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.
SP_C1_f.fastq
quality trimmed RNAseq reads: Spain, 'crab' ecotype, sample 1, forward reads
SP_C1_r.fastq
quality trimmed RNAseq reads: Spain, 'crab' ecotype, sample 1, reverse reads
SP_C2_f.fastq
quality trimmed RNAseq reads: Spain, 'crab' ecotype, sample 2, forward reads
SP_C2_r.fastq
quality trimmed RNAseq reads: Spain, 'crab' ecotype, sample 2, reverse reads
SP_W1_f.fastq
quality trimmed RNAseq reads: Spain, 'wave' ecotype, sample 1, forward reads
SP_W1_r.fastq
quality trimmed RNAseq reads: Spain, 'wave' ecotype, sample 1, reverse reads
SP_W2_f.fastq
quality trimmed RNAseq reads: Spain, 'wave' ecotype, sample 2, forward reads
SP_W2_r.fastq
quality trimmed RNAseq reads: Spain, 'wave' ecotype, sample 2, reverse reads
SW_C1_f.fastq
quality trimmed RNAseq reads: Sweden, 'crab' ecotype, sample 1, forward reads
SW_C1_r.fastq
quality trimmed RNAseq reads: Sweden, 'crab' ecotype, sample 1, reverse reads
SW_C2_f.fastq
quality trimmed RNAseq reads: Sweden, 'crab' ecotype, sample 2, forward reads
SW_C2_r.fastq
quality trimmed RNAseq reads: Sweden, 'crab' ecotype, sample 2, reverse reads
SW_W1_f.fastq
quality trimmed RNAseq reads: Sweden, 'wave' ecotype, sample 1, forward reads
SW_W1_r.fastq
quality trimmed RNAseq reads: Sweden, 'wave' ecotype, sample 1, reverse reads
SW_W2_f.fastq
quality trimmed RNAseq reads: Sweden, 'wave' ecotype, sample 2, forward reads
SW_W2_r.fastq
quality trimmed RNAseq reads: Sweden, 'wave' ecotype, sample 2, reverse reads
UK_C1_f.fastq
quality trimmed RNAseq reads: United Kingdom, 'crab' ecotype, sample 1, forward reads
UK_C1_r.fastq
quality trimmed RNAseq reads: United Kingdom, 'crab' ecotype, sample 1, reverse reads
UK_C2_f.fastq
quality trimmed RNAseq reads: United Kingdom, 'crab' ecotype, sample 2, forward reads
UK_C2_r.fastq
quality trimmed RNAseq reads: United Kingdom, 'crab' ecotype, sample 2, reverse reads
UK_W1_f.fastq
quality trimmed RNAseq reads: United Kingdom, 'wave' ecotype, sample 1, forward reads
UK_W1_r.fastq
quality trimmed RNAseq reads: United Kingdom, 'wave' ecotype, sample 1, reverse reads
UK_W2_f.fastq
quality trimmed RNAseq reads: United Kingdom, 'wave' ecotype, sample 2, forward reads
UK_W2_r.fastq
quality trimmed RNAseq reads: United Kingdom, 'wave' ecotype, sample 2, reverse reads
Littorina.mpileup
mpileup 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.gz
Littorina_analysed_genome_contigs.fasta
Contains 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.