Phylogenomics of the Choristoneura fumiferana species complex (Lepidoptera: Tortricidae)
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Abstract
The phylogenetic relationships of the destructive spruce budworm group of forest pests (Choristoneura fumiferana species complex) have previously been explored using allozymes, microsatellites, mitochondrial genes and a nuclear gene, but remain poorly resolved with conflicting topologies. I used mass sampling of single nucleotide polymorphisms (SNPs) across their genome in a genotyping-by-sequencing approach. Over 100 000 SNPs with greater than 75% coverage in 99 specimens (ApeKI restriction enzyme digest) or 144 specimens (PstI-MspI digest) resolved C. fumiferana, C. carnana, C. retiniana, and C. pinus as strongly-supported monophyletic species. The most distinct species, C. pinus, yielded 945 autapomorphic SNPs, and was definitively placed as basal to the whole species complex, contrasting with previous mtDNA results. The functions of genes homologous to the sequence surrounding the diagnostic C. pinus SNPs included detoxification, morphological differences, flight, and sensory perception, providing insights into the genetic basis of species differences.