DOI: 10.5061/dryad.vt4b8gtnv
title: Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species

description: 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.
description: A total of 1,141 lobster samples
 were collected from 21 sites between May and July in 2016 in the southern
 area of the Gulf of St-Lawrence. DNA was extracted from half of the
 walking leg of each lobster using salt extraction
 (Aljanabi & Martinez,
 1997) with an additional RNAse treatment following the manufacturer’s
 instructions. DNA quality was assessed using 1% agarose gel
 electrophoresis. Genomic DNA concentrations were normalized to 20ng/µl
 based on a fluorescence quantification method (AccuClear™ Ultra High
 Sensitivity dsDNA Quantitation
 Solution). Individual reduced-representation
 shotgun sequencing (i.e. RRS) libraries were prepared following the
 Rapture approach (Ali et al., 2016). Briefly, the Rapture approach is a
 form of RRS sequencing which combines double-digested libraries (i.e. GBS,
 ddRADseq) with a sequence capture step using DNA probes designed from
 known genomic sequences. Here, we used the same 9,818 targeted loci
 previously used for the American lobster and all the details about the wet
 protocol are described in Dorant et al. (2019). All Rapture libraries were
 sequenced on the Ion Torrent p1v3 chip at the Plateforme d’analyses
 génomiques of the Institute of Integrative and Systems Biology (IBIS,
 Université Laval, Québec, Canada
 http://www.ibis.ulaval.ca/en/home/). Two rounds of sequencing (i.e. two separated chips) were conducted for all Rapture libraries.
description: <strong>Raw VCF consisted of 44374 unfiltered
 SNPs</strong><br> batch_1.vcf
 <strong>File containing estimated metrics for SNPs
 caracterization (i.e. singleton, duplicated, diverged, low
 confidence)</strong><br>
 SNPs_caracterization_metrics.txt <strong>Filtered
 VCF of 14534 SNPs identified as singletons</strong><br>
 filtered_singleton_SNPs.vcf <strong>Filtered VCF
 of 9659 SNPs identified as duplicated</strong><br>
 filtered_duplicated_SNPs.vcf <strong>Martix of
 normalized read depth for CNV loci</strong><br>
 CNVs_normalized_read_depth.txt <strong>Sea
 surface temperature data</strong><br>
 Sea_surface_temperatures.txt <strong>Script for
 SNPs classification (singleton, duplicated)</strong><br>
 00_classify_snps_lobster_Rapture.R<br> <br>
 <strong>Script for CNV data normalization</strong><br>
 01-edgeR_normalization_CNVs_data.R