Genetic Patterns in European Geometrid Moths Revealed by the Barcode Index Number (BIN) System

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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.

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The integrative future of taxonomy

José M. Padial, Aurélien Miralles, Ignacio De la Riva … (2010)

Background Taxonomy is the biological discipline that identifies, describes, classifies and names extant and extinct species and other taxa. Nowadays, species taxonomy is confronted with the challenge to fully incorporate new theory, methods and data from disciplines that study the origin, limits and evolution of species. Results Integrative taxonomy has been proposed as a framework to bring together these conceptual and methodological developments. Here we review perspectives for an integrative taxonomy that directly bear on what species are, how they can be discovered, and how much diversity is on Earth. Conclusions We conclude that taxonomy needs to be pluralistic to improve species discovery and description, and to develop novel protocols to produce the much-needed inventory of life in a reasonable time. To cope with the large number of candidate species revealed by molecular studies of eukaryotes, we propose a classification scheme for those units that will facilitate the subsequent assembly of data sets for the formal description of new species under the Linnaean system, and will ultimately integrate the activities of taxonomists and molecular biologists.

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DNA barcodes distinguish species of tropical Lepidoptera.

Mehrdad Hajibabaei, Daniel Janzen, John M Burns … (2006)

Although central to much biological research, the identification of species is often difficult. The use of DNA barcodes, short DNA sequences from a standardized region of the genome, has recently been proposed as a tool to facilitate species identification and discovery. However, the effectiveness of DNA barcoding for identifying specimens in species-rich tropical biotas is unknown. Here we show that cytochrome c oxidase I DNA barcodes effectively discriminate among species in three Lepidoptera families from Area de Conservación Guanacaste in northwestern Costa Rica. We found that 97.9% of the 521 species recognized by prior taxonomic work possess distinctive cytochrome c oxidase I barcodes and that the few instances of interspecific sequence overlap involve very similar species. We also found two or more barcode clusters within each of 13 supposedly single species. Covariation between these clusters and morphological and/or ecological traits indicates overlooked species complexes. If these results are general, DNA barcoding will significantly aid species identification and discovery in tropical settings.

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Sequence-based species delimitation for the DNA taxonomy of undescribed insects.

Jesús F. Zurita, Anabela Cardoso, Alfried Vogler … (2006)

Cataloging the very large number of undescribed species of insects could be greatly accelerated by automated DNA based approaches, but procedures for large-scale species discovery from sequence data are currently lacking. Here, we use mitochondrial DNA variation to delimit species in a poorly known beetle radiation in the genus Rivacindela from arid Australia. Among 468 individuals sampled from 65 sites and multiple morphologically distinguishable types, sequence variation in three mtDNA genes (cytochrome oxidase subunit 1, cytochrome b, 16S ribosomal RNA) was strongly partitioned between 46 or 47 putative species identified with quantitative methods of species recognition based on fixed unique ("diagnostic") characters. The boundaries between groups were also recognizable from a striking increase in branching rate in clock-constrained calibrated trees. Models of stochastic lineage growth (Yule models) were combined with coalescence theory to develop a new likelihood method that determines the point of transition from species-level (speciation and extinction) to population-level (coalescence) evolutionary processes. Fitting the location of the switches from speciation to coalescent nodes on the ultrametric tree of Rivacindela produced a transition in branching rate occurring at 0.43 Mya, leading to an estimate of 48 putative species (confidence interval for the threshold ranging from 47 to 51 clusters within 2 logL units). Entities delimited in this way exhibited biological properties of traditionally defined species, showing coherence of geographic ranges, broad congruence with morphologically recognized species, and levels of sequence divergence typical for closely related species of insects. The finding of discontinuous evolutionary groupings that are readily apparent in patterns of sequence variation permits largely automated species delineation from DNA surveys of local communities as a scaffold for taxonomy in this poorly known insect group.

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Author and article information

Contributors

Sebastian D. Fugmann: Role: Editor

Journal

Journal ID (nlm-ta): PLoS One

Journal ID (iso-abbrev): PLoS ONE

Journal ID (publisher-id): plos

Journal ID (pmc): plosone

Title: PLoS ONE

Publisher: Public Library of Science (San Francisco, USA )

ISSN (Electronic): 1932-6203

Publication date Collection: 2013

Publication date (Electronic): 17 December 2013

Volume: 8

Issue: 12

Electronic Location Identifier: e84518

Affiliations

[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

Chang Gung University, Taiwan

Author notes

* E-mail: axel.hausmann@ 123456zsm.mwn.de

Competing Interests: The authors have declared that no competing interests exist.

Conceived and designed the experiments: AH SR PDNH. Performed the experiments: AH. Analyzed the data: AH. Contributed reagents/materials/analysis tools: AH PH HCJG RR EN MM SR PDNH. Wrote the manuscript: AH MM RR HCJG PDNH. Provided input into the manuscript: AH PH HCJG RR EN MM SR PDNH.

Article

Publisher ID: PONE-D-13-31971

DOI: 10.1371/journal.pone.0084518

PMC ID: 3866169

PubMed ID: 24358363

SO-VID: 75a05b52-19d6-4875-8d8b-dcff7076799e

License:

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.

History

Date received : 5 August 2013

Date accepted : 14 November 2013

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.

Genetic Patterns in European Geometrid Moths Revealed by the Barcode Index Number (BIN) System

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Abstract

Background

Methodology/Principal Findings

Conclusions/Significance

Related collections

PLOS Climate

Most cited references 14

The integrative future of taxonomy

DNA barcodes distinguish species of tropical Lepidoptera.

Sequence-based species delimitation for the DNA taxonomy of undescribed insects.

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