Inadequate molecular identification protocols for invasive pests threaten biosecurity

Doorenweerd, Camiel; Jose, Michael San; Leblanc, Luc; Rubinoff, Daniel

doi:10.1111/syen.12581

Cited by 4 publications

(6 citation statements)

References 56 publications

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“…As such, a combination of data sources for species delimitation—i.e., morphology, biogeography, host records, lure attraction and genomic data, as well as robust and continued sampling across the distribution of species—will likely remain the best way forward in the foreseeable future. Increased accuracy of species delimitation and increased rates of species discovery will be crucial to ensure biosecurity across the globe to protect agricultural production (Doorenweerd et al 2023).…”

Section: Discussionmentioning

confidence: 99%

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Genomic data reveal new species and the limits of mtDNA barcode diagnostics to contain a global pest species complex (Diptera: Tephritidae: Dacinae)

Doorenweerd,

San Jose,

Geib

et al. 2023

Systematic Entomology

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The Oriental fruit fly Bactrocera dorsalis (Hendel), a global pest that can decimate regional fruit industries and elicit international quarantines, has been the subject of considerable taxonomic confusion. Previous phylogenetic work revealed that B. dorsalis is part of a monophyletic clade containing 12 species. We present restriction site‐associated DNA sequencing (RAD‐seq) genomic data for 2,292 specimens, which unequivocally supports the delimitation of two new species, here described as Bactrocera borneoensis sp. n. Doorenweerd & San Jose and B. incognita sp. n. Doorenweerd & San Jose. We additionally obtained 1,985 Cytochrome C oxidase I (COI) sequences for a subset of the specimens to see which species can be diagnosed with this mtDNA marker and conclude that B. dorsalis, B. incognita, B. carambolae Drew & Hancock, B. raiensis Drew & Hancock, B. occipitalis (Bezzi) and B. kandiensis Drew & Hancock cannot be identified reliably using COI due to introgression—but the newly described species B. borneoensis can be identified using COI. The supposed innocuous species B. raiensis distribution is underestimated in Asia and Africa. Bactrocera kandiensis COI genotypes occur in African flies, but RAD‐seq data confirm that these are B. dorsalis with introgressed B. kandiensis COI. The phylogenomic dataset brings new light to the extent of the B. dorsalis s.l. clade and the morphological and molecular confusion based on COI. This will have ramifications for ecological data—including host and distribution ranges—associated with B. dorsalis s.l. clade species, pest identification protocols and our understanding of the economic importance of the various species in the clade.

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Section: Discussionmentioning

confidence: 99%

“…Increased accuracy of species delimitation and increased rates of species discovery will be crucial to ensure biosecurity across the globe to protect agricultural production (Doorenweerd et al 2023).…”

Section: Phylogenomics To Reveal Cryptic Taxamentioning

confidence: 99%

Genomic data reveal new species and the limits of mtDNA barcode diagnostics to contain a global pest species complex (Diptera: Tephritidae: Dacinae)

Doorenweerd,

San Jose,

Geib

et al. 2023

Systematic Entomology

Self Cite

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“…We recognize several issues that can be addressed in future studies of the utility of barcodes. The first is the comprehensive sampling of intraspecific genetic diversity [13,39]. Our datasets had various amounts of intraspecific sampling, but likely none represented the maximum genetic distance among conspecifics due to research constraints (such as time and funding).…”

Section: Discussionmentioning

confidence: 99%

“…More than 12 million sequences have been generated in the past 20 years (https://boldsystems.org, accessed on 23 January 2023) and have been included in more than 3700 "DNA barcoding" studies [12]. Although the utility of mtDNA COI sequences to help resolve taxonomic mysteries is undeniable, reliance on one "barcode" gene has been discussed [13]. The unique properties of mtDNA genes make them subject to several issues that can lead to misidentifications.…”

Section: Introductionmentioning

confidence: 99%

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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“…Despite its crucial importance, the entry process remains the most poorly studied stage of pest invasions due to the difficulties in detecting very small populations at the early stage of dispersal 16 . Besides, issues might occur in the identification of some taxa 17 , 18 , mainly due to difficulties in taxonomically delineating species or because of unspecificity of signs or symptoms. Thus, organisms might be detected only later in the invasion process when already spreading and causing damage 19 .…”

Section: Background and Summarymentioning

confidence: 99%

A spatio-temporal dataset of plant pests’ first introductions across the EU and potential entry pathways

Rosace,

Cendoya,

Mattion

et al. 2023

Sci Data

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World trade has greatly increased in recent decades, together with a higher risk of introducing non-indigenous pests. Introduction trends show no sign of saturation, and it seems likely that many more species will enter and establish in new territories in the future. A key challenge in analysing pest invasion patterns is the paucity of historical data on pest introductions. A comprehensive dataset of pests’ introductions in the EU, including their spatial occurrences, is not currently available and information is scattered across different sources or buried in the scientific literature. Therefore, we collected pests’ introduction information (e.g., year, host) from online scientific databases and literature; we then gathered primary spatial data related to the site of first introductions. Finally, we identified the potential pathways of entry for each pest. The dataset contains expert-revised data on 278 pests introduced in the EU between 1999 and 2019, alongside their spatial occurrence and potential pathways of entry, providing a basis to better understand the factors associated with the likelihood of pest introduction. It is important to note that this dataset does not contain the current distribution of the introduced pests, but only records of their first introduction in the EU.

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Inadequate molecular identification protocols for invasive pests threaten biosecurity

Abstract: Molecular markers are crucial to identify new pest invasions before they can become established but current methods are often inadequate.

Cited by 4 publications

References 56 publications

Genomic data reveal new species and the limits of mtDNA barcode diagnostics to contain a global pest species complex (Diptera: Tephritidae: Dacinae)

Genomic data reveal new species and the limits of mtDNA barcode diagnostics to contain a global pest species complex (Diptera: Tephritidae: Dacinae)

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

A spatio-temporal dataset of plant pests’ first introductions across the EU and potential entry pathways

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