Data from: Genetic architecture in a marine hybrid zone: comparing outlier detection and genomic clines analysis in the bivalve Macoma balthica

The role of natural selection in speciation has received increasing
attention and support in recent years. Different types of approaches have
been developed that can detect genomic regions influenced by selection.
Here we address the question whether two highly different methods - Fst
outlier analysis and admixture analysis - detect largely the same set of
non-neutral genomic elements or, instead, complementary sets. We study
genetic architecture in a natural secondary contact zone where extensive
admixture occurs. The marine bivalves Macoma balthica rubra and M. b.
balthica descend from two independent trans-Arctic invasions of the north
Atlantic and hybridize extensively where they meet, for example in the
Kattegat - Danish Straits - Baltic Sea region. The Kattegat - Danish
Straits region forms a steep salinity cline and is the only entrance to
the recently (ca 8000 years ago) established brackish water basin the
Baltic Sea. Salinity along the contact zone drops from 30‰ (Skagerrak,
M.b.rubra) to 3‰ (Baltic, M.b.balthica). Both outlier analysis and genomic
clines analysis suggest that large parts of the genome are influenced by
non-neutral effects. Contrasting samples from well outside the hybrid
zone, outlier analysis detects 16 of 84 amplified fragment length
polymorphism (AFLP) markers as significant Fst outliers. Genomic clines
analysis detects 31 out of 84 markers as non-neutral inside the hybrid
zone. Remarkably, only three markers are detected by both methods. We
conclude that the two methods together identify a suite of markers that
are under the influence of non-neutral effects.