Long-term reciprocal gene flow in wild and domestic geese reveals complex domestication history

Heikkinen, Marja E.; Ruokonen, Minna; White, Thomas A.; Alexander, Michelle M.; Gündüz, İslam; Dobney, Keith M.; Aspi, Jouni; Searle, Jeremy B.; Pyhäjärvi, Tanja

Hybridisation can substantially impact genetic diversity of domesticates, but this situation has not been widely studied. We analysed the impact of hybridisation on the genome-wide genetic variation in current populations of the European domestic goose and its wild progenitor: the greylag goose (Anser anser). Our dataset consisted of 58 wild greylag and 75 domestic geese genotyped for 33,527 single nucleotide polymorphisms (SNPs) identified by genotyping-by-sequencing (GBS). Demographic reconstruction and clustering analysis suggested that divergence between wild and domestic geese around 5,300 generations ago was followed by long-term genetic exchange, and that greylag populations have 3.2–58.0% admixture proportions with domestic geese, that also varies geographically. Many modern European breeds share considerable (> 10%) ancestry with Chinese domestic geese (derived from the swan goose A. cygnoid). This study shows a domestication process progressing despite continued and pervasive gene flow from the wild form.