Genetic patterns in European geometrid moths revealed by the Barcode Index Number (BIN) system Axel Hausmann, H. Charles J. Godfray, Peter Huemer, Marko Mutanen, Rodolphe Rougerie, Erik J van Nieukerken, Sujeevan Ratnasingham, Paul D. N. Hebert To cite this version: Axel Hausmann, H. Charles J. Godfray, Peter Huemer, Marko Mutanen, Rodolphe Rougerie, et al.. Genetic patterns in European geometrid moths revealed by the Barcode Index Number (BIN) system. PLoS ONE, Public Library of Science, 2013, 8 (12), 11 p. 10.1371/journal.pone.0084518. hal- 02650363 HAL Id: hal-02650363 https://hal.inrae.fr/hal-02650363 Submitted on 29 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Genetic Patterns in European Geometrid Moths Revealed by the Barcode Index Number (BIN) System Axel Hausmann1,2*, H. Charles J. Godfray3, Peter Huemer4, Marko Mutanen5, Rodolphe Rougerie6,7, Erik J. van Nieukerken8, Sujeevan Ratnasingham9, Paul D. N. Hebert9 1 Entomology Department, Bavarian State Collection of Zoology, Munich, Germany, 2 Bavarian Natural History Collections, Munich, Germany, 3 Department of Zoology, University of Oxford, Oxford, United Kingdom, 4 Naturwissenschaftliche Sammlungen, Tiroler Landesmuseen Betriebsgesellschaft, Innsbruck, Austria, 5 Zoological Museum of the Department of Biology, University of Oulu, Oulu, Finland, 6 Laboratoire d'Ecologie, Université de Rouen, Mont-Saint-Aignan, France, 7 Unité de Recherche en Zoologie Forestière, Orléans, France, 8 Naturalis Biodiversity Center, Leiden, The Netherlands, 9 Biodiversity Institute of Ontario, University of Guelph, Guelph, Canada Abstract Background: The geometrid moths of Europe are one of the best investigated insect groups in traditional taxonomy making them an ideal model group to test the accuracy of the Barcode Index Number (BIN) system of BOLD (Barcode of Life Datasystems), a method that supports automated, rapid species delineation and identification. Methodology/Principal Findings: This study provides a DNA barcode library for 219 of the 249 European geometrid moth species (88%) in five selected subfamilies. The data set includes COI sequences for 2130 specimens. Most species (93%) were found to possess diagnostic barcode sequences at the European level while only three species pairs (3%) were genetically indistinguishable in areas of sympatry. As a consequence, 97% of the European species we examined were unequivocally discriminated by barcodes within their natural areas of distribution. We found a 1:1 correspondence between BINs and traditionally recognized species for 67% of these species. Another 17% of the species (15 pairs, three triads) shared BINs, while specimens from the remaining species (18%) were divided among two or more BINs. Five of these species are mixtures, both sharing and splitting BINs. For 82% of the species with two or more BINs, the genetic splits involved allopatric populations, many of which have previously been hypothesized to represent distinct species or subspecies. Conclusions/Significance: This study confirms the effectiveness of DNA barcoding as a tool for species identification and illustrates the potential of the BIN system to characterize formal genetic units independently of an existing classification. This suggests the system can be used to efficiently assess the biodiversity of large, poorly known assemblages of organisms. For the moths examined in this study, cases of discordance between traditionally recognized species and BINs arose from several causes including overlooked species, synonymy, and cases where DNA barcodes revealed regional variation of uncertain taxonomic significance. Citation: Hausmann A, Godfray HCJ, Huemer P, Mutanen M, Rougerie R, et al. (2013) Genetic Patterns in European Geometrid Moths Revealed by the Barcode Index Number (BIN) System. PLoS ONE 8(12): e84518. doi:10.1371/journal.pone.0084518 Editor: Sebastian D. Fugmann, Chang Gung University, Taiwan Received August 5, 2013; Accepted November 14, 2013; Published December 17, 2013 Copyright: © 2013 Hausmann et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This study represents a contribution to WG1.9 of the International Barcode of Life Project. Sequence analysis was supported by Genome Canada through the Ontario Genomics Institute, while informatics support was provided through a grant from the Ontario Ministry of Research and Innovation. The collection and processing of specimens were funded as components of the “Barcoding Fauna Bavarica” project by the Bavarian Ministry of Science, Research and Art (Bayerisches Staatsministerium für Wissenschaft, Forschung und Kunst, Munich, Germany), the “German Barcode of Life” project by the German Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung; 01 LI 1101 B), the project on Barcoding Lepidoptera of Finland by the Finnish Cultural Foundation, Kone Foundation and the project on Barcoding Lepidoptera of northern France by the Conseil Régional de Haute-Normandie. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist. * E-mail: [email protected] Introduction CO1 gene have gained acceptance as an important molecular component of integrated taxonomic analyses [5-8]. As the In the decade since DNA barcodes were proposed as a tool number of DNA barcode campaigns has increased, and large for species identification [1], many studies have shown that this libraries of barcodes have been assembled, efforts have been approach yields excellent results for most groups of animals directed towards the development of methods for automated [2-4]. Furthermore, DNA barcodes based on the mitochondrial species delineation [9-12]. Initial work in this area focused on PLOS ONE | www.plosone.org 1 December 2013 | Volume 8 | Issue 12 | e84518 European Geometrid Moths and Barcode Index Numbers the development of approaches enabling the estimation of Lepidoptera campaign which was launched in 2011 at the species boundaries within the sequences gathered in a XVIIth European Congress of Lepidopterology in Luxembourg. particular study. Ratnasingham & Hebert [13] recently Summaries of the taxonomy and nomenclature of European implemented the Barcode Index Number (BIN) system as a geometrids are provided by the Fauna of Europe project [18], registry for all records on the Barcode of Life Datasystems and the book series ‘Geometrid Moths of Europe’ [19,20]. (BOLD, www.boldsystems.org) [14,15]. The BIN system employs a two-stage algorithm (Refined Single Linkage) that Materials and Methods couples single linkage and Markov clustering to assign sequences to a sequence cluster that is subsequently assigned Sampling a unique identifier termed a Barcode Index Number. The Specimens were sampled across Europe which was defined Refined Single Linkage algorithm matches the taxonomic performance of competing approaches, but couples this with using the same boundaries as in Hausmann [19,20]: i.e. from protocols that are simple enough to allow the automated Iceland to the Urals and northern foothills of the Caucasus, and assignment of all new barcode records to a BIN. BOLD from Malta to the Northern Cape, excluding Cyprus and currently hosts nearly 2.5 million DNA barcode sequences, Macaronesia. deriving from more than 190,000 formally named species, and This study covers five of the seven subfamilies of is used daily by hundreds of researchers. The development of Geometridae known from Europe: Archiearinae, the BIN system provides a new tool accessible to all users. Desmobathrinae, Orthostixinae, Geometrinae and Sterrhinae, Although the BIN system is potentially of great importance to which jointly include 249 recognized species [19,20]. The two the barcode research community, its performance has seen other subfamilies, the Larentiinae and Ennominae, include limited examination. another 733 species which will be addressed in another paper. In this paper we report the assembly of a comprehensive Specimens were sampled by the community of lepidopterists DNA barcode library for a taxonomically very well-known fauna involved in assembling a comprehensive DNA barcode library - five of the seven subfamilies of European geometrid moths. for European Lepidoptera. In total, DNA was extracted from We use this data to test the correspondence between the BIN 2150 European specimens, representing 195 different species. system currently implemented in BOLD and recognised Specimens collected outside Europe were included for 32 of species boundaries. the 54 missing species, adding an additional 520 specimens. The specific aims of this study are (a) to present a public The data set is somewhat geographically biased with Eastern data release of DNA barcodes for five subfamilies of European