Unknown Biases: Understanding How Anthropogenic Hybridization Impacts Genomic Diversity and Demographic Estimates

Understanding the genomic consequences of increasing anthropogenic hybridization between wild species and their domesticated forms requires careful consideration. The mallard (Anas platyrhynchos) and its sister species provide a unique system, as the worldwide release of domesticated game-farm mallards has resulted in widespread anthropogenic hybridization with wild mallards or endemic mallard-like congeners. While game-farm mallards continue to be released in mainland North America, they also gave rise to feral populations in Hawaii and New Zealand that interbred with endemic Hawaiian ducks (Anas wyvilliana) and New Zealand grey ducks (Anas superciliosa superciliosa), respectively. Here, we re-sequenced whole genomes representing domestic and wild congeners, as well as the resulting hybrids spanning a range of admixture levels. Wild genomes consistently harbored higher levels of genetic diversity and lower runs of homozygosity than domestic lineages. Among ecoregions, we recovered the strongest statistical correlation between ancestry and summary statistics for North America, where stocking continues. Conversely, in New Zealand and Hawaii, where stocking efforts largely ceased or are limited, we find an uncoupling of summary statistics, likely as a result of genetic drift and/or adaptive introgression. Finally, demographic inferences from domesticated or hybrid genomes produced biased estimates of effective population size (NE) and divergence times, suggesting careful consideration when attempting to infer such histories with inbred and/or admixed individuals.