title: Genome-wide SNPs resolve phylogenetic relationships in the North American spruce budworm (Choristoneura fumiferana) species complex.
abstract: 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.
authors.affiliation: Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, Alberta T6G 2E9, Canada. Electronic address: jrdupuis@hawaii.edu.
authors.forename: J R
authors.initials: JR
authors.lastname: Dupuis
authors.affiliation: Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, Alberta T6G 2E9, Canada.
authors.forename: B M T
authors.initials: BMT
authors.lastname: Brunet
authors.affiliation: Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, Alberta T6G 2E9, Canada.
authors.forename: H M
authors.initials: HM
authors.lastname: Bird
authors.affiliation: Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, Alberta T6G 2E9, Canada; Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du PEPS, PO Box 10380, Stn. Ste-Foy, Quebec City, Canada.
authors.forename: L M
authors.initials: LM
authors.lastname: Lumley
authors.affiliation: Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, Alberta T6G 2E9, Canada; Pontificia Universidad Javeriana, Department of Biology, Carrera 7 No. 40-62, Bogotá D.C., Colombia.
authors.forename: G
authors.initials: G
authors.lastname: Fagua
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada.
authors.forename: B
authors.initials: B
authors.lastname: Boyle
authors.affiliation: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada.
authors.forename: R
authors.initials: R
authors.lastname: Levesque
authors.affiliation: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du PEPS, PO Box 10380, Stn. Ste-Foy, Quebec City, Canada.
authors.forename: M
authors.initials: M
authors.lastname: Cusson
authors.affiliation: Department of Environmental Science, Policy and Management, University of California at Berkeley, 130 Mulford Hall #3114, Berkeley, CA, USA.
authors.forename: J A
authors.initials: JA
authors.lastname: Powell
authors.affiliation: Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, Alberta T6G 2E9, Canada.
authors.forename: F A H
authors.initials: FAH
authors.lastname: Sperling
mesh_terms: D000818:Animals; D016002:Discriminant Analysis; D049810:Genetic Speciation; D005828:Genetics, Population; D049750:Genome, Insect; D005838:Genotype; D005843:Geography; D009036:Moths / Q000235:genetics*; D009656:North America; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D025341:Principal Component Analysis; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D014481:United States
keywords: Genotyping-by-sequencing; Phylogenomics; Population genetics; RAD-seq; Species relationships; Systematics