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

• Published in: Systematic entomology Vol. 49; no. 2; pp. 279 - 293
• Main Authors: Doorenweerd, Camiel, San Jose, Michael, Geib, Scott, Barr, Norman, Rubinoff, Daniel
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.04.2024; Wiley Subscription Services, Inc
• Subjects: Africa; Asia; Bactrocera dorsalis; Bactrocera kandiensis; Bactrocera raiensis; cryptic species; Cytochrome-c oxidase; data collection; diagnostic techniques; DNA; DNA barcoding; DNA sequencing; Economic importance; entomology; fruits; Genomics; Genotypes; Geographical distribution; introgression; invasive species; Mitochondrial DNA; monophyly; New species; Oriental fruit fly; pest identification; Pests; Phylogeny; RAD‐seq; taxonomy; Asia; Africa
• ISSN: 0307-6970; 1365-3113
• DOI: 10.1111/syen.12616

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. Our RAD‐seq genomic dataset with 2295 specimens clearly delimits 12 species in the Oriental fruit fly clade. Two species are newly described, which were previously confused with B. dorsalis. COI sequences cannot be used to identify the majority of the species in the clade because of introgression.