Data from: Mito-nuclear discord in six congeneric lineages of Holarctic ducks (genus Anas)

Many species have Holarctic distributions that extend across Europe, Asia, and North America. Most genetics research on these species has examined only mitochondrial (mt) DNA, which has revealed wide variance in divergence between Old World (OW) and New World (NW) populations, ranging from shallow, unstructured genealogies to deeply divergent lineages. In this study, we sequenced 20 nuclear introns to test for concordant patterns of OW-NW differentiation between mtDNA and nuclear (nu) DNA for six lineages of Holarctic ducks (genus Anas). Genetic differentiation for both marker types varied widely among these lineages (idiosyncratic population histories), but mtDNA and nuDNA divergence within lineages was not significantly correlated. Moreover, compared to the association between mtDNA and nuDNA divergence observed among different species, OW-NW nuDNA differentiation was generally lower than mtDNA divergence, at least for lineages with deeply divergent mtDNA. Furthermore, coalescent estimates indicated significantly higher rates of gene flow for nuDNA than mtDNA for four of the six lineages. Thus, Holarctic ducks show prominent mito-nuclear discord between OW and NW populations, and we reject differences in sorting rates as the sole cause of the within-species discord. Male-mediated intercontinental gene flow is likely a leading contributor to this discord, although selection could also cause elevated mtDNA divergence relative to weak nuDNA differentiation. The population genetics of these ducks contribute to growing evidence that mtDNA can be an unreliable indicator of stage of speciation, and that more holistic approaches are needed for species delimitation.

诸多类群具有全北界（Holarctic）分布格局，分布范围横跨欧洲、亚洲与北美。针对此类类群的多数遗传学研究仅以线粒体（mt）DNA为研究对象，相关结果显示旧世界（OW）与新世界（NW）种群间的分化程度差异显著，涵盖从浅分化无结构的基因谱系到深度分化支系的各类情况。本研究对20个核内含子（nuclear introns）进行测序，旨在检验6个全北界鸭类（鸭属*Anas*）支系的旧世界-新世界分化模式在线粒体DNA与核（nu）DNA之间是否存在一致性。两类分子标记的遗传分化在各支系间均存在广泛差异，对应各支系独特的种群历史，但各支系内线粒体DNA与核DNA的分化程度并无显著相关性。此外，相较于不同物种间观察到的线粒体DNA与核DNA分化关联模式，旧世界-新世界的核DNA分化程度整体低于线粒体DNA分化，对于线粒体DNA深度分化的支系而言尤为明显。进一步的溯祖估计（coalescent estimates）结果显示，6个支系中有4个支系的核DNA基因流（gene flow）速率显著高于线粒体DNA。综上，全北界鸭类的旧世界与新世界种群间存在显著的线粒体-核基因座分化不一致现象，我们不支持“分化分选速率差异是种内分化不一致的唯一原因”这一假说。雄性介导的跨大陆基因流可能是导致该不一致现象的主要因素，不过选择作用也可能造成线粒体DNA分化程度高于核DNA分化的情况。此类鸭类的种群遗传学研究结果进一步佐证了日益增多的证据：线粒体DNA或许无法可靠反映物种形成（speciation）进程，物种界定（species delimitation）亟需更为全面的研究方法。