Data from: Behavioral vs. molecular sources of conflict between nuclear and mitochondrial DNA: the role of male-biased dispersal in a Holarctic sea duck

Genetic studies of waterfowl (Anatidae) have observed the full spectrum of mitochondrial (mt) DNA population divergence, from panmixia to deep, reciprocally monophyletic lineages. Yet these studies generally found weak or no nuclear (nu) DNA structure which was often attributed to sex-biased gene flow (i.e., male dispersal and female philopatry), a common behavior within this family. An alternative explanation for this “conflict” is that the smaller effective population size and faster sorting rate of mtDNA relative to nuDNA leads to different signals of population structure. To test these alternatives, we simulated expected nuDNA differentiation based on mtDNA patterns of effective population sizes, gene flow, and divergence times in a Holarctic pair of waterfowl subspecies, the goosander (Mergus merganser merganser) and common merganser (M. m. americanus). We compared simulated results to empirical data from 12 nuDNA introns sampled from the species’ global range. Between Europe and North America, nuDNA ФST was 3.4-fold lower than mtDNA ФST, a result consistent with differences in sorting rates. However, despite geographically structured and monophyletic mtDNA lineages within continents, nuDNA ФST values were generally < 0 and significantly lower than predicted. This between- and within-continent contrast held when comparing mtDNA and nuDNA among published studies of ducks. Thus, male-mediated gene flow is a better explanation than slower sorting rates for limited nuDNA differentiation within continents, which is also supported by non-molecular data. This study illustrates the value of quantitatively testing discrepancies between mtDNA and nuDNA to reject the null hypothesis that conflict simply reflects different sorting rates.

针对水禽（鸭科Anatidae）的遗传学研究已观测到线粒体（mtDNA）种群分化的完整谱系，从随机泛交直至深度互惠单系分支。然而此类研究普遍发现核（nuDNA）群体结构信号微弱甚至缺失，该现象常被归因于该类群普遍存在的性别偏向性基因流——即雄性扩散与雌性恋巢行为。针对这一冲突，另一解释为：相较于核DNA，线粒体DNA拥有更小的有效种群规模与更快的谱系分选速率，由此导致二者呈现出截然不同的种群结构信号。为检验这两种假说，本研究基于全北界分布的一对水禽亚种——普通秋沙鸭指名亚种（Mergus merganser merganser）与普通秋沙鸭美洲亚种（M. m. americanus）的有效种群大小、基因流与分化时间的线粒体DNA模式，模拟了预期的核DNA分化水平。研究将模拟结果与基于该物种全球分布范围采样的12个核DNA内含子的实证数据进行了比对。在欧洲与北美之间，核DNA ФST值较线粒体DNA ФST低3.4倍，该结果与谱系分选速率差异的预期相符。然而，尽管各大陆内部存在地理结构化且单系的线粒体DNA分支，核DNA ФST值普遍小于0，且显著低于预测值。这种大陆间与大陆内的差异模式，在已发表的鸭类线粒体DNA与核DNA相关研究中同样存在。因此，相较于较慢的谱系分选速率，雄性介导的基因流更能解释大陆内部有限的核DNA分化现象，该结论也得到了非分子数据的支持。本研究阐明了定量检验线粒体DNA与核DNA之间差异的重要价值，以此驳斥“二者的冲突仅反映不同谱系分选速率”的零假设。