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We test between possible outcomes of human\u2010mediated secondary contact using genomic techniques at both historical and contemporary timescales for two iconic duck species. First, we sequence several thousand ddRAD\u2010seq loci for contemporary mallards (<jats:italic>Anas platyrhynchos<\/jats:italic>) throughout North America and two domestic mallard types (i.e., known game\u2010farm mallards and feral Khaki Campbell's). We show that North American mallards may well be becoming a hybrid swarm due to interbreeding with domesticated game\u2010farm mallards released for hunting. Next, to attain a historical perspective, we applied a bait\u2010capture array targeting thousands of loci in century\u2010old (1842\u20131915) and contemporary (2009\u20132010) mallard and American black duck (<jats:italic>Anas rubripes<\/jats:italic>) specimens. We conclude that American black ducks and mallards have always been closely related, with a divergence time of ~600,000\u00a0years before present, and likely evolved through prolonged isolation followed by limited bouts of gene flow (i.e., secondary contact). They continue to maintain genetic separation, a finding that overturns decades of prior research and speculation suggesting the genetic extinction of the American black duck due to contemporary interbreeding with mallards. Thus, despite having high rates of hybridization, actual gene flow is limited between mallards and American black ducks. Conversely, our historical and contemporary data confirm that the intensive stocking of game\u2010farm mallards during the last ~100\u00a0years has fundamentally changed the genetic integrity of North America's wild mallard population, especially in the east. It thus becomes of great interest to ask whether the iconic North American mallard is declining in the wild due to introgression of maladaptive traits from domesticated forms. Moreover, we hypothesize that differential gene flow from domestic game\u2010farm mallards into the wild mallard population may explain the overall temporal increase in differentiation between wild black ducks and mallards, as well as the uncoupling of genetic diversity and effective population size estimates across time in our results. Finally, our findings highlight how genomic methods can recover complex population histories by capturing DNA preserved in traditional museum specimens.<\/jats:p>","DOI":"10.1111\/mec.15343","type":"journal-article","created":{"date-parts":[[2019,12,24]],"date-time":"2019-12-24T03:46:12Z","timestamp":1577159172000},"page":"578-595","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":64,"title":["Assessing changes in genomic divergence following a century of human\u2010mediated secondary contact among wild and captive\u2010bred ducks"],"prefix":"10.1111","volume":"29","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5904-8821","authenticated-orcid":false,"given":"Philip","family":"Lavretsky","sequence":"first","affiliation":[{"name":"Department of Biological Sciences The University of Texas at El Paso El Paso TX USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nancy Rotzel","family":"McInerney","sequence":"additional","affiliation":[{"name":"Center for Conservation Genomics Smithsonian Conservation Biology Institute Smithsonian Institution Washington DC USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathon E.","family":"Mohl","sequence":"additional","affiliation":[{"name":"Border Biomedical Research Center The University of Texas at El Paso El Paso TX USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua I.","family":"Brown","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences The University of Texas at El Paso El Paso TX USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2495-6133","authenticated-orcid":false,"given":"Helen F.","family":"James","sequence":"additional","affiliation":[{"name":"Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington DC USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin G.","family":"McCracken","sequence":"additional","affiliation":[{"name":"Department of Biology University of Miami Coral Gables FL USA"},{"name":"Department of Marine Biology and Ecology Rosenstiel School of Marine and Atmospheric Sciences University of Miami Miami FL USA"},{"name":"Human Genetics and Genomics Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA"},{"name":"Institute of Arctic Biology University of Alaska Museum University of Alaska Fairbanks Fairbanks AK USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert C.","family":"Fleischer","sequence":"additional","affiliation":[{"name":"Center for Conservation Genomics Smithsonian Conservation Biology Institute Smithsonian Institution Washington DC USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2020,1,8]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.13685"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-12-246"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.094052.109"},{"key":"e_1_2_9_5_1","volume-title":"Admixture 1.22 software manual","author":"Alexander D. 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