Data from: The roles of plasticity and selection in rapid phenotypic changes at the Pacific oyster invasion front in Europe
Data files
Feb 06, 2025 version files 19.15 GB
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1_Adults.vcf.gz
3.89 GB
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2_Larvae.vcf.gz
15.26 GB
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README.md
3.80 KB
Abstract
Invasive species are a major challenge to managers worldwide due to their ability to rapidly change their niche space and behavior in order to reproduce and survive in a novel environment. One globally distributed invasive species, the Pacific oyster, Crassostrea (Magallana) gigas, first arrived in Sweden in 2006. To date, they have not colonized the low salinity waters of the Baltic Sea, and it has generally been assumed that the inability of Pacific oysters to reproduce in low salinities has acted as a barrier. We have studied differences in fertilization rates among oysters along the invasion range, and examined heritability of salinity tolerance through classic mating designs across five different salinity levels. We found that fertilization rates in low salinities increased with proximity to the range front, and that there was a strong heritable component to these differences. We then used whole genome sequence data to identify genomic regions that diverged significantly from expected Mendelian inheritance in larval full-sib families that survived in low salinities. Our results show that a chromosomal region containing coding sequences for all histones forming the nucleosome, as well as a region containing LSU and SSU subunit ribosomal DNA in the sperm, are involved in low-salinity tolerance at fertilization and early development. We also found no evidence of recent bottlenecks or reductions in genetic diversity along the invasion front compared to more established populations. We therefore conclude that the Pacific oyster has the potential to adapt further to low-salinity conditions and may invade the Baltic Sea.
https://doi.org/10.5061/dryad.v6wwpzh5q
Description of the data and file structure
Detailed description of the methods can be found in our paper: **The roles of plasticity and selection in rapid phenotypic changes at the Pacific oyster invasion front in Europe in Molecular Ecology **
Sexually mature Pacific oysters (C. gigas) were obtained from the present invasion front in southwestern Sweden (Hallands Väderö). Gametes were extracted from the gonads by strip-spawning. We created multiple blocks of diallel crosses of 3 Males ´ 3 Females following a classic animal breeding design (North Carolina II; Lynch & Walsh 1998). Each block used gametes from 6 new adults (total of 9 crosses [3M ´ 3F] fertilized in 2 salinities (13 and 23 ‰), we obtained 5 experimental blocks for a total of 15 males and 15 females. 24 hours post-fertilization, larval full-sub families were placed in ethanol. Mantle tissue from all parents were also placed in ethanol. DNA was extracted from the tissue samples and from the pools of D-stage larvae from the two salinities using a Qiagen DNEasy Blood & Tissue kit with the standard protocol. DNA from the pools of larvae were further purified using a Zymo Clean and Concentrator kit, after which DNA amount was assessed using a QuBit BR assay. Sequencing libraries were prepared using the Illumina DNA PCR-free protocol (https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/dna-pcr-free-prep.html) at the Swedish National Genomics Infrastructure. Due to low DNA amounts, successful libraries were prepared for 37 pools of larvae from 23 ‰ and from 35 families in 13 ‰ (of which 33 families were present in both salinities). Parents and larvae were multiplexed and sequenced in one lane of a S4-600 flowcell in an Illumina NovaSeq6000 (2150 bp reads). To increase coverage in the larval pools for accurate allele frequency estimations, libraries were additionally sequenced in two 10B-300 flowcell lanes in an NovaSeqXPlus instrument (2150 bp reads).
All custom scripts and commands used in bioinformatic data analysis can be found here: https://github.com/DeWitP/gigas_lowsal_adaptation.
Files and variables
File: 1_Adults.vcf.gz
Description: vcf file of SNV calls in the parental oysters collected from Hallands Väderö, 12 April 2022. Generated using GATK 3.8
File: 2_Larvae.vcf.gz
Description: vcf file of SNV calls in pool-seq data from full-sib families of 24 hour old oyster larvae. Each sample contains 100s of larvae. vcf file generated using FreeBayes.
File named 1_Adults.vcf.gz: gzipped vcf file with filtered SNP variants from adult oysters collected in Sweden, Hallands Väderö.
File named 2_Larvae.vcf.gz: gzipped vcf file with filtered SNP variants from larval (24 h post-fertilization) full-sib families (obtained through pool-seq) obtained through controlled crosses of the adult oysters in file 1.
Bioinformatic pipeline for creating these variant call sets can be found at: https://github.com/DeWitP/gigas_lowsal_adaptation
Code/software
All custom scripts and commands used in bioinformatic data analysis can be found here: https://github.com/DeWitP/gigas_lowsal_adaptation
Access information
Other publicly accessible locations of the data:
- Raw fastq data can be found on NCBI SRA, under BioProject PRJNA1190893.