Genome-wide SNPs resolve phylogenetic relationships in the North American spruce budworm (Choristoneura fumiferana) species complex

J. R. Dupuis, B. M.T. Brunet, H. M. Bird, L. M. Lumley, G. Fagua, B. Boyle, R. Levesque, M. Cusson, J. A. Powell, F. A.H. Sperling

Research output: Contribution to journalArticlepeer-review

27 Scopus citations


High throughput sequencing technologies have revolutionized the potential to reconcile incongruence between gene and species trees, and numerous approaches have been developed to take advantage of these advances. Genotyping-by-sequencing is becoming a regular tool for gathering phylogenetic data, yet comprehensive evaluations of phylogenetic methods using these data are sparse. Here we use multiple phylogenetic and population genetic methods for genotyping-by-sequencing data to assess species relationships in a group of forest insect pests, the spruce budworm (Choristoneura fumiferana) species complex. With few exceptions, all methods agree on the same relationships, most notably placing C. pinus as basal to the remainder of the group, rather than C. fumiferana as previously suggested. We found strong support for the monophyly of C. pinus, C. fumiferana, and C. retiniana, but more ambiguous relationships and signatures of introgression in a clade of western lineages, including C. carnana, C. lambertiana, C. occidentalis occidentalis, C. occidentalis biennis, and C. orae. This represents the most taxonomically comprehensive genomic treatment of the spruce budworm species group, which is further supported by the broad agreement among multiple methodologies.

Original languageEnglish
Pages (from-to)158-168
Number of pages11
JournalMolecular Phylogenetics and Evolution
StatePublished - Jun 1 2017

Bibliographical note

Funding Information:
We thank Alberta Environment and Sustainable Resource Development, G. Anweiler, S. Brunet, Canadian Forest Service, J. De Benedictis, J. Dombroskie, J. Doucette, A. Hundsdoerfer, J.F. Landry, L. Nolan, B. Proshek, A. Roe, D. Rubinoff, Saskatchewan Environment, and C. Whitehouse for assistance in specimen collection and two anonymous reviewers for comments. Funding was provided by an Alberta Innovates Bio Solutions grant (# VCS-11-034) and National Science and Engineering Research Council Discovery grant (# 217174) to FAHS, a Genomics Research and Development Initiative (GRDI) grant to M. Cusson, a Genome Quebec grant (GreenSNPs project) to R. Levesque, and a scholarship from the Academic Vice rectory of the ?Pontificia Universidad Javeriana-Bogot?? (Agreement DJE-012-2011)-Administrative Department of Science, Technology and Innovation of Colombia (COLCIENCIAS, APCC-80-134) to G. Fagua. This research was enabled in part by support provided by WestGrid ( and Compute Canada Calcul Canada (


  • Genotyping-by-sequencing
  • Phylogenomics
  • Population genetics
  • RAD-seq
  • Species relationships
  • Systematics

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics


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