Data from: History, geography, and host use shape genome-wide patterns of genetic variation in the redheaded pine sawfly (Neodiprion lecontei)

Divergent host use has long been suspected to drive population
differentiation and speciation in plant-feeding insects. Evaluating the
contribution of divergent host use to genetic differentiation can be
difficult, however, as dispersal limitation and population structure may
also influence patterns of genetic variation. In this study, we use
double-digest restriction-associated DNA (ddRAD) sequencing to test the
hypothesis that divergent host use contributes to genetic differentiation
among populations of the redheaded pine sawfly (Neodiprion lecontei), a
widespread pest that uses multiple Pinus hosts throughout its range in
eastern North America. Because this species has a broad range and
specializes on host plants known to have migrated extensively during the
Pleistocene, we first assess overall genetic structure using model-based
and model-free clustering methods, and identify three geographically
distinct genetic clusters. Next, using a composite-likelihood approach
based on the site frequency spectrum and a novel strategy for maximizing
the utility of linked RAD markers, we infer the population topology and
date divergence to the Pleistocene. Based on existing knowledge of Pinus
refugia, estimated demographic parameters, and patterns of diversity among
sawfly populations, we propose a Pleistocene divergence scenario for N.
lecontei. Finally, using Mantel and partial Mantel tests, we identify a
significant relationship between genetic distance and geography in all
clusters, and between genetic distance and host use in two of three
clusters. Overall, our results indicate that Pleistocene isolation,
dispersal limitation, and ecological divergence all contribute to
genome-wide differentiation in this species, and support the hypothesis
that host use is a common driver of population divergence in
host-specialized insects.