A population genomics approach to uncover the CNVs, and their evolutionary significance, hidden in reduced‐representation sequencing data sets

Abstract

Population genetics studies, both theoretical and empirical, have primarily focused on sequence variation since the dawn of the discipline in the 1920s, even though genetic structural variation was discovered almost at the same time (McClintock, 1931; Sturtevant, 1913). Among the many great contributions of high-throughput sequencing to biology, the renewed, yet vastly greater, appreciation for structural variation stands out. In recent years, many structural variants (SVs) have been associated with traits involved in speciation and adaptation, highlighting their role in micro-and macroevolutionary processes (Mérot et al., 2020; Wellenreuther et al., 2019). Among SVs, copy number variants (CNVs), which encompass all the SVs in which a sequence varies in number of copies among individuals including duplications, insertions, deletions and transposable elements (TEs), have been linked to adaptation to pollution, pesticides, domestication, and high and low temperatures (Axelsson

Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish

“…We therefore encourage further simulation studies to compare the efficiency of RAD‐seq and whole‐genome (read‐pair, read‐depth, split‐read, and de novo assembly approaches; Pirooznia et al, 2015) CNV analyses, considering contrasted levels of reference genome quality. Overall, despite its technical limitations, RAD‐seq CNV analysis provides a robust, novel tool for improving our knowledge on the evolutionary role of duplicated regions and TEs in nonmodel species by permitting studies involving hundreds of individuals or more from dozens of populations (Tigano, 2020).…”

“…However, with the exception of targeted candidate genes studies, CNV genotyping remained expensive until recently as it required whole genome sequencing data with deep coverage (Makałowski et al, 2019; Pirooznia et al, 2015), precluding the use of these markers in population genomic studies that involve thousands of samples from dozens of populations. This situation has recently changed through the development of a novel methodological approach allowing the identification of CNVs in a cost‐effective way using RAD‐seq (restriction site associated DNA sequencing) data (Dorant et al, 2020; McKinney et al, 2017; Tigano, 2020). Using this method, Dorant et al (2020) recently showed that CNVs can be more efficient than SNPs at revealing genotype–temperature associations in marine invertebrates, namely the American lobster.…”

“…Using this method, Dorant et al (2020) recently showed that CNVs can be more efficient than SNPs at revealing genotype–temperature associations in marine invertebrates, namely the American lobster. Yet, the usefulness of CNVs from RAD‐seq data as valuable DNA markers for population genomic studies still needs to be more broadly exemplified (Tigano, 2020). In particular, it needs to be investigated whether these CNVs may be associated with variation in fitness‐related phenotypic traits and can be informative for organisms with a small‐size genome containing far fewer repeated elements than that of the American lobster (~4.5 Gbp; Jimenez et al, 2010).…”