High degree of cryptic population differentiation in the Baltic Sea herring Clupea harengus

Marine fish species are characterised by a low degree of population differentiation at putatively neutral marker genes. This has been traditionally attributed to ecological homogeneity and a lack of obvious dispersal barriers in marine habitats, as well as to large (effective) population sizes of most marine fish species. The herring (Clupea harengus) is a case in point – the levels of population differentiation at neutral markers, even across vast geographic areas, are typically very low (FST ≈ 0.005). We used a RAD-sequencing approach to identify 5985 novel SNPs in the herring, and estimated genome-wide levels of divergence using pooled DNA-samples between two Baltic Sea populations separated by 387 km. We found a total of 4756 divergent SNPs (79% of all SNPs) between the populations, of which 117 showed evidence of substantial divergence, corresponding to FST = 0.128 (0.125,0.131) after accounting for possible biases due to minor alleles and uneven DNA amplification over the pooled s...