History, geography and host use shape genomewide patterns of genetic variation in the redheaded pine sawfly (Neodiprion lecontei)

Robin K. Bagley, Vitor C. Sousa, Matthew L. Niemiller, Catherine R. Linnen

Research output: Contribution to journalArticlepeer-review

29 Scopus citations


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 genomewide differentiation in this species and support the hypothesis that host use is a common driver of population divergence in host-specialized insects.

Original languageEnglish
Pages (from-to)1022-1044
Number of pages23
JournalMolecular Ecology
Issue number4
StatePublished - Feb 1 2017

Bibliographical note

Funding Information:
We thank Brant Peterson, Emily Kay and Jesse Weber for advice on ddRAD library preparation and demultiplexing; Gideon Bradburd for helpful discussions on IBD and IBE; Laurent Excoffier for his advice regarding demographic analyses; and five anonymous reviewers whose comments helped improve this manuscript. We thank the past and present members of the Linnen laboratory, especially Joanna Larson, Kim Vertacnik, Emily Bendall, John Terbot II, Danielle Herrig, Rachael Ziembroski and Mary Collins, for comments on the manuscript, assistance in the field and maintenance of sawfly colonies. Michael Hillstrom, Jeff Kastle, Scott Lint, Jen Weimer, Kyle Lombard, A. Zeppa, T. Frontz, Laurie Reid, Kaye Murray, Doug Audley, Rob McFerrin, Bev Taulbee, Jill Bagley, Keith Cals, Duane (Spike) Bagley, Maryanna Bagley and Jackson Mosely provided N. lecontei samples. Collecting permits were provided by the Florida Park Service. Funding for this research was provided by the National Science Foundation (DEB-1257739; CRL); a University of Kentucky Multi-Year Fellowship, Daniel R Reedy award and Ribble mini-grant (RKB); a USDA-NIFA Predoctoral Fellowship (2015-67011-22803; RKB); Swiss NSF grants (31003A-143393 and 310030B-166605; VCS); and national funds through Fundação para a Ciência e a Tecnologia (UID/BIA/00329/2013; VCS). This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1053575.

Publisher Copyright:
© 2016 John Wiley & Sons Ltd


  • Pleistocene divergence
  • demographic modelling
  • ecological speciation
  • isolation by colonization
  • isolation by distance
  • isolation by environment

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics


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