Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species

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.