Data from: Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes

Understanding the evolutionary mechanisms generating parallel genomic divergence patterns among replicate ecotype pairs remains an important challenge in speciation research. We investigated the genomic divergence between the anadromous parasitic river lamprey (Lampetra fluviatilis) and the freshwater-resident nonparasitic brook lamprey (Lampetra planeri) in nine population pairs displaying variable levels of geographic connectivity. We genotyped 338 individuals with RAD sequencing and inferred the demographic divergence history of each population pair using a diffusion approximation method. Divergence patterns in geographically connected population pairs were better explained by introgression after secondary contact, whereas disconnected population pairs have retained a signal of ancient migration. In all ecotype pairs, models accounting for differential introgression among loci outperformed homogeneous migration models. Generating neutral predictions from the inferred divergence scenarios to detect highly differentiated markers identified greater proportions of outliers in disconnected population pairs than in connected pairs. However, increased similarity in the most divergent genomic regions was found among connected ecotype pairs, indicating that gene flow was instrumental in generating parallelism at the molecular level. These results suggest that heterogeneous genomic differentiation and parallelism among replicate ecotype pairs have partly emerged through restricted introgression in genomic islands.

解析重复生态型配对间平行基因组分化模式的演化机制，仍是物种形成研究领域的重要科学难题。本研究针对9个地理连通性水平存在差异的种群对，探究了溯河寄生型七鳃鳗（Lampetra fluviatilis）与淡水定居非寄生型溪七鳃鳗（Lampetra planeri）之间的基因组分化特征。我们通过限制性位点关联DNA（RAD）测序对338个个体开展基因分型，并采用扩散近似法推断了每个种群对的种群分化历史。地理连通种群对的分化模式更符合二次接触后发生基因渐渗的假说，而地理隔离种群对则保留了古代基因交流的信号。在所有生态型配对中，考虑位点间差异化基因渐渗的模型，其拟合表现均优于均一化基因流模型。基于推断的分化场景生成中性演化预测以筛选高分化标记时，地理隔离种群对中的异常位点占比高于地理连通种群对。不过，地理连通的生态型配对间，高度分化的基因组区域的相似性反而更高，这表明基因流在分子层面的平行演化过程中起到了关键推动作用。本研究结果表明，重复生态型配对间的异质性基因组分化与平行演化模式，部分是通过基因组岛内的受限基因渐渗形成的。