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

Dupuis, Julian R.; Brunet, Bryan M. T.; Bird, Heather M; Lumley, Lisa M.; Fagua, Giovanny; Boyle, B.; Levesque, Roger C.; Cusson, Michel; Powell, Jerry A.; Sperling, Felix A. H.

doi:10.1016/j.ympev.2017.04.001

Cited by 30 publications

(36 citation statements)

References 90 publications

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“…Although the resolution of internal relationships within the SBW species complex was not a goal of our study, such phylogenetic instability could result from recent divergences, incomplete lineage sorting, and hybridization between lineages (Lumley and Sperling ; Brunet et al . ; Dupuis et al ., ), as well as from rapid, simultaneous divergences during the Pliocene–Pleistocene transition (Fig. ), similar to the diversification proposed for Ditrysian lineages (Heikkilä et al ., ).…”

Section: Discussionsupporting

confidence: 85%

“…This was consistent with the observed high instability in the internal topology of the SBW in other analyses (Appendix File S6; Figs S1–S3) and previous studies (e.g. Stock & Castrovillo, ; Castrovillo, ; Sperling & Hickey, , ; Lumley & Sperling, ; Bird, ; Dupuis et al ., ).…”

Section: Resultsmentioning

confidence: 97%

“…Other well‐known species are the large aspen tortrix, C. conflictana (Walker), and a pest of plants in the rose family, C. rosaceana (Harris) (Reissig, ; Holsten & Hard, ). Previous studies on the phylogeny of Choristoneura have dealt with the morphology of species from North America and Eurasia based on male genitalia (Dang, ) or were included in commentaries or reviews (Razowski, , , , , ; Jinbo, ), while molecular phylogenetic studies have focused on the SBW complex (Sperling & Hickey, , ; Lumley & Sperling, , ; Dupuis et al ., ) and Archipini (Dombroskie & Sperling, ). Despite continuing attention, the delimitation of the genus remains unresolved and a stable phylogeny is lacking, due in part to low taxon sampling of key species (e.g.…”

Section: Introductionmentioning

confidence: 99%

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Genus delimitation, biogeography and diversification of Choristoneura Lederer (Lepidoptera: Tortricidae) based on molecular evidence

Fagua

Condamine

Dombroskie

et al. 2018

Systematic Entomology

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Widely known for pest species that include major modulators of temperate forests, the genus Choristoneura is part of the species-rich tribe Archipini of leafroller moths (Tortricidae). Delimitation of the genus has remained unresolved because no phylogeny has included species endemic to Africa and studies have often omitted the type species of the genus. Further taxonomic confusion has been generated by the transfer of Archips occidentalis (Walsingham) to Choristoneura, creating a homonym with Choristoneura occidentalis Freeman, an important defoliator of North American forests. To define the limits of the genus, we reconstructed a phylogeny using DNA sequences for mitochondrial cytochrome oxidase subunit I and nuclear ribosomal 28S genes. Our ingroup included 23 Choristoneura species-level taxa, complemented by a large sample of outgroups comprising 82 species of Archipini and other Tortricidae. We generated a time-calibrated tree using fossil and secondary calibrations and we inferred biogeographic and diversification processes in Choristoneura. Our analysis recovered the genus as polyphyletic, with Archips occidentalis, Choristoneura simonyi and Choristoneura evanidana excluded from the main clade. Based on the recovered phylogenies and a redefinition, we restrict Choristoneura primarily to species with a northern hemisphere distribution. Our analysis supports A. occidentalis as the sister group of Cacoecimorpha pronubana, C. simonyi as the sister of 'Xenotemna' pallorana, and C. evanidana as the sister of Archips purpurana. A new combination is proposed: Archips evanidana comb.n.; the availability of 'Xenotemna' as a valid name is discussed and A. occidentalis is considered as an orphaned name within the Archipini. We found support for a Holarctic origin of Choristoneura about 23 Ma, followed by early divergence in the Palearctic region. The main divergence occurred at 16 Ma, with one clade in the Nearctic and another in the Palearctic. Subsequent cladogenetic events were synchronous and related to herbivorous specialization, with each clade divided into coniferophagous and polyphagous lineages. Their specialization as conifer feeders temporally matched the expansion of boreal forest during the Miocene. or Zelotherses. Our phylogenetic analysis indicates the closest relationship to Cacoecimorpha; however, we need a larger sample of African and Far East Archipini to corroborate the hypothesis.

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Section: Discussionsupporting

confidence: 85%

Section: Resultsmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

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Genus delimitation, biogeography and diversification of Choristoneura Lederer (Lepidoptera: Tortricidae) based on molecular evidence

Fagua

Condamine

Dombroskie

et al. 2018

Systematic Entomology

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“…A statement as to whether (1) all criteria assessed by EFSA above for consideration as a potential quarantine pest were met and (2) if not, which one(s) were not met A statement as to whether (1) all criteria assessed by EFSA above for consideration as potential protected zone quarantine pest were met, and (2) if not, which one(s) were not met A statement as to whether (1) all criteria assessed by EFSA above for consideration as a potential regulated nonquarantine pest were met, and (2) if not, which one(s) were not met not exist anymore in the current catalogue. Of particular interest from the standpoint of forest health is the 'spruce budworm (Choristoneura fumiferana) species complex' (henceforth SBW), which comprises C. pinus, C. fumiferana, C. retiniana, C. carnana, C. lambertiana, C. occidentalis occidentalis, C. occidentalis biennis, and C. orae (Dupuis et al, 2017).…”

Section: Conclusion Of Pest Categorisation (Section 4)mentioning

confidence: 99%

“…() refer to ‘ C. occidentalis ’ in southern British Columbia without specifying the subspecies, or Stark and Borden () refer to C. lambertiana subretiniana , a subspecies which does not exist anymore in the current catalogue. Of particular interest from the standpoint of forest health is the ‘spruce budworm ( Choristoneura fumiferana ) species complex’ (henceforth SBW), which comprises C. pinus , C. fumiferana , C. retiniana , C. carnana , C. lambertiana , C. occidentalis occidentalis , C. occidentalis biennis , and C. orae (Dupuis et al., ).…”

mentioning

confidence: 99%

Pest categorisation of non‐EU Choristoneura spp.

Bragard¹,

Dehnen‐Schmutz²,

Serio³

et al. 2019

EFS2

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The Panel on Plant Health performed a pest categorisation of non-EU Choristoneura spp. Choristoneura is a well-defined insect genus in the family Tortricidae (Insecta: Lepidoptera). Species can be identified using taxonomic keys and molecular methods. The genus includes 52 species and subspecies colonising conifers and non-conifer trees in many areas in the world, among which five species are present in the EU. The non-EU species are listed in Annex IAI of Council Directive 2000/29/EC as Choristoneura spp. (non-European). Some Choristoneura species are important defoliators in North America, mainly on conifers but also on several broadleaf tree species and on non-forest crops. Females lay eggs in batches on the needles or the leaves, and overwintering occurs at the larval stage in a silken hibernaculum. Most species are univoltine, some are bivoltine and at least one subspecies has a 2-year life cycle. Pupation occurs on the twigs of conifers or in folded leaves of broadleaf trees. The adults are strong flyers, and the larvae can disperse by ballooning. The main pathways for entry are plants for planting, cut branches, fruits of host plants (including cones), round wood with bark and bark. Suitable host plants and climate would allow the establishment in the EU of the known, North American harmful species. Non-EU Choristoneura spp. satisfy all the criteria to be considered as Union quarantine pests. Measures are in place to prevent the introduction of non-EU Choristoneura spp. through the pathways described above. As non-EU Choristoneura spp. are not present in the EU and plants for planting are not the major pathway for spread, non-EU Choristoneura spp. do not meet the criteria to be considered as regulated non-quarantine pests.

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Continent‐wide population genomic structure and phylogeography of North America’s most destructive conifer defoliator, the spruce budworm (Choristoneura fumiferana)

Lumley

Pouliot

Laroche

et al. 2020

Ecology and Evolution

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The spruce budworm, Choristoneura fumiferana, is presumed to be panmictic across vast regions of North America. We examined the extent of panmixia by genotyping 3,650 single nucleotide polymorphism (SNP) loci in 1975 individuals from 128 collections across the continent. We found three spatially structured subpopulations:Western (Alaska, Yukon), Central (southeastern Yukon to the Manitoba-Ontario border), and Eastern (Manitoba-Ontario border to the Atlantic). Additionally, the most diagnostic genetic differentiation between the Central and Eastern subpopulations was chromosomally restricted to a single block of SNPs that may constitute an island of differentiation within the species. Geographic differentiation in the spruce budworm parallels that of its principal larval host, white spruce (Picea glauca), providing evidence that spruce budworm and spruce trees survived in the Beringian refugium through the Last Glacial Maximum and that at least two isolated spruce budworm populations diverged with spruce/fir south of the ice sheets. Gene flow in the spruce budworm may also be affected by mountains in western North America, habitat isolation in West Virginia, regional adaptations, factors related to dispersal, and proximity of other species in the spruce budworm species complex. The central and eastern geographic regions contain individuals that assign to Eastern and Central subpopulations, respectively, indicating that these barriers are not complete.Our discovery of previously undetected geographic and genomic structure in the spruce budworm suggests that further population modelling of this ecologically important insect should consider regional differentiation, potentially co-adapted blocks of genes, and gene flow between subpopulations. K E Y W O R D SChoristoneura, comparative phylogeography, genotyping-by-sequencing, Picea glauca | 915 LUMLEY Et aL.

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

Cited by 30 publications

References 90 publications

Genus delimitation, biogeography and diversification of Choristoneura Lederer (Lepidoptera: Tortricidae) based on molecular evidence

Genus delimitation, biogeography and diversification of Choristoneura Lederer (Lepidoptera: Tortricidae) based on molecular evidence

Pest categorisation of non‐EU Choristoneura spp.

Continent‐wide population genomic structure and phylogeography of North America’s most destructive conifer defoliator, the spruce budworm (Choristoneura fumiferana)

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