DOI: 10.5061/dryad.21pf0
title: Data from: Do the same genes underlie parallel phenotypic divergence in different Littorina saxatilis populations?

description: Parallel patterns of adaptive divergence and speciation are cited as
 powerful evidence for the role of selection driving these processes.
 However, it is often not clear whether parallel phenotypic divergence is
 underlain by parallel genetic changes. Here, we asked about the genetic
 basis of parallel divergence in the marine snail Littorina saxatilis,
 which has repeatedly evolved coexisting ecotypes adapted to either crab
 predation or wave action. We sequenced the transcriptome of snails of both
 ecotypes from three distant geographical locations (Spain, Sweden and
 United Kingdom) and mapped the reads to the L. saxatilis reference genome.
 We identified genomic regions potentially under divergent selection
 between ecotypes within each country, using an outlier approach based on
 FST values calculated per locus. In line with previous studies indicating
 that gene reuse is generally common, we expected to find extensive sharing
 of outlier loci due to recent shared ancestry and gene flow between at
 least two of the locations in our study system. Contrary to our
 expectations, we found that most outliers were country specific,
 suggesting that much of the genetic basis of divergence is not shared
 among locations. However, we did find that more outliers were shared than
 expected by chance and that differentiation of shared outliers is often
 generated by the same SNPs. We discuss two mechanisms potentially
 explaining the limited amount of sharing we observed. First, a polygenic
 basis of divergent traits might allow for multiple distinct molecular
 mechanisms generating the same phenotypic patterns. Second, additional,
 location-specific axes of selection that we did not focus on in this study
 may produce distinct patterns of genetic divergence within each site.
description: SP_C1_f.fastqquality trimmed RNAseq reads: Spain, 'crab' ecotype, sample 1, forward readsSP_C1_r.fastqquality trimmed RNAseq reads: Spain, 'crab' ecotype, sample 1, reverse readsSP_C2_f.fastqquality trimmed RNAseq reads: Spain, 'crab' ecotype, sample 2, forward readsSP_C2_r.fastqquality trimmed RNAseq reads: Spain, 'crab' ecotype, sample 2, reverse readsSP_W1_f.fastqquality trimmed RNAseq reads: Spain, 'wave' ecotype, sample 1, forward readsSP_W1_r.fastqquality trimmed RNAseq reads: Spain, 'wave' ecotype, sample 1, reverse readsSP_W2_f.fastqquality trimmed RNAseq reads: Spain, 'wave' ecotype, sample 2, forward readsSP_W2_r.fastqquality trimmed RNAseq reads: Spain, 'wave' ecotype, sample 2, reverse readsSW_C1_f.fastqquality trimmed RNAseq reads: Sweden, 'crab' ecotype, sample 1, forward readsSW_C1_r.fastqquality trimmed RNAseq reads: Sweden, 'crab' ecotype, sample 1, reverse readsSW_C2_f.fastqquality trimmed RNAseq reads: Sweden, 'crab' ecotype, sample 2, forward readsSW_C2_r.fastqquality trimmed RNAseq reads: Sweden, 'crab' ecotype, sample 2, reverse readsSW_W1_f.fastqquality trimmed RNAseq reads: Sweden, 'wave' ecotype, sample 1, forward readsSW_W1_r.fastqquality trimmed RNAseq reads: Sweden, 'wave' ecotype, sample 1, reverse readsSW_W2_f.fastqquality trimmed RNAseq reads: Sweden, 'wave' ecotype, sample 2, forward readsSW_W2_r.fastqquality trimmed RNAseq reads: Sweden, 'wave' ecotype, sample 2, reverse readsUK_C1_f.fastqquality trimmed RNAseq reads: United Kingdom, 'crab' ecotype, sample 1, forward readsUK_C1_r.fastqquality trimmed RNAseq reads: United Kingdom, 'crab' ecotype, sample 1, reverse readsUK_C2_f.fastqquality trimmed RNAseq reads: United Kingdom, 'crab' ecotype, sample 2, forward readsUK_C2_r.fastqquality trimmed RNAseq reads: United Kingdom, 'crab' ecotype, sample 2, reverse readsUK_W1_f.fastqquality trimmed RNAseq reads: United Kingdom, 'wave' ecotype, sample 1, forward readsUK_W1_r.fastqquality trimmed RNAseq reads: United Kingdom, 'wave' ecotype, sample 1, reverse readsUK_W2_f.fastqquality trimmed RNAseq reads: United Kingdom, 'wave' ecotype, sample 2, forward readsUK_W2_r.fastqquality trimmed RNAseq reads: United Kingdom, 'wave' ecotype, sample 2, reverse readsLittorina.mpileupmpileup file of Littorina saxatilis RNAseq reads from 12 samples mapped to the reference genome. sample 1: Spain, crab ecotype, replicate 1. sample 2: Spain, crab ecotype, replicate 2. sample 3: Spain, wave ecotype, replicate 1. sample 4: Spain, wave ecotype, replicate 2. sample 5: Sweden, crab ecotype, replicate 1. sample 6: Sweden, crab ecotype, replicate 2. sample 7: Sweden, wave ecotype, replicate 1. sample 8: Sweden, wave ecotype, replicate 2. sample 9: UK, crab ecotype, replicate 1. sample 10: UK, crab ecotype, replicate 2. sample 11: UK, wave ecotype, replicate 1. sample 12: UK, wave ecotype, replicate 2.littorina.mpileup.gzLittorina_analysed_genome_contigs.fastaContains the 6790 Littorina saxatilis genome contigs to which RNAseq reads could be mapped and that passed filters. These are the contigs that outlier analyses in the paper are based on.