species. Here, we measure population genetic structure and connectivity across the respective ranges of two sister species of Goldeneye, Barrow’s Goldeneye (Bucephala islandica) and Common Goldeneye (B. clangula). We use two different marker types: 7 nuclear microsatellite loci assayed across 229 samples and 3,678 double digest Restriction-site Associated DNA Sequencing (ddRAD-seq) loci assayed across 61 samples. First, both datasets failed to uncover genetic structure within Common or Barrow’s Goldeneye, including between North American and European samples of Common Goldeneye. These results are in contrast with previous mitochondrial DNA, band recovery, and telemetry data which suggests that goldeneyes are structured across their range. We posit that the discordance between autosomal genetic markers and other data types suggests that males, possibly subadult males, may be maintaining genetic connectivity across each species’ respective ranges. 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 Barrow’s Goldeneye and Common Goldeneye of ~1.6 million years before present and that the genomes of both species have been under similar evolutionary constraints.

FASTA, ADMIXTURE/SIMULATIONS, PCA, fineRADstructure, and ∂a∂i INPUT FILES