University of Oulu

Lopez-Vaamonde C, Kirichenko N, Cama A, Doorenweerd C, Godfray HCJ, Guiguet A, Gomboc S, Huemer P, Landry J-F, Laštůvka A, Laštůvka Z, Lee KM, Lees DC, Mutanen M, van Nieukerken EJ, Segerer AH, Triberti P, Wieser C and Rougerie R (2021) Evaluating DNA Barcoding for Species Identification and Discovery in European Gracillariid Moths. Front. Ecol. Evol. 9:626752. doi: 10.3389/fevo.2021.626752

Evaluating DNA barcoding for species identification and discovery in European Gracillariid moths

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Author: Lopez-Vaamonde, Carlos1,2; Kirichenko, Natalia3,4; Cama, Alain5;
Organizations: 1INRAE, URZF, Orléans, France
2IRBI, UMR 7261, CNRS-Université de Tours, Tours, France
3Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Federal Research Center “Krasnoyarsk Science Center SB RAS,” Krasnoyarsk, Russia
4Siberian Federal University, Krasnoyarsk, Russia
5La Chapelle sur Loire, France
6Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, United States
7Naturalis Biodiversity Center, Leiden, Netherlands
8Department of Zoology, University of Oxford, Oxford, United Kingdom
9Department of Biology, The Pennsylvania State University, University Park, PA, United States
10Gancani, Beltinci, Slovenia
11Tiroler Landesmuseen Betriebsges.m.b.H., Sammlungs- und Forschungszentrum, Hall in Tirol, Austria
12Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
13Prostějov, Czechia
14Faculty of Agronomy, Mendel University, Brno, Czechia
15Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
16Department of Life Sciences, Natural History Museum, London, United Kingdom
17Staatliche Naturwissenschaftliche Sammlungen Bayerns, Zoologische Staatssammlung München (SNSB-ZSM), Munich, Germany
18Museo Civico di Storia Naturale, Zoologia, Verona, Italy
19Landesmuseum für Kärnten, Abteilung Zoologie, Sammlungs- und Wissenschaftszentrum, Klagenfurt, Austria
20Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 1.7 MB)
Persistent link: http://urn.fi/urn:nbn:fi-fe2021042820711
Language: English
Published: Frontiers Media, 2021
Publish Date: 2021-04-28
Description:

Abstract

Gracillariidae is the most species-rich leaf-mining moth family with over 2,000 described species worldwide. In Europe, there are 263 valid named species recognized, many of which are difficult to identify using morphology only. Here we explore the use of DNA barcodes as a tool for identification and species discovery in European gracillariids. We present a barcode library including 6,791 COI sequences representing 242 of the 263 (92%) resident species. Our results indicate high congruence between morphology and barcodes with 91.3% (221/242) of European species forming monophyletic clades that can be identified accurately using barcodes alone. The remaining 8.7% represent cases of non-monophyly making their identification uncertain using barcodes. Species discrimination based on the Barcode Index Number system (BIN) was successful for 93% of species with 7% of species sharing BINs. We discovered as many as 21 undescribed candidate species, of which six were confirmed from an integrative approach; the other 15 require additional material and study to confirm preliminary evidence. Most of these new candidate species are found in mountainous regions of Mediterranean countries, the South-Eastern Alps and the Balkans, with nine candidate species found only on islands. In addition, 13 species were classified as deep conspecific lineages, comprising a total of 27 BINs with no intraspecific morphological differences found, and no known ecological differentiation. Double-digest restriction-site associated DNA sequencing (ddRAD) analysis showed strong mitonuclear discrepancy in four out of five species studied. This discordance is not explained by Wolbachia-mediated genetic sweeps. Finally, 26 species were classified as “unassessed species splits” containing 71 BINs and some involving geographical isolation or ecological specialization that will require further study to test whether they represent new cryptic species.

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Series: Frontiers in ecology and evolution
ISSN: 2296-701X
ISSN-E: 2296-701X
ISSN-L: 2296-701X
Volume: 9
Article number: 626752
DOI: 10.3389/fevo.2021.626752
OADOI: https://oadoi.org/10.3389/fevo.2021.626752
Type of Publication: A1 Journal article – refereed
Field of Science: 1181 Ecology, evolutionary biology
Subjects:
Funding: This work was funded by the Studium (France) to both NK and DL to work as research fellows at INRAE Orléans; the Russian Foundation for Basic Research (No. 19-04-01029-a) and the basic project of Sukachev Institute of Forest SB RAS (project No. 0287-2021-0011) to NK; the Région Centre (France) project ENDOFEED (201000047141) to CL-V; the Ministry of Agriculture (France) project PASSIFOR to CL-V and RR; the Academy of Finland (grant number: 277984) to MM and the Kvantum Institute to KL; Kone foundation, Finnish Cultural foundation for financing the FinBOL (Finnish Barcode of Life) 2011-2015, and the Academy of Finland for financing FinBOL through the FinBIF national infrastructure project since 2014; Agriculture & Agri-Food Canada, Science and Technology Branch (projects Nos. J-000977 and J-002279) to J-FL; Promotion of Educational Policies, University and Research Department of the Autonomous Province of Bolzano – South Tyrol and Austrian Federal Ministry of Science, Research and Economics in the framework of ABOL (Austrian Barcode of Life) to PH. CD’s salary and all DNA sequencing at Naturalis Biodiversity Center was funded through the Dutch Economic Restructuring Fund (FES). AS was supported by the Bavarian Ministry of Science and Art (Germany) project BFB and the Federal Ministry of Education and Research (Germany) project GBOL. Funding for DNA barcoding was also partly provided by the Government of Canada through Genome Canada, the Ontario Genomics Institute in support of the International Barcode of Life project, and by the National Science and Engineering Research Council of Canada.
Academy of Finland Grant Number: 277984
Detailed Information: 277984 (Academy of Finland Funding decision)
Copyright information: © 2021 Lopez-Vaamonde, Kirichenko, Cama, Doorenweerd, Godfray, Guiguet, Gomboc, Huemer, Landry, Laštůvka, Laštůvka, Lee, Lees, Mutanen, van Nieukerken, Segerer, Triberti, Wieser and Rougerie. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
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