RAD sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic Eels
RAD sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic Eels
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DOI：
10.1111/mec.13466
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发表时间：
2016-01-01
影响因子：
4.9
通讯作者：
Bernatchez，L.
中科院分区：
文献类型：
--
作者：
Laporte，M.;Pavey，S. A.;Bernatchez，L.
测量人类改变的环境对基因组的选择影响是目前生态基因组学的主要目标。鉴于大多数表型性状的多基因基础，数量遗传理论预测，选择预计会导致微妙的等位基因的变化之间的协变基因座，而不是显着的变化，在少数几个基因座的大的影响。本研究的目的是测试多基因选择在北大西洋鳗鱼（欧洲鳗，安圭拉和美洲鳗，A。rostrata），使用一种方法，搜索基因座之间的协变，将区分鳗鱼从“控制”与“污染”的环境，并与特定的污染物作为推定的选择剂。RAD‐seq文库分别产生了欧洲和美国鳗鱼的23 659和14 755个过滤位点。共获得142和141个协变标记区分欧洲和美国鳗鱼从“控制”与“污染”的采样地点，使用随机森林算法。使用基于距离的冗余分析（db-RDAs）来评估这些共变标记物与每只鳗鱼测量的34种污染物浓度之间的关系。PCB 153、4′4′DDE和硒与两种物种的共变标记相关，因此指出这些污染物是污染场地的主要选择性因子。基因富集分析表明，固醇调节在鳗鱼在“污染”环境中的差异生存中起着重要作用。这项研究说明了在旨在记录基因组水平上的选择动态的研究中，特别是在人类改变的环境中，检测多基因选择信号和将标记变异与推定的选择剂相关联的方法的组合的力量。
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 anguillaand 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.