Dorant Yann, Cayuela Hugo, Wellband Kyle, Laporte Martin, Rougemont Quentin, Mérot Claire, Normandeau Eric, Rochette Rémy, Bernatchez Louis
Institut de Biologie Intégrative des Systèmes (IBIS), Université Laval, Québec, QC, Canada.
Department of Biology, University of New Brunswick, Saint John, NB, Canada.
Mol Ecol. 2020 Dec;29(24):4765-4782. doi: 10.1111/mec.15565. Epub 2020 Aug 17.
Copy number variants (CNVs) are a major component of genotypic and phenotypic variation in genomes. To date, our knowledge of genotypic variation and evolution has largely been acquired by means of single nucleotide polymorphism (SNPs) analyses. Until recently, the adaptive role of structural variants (SVs) and particularly that of CNVs has been overlooked in wild populations, partly due to their challenging identification. Here, we document the usefulness of Rapture, a derived reduced-representation shotgun sequencing approach, to detect and investigate copy number variants (CNVs) alongside SNPs in American lobster (Homarus americanus) populations. We conducted a comparative study to examine the potential role of SNPs and CNVs in local adaptation by sequencing 1,141 lobsters from 21 sampling sites within the southern Gulf of St. Lawrence, which experiences the highest yearly thermal variance of the Canadian marine coastal waters. Our results demonstrated that CNVs account for higher genetic differentiation than SNP markers. Contrary to SNPs, for which no significant genetic-environment association was found, 48 CNV candidates were significantly associated with the annual variance of sea surface temperature, leading to the genetic clustering of sampling locations despite their geographic separation. Altogether, we provide a strong empirical case that CNVs putatively contribute to local adaptation in marine species and unveil stronger spatial signal of population structure than SNPs. Our study provides the means to study CNVs in nonmodel species and highlights the importance of considering structural variants alongside SNPs to enhance our understanding of ecological and evolutionary processes shaping adaptive population structure.
拷贝数变异（CNV）是基因组中基因型和表型变异的主要组成部分。迄今为止，我们对基因型变异和进化的认识很大程度上是通过单核苷酸多态性（SNP）分析获得的。直到最近，结构变异（SV）尤其是CNV在野生种群中的适应性作用一直被忽视，部分原因是其鉴定具有挑战性。在这里，我们记录了Rapture（一种衍生的简化代表性鸟枪法测序方法）在美国龙虾（美洲螯龙虾）种群中检测和研究拷贝数变异（CNV）以及SNP的实用性。我们进行了一项比较研究，通过对圣劳伦斯湾南部21个采样点的1141只龙虾进行测序，来检验SNP和CNV在局部适应性中的潜在作用，圣劳伦斯湾是加拿大沿海水域中每年热变化最大的区域。我们的结果表明，CNV比SNP标记导致更高的遗传分化。与未发现显著遗传-环境关联的SNP相反，48个CNV候选位点与海表温度的年变化显著相关，尽管采样地点在地理上是分开的，但仍导致了遗传聚类。总之，我们提供了一个有力的实证案例，证明CNV可能有助于海洋物种的局部适应，并揭示了比SNP更强的种群结构空间信号。我们的研究提供了在非模式物种中研究CNV的方法，并强调了在考虑SNP的同时考虑结构变异以增强我们对塑造适应性种群结构的生态和进化过程理解的重要性。
