Along with manipulating habitat, the direct release of domesticated individuals into the wild is a practice used worldwide to augment wildlife populations. We test between possible outcomes of human-mediated secondary contact using genomic techniques at both historical and contemporary timescales for two iconic duck species. First, we sequence several thousand ddRAD-seq loci for contemporary mallards (Anas platyrhynchos) throughout North America and two domestic mallard types (i.e., known game-farm 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-farm mallards released for hunting. Next, to attain a historical perspective, we applied a bait-capture array targeting thousands of loci in century-old (1842-1915) and contemporary (2009-2010) mallard and American black duck (Anas rubripes) specimens. We conclude that American black ducks and mallards have always been closely related, with a divergence time of ~600,000 years 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-farm mallards during the last ~100 years 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-farm 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.

中文翻译：

---

经过一个世纪的人类介导的野鸭和圈养鸭之间的二次接触，评估基因组差异的变化。

除了操纵栖息地外，将驯养的个体直接释放到野外是全世界范围内用来增加野生动植物种群的一种做法。我们使用基因组学技术，在两个标志性鸭子物种的历史和当代时间尺度上，测试了人类介导的二次接触的可能结果。首先，我们对整个北美的当代野鸭（Anas platyrhynchos）和两种国内野鸭类型（即已知的野战野鸭和野性的卡其色的野鸭）排序了数千个ddRAD-seq位点。我们表明，由于与为狩猎而发行的驯养的野外野鸭杂交，北美野鸭很可能成为混合种群。接下来，要获得历史观点，我们应用了一个诱饵捕获阵列，该阵列针对百年历史（1842-1915）和当代（2009-2010）绿头野鸭和美国黑鸭（Anas rubripes）标本中的数千个基因座。我们得出的结论是，美国黑鸭和野鸭之间一直存在着密切的联系，它们之间的分歧时间约为60万年前，并且可能是由于长时间的隔离以及随后有限的基因流动（即二次接触）而演变而来的。他们继续保持遗传分离，这一发现推翻了数十年的先前研究和推测，表明由于当代与野鸭的杂交，美洲黑鸭已灭绝。因此，尽管杂交率很高，但是野鸭和美国黑鸭之间的实际基因流却受到限制。反过来，我们的历史和当代数据证实，在过去约100年中，密集的野鸭野鸭种群已从根本上改变了北美野生野鸭种群的遗传完整性，尤其是在东部。因此，人们非常有兴趣地问一下，由于驯化形式的不良适应性特征的渗入，标志性的北美野鸭是否在野外减少。此外，我们假设从家养农场野鸭到野生野鸭种群的差异基因流可能解释了野生黑鸭和野鸭之间总体分化的暂时性增加，以及整个时期遗传多样性和有效种群规模估计的解耦。我们的结果。最后，