Data from: Historical introgression and the role of selective vs. neutral processes in structuring nuclear genetic variation (AFLP) in a circumpolar marine fish, the capelin (Mallotus villosus)

The capelin (Mallotus villosus) is a widespread marine fish species for which previous work has identified geographically distinct mtDNA clades, the frontiers of which are well within adult and larval dispersal capabilities. Here, we use AFLPs to test for the presence of nuclear gene flow among clades. In addition, we evaluate genetic structuring within one clade, the Northwest Atlantic (NWA). We found that each of the mtDNA clades corresponds with a unique nuclear DNA genetic cluster. Within the NWA clade, we detected individuals with small but significant amounts of genetic ancestry from other clades, likely due to historical introgression. Further support for historical introgression comes from analyses of variance in locus-specific differentiation, which support introgression between some clades and divergence without gene flow between others. Within the NWA, we identified two genetic clusters that correspond to sites in geographically adjacent areas. However, these clusters differ primarily at ‘outlier’ loci, and a genetic subdivision (K = 2) was not supported by genetic clustering programs using neutral loci. Significant neutral FST differentiation was found only between sites that otherwise differed at outlier loci. Thus, these populations may be in the initial stages of ‘isolation by adaptation’. These results suggest strong between-clade reproductive isolation despite opportunities for gene flow and support the hypothesis that selection can contribute to divergence in otherwise ‘open’ systems.

毛鳞鱼（capelin，Mallotus villosus）是一种广布性海洋鱼类，既往研究已识别出其具有地理分化的线粒体DNA（mtDNA）支系，且这些支系的分布边界均处于成体与幼体的扩散能力范围内。本研究采用扩增片段长度多态性（AFLPs, Amplified Fragment Length Polymorphism）标记，检验不同mtDNA支系间是否存在核基因流。此外，我们还对其中一个支系——西北大西洋（Northwest Atlantic, NWA）支系——内部的遗传结构进行了评估。研究发现，每个mtDNA支系均对应一个独特的核DNA遗传簇。在NWA支系内部，我们检测到部分个体携带来自其他支系的少量但显著的遗传祖源成分，这一现象大概率由历史遗传渐渗所致。进一步支持历史渐渗的证据来自位点特异性分化方差分析，该分析结果证实部分支系间存在遗传渐渗，而其余支系间仅发生分化而无基因流。在NWA支系内部，我们识别出两个遗传簇，其对应地理上相邻的采样位点。然而，这两个簇的遗传差异主要集中在离群位点（outlier loci），而基于中性位点的遗传聚类软件并不支持K=2的遗传分化划分。仅在那些本身在离群位点存在遗传分化的采样位点之间，才检测到显著的中性FST遗传分化。因此，这些种群可能正处于‘适应依赖型隔离’（isolation by adaptation）的初始阶段。本研究结果表明，尽管存在发生基因流的潜在条件，但各支系间仍存在强烈的生殖隔离，同时支持了“选择作用可在本应‘开放’的系统中推动种群分化”这一假说。