The Essential Role of Taxonomic Expertise in the Creation of DNA Databases for the Identification and Delimitation of Southeast Asian Ambrosia Beetle Species (Curculionidae: Scolytinae: Xyleborini)
DNA holds great potential for species identification and efforts to create a DNA database of all animals and plants currently contains >7.5 million sequences representing ~300,000 species. This promise of a universally applicable identification tool suggests that morphologically based tools a...
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Frontiers Media S.A.
2020-02-01
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Series: | Frontiers in Ecology and Evolution |
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Online Access: | https://www.frontiersin.org/article/10.3389/fevo.2020.00027/full |
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record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Anthony I. Cognato Gina Sari Sarah M. Smith Roger A. Beaver You Li Jiri Hulcr Bjarte H. Jordal Hisashi Kajimura Ching-Shan Lin Thai Hong Pham Sudhir Singh Wisut Sittichaya |
spellingShingle |
Anthony I. Cognato Gina Sari Sarah M. Smith Roger A. Beaver You Li Jiri Hulcr Bjarte H. Jordal Hisashi Kajimura Ching-Shan Lin Thai Hong Pham Sudhir Singh Wisut Sittichaya The Essential Role of Taxonomic Expertise in the Creation of DNA Databases for the Identification and Delimitation of Southeast Asian Ambrosia Beetle Species (Curculionidae: Scolytinae: Xyleborini) Frontiers in Ecology and Evolution CAD COI DNA barcoding species delimitation species identification |
author_facet |
Anthony I. Cognato Gina Sari Sarah M. Smith Roger A. Beaver You Li Jiri Hulcr Bjarte H. Jordal Hisashi Kajimura Ching-Shan Lin Thai Hong Pham Sudhir Singh Wisut Sittichaya |
author_sort |
Anthony I. Cognato |
title |
The Essential Role of Taxonomic Expertise in the Creation of DNA Databases for the Identification and Delimitation of Southeast Asian Ambrosia Beetle Species (Curculionidae: Scolytinae: Xyleborini) |
title_short |
The Essential Role of Taxonomic Expertise in the Creation of DNA Databases for the Identification and Delimitation of Southeast Asian Ambrosia Beetle Species (Curculionidae: Scolytinae: Xyleborini) |
title_full |
The Essential Role of Taxonomic Expertise in the Creation of DNA Databases for the Identification and Delimitation of Southeast Asian Ambrosia Beetle Species (Curculionidae: Scolytinae: Xyleborini) |
title_fullStr |
The Essential Role of Taxonomic Expertise in the Creation of DNA Databases for the Identification and Delimitation of Southeast Asian Ambrosia Beetle Species (Curculionidae: Scolytinae: Xyleborini) |
title_full_unstemmed |
The Essential Role of Taxonomic Expertise in the Creation of DNA Databases for the Identification and Delimitation of Southeast Asian Ambrosia Beetle Species (Curculionidae: Scolytinae: Xyleborini) |
title_sort |
essential role of taxonomic expertise in the creation of dna databases for the identification and delimitation of southeast asian ambrosia beetle species (curculionidae: scolytinae: xyleborini) |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Ecology and Evolution |
issn |
2296-701X |
publishDate |
2020-02-01 |
description |
DNA holds great potential for species identification and efforts to create a DNA database of all animals and plants currently contains >7.5 million sequences representing ~300,000 species. This promise of a universally applicable identification tool suggests that morphologically based tools and taxonomists will soon not have utility. Here we demonstrate that DNA-based identification is not reliable without the contributions of taxonomic experts. We use ambrosia beetles (Xyleborini), which are known for great diversity as well as global invasions and damage, as a test case. Recent xyleborine introductions have caused major economic and ecological losses, thus timely species identifications of new invaders are necessary. This need is hampered by a paucity of identification tools and a fauna that is only moderately documented. To help alleviate deficiencies in their identification, we created COI and CAD DNA barcode databases (490 and 429 specimens), representing over half of the known fauna of Southeast Asia (165/316 species). Taxonomic experts identified species based on original descriptions and type specimens. Tree, distance, and iterative methods were used to assess the identification and delimitation of species. High intra- and interspecific COI distances were observed for congeneric species and attributed to the beetle's inbreeding system. Neither of the two markers provided 100% identification success but with the neighbor-joining tree-based method, 80% of species were identified by both genes. As for species delimitation, an obvious barcode gap between intra- and interspecific differences was not observed. Correspondence between distance-based groups and morphology-based species was poor. In a demonstration of iterative taxonomy, we constructed parsimony-based phylogenies using COI and CAD sequences for two genera. Although not all clades were resolved or supported, we provided better explanations for species boundaries in light of morphological and DNA sequence differences. Confident species identifications demonstrated <3% COI and <1% CAD difference and recognition of new species became more probable when there was >10–12% COI and/or >2–3% CAD. Involvement of taxonomic experts from the start of this project was essential for the creation of a stable foundation for the DNA identification of xyleborine species. In general, their role in DNA barcoding cannot be underestimated and is further discussed. |
topic |
CAD COI DNA barcoding species delimitation species identification |
url |
https://www.frontiersin.org/article/10.3389/fevo.2020.00027/full |
work_keys_str_mv |
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doaj-27ea5772b54343c1871dd2159cf8a78f2020-11-25T00:01:46ZengFrontiers Media S.A.Frontiers in Ecology and Evolution2296-701X2020-02-01810.3389/fevo.2020.00027502805The Essential Role of Taxonomic Expertise in the Creation of DNA Databases for the Identification and Delimitation of Southeast Asian Ambrosia Beetle Species (Curculionidae: Scolytinae: Xyleborini)Anthony I. Cognato0Gina Sari1Sarah M. Smith2Roger A. Beaver3You Li4Jiri Hulcr5Bjarte H. Jordal6Hisashi Kajimura7Ching-Shan Lin8Thai Hong Pham9Sudhir Singh10Wisut Sittichaya11Department of Entomology, Michigan State University, East Lansing, MI, United StatesIndonesia Agricultural Quarantine Agency, Jakarta, IndonesiaDepartment of Entomology, Michigan State University, East Lansing, MI, United StatesRetired, Chiang Mai, ThailandSchool of Forest Resources and Conservation, University of Florida, Gainesville, FL, United StatesSchool of Forest Resources and Conservation, University of Florida, Gainesville, FL, United StatesUniversity Museum of Bergen, University of Bergen, Bergen, NorwayGraduate School of Bioagricultural Sciences, Nagoya University, Nagoya, JapanDepartment of Entomology, National Taiwan University, Taipei, TaiwanVietnam National Museum of Nature and Graduate School of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, VietnamForest Entomology Division, Forest Research Institute, New Forest, Dehradun, Uttarakhand, India0Department of Pest Management, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, ThailandDNA holds great potential for species identification and efforts to create a DNA database of all animals and plants currently contains >7.5 million sequences representing ~300,000 species. This promise of a universally applicable identification tool suggests that morphologically based tools and taxonomists will soon not have utility. Here we demonstrate that DNA-based identification is not reliable without the contributions of taxonomic experts. We use ambrosia beetles (Xyleborini), which are known for great diversity as well as global invasions and damage, as a test case. Recent xyleborine introductions have caused major economic and ecological losses, thus timely species identifications of new invaders are necessary. This need is hampered by a paucity of identification tools and a fauna that is only moderately documented. To help alleviate deficiencies in their identification, we created COI and CAD DNA barcode databases (490 and 429 specimens), representing over half of the known fauna of Southeast Asia (165/316 species). Taxonomic experts identified species based on original descriptions and type specimens. Tree, distance, and iterative methods were used to assess the identification and delimitation of species. High intra- and interspecific COI distances were observed for congeneric species and attributed to the beetle's inbreeding system. Neither of the two markers provided 100% identification success but with the neighbor-joining tree-based method, 80% of species were identified by both genes. As for species delimitation, an obvious barcode gap between intra- and interspecific differences was not observed. Correspondence between distance-based groups and morphology-based species was poor. In a demonstration of iterative taxonomy, we constructed parsimony-based phylogenies using COI and CAD sequences for two genera. Although not all clades were resolved or supported, we provided better explanations for species boundaries in light of morphological and DNA sequence differences. Confident species identifications demonstrated <3% COI and <1% CAD difference and recognition of new species became more probable when there was >10–12% COI and/or >2–3% CAD. Involvement of taxonomic experts from the start of this project was essential for the creation of a stable foundation for the DNA identification of xyleborine species. In general, their role in DNA barcoding cannot be underestimated and is further discussed.https://www.frontiersin.org/article/10.3389/fevo.2020.00027/fullCADCOIDNA barcodingspecies delimitationspecies identification |