Data from: RAD-sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic Eels

Measuring the effects of selection on the genome imposed by human-altered environment is currently a major goal in ecological genomics. Given the polygenic basis of most phenotypic traits, quantitative genetic theory predicts that selection is expected to cause subtle allelic changes among covarying loci rather than pronounced changes at few loci of large effects. The goal of this study was to test for the occurrence of polygenic selection in both North Atlantic eels (European Eel, Anguilla anguilla and American Eel, A. rostrata), using a method that searches for covariation among loci that would discriminate eels from “control” vs. “polluted” environments and be associated with specific contaminants acting as putative selective agents. RAD-seq libraries resulted in 23,659 and 14,755 filtered loci for the European and American Eels respectively. A total of 142 and 141 covarying markers discriminating European and American Eels from “control” vs. “polluted” sampling localities were obtained using the Random Forest algorithm. Distance-based redundancy analyses (db-RDAs) were used to assess the relationships between these covarying markers and concentration of 34 contaminants measured for each individual eel. PCB153, 4'4'DDE and selenium were associated with covarying markers for both species, thus pointing to these contaminants as major selective agents in contaminated sites . Gene enrichment analyses suggested that sterol regulation plays an important role in the differential survival of eels in “polluted” environment. This study illustrates the power of combining methods for detecting signals of polygenic selection and for associating variation of markers with putative selective agents in studies aiming at documenting the dynamics of selection at the genomic level, and particularly so in human altered environments.

解析人类活动干扰环境对基因组施加的选择效应，是当前生态基因组学（ecological genomics）的核心研究目标之一。鉴于多数表型性状均具有多基因基础，数量遗传学理论预测，选择作用更易引发共变异位点间的微小等位基因频率变化，而非少数大效应位点的显著变异。本研究旨在针对北大西洋鳗鲡（欧洲鳗鲡*Anguilla anguilla*与美洲鳗鲡*A. rostrata*）检验多基因选择的存在性，所用方法为筛选可区分鳗鲡“对照”与“污染”生境的位点共变异模式，且这些位点与作为潜在选择因子的特定污染物相关联。通过限制性酶切位点相关DNA测序（RAD-seq）文库构建，欧洲鳗鲡与美洲鳗鲡分别获得23659个和14755个过滤后的位点。借助随机森林（Random Forest）算法，本研究分别获得142个和141个可区分欧洲鳗鲡、美洲鳗鲡“对照”与“污染”采样点的共变异标记。采用基于距离的冗余分析（db-RDA），评估这些共变异标记与每条鳗鲡个体所检测的34种污染物浓度之间的关联关系。两种鳗鲡的共变异标记均与多氯联苯153（PCB153）、4,4'-二氯二苯二氯乙烯（4'4'DDE）及硒元素存在关联，表明上述污染物为污染生境中的主要选择因子。基因富集分析结果显示，固醇调控过程在污染生境中鳗鲡的差异化存活中发挥关键作用。本研究证实，在旨在解析基因组水平选择动态的研究中，尤其是人类活动干扰环境下的相关研究，联合使用多基因选择信号检测方法与标记变异-潜在选择因子关联分析方法的有效性。