Data from: Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact

Ecophenotypic differentiation among replicate ecotype pairs within a species complex is often attributed to independent outcomes of parallel divergence driven by adaptation to similar environmental contrasts. However, the extent to which parallel phenotypic and genetic divergence patterns have emerged independently is increasingly questioned by population genomic studies. Here, we document the extent of genetic differentiation within and among two geographic replicates of the coastal and marine ecotypes of the European anchovy (Engraulis encrasicolus) gathered from Atlantic and Mediterranean locations. Using a genome-wide data set of RAD-derived SNPs, we show that habitat type (marine vs. coastal) is the most important component of genetic differentiation among populations of anchovy. By analysing the joint allele frequency spectrum of each coastal-marine ecotype pair, we show that genomic divergence patterns between ecotypes can be explained by a postglacial secondary contact following a long period of allopatric isolation (c. 300 kyrs). We found strong support for a model including heterogeneous migration among loci, suggesting that secondary gene flow has eroded past differentiation at different rates across the genome. Markers experiencing reduced introgression exhibited strongly correlated differentiation levels among Atlantic and Mediterranean regions. These results support that partial reproductive isolation and parallel genetic differentiation among replicate pairs of anchovy ecotypes are largely due to a common divergence history prior to secondary contact. They moreover provide comprehensive insights into the origin of a surprisingly strong fine-scale genetic structuring in a high gene flow marine fish, which should improve stock management and conservation actions.

物种复合群内各重复生态型对之间的生态表型分化（ecophenotypic differentiation），以往多被归因于适应相似环境差异所驱动的平行分化的独立演化结局。然而，群体基因组学研究（population genomic studies）愈发对平行表型与遗传分化模式是否独立形成提出了质疑。本研究针对采集自大西洋与地中海海域的欧洲鳀（Engraulis encrasicolus）沿岸与海洋生态型的2组地理重复样本，解析了其种群内部及种群间的遗传分化程度。我们利用限制性酶切位点相关DNA单核苷酸多态性（RAD-derived SNPs）的全基因组数据集，证实生境类型（海洋vs. 沿岸）是鳀鱼种群间遗传分化的最核心驱动因素。通过分析每一组沿岸-海洋生态型对的联合等位基因频率谱（joint allele frequency spectrum），我们发现生态型间的基因组分化模式，可以用经长达约30万年的异域隔离（allopatric isolation）后发生的冰期后二次接触（postglacial secondary contact）来解释。本研究强烈支持包含位点间异质迁移（heterogeneous migration among loci）的演化模型，表明二次基因流在全基因组范围内以不同速率消除了既往的遗传分化。表现出降低基因渐渗（introgression）程度的遗传标记，在大西洋与地中海区域均呈现出显著相关的分化水平。上述结果证实，鳀鱼重复生态型对之间的部分生殖隔离（reproductive isolation）与平行遗传分化，主要源于二次接触前共同的分化历史。本研究还为解析高基因流海洋鱼类中出乎意料的精细尺度强遗传结构的起源提供了全面见解，相关成果将有助于优化种群管理与保护实践。