Evaluating species boundaries using coalescent delimitation in pine-killing Monochamus (Coleoptera: Cerambycidae) sawyer beetles

Gorring, Patrick; Farrell, Brian D.

doi:10.1016/j.ympev.2023.107777

Cited by 7 publications

(9 citation statements)

References 95 publications

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“…Nucleotide diversity at the species level, especially in third positions, allows for the discrimination of recently diverged taxa, even though no intron is usually present. CAD is a single-copy gene, and CPS barcode lengths under 1000 bp can be confidently amplified using a nested PCR procedure [31,33] and primers (Table 1). The locus is evolving quickly enough to discriminate species, while not so fast as to saturate within a tribe.…”

Section: Discussionmentioning

confidence: 99%

“…The carbamoyl-phosphate synthetase 2 locus of CAD has been useful in specieslevel phylogenetic studies [32,37,40] and species diagnostics [21] (Gorring unpub.). We evaluated the <1000 bp region sequenced for each genus and reduced the length of certain long Bembidion sequences to a shorter shared region.…”

Section: Taxon and Gene Selectionmentioning

confidence: 99%

“…Xyleborus placed all outgroups properly for CAD, while the outgroup genus Euwallacea was placed incorrectly in the COI tree. The "true" multigene published trees with substitutions modeled by partition always excluded the outgroup taxa except with Monochamus, where the Goes genus was not placed with high confidence either inside or outside Monochamus [33].…”

Section: Taxon Placement and Diagnostic Potentialmentioning

confidence: 99%

“…In a few studies, partial CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase) nuclear gene sequences were useful in the identification of fly and beetle species [20,28,29]. Given the development and use of the CAD CPS (carbamoyl-phosphate synthetase 2) region in beetle phylogenetic studies [30][31][32][33], data exist to explore its use as a nuclear barcode gene for beetles. For example, Cognato et al [20] created a barcoding database of partial CAD sequences for ambrosia beetles (Scolytinae: Xyleborini).…”

Section: Introductionmentioning

confidence: 99%

“…Given this preliminary evidence, we investigated the potential of CAD as a nuclear barcoding gene for beetles. We assembled previously published COI and CAD sequences with sufficient intraspecific sampling for beetle families Cerambycidae [33], Curculionidae: Scolytinae [20,[34][35][36], and Carabidae [31,37]. We analyzed these datasets by evaluating their composition, performing taxon placement tests, and measuring intra-and interspecific differences to assess the occurrence of barcoding gaps.…”

Section: Introductionmentioning

confidence: 99%

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The Case for a Nuclear Barcode: Using the CAD CPS Region for Species and Genus Level Discrimination in Beetles

Gorring

Cognato

2023

Diversity

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DNA barcoding has revolutionized how we discover, identify, and detect species. A substantial foundation has been established with millions of mitochondrial cytochrome c oxidase I sequences freely available for eukaryotes. However, issues with COI ranging from uniparental inheritance and small genetic population sizes to nuclear and asymmetric introgression can impede its use. We propose using CAD as the “nuclear barcode” to complement the COI barcode and ameliorate these concerns. We focused on beetles from taxonomically diverse species-level studies that used COI and CAD. An ambiguous barcode gap was present between intra- and interspecific genetic distances in CAD and COI; this led to difficulty with automated gap detection methods. We found pseudogenes, problematic population structure, introgression, and incomplete lineage sorting represented in the COI data. A CAD gene tree illuminated these cryptic problems. Placement tests of species and outgroups using distance-based tree building were largely successful for CAD, demonstrating its phylogenetic signal at the species and genus levels. Species placement issues were typically unique to one locus, allowing for recognition of misdiagnosis. We conclude that a CAD barcode is a valuable tool for beetle diagnostics, metabarcoding, and faunistic surveys.

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Section: Discussionmentioning

confidence: 99%

Section: Taxon and Gene Selectionmentioning

confidence: 99%

Section: Taxon Placement and Diagnostic Potentialmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The Case for a Nuclear Barcode: Using the CAD CPS Region for Species and Genus Level Discrimination in Beetles

Gorring

Cognato

2023

Diversity

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Disentangling disjunctus: an integrated analysis of the patent leather beetle, Odontotaenius disjunctus complex (Passalidae: Coleoptera) with the description of two new species

Fontanella,

Whitaker,

Smallwood

et al. 2024

Systematics and Biodiversity

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Non‐destructive molecular methods to identify Monochamus alternatus (Coleoptera: Cerambycidae), a major vector of Bursaphelenchus xylophilus (Nematoda: Aphelenchoididae)

Qi,

Nan,

Zhao

et al. 2024

J Applied Entomology

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Monochamus alternatus is one of the most important borers of conifers and the main vector of the pinewood nematode, Bursaphelenchus xylophilus, the causal agent of pine wilt disease. It causes massive death of pine trees and seriously affects the health of forest ecosystems. Traditionally, adults or larvae are identified by morphological or molecular methods. However, diagnosing M. alternatus larvae at different instars collected from forests is expensive and time‐consuming. Non‐destructive molecular diagnostic protocols are, therefore, being developed to detect biological traces (i.e. exuviae, excreta) and to determine the distribution and spread of this pest. In this study, based on the alignment of mitochondrial DNA cytochrome oxidase subunit I (COI) gene sequences of M. alternatus and other insect species, we designed the primer pair of Mal‐SF/Mal‐SR and probe of Mal‐P for M. alternatus. TaqMan probe‐based qPCR was developed to identify the occurrence of M. alternatus in forests by amplifying the DNA samples obtained from its adult, larva, frass, excreta and exuviae. The amplification results were very effective. The lowest amount of M. alternatus DNA that could be detected with a Cq of 31.93 in the mixed samples was 0.64 pg, showing very high sensitivity. This assay can easily identify M. alternatus from other non‐target wood‐borer species using its frass and exuviae, providing a new diagnostic protocol for monitoring the occurrence and distribution of M. alternatus in forests.

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Evaluating species boundaries using coalescent delimitation in pine-killing Monochamus (Coleoptera: Cerambycidae) sawyer beetles

Cited by 7 publications

References 95 publications

The Case for a Nuclear Barcode: Using the CAD CPS Region for Species and Genus Level Discrimination in Beetles

The Case for a Nuclear Barcode: Using the CAD CPS Region for Species and Genus Level Discrimination in Beetles

Disentangling disjunctus: an integrated analysis of the patent leather beetle, Odontotaenius disjunctus complex (Passalidae: Coleoptera) with the description of two new species

Non‐destructive molecular methods to identify Monochamus alternatus (Coleoptera: Cerambycidae), a major vector of Bursaphelenchus xylophilus (Nematoda: Aphelenchoididae)

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