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格局的形成机制，仍是物种形成研究领域的核心科学难题之一。本研究以9个地理连通性水平存在差异的种群对为研究对象，分析了溯河洄游寄生型七鳃鳗（Lampetra fluviatilis）与淡水定居非寄生型溪七鳃鳗（Lampetra planeri）之间的基因组分化模式。研究团队通过限制性位点关联DNA测序（RAD-sequencing）对338个个体进行基因分型，并采用扩散近似法推断了每个种群对的分化种群历史动态。地理连通种群对的分化格局更符合二次接触后的基因渐渗模型，而地理隔离种群对则保留了远古基因迁移的信号特征。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基因流模型。通过推断的分化情景生成中性预测以筛选高度分化的遗传标记，结果显示地理隔离种群对的异常分化位点占比高于地理连通种群对。但地理连通的生态型对间，分化程度最高的基因组区域相似度显著更高，这表明基因流在推动分子层面平行演化的过程中发挥了关键作用。本研究结果表明，重复生态型对间的异质性基因组分化与平行演化格局，部分源于基因组岛（genomic islands）内受限的基因渐渗过程。