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