Data from: Shared and non-shared genomic divergence in parallel ecotypes of Littorina saxatilis at a local scale

• Main Authors: Ravinet, Mark, Westram, Anja, Johannesson, Kerstin, Butlin, Roger, André, Carl, Panova, Marina
• Format: Dataset
• Language: English
• Published: Dryad 2015
• Subjects: Parallel speciation; null alleles; genome scan; shared genomic divergence; RAD sequencing; Close Islands; Jutholmen
• Online Access: https://dx.doi.org/10.5061/dryad.g466r; http://datadryad.org/stash/dataset/doi:10.5061/dryad.g466r

Parallel speciation occurs when selection drives repeated, independent adaptive divergence that reduces gene flow between ecotypes. Classical examples show parallel speciation originating from shared genomic variation, but this does not seem to be the case in the rough periwinkle (Littorina saxatilis) that has evolved considerable phenotypic diversity across Europe, including several distinct ecotypes. Small ‘wave’ ecotype snails inhabit exposed rocks and experience strong wave action, while thick-shelled, ‘crab’ ecotype snails are larger and experience crab predation on less exposed shores. Crab and wave ecotypes appear to have arisen in parallel and recent evidence suggests only marginal sharing of molecular variation linked to evolution of similar ecotypes in different parts of Europe. However the extent of genomic sharing is expected to increase with gene flow and more recent common ancestry. To test this we used de novo RAD-sequencing to quantify the extent of shared genomic divergence associated with phenotypic similarities among ecotype-pairs on three close islands (< 10 km distance) connected by weak gene flow (Nm~0.03) and with recent common ancestry (< 10,000 years). After accounting for technical issues, including a large proportion of null alleles due to a large effective population size, we found ~8-28% of positive outliers were shared between two islands and ~2-9% were shared among all three islands. This low level of sharing suggests that parallel phenotypic divergence in this system is not matched by shared genomic divergence despite a high probability of gene flow and standing genetic variation. : Haplotype and genepop datasetsAll haplotype files generated by Stacks assembly and genepop files created by custom conversion. See README for additional information.haplotype_genepop_files.zipOutlier lociOutlier loci identified using FreeNA corrected FST and He values in fdist. Each file is a fasta file with two lines - the locus identifier from the main catalogue and a consensus haplotype sequence. See README for a description of filenames.outlier_loci.zipfdist outputfdist output from each of the analyses performed in the main and supplementary text. See README file for more information.fdist.zipFinal stacks catalogueFinal stacks catalogue constructed using Stacks v1.21. See README for additional explanationfinal_catalogue.zipGeometric morphometrics dataGeometric morphometrics data for Littorina ecotypes. Columns are sample, ecotype, population (island), population x ecotype. Columns with 'proc' are size adjusted procrustes coordinates. Columns with 'PC' are principle components. Columns with 'CV' are canonical variates.geometric_morphometrics.csvSample metatableMetatable of all samples used in study for both RAD-seq and morphometrics. Columns are sample, population (island), ecotype, sex (NS = not sexed), whether sample was RAD-sequenced, whether sample was used in initial catalogue, whether sample was used in final catalogue, whether sample was used in morphometrics and ENA accession number for sequenced individuals.metatable.csvvcf_filesVCF files for Salto, Jutholmen, Ramso and the all-island dataset.Diversity statisticsDiversity statistics calculated from haplotype data. See README for indepth explanation.diversity_statistics.zip