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

• Published in: Molecular phylogenetics and evolution 2017-06, Vol.111, p.158-168
• Main Authors: Dupuis, J.R., Brunet, B.M.T., Bird, H.M., Lumley, L.M., Fagua, G., Boyle, B., Levesque, R., Cusson, M., Powell, J.A., Sperling, F.A.H.
• Format: Article
• Language: English
• Subjects: Animals; Discriminant Analysis; Genetic Speciation; Genetics, Population; Genome, Insect; Genotype; Genotyping-by-sequencing; Geography; Moths - genetics; North America; Phylogenomics; Phylogeny; Polymorphism, Single Nucleotide - genetics; Population genetics; Principal Component Analysis; RAD-seq; Sequence Analysis, DNA; Species relationships; Species Specificity; Systematics; United States
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2017.04.001

[Display omitted] •Genotyping-by-sequencing has resolved relationships in the spruce budworm complex.•Multiple analyses agreed on an unexpectedly basal placement forChoristoneura pinus.•Relationships remain ambiguous for a clade of western species.•Speciation has likely been driven by a combination of ecological factors. 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.