Data from: Do the same genes underlie parallel phenotypic divergence in different Littorina saxatilis populations?

Parallel patterns of adaptive divergence and speciation are cited as powerful evidence for the role of selection driving these processes. However, it is often not clear whether parallel phenotypic divergence is underlain by parallel genetic changes. Here, we asked about the genetic basis of parallel divergence in the marine snail Littorina saxatilis, which has repeatedly evolved coexisting ecotypes adapted to either crab predation or wave action. We sequenced the transcriptome of snails of both ecotypes from three distant geographical locations (Spain, Sweden and United Kingdom) and mapped the reads to the L. saxatilis reference genome. We identified genomic regions potentially under divergent selection between ecotypes within each country, using an outlier approach based on FST values calculated per locus. In line with previous studies indicating that gene reuse is generally common, we expected to find extensive sharing of outlier loci due to recent shared ancestry and gene flow between at least two of the locations in our study system. Contrary to our expectations, we found that most outliers were country specific, suggesting that much of the genetic basis of divergence is not shared among locations. However, we did find that more outliers were shared than expected by chance and that differentiation of shared outliers is often generated by the same SNPs. We discuss two mechanisms potentially explaining the limited amount of sharing we observed. First, a polygenic basis of divergent traits might allow for multiple distinct molecular mechanisms generating the same phenotypic patterns. Second, additional, location-specific axes of selection that we did not focus on in this study may produce distinct patterns of genetic divergence within each site.

适应性分化与物种形成的平行模式，常被视为选择驱动此类演化过程的有力佐证。然而，学界始终难以明确：平行的表型分化是否以平行的遗传变异为基础。本研究以粗面滨螺（Littorina saxatilis）为研究对象，该物种多次独立演化出两类共存的生态型，分别适应蟹类捕食与海浪冲击两种环境压力。我们对来自三个相距遥远的地理种群（西班牙、瑞典与英国）的两类生态型个体进行了转录组测序，并将测序读段比对至粗面滨螺的参考基因组。我们采用基于每位点FST（群体固定指数）值的异常值检测方法，识别出每个地理种群内两类生态型间可能受分化选择作用的基因组区域。过往研究表明基因重用现象普遍存在，基于此我们曾预期：由于本研究体系中至少两个地理种群间存在近期共同祖先与基因交流，异常值位点的共享现象会广泛存在。但本研究结果与预期相悖：绝大多数异常值位点具有种群特异性，这表明分化的遗传基础在不同地理种群间大多并不共享。不过我们确实发现，存在共享的异常值位点，且其数量多于随机预期；且共享异常值位点的遗传分化，往往由相同的SNP（单核苷酸多态性）所介导。针对观测到的共享程度有限这一现象，我们探讨了两种潜在的解释机制：其一，分化性状的多基因基础，可能允许存在多种不同的分子机制，最终产生相同的表型模式；其二，本研究未聚焦的其他种群特异性选择压力，可能在每个采样位点产生独特的遗传分化模式。