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.

在物种形成研究领域，阐明重复生态型对（ecotype pairs）间平行基因组分化格局的形成机制，仍是一项核心科学挑战。本研究选取9个地理连通度存在显著差异的种群对，探究了溯河寄生性七鳃鳗（Lampetra fluviatilis）与淡水定居非寄生性溪七鳃鳗（Lampetra planeri）之间的基因组分化模式。研究团队通过限制性位点相关DNA测序（RAD sequencing）对338个个体进行基因分型，并采用扩散近似法（diffusion approximation method）推断各种群对的种群分化人口学历史。结果显示，地理连通的种群对的分化格局更适合用二次接触后的基因渐渗（introgression）加以解释；而地理隔离的种群对则保留了远古迁移的信号特征。在所有生态型对中，考虑位点间差异化渐渗的进化模型，其拟合表现均优于同质化基因流模型。通过基于推断的分化场景生成中性预测以筛选高度分化的遗传标记，研究发现地理隔离种群对中的异常分化位点占比，高于地理连通的种群对。然而，地理连通的生态型对之间，高度分化的基因组区域的相似性显著提升，这表明基因流（gene flow）在分子水平的平行性形成过程中起到了关键作用。本研究结果表明，重复生态型对间的异质基因组分化与平行性，部分是通过基因组岛（genomic islands）中的受限渐渗演化形成的。