RAD-Seq Reveals Patterns of Additive Polygenic Variation Caused by Spatially-Varying Selection in the American Eel (Anguilla rostrata).
RAD-Seq Reveals Patterns of Additive Polygenic Variation Caused by Spatially-Varying Selection in the American Eel (Anguilla rostrata).
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DOI：
10.1093/gbe/evx226
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发表时间：
2017-11-01
影响因子：
3.3
通讯作者：
Bernatchez L
中科院分区：
文献类型：
--
作者：
Babin C;Gagnaire PA;Pavey SA;Bernatchez L
美洲鳗（Anguilla rostrata）具有独特的生命周期，其特点是在亚热带到亚北极纬度高度异质的栖息地中进行物种规模的泛生养繁殖，随机分布和选择。在这个物种中，空间变化选择的遗传后果已经被研究了几十年，揭示了在一些位点上等位基因频率的微妙变化，与绝大多数基因组的完全泛群形成对比。由于每一代的繁殖都使等位基因频率均匀，因此在这种情况下，采样大小和基因组覆盖率对于达到足够的功率来检测选定的基因座至关重要。本研究利用来自12个地点的710个个体和12098个高质量的单核苷酸多态性，重新评估了局部选择对该物种遗传多样性空间分布的影响程度。我们使用环境关联方法鉴定了空间变化选择下的标记，结果表明选择影响了约1.5%的基因组。然后，我们使用加性多基因评分评估候选标记集体随环境因素变化的程度。结果表明，多基因得分与纬度、经度和温度之间存在显著的相关性，这与多基因选择在不同生境中对不适应基因型的影响是一致的。胰岛素信号通路中与异常标记相关的基因功能显著富集，表明占据如此大的分布范围所固有的权衡涉及代谢调节。总的来说，这项研究强调了加性多基因评分方法在复杂环境中检测选择效应的潜力。
The American Eel (Anguilla rostrata) has an exceptional life cycle characterized by panmictic reproduction at the species scale, random dispersal, and selection in a highly heterogeneous habitat extending from subtropical to subarctic latitudes. The genetic consequences of spatially-varying selection in this species have been investigated for decades, revealing subtle clines in allele frequency at a few loci that contrast with complete panmixia on the vast majority of the genome. Because reproduction homogenizes allele frequencies every generation, sampling size, and genomic coverage are critical to reach sufficient power to detect selected loci in this context. Here, we used a total of 710 individuals from 12 sites and 12,098 high-quality single nucleotide polymorphisms to re-evaluate the extent to which local selection affects the spatial distribution of genetic diversity in this species. We used environmental association methods to identify markers under spatially-varying selection, which indicated that selection affects ∼1.5% of the genome. We then evaluated the extent to which candidate markers collectively vary with environmental factors using additive polygenic scores. We found significant correlations between polygenic scores and latitude, longitude and temperature which are consistent with polygenic selection acting against maladapted genotypes in different habitats occupied by eels throughout their range of distribution. Gene functions associated with outlier markers were significantly enriched for the insulin signaling pathway, indicating that the trade-offs inherent to occupying such a large distribution range involve the regulation of metabolism. Overall, this study highlights the potential of the additive polygenic scores approach in detecting selective effects in a complex environment.
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