Data from: Historical introgression and the role of selective vs. neutral processes in structuring nuclear genetic variation (AFLP) in a circumpolar marine fish, the capelin (Mallotus villosus)

The capelin (Mallotus villosus) is a widespread marine fish species for
which previous work has identified geographically distinct mtDNA clades,
the frontiers of which are well within adult and larval dispersal
capabilities. Here, we use AFLPs to test for the presence of nuclear gene
flow among clades. In addition, we evaluate genetic structuring within one
clade, the Northwest Atlantic (NWA). We found that each of the mtDNA
clades corresponds with a unique nuclear DNA genetic cluster. Within the
NWA clade, we detected individuals with small but significant amounts of
genetic ancestry from other clades, likely due to historical
introgression. Further support for historical introgression comes from
analyses of variance in locus-specific differentiation, which support
introgression between some clades and divergence without gene flow between
others. Within the NWA, we identified two genetic clusters that correspond
to sites in geographically adjacent areas. However, these clusters differ
primarily at ‘outlier’ loci, and a genetic subdivision (K = 2) was not
supported by genetic clustering programs using neutral loci. Significant
neutral FST differentiation was found only between sites that otherwise
differed at outlier loci. Thus, these populations may be in the initial
stages of ‘isolation by adaptation’. These results suggest strong
between-clade reproductive isolation despite opportunities for gene flow
and support the hypothesis that selection can contribute to divergence in
otherwise ‘open’ systems.