Data from: Evidence for adaptation from standing genetic variation on an antimicrobial peptide gene in the mussel Mytilus edulis

Genome scans of population differentiation identify candidate loci for adaptation but provide little information on how selection has influenced the genetic structure of these loci. Following a genome scan, we investigated the nature of the selection responsible for the outlying differentiation observed between populations of the marine mussel Mytilus edulis at a leucine/arginine polymorphism (L31R) in the antimicrobial peptide MGD2. We analysed DNA sequence polymorphisms, allele frequencies and population differentiation of polymorphisms closely linked to L31R, and pairwise and third-order linkage disequilibria. An outlying level of population differentiation was observed at L31R only, while no departure from panmixia was observed at linked loci surrounding L31R, as in most of the genome. Selection therefore seems to affect L31R directly. Three hypotheses can explain the lack of differentiation in the chromosomal region close to L31R: (i) hitchhiking has occurred but migration and recombination subsequently erased the signal, (ii) selection was weak enough and recombination strong enough to limit the hitchhiking effect to a very small chromosomal region or (iii) selection acted on a pre-existing polymorphism (i.e. standing variation) at linkage equilibrium with its background. Linkage equilibrium was observed between L31R and linked polymorphisms in every population analysed, as expected under the three hypotheses. However, linkage disequilibrium was observed in some populations between pairs of loci located upstream and downstream to L31R, generating a complex pattern of third-order linkage disequilibria which is best explained by the hypothesis of selection on a pre-existing polymorphism. We hypothesise that selection could be either balanced, maintaining alleles at different frequencies depending on the pathogen community encountered locally by mussels, or intermittent, resulting in sporadic fluctuations in allele frequency.群体分化基因组扫描（genome scan）能够鉴定适应相关的候选位点，但却难以揭示选择作用如何影响这些位点的遗传结构。在完成基因组扫描后，我们针对紫贻贝（Mytilus edulis）种群间在抗菌肽（antimicrobial peptide）MGD2中一处亮氨酸/精氨酸多态性位点（L31R）上观测到的异常分化，解析了背后的选择作用本质。我们分析了与L31R紧密连锁的多态性位点的DNA序列多态性、等位基因频率及群体分化水平，同时也分析了位点间的成对连锁不平衡与三阶连锁不平衡。仅在L31R位点观测到异常的群体分化水平；而与L31R相邻的连锁位点，正如基因组绝大多数区域一样，并未出现偏离随机交配（panmixia）的情况。由此推测，选择作用直接作用于L31R位点。针对L31R附近染色体区域未出现分化的现象，可通过三种假说解释：（1）曾发生遗传搭车（hitchhiking）事件，但后续的基因流与重组清除了该信号；（2）选择作用强度较弱且重组频率较高，将搭车效应限制在了极小的染色体区域内；（3）选择作用于与背景位点处于连锁平衡的预先存在的多态性（即现存遗传变异（standing variation））。正如三种假说所预期的那样，在所有分析的种群中，L31R与连锁多态性位点之间均观测到连锁平衡。然而，在部分种群中，L31R上下游的成对位点间观测到了连锁不平衡，由此形成了复杂的三阶连锁不平衡模式，这一结果最符合预先存在多态性位点上的选择作用假说。我们推测，该选择作用可能为平衡选择，通过维持与贻贝本地遭遇的病原群落相适配的等位基因频率，亦或是间歇性选择，进而导致等位基因频率出现偶发波动。