Data from: Low reproductive isolation and highly variable levels of gene flow reveal limited progress toward speciation between European river and brook lampreys

Ecologically based divergent selection is a factor that could drive reproductive isolation even in the presence of gene flow. Population pairs arrayed along a continuum of divergence provide a good opportunity to address this issue. Here we used a combination of mating trials, experimental crosses and population genetics analyses to investigate the evolution of reproductive isolation between two closely related species of lampreys with distinct life histories. We used microsatellite markers to genotype over 1000 individuals of the migratory parasitic river lamprey (Lampetra fluviatilis) and freshwater-resident nonparasitic brook lamprey (L. planeri) distributed in 10 sympatric and parapatric population pairs in France. Mating trials, parentage analyses and artificial fertilizations demonstrated a low level of reproductive isolation between species even though size assortative mating may contribute to isolation. Most parapatric population pairs were strongly differentiated due to the joint effects of geographic distance and barriers to migration. In contrast, we found variable levels of gene flow between sympatric populations ranging from panmixia to moderate differentiation, which indicates a gradient of divergence with some population pairs that may correspond to alternative morphs or ecotypes of a single species and others that remain partially isolated. Ecologically-based divergent selection may explain these variable levels of divergence among sympatric population pairs but incomplete genome swamping following secondary contact could have also played a role. Overall, this study illustrates how highly differentiated phenotypes can be maintained despite high levels of gene flow that limit the progress toward speciation.基于生态的歧化选择（Ecologically based divergent selection）是即便存在基因流，仍可推动生殖隔离形成的关键因素之一。沿分化梯度排布的种群对为探究该科学问题提供了绝佳研究契机。本研究结合交配试验、杂交实验与种群遗传学分析，对两种具有独特生活史的近缘七鳃鳗物种间的生殖隔离演化过程展开研究。我们使用微卫星标记（microsatellite markers），对分布于法国10个同域及邻域种群对的1000余尾个体进行基因分型，这些个体涵盖洄游寄生型七鳃鳗（Lampetra fluviatilis）与淡水定居型非寄生溪七鳃鳗（L. planeri）。交配试验、亲权分析与人工授精结果显示，尽管体型选型交配（size assortative mating）可能对生殖隔离存在一定贡献，但两物种间的生殖隔离整体水平较低。多数邻域种群对因地理距离与迁移障碍的共同作用，呈现出显著的遗传分化。与之形成鲜明对比的是，我们发现同域种群间的基因流水平存在显著差异，从泛交（panmixia，随机交配）到中等程度分化不等，这表明种群间的分化存在梯度：部分种群对可能对应单一物种的不同形态或生态型，而其余种群则仍存在部分生殖隔离。基于生态的歧化选择或许可以解释同域种群对间的分化差异，但次生接触后未发生完全的基因组淹没（genome swamping）也可能在其中发挥了作用。总体而言，本研究阐明了在高基因流限制物种形成进程的背景下，高度分化的表型仍可得以维持的内在机制。