Datasets for genomic signals of adaptation along a natural CO2 gradient over striking microgeographic scale

Description

Genpop file obtained using 2b-RADseq which comprises a total of 14,881 loci for 74 individuals of the black sea urchin Arbacia lixula. The individuals were collected along a natural CO2 gradient from the island of La Palma in the Canary Archipelago, Spain.

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Genomic DNA was extracted using a modified protocol adapted from Panova et al. (2016). DNA samples were obtained from 10-20 individuals per site, and individual 2b-RAD libraries were constructed following the laboratory protocol by Galina Aglyamova and Mikhail Matz, which can be found at https://github.com/z0on/2bRAD_denovo. The equimolarly pooled libraries were sequenced on the Illumina NovaSeq 6000 SP flowcell, generating 50bp pair-end sequences. Sequencing was conducted at the Science for Life Laboratory (SciLifeLab) – Genomics, SNPandSEQ Technology Platform, located at Uppsala University in Sweden. The bioinformatic analyses were performed on the computer cluster 'Albiorix' at the University of Gothenburg, Sweden. The analysis followed a modified de novo pipeline available at https://github.com/crustaceana/TheFucusProject, originally developed by Mikhail Matz (https://github.com/z0on/2bRAD_denovo). Loci with over 75% heterozygosity were removed to mitigate sequencing errors. The data were initially thinned to retain one Single Nucleotide Polymorphism (SNP) per RAD fragment, provided the fragment had less than 50% missing data. Technical replicates were subsequently excluded from the dataset. Further thinning was performed using Poppr (Kamvar et al., 2014) to eliminate loci or genotypes with over 5% missing data and to retain only informative loci with at least two differing observations. The raw 2b-RAD sequences have been deposited in the Sequence Read Archive Repository at the National Centre for Biotechnology and Information (Bioproject PRJNA948020). References: Panova M, Aronsson H, Cameron R A, Dahl P, Godhe A, Lind U and Blomberg A. 2016. DNA extraction protocols for wholegenome sequencing in marine organisms. Marine Genomics. Humana Press, New York, pp. 13–44. Kamvar ZN, Tabima JF, Grünwald NJ. 2014. Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2:e281 https://doi.org/10.7717/peerj.281

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