IBIS (Institut de biologie intégrative et des systèmes), Département de biologie, Université Laval, Québec, Canada.
Institut des Sciences de l'Évolution-Montpellier (ISEM-CNRS UMR5554), SMEL, Sète, France.
Genome Biol Evol. 2017 Nov 1;9(11):2974-2986. doi: 10.1093/gbe/evx226.
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.
美洲鳗（Anguilla rostrata）具有独特的生命周期，其特点是在物种尺度上进行混合繁殖、随机扩散以及在从亚热带到亚北极的高度异质生境中进行选择。几十年来，人们一直在研究该物种中空间变化选择的遗传后果，发现少数几个基因座的等位基因频率存在细微的梯度，而绝大多数基因组则完全混合。由于繁殖每代都会使等位基因频率均匀化，因此在这种情况下，采样量和基因组覆盖率对于达到检测选定基因座的足够效力至关重要。在这里，我们使用了来自 12 个地点的总共 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来识别受空间变化选择影响的标记，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与环境因素共同变化的程度。我们发现多基因评分与纬度、经度和温度之间存在显著相关性，这与在美洲鳗分布范围内不同生境中选择不利于适应不良基因型的多基因选择一致。与异常标记相关的基因功能显著富集到胰岛素信号通路，表明在如此大的分布范围内进行权衡涉及到代谢的调节。总的来说，这项研究强调了加性多基因评分方法在检测复杂环境中选择效应的潜力。
