Towards a better future for DNA barcoding: Evaluating monophyly- and distance-based species identification using COI gene fragments of Dacini fruit flies.

Autor: Doorenweerd C; Entomology Section, Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA., San Jose M; Entomology Section, Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA., Leblanc L; Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, Idaho, USA., Barr N; United States Department of Agriculture, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science & Technology, Insect Management and Molecular Diagnostics Laboratory, Edinburg, Texas, USA., Geib SM; Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, Hawaii, USA., Chung AYC; Forest Research Centre, Sabah Forestry Department, Sandakan, Sabah, Malaysia., Dupuis JR; Department of Entomology, University of Kentucky, Lexington, Kentucky, USA., Ekayanti A; Niogret Ecology Consulting LLC, Wotu, Luwu Timor, Sulawesi Seleaton, Indonesia., Fiegalan E; Department of Crop Protection, College of Agriculture, Central Luzon State University, Science City of Muñoz, Nueva Ecija, Philippines., Hemachandra KS; Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka., Aftab Hossain M; Insect Biotechnology Division, Institute of Food and Radiation Biology, Bangladesh Atomic Energy Commission, Dhaka, Bangladesh., Huang CL; Institute of Oceanography, Minjiang University, Fuzhou, Fujian, China., Hsu YF; Department of Life Science, National Taiwan Normal University, Taipei, Taiwan, ROC., Morris KY; Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, Hawaii, USA., Maryani A Mustapeng A; Forest Research Centre, Sabah Forestry Department, Sandakan, Sabah, Malaysia., Niogret J; Centre for Tropical Environmental & Sustainability Science, Nguma-Bada Campus, James Cook University, Smithfield, Queensland, Australia., Pham TH; Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology (VAST), Hue, Vietnam.; Vietnam National Museum of Nature & Graduate School of Science and Technology, VAST, Hanoi, Vietnam., Thi Nguyen N; Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi, Vietnam., Sirisena UGAI; Department of Plant Sciences, Faculty of Agriculture, Rajarata University of Sri Lanka, Mihintale, Sri Lanka., Todd T; United States Department of Agriculture, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science & Technology, Insect Management and Molecular Diagnostics Laboratory, Edinburg, Texas, USA., Rubinoff D; Entomology Section, Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA.
Jazyk: angličtina
Zdroj: Molecular ecology resources [Mol Ecol Resour] 2024 Aug; Vol. 24 (6), pp. e13987. Date of Electronic Publication: 2024 Jul 02.
DOI: 10.1111/1755-0998.13987
Abstrakt: The utility of a universal DNA 'barcode' fragment (658 base pairs of the Cytochrome C Oxidase I [COI] gene) has been established as a useful tool for species identification, and widely criticized as one for understanding the evolutionary history of a group. Large amounts of COI sequence data have been produced that hold promise for rapid species identification, for example, for biosecurity. The fruit fly tribe Dacini holds about a thousand species, of which 80 are pests of economic concern. We generated a COI reference library for 265 species of Dacini containing 5601 sequences that span most of the COI gene using circular consensus sequencing. We compared distance metrics versus monophyly assessments for species identification and although we found a 'soft' barcode gap around 2% pairwise distance, the exceptions to this rule dictate that a monophyly assessment is the only reliable method for species identification. We found that all fragments regularly used for Dacini fruit fly identification >450 base pairs long provide similar resolution. 11.3% of the species in our dataset were non-monophyletic in a COI tree, which is mostly due to species complexes. We conclude with recommendations for the future generation and use of COI libraries. We revise the generic assignment of Dacus transversus stat. rev. Hardy 1982, and Dacus perpusillus stat. rev. Drew 1971 and we establish Dacus maculipterus White 1998 syn. nov. as a junior synonym of Dacus satanas Liang et al. 1993.
(© 2024 John Wiley & Sons Ltd.)
Databáze: MEDLINE
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