Data from: Targeted re-sequencing reveals geographic 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塑造生物多样性过程中的作用提供了佐证。近期研究显示，不同地理区域内的平行表型分化未必拥有相同的遗传基础——异常位点（outlier loci，即潜在受趋异选择影响的位点）在多起平行表型分化案例中往往并不共享。然而，若存在假阳性异常位点，共享程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，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环境。我们提出如下假说：若该类群此前研究中观测到的共享程度偏低是由抽样效应导致的，那么当我们对原始种群的新样本进行测序时，前述异常位点将不会表现出升高的FST值，也不会遵循升高FST的可预测地理分布模式。本研究采用分层抽样设计（国家内与国家间），靶向此前研究中的异常位点与对照位点开展捕获测序。我们发现，异常位点在其起源种群中再次表现出升高的FST水平，这表明它们并非由抽样效应产生。此外，异常位点在地理距离较近的种群中更易表现出升高的FST值，这一现象可通过与远距种群相比，近距种群间存在更高的基因流水平或共享更多的祖先遗传变异来解释。不过，与此前的研究结果不同，我们还发现部分异常位点类型在地理距离较远的种群中也表现出升高的FST值。我们就这一意外结果的潜在解释展开了讨论。