RAD sequencing reveals parallel and non-parallel divergence in Swedish Littorina saxatilis populations

How parallel is adaptation within a species? Adaptation to similar environments by independent populations may appear phenotypically parallel but does the same genetic architecture underlie these traits? Widely available genome reduction and genotyping-by-sequencing methods mean that it is now possible to ask these questions in non-model organisms.

The rough periwinkle, Littorina saxatilis has evolved considerable morphological, ecological and behavioural diversity within its European distribution. In Western Sweden, crab and wave ecotypes appear to have arisen independently in parapatry multiple times as a result of divergent ecological selection. Wave ecotypes inhabit exposed rocks and are small with a larger relative foot area in order to withstand wave action. Crab individuals experience considerable crab predation and are typically larger with a thicker shell.

Using restriction-site associated sequencing (RAD-seq) we have identified thousands of polymorphic markers in three independent populations of Littorina saxatilis. However a large effective population size, high levels of heterozygosity and subsequently large numbers of null alleles in this species have hampered accurate de novo assembly. To account for biases in the dataset, we performed extensive sensitivity tests and applied a null allele correction factor. Using an FST based outlier approach on our corrected dataset, we have identified multiple loci putatively under positive selection between ecotypes at all three localities. Our results represent a first step towards identifying the parallel genomic basis of adaptation in this system and a cautionary tale for the use of de novo RAD sequencing.