Data from: Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and non-parasitic 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 non-parasitic 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。本研究针对地理连通性水平各异的9个种群对，探究了洄游寄生型河七鳃鳗（Lampetra fluviatilis）与淡水定居非寄生型溪七鳃鳗（Lampetra planeri）间的基因组分化模式。我们通过RAD测序（RAD-sequencing）对338个个体进行了基因分型，并利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演化场景；而地理隔离种群对则保留了远古迁徙的遗传信号。在所有生态型对中，考虑位点间差异化基因渐渗的模型，其拟合效果均优于均一化迁徙模型。通过从推断的分化场景生成中性预测以筛选高度分化的分子标记，我们发现地理隔离种群对的异常位点占比高于地理连通种群对。但地理连通的生态型对间，高度分化的基因组区域的相似性显著提升，这说明基因流是推动分子水平平行演化的关键因素。本研究结果显示，重复生态型对间的异质基因组分化与平行演化，部分是通过基因组岛（genomic islands）内受限的基因渐渗实现的。