ddRAD sequences of mallards and black ducks from North Carolina

We assessed the genetic integrity, hybridization rates, and population structure of a breeding population of American black ducks in North Carolina. Data includes ddRAD sequences of genomic DNA extracted from chorioallantoic membranes and contour feathers. Through various analyses, we recover strong population structure and high coancestry across genetic markers due to interrelatedness among sampled nests in North Carolina, and conclude that black ducks have been locally breeding in this area for some time. Despite a high level of interrelatedness among our samples, nucleotide diversity was similar to the reference continental black duck population, suggesting little effect of genetic drift, including inbreeding on this relatively small North Carolina population. Additionally, we conclude that molecular diversity of pure black ducks in North Carolina is likely maintained at reference population levels largely through the influx of genetic material from unrelated, migrating male black ducks. Finally, we conclude that due to high rates of interspecific hybridization and successive backcrossing events, introgression from wild and feral mallards is occurring into this population of breeding black ducks that requires careful consideration in future management efforts.