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 non-parasitic 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.

基于生态的分化选择（ecologically based divergent selection）是即便存在基因流（gene flow），也可推动生殖隔离（reproductive isolation）形成的关键因素之一。沿分化连续谱系分布的种群对，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，对两种具有截然不同生活史的近缘七鳃鳗（lamprey）物种间生殖隔离的演化机制展开探究。我们利用微卫星标记（microsatellite marker）对法国境内10个同域（sympatric）与邻域（parapatric）种群对中的1000余尾个体进行基因分型，这些个体分属洄游寄生型河七鳃鳗（*Lampetra fluviatilis*）与淡水定居非寄生型溪七鳃鳗（*L. planeri*）。交配试验、亲权鉴定分析与人工授精实验结果显示，尽管体型选型交配（assortative mating）可能对生殖隔离存在一定贡献，但两类物种间的生殖隔离程度整体偏低。多数邻域种群对因地理距离与洄游障碍的共同作用，呈现出高度的遗传分化。与之相反，我们发现同域种群间的基因流水平存在显著差异，范围从泛交（panmixia）到中等程度的遗传分化，这表明存在分化梯度：部分种群对可能对应单一物种的不同形态或生态型（ecotype），而其余种群对则处于部分生殖隔离状态。基于生态的分化选择可解释同域种群对间分化水平的差异，但二次接触（secondary contact）后未完全发生的基因组淹没（genome swamping）或许也起到了一定作用。总体而言，本研究阐明了：即便存在限制物种形成（speciation）进程的高强度基因流，高度分化的表型（phenotype）仍可得以维持。