DOI: 10.5061/dryad.hx3ffbgbp
title: Data from: Shared ancestral polymorphism and chromosomal rearrangements as potential drivers of local adaptation in a marine fish

description: Gene flow has tremendous importance on local adaptation, by influencing
 the fate of de novo mutations, maintaining standing genetic variation, and
 driving adaptive introgression. Furthermore, structural variation as
 chromosomal rearrangements may facilitate adaptation despite high gene
 flow. However, our understanding of evolutionary mechanisms impending or
 favoring local adaptation in the presence of gene flow is still limited to
 a restricted number of study systems. In this study, we examined how
 demographic history, shared ancestral polymorphism, and gene flow among
 glacial lineages contribute to local adaptation to sea conditions in a
 marine fish, the capelin (Mallotus villosus). We first assembled a 490 Mbp
 draft genome of M. villosus to map our RAD sequence reads. Then, we used a
 large dataset of genome-wide single nucleotide polymorphisms (25,904
 filtered SNPs) genotyped in 1,310 individuals collected from 31 spawning
 sites in the northwest Atlantic. We reconstructed the history of
 divergence among three glacial lineages and showed that they likely
 diverged from 3.8 to 1.8 MyA and experienced secondary contacts. Within
 each lineage, our analyses provided evidence for large Ne and high gene
 flow among spawning sites. Within the NWA lineage, we detected a
 polymorphic chromosomal rearrangement leading to the occurrence of three
 haplogroups. Genotype-environment associations revealed molecular
 signatures of local adaptation to environmental conditions prevailing at
 spawning sites. Our study also suggests that, both shared polymorphism
 among lineages, resulting from standing genetic variation or
 introgression, and chromosomal rearrangements may contribute to local
 adaptation in the presence of high gene flow.
description: We provide the filtered vcf of GBS data and the environmental
 variables (bottom temperature and chlorophyll) used in our study. Below,
 we give information about sampling area and molecular analyses.
 A total of 1,359 capelins were sampled from 31 sites in the
 Northwest Atlantic, both in Canadian and Greenland waters, which were
 expected to include representatives from the three lineages according to a
 previous study using mitochondrial DNA and microsatellite genetic markers
 (Dodson et al. 2007). We sampled 25 spawning sites within the presumed NWA
 lineage including three demersal shallow-water sites, three demersal
 deep-water sites, and 18 beach spawning sites. These sites were located in
 four geographic regions : Kuururjuaq, Labrador, Newfoundland, and St.
 Lawrence. In parallel, we sampled two sites (beach-spawning fishes) within
 the presumed range of the ARC lineage and four offshore sampling sites in
 the range of the GRE lineage. The median sample size was 46.5 (range: 19
 to 50) individuals per site. Fish were collected during the breeding
 period (captured by hand at beach spawning sites and using nets at
 demersal spawning sites), sexed, and a piece of fin was preserved in
 RNAlater. The DNA extraction procedure follows
 protocols fully described elsewhere (Moore et al. 2017; Rougemont et al.
 2019) and is described briefly below. DNA was extracted with a salt-based
 method and an RNAse A (Qiagen) treatment was applied following the
 manufacturer’s recommendation. DNA quality was assessed using gel
 electrophoresis. DNA was quantified using a NanoDrop spectrophotometer
 (Thermo Scientific) and then using QuantiT Picogreen dsDNA Assay Kit
 (Invitrogen). Concentration of DNA was normalized to 20 ng/μl. Libraries
 were constructed following a double-digest RAD (restriction
 site-associated DNA sequencing; Peterson et al. 2012) protocol modified
 from Mascher et al. (2013). Genomic DNA was digested with two restriction
 enzymes (PstI and MspI, Poland et al. 2013) by incubating at 37°C for two
 hours followed by enzyme inactivation by incubation at 65°C for 20 min.
 Sequencing adaptors and a unique individual barcode were ligated to each
 sample using a ligation master mix including T4 ligase. The ligation
 reaction was completed at 22°C for 2 hours followed by 65°C for 20 min to
 deactivate the enzymes. Samples were pooled in multiplexes of 48
 individuals, ensuring that individuals from each sampling location were
 sequenced as part of at least six different multiplexes to avoid pool
 effects. Libraries were size-selected using a BluePippin prep (Sage
 Science), amplified by PCR and sequenced on the Ion Proton P1v2 chip
 (producing single-end reads with 80 million bp per chip). Eighty-two
 individuals were sequenced per chip.