Data from: Genome divergence between European anchovy ecotypes fuelled by structural variants originating from trans-equatorial admixture

The European anchovy (Engraulis encrasicolus) is known to be subdivided
into marine and coastal ecotypes, and their divergence shows patterns that
are consistent with SVs. Here, we present the first genome-scale study
investigating genetic structure in the E. encrasicolus species complex. We
generated a reference genome and produced whole-genome resequencing data
for anchovies from the North-East Atlantic and Mediterranean Sea, as well
as from South Africa. We complemented this approach with the analysis of
RAD-seq data in order to study ecotypic structure across the entire
distribution range. We found that genetic diversity is not only
characterised by the presence of two genetic clusters, namely the marine
and coastal ecotypes, but also by a third ancestry which corresponds to a
southern Atlantic lineage. Genomic landscapes of differentiation showed
evidence for large regions of high linkage disequilibrium, likely
representing SVs that differentiate the three anchovy lineages.