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.