Data from: Targeted resequencing reveals geographical patterns of differentiation for loci implicated in parallel evolution

Parallel divergence and speciation provide evidence for the role of divergent selection in generating biological diversity. Recent studies indicate that parallel phenotypic divergence may not have the same genetic basis in different geographical locations - “outlier loci” (loci potentially affected by divergent selection) are often not shared among parallel instances of phenotypic divergence. However, limited sharing may be due, in part, to technical issues if false positive outliers occur. Here, we test this idea in the marine snail Littorina saxatilis, which has evolved two partly isolated ecotypes (adapted to crab predation vs. wave action) in multiple locations independently. We argue that if the low extent of sharing observed in earlier studies in this system is due to sampling effects, we expect outliers not to show elevated FST when sequenced in new samples from the original locations, and also not to follow predictable geographical patterns of elevated FST. Following a hierarchical sampling design (within vs. between country), we applied capture sequencing, targeting outliers from earlier studies and control loci. We found that outliers again showed elevated levels of FST in their original location, suggesting they were not generated by sampling effects. Outliers were also likely to show increased FST in geographically close locations, which may be explained by higher levels of gene flow or shared ancestral genetic variation compared to more distant locations. However, in contrast to earlier findings, we also found some outlier types to show elevated FST in geographically distant locations. We discuss possible explanations for this unexpected result.

平行分化与物种形成为趋异选择在生物多样性产生中的作用提供了实证依据。近期研究表明，不同地理区域的平行表型分化可能具有不同的遗传基础——“异常位点（outlier loci）”（即潜在受趋异选择作用的基因座）在平行表型分化的不同实例间通常并不共享。然而，若出现假阳性异常位点，则共享度偏低的现象可能部分源于技术层面的问题。本研究以滨螺（Littorina saxatilis）为研究对象对该假说进行验证：该物种已在多个地理区域独立演化出两种部分隔离的生态型——分别适应螃蟹捕食与海浪冲击。我们提出，若该类群此前研究中观测到的共享度偏低源于抽样效应，那么当对原采样地点的新样本进行测序时，异常位点不应表现出升高的遗传分化系数（FST），也不会呈现出可预测的FST升高地理模式。本研究采用分层采样设计（国家内与国家间），针对此前研究中的异常位点与对照基因座开展捕获测序。研究结果显示，异常位点在其原采样地点再次表现出升高的FST水平，表明其并非由抽样效应所产生。异常位点在地理邻近的采样地点中也更可能表现出升高的FST，这一结果可通过与远距地点相比，近距地点具有更高的基因流水平或共享更多祖先遗传变异来解释。但与此前研究结果不同的是，本研究还发现部分异常位点类型在地理远距的采样地点中也表现出升高的FST。本研究最后对这一意外结果的潜在成因展开讨论。