Data from: Genetic divergence with ongoing gene flow is maintained by the use of different hosts in phytophagous ladybird beetles genus Henosepilachna

Adaptation to different environments can promote population divergence via
natural selection even in the presence of gene flow–a phenomenon that
typically occurs during ecological speciation. To elucidate how natural
selection promotes and maintains population divergence during speciation,
we investigated the population genetic structure, degree of gene flow and
heterogeneous genomic divergence in three closely related Japanese
phytophagous ladybird beetles: Henosepilachna pustulosa, H. niponica and
H. yasutomii. These species act as a generalist, a wild thistle (Cirsium
spp.) specialist and a blue cohosh (Caulophyllum robustum) specialist,
respectively, and their ranges differ accordingly. The two specialist
species widely co-occur but are reproductively isolated solely due to
their high specialisation to a particular host plant. Genome-wide
amplified fragment-length polymorphism (AFLP) markers and mitochondrial
cytochrome c oxidase subunit I (COI) gene sequences demonstrated obvious
genome-wide divergence associated with both geographic distance and
ecological divergence. However, a hybridisation assessment for both AFLP
loci and the mitochondrial sequences revealed a certain degree of
unidirectional gene flow between the two sympatric specialist species.
Principal coordinates analysis (PCoA) based on all of the variable AFLP
loci demonstrated that there are genetic similarities between populations
from adjacent localities irrespective of the species (i.e. host range).
However, a further comparative genome scan identified a few fractions of
loci representing approximately 1% of all loci as different-host
associated outliers. These results suggest that these three species had a
complex origin, which could be obscured by current gene flow, and that
ecological divergence can be maintained with only a small fraction of the
genome is related to different host use even when there is a certain
degree of gene flow between sympatric species pairs.