Testing DNA Barcode Performance in 1000 Species of European Lepidoptera: Large Geographic Distances Have Small Genetic Impacts

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Abstract

This study examines the performance of DNA barcodes (mt cytochrome c oxidase 1 gene) in the identification of 1004 species of Lepidoptera shared by two localities (Finland, Austria) that are 1600 km apart. Maximum intraspecific distances for the pooled data were less than 2% for 880 species (87.6%), while deeper divergence was detected in 124 species. Despite such variation, the overall DNA barcode library possessed diagnostic COI sequences for 98.8% of the taxa. Because a reference library based on Finnish specimens was highly effective in identifying specimens from Austria, we conclude that barcode libraries based on regional sampling can often be effective for a much larger area. Moreover, dispersal ability (poor, good) and distribution patterns (disjunct, fragmented, continuous, migratory) had little impact on levels of intraspecific geographic divergence. Furthermore, the present study revealed that, despite the intensity of past taxonomic work on European Lepidoptera, nearly 20% of the species shared by Austria and Finland require further work to clarify their status. Particularly discordant BIN (Barcode Index Number) cases should be checked to ascertain possible explanatory factors such as incorrect taxonomy, hybridization, introgression, and Wolbachia infections.

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DNA barcodes for 1/1000 of the animal kingdom

Paul Hebert, Jeremy deWaard, Jean-François Landry (2009)

This study reports DNA barcodes for more than 1300 Lepidoptera species from the eastern half of North America, establishing that 99.3 per cent of these species possess diagnostic barcode sequences. Intraspecific divergences averaged just 0.43 per cent among this assemblage, but most values were lower. The mean was elevated by deep barcode divergences (greater than 2%) in 5.1 per cent of the species, often involving the sympatric occurrence of two barcode clusters. A few of these cases have been analysed in detail, revealing species overlooked by the current taxonomic system. This study also provided a large-scale test of the extent of regional divergence in barcode sequences, indicating that geographical differentiation in the Lepidoptera of eastern North America is small, even when comparisons involve populations as much as 2800 km apart. The present results affirm that a highly effective system for the identification of Lepidoptera in this region can be built with few records per species because of the limited intra-specific variation. As most terrestrial and marine taxa are likely to possess a similar pattern of population structure, an effective DNA-based identification system can be developed with modest effort.

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Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding.

Winnie Hallwachs, Mehrdad Hajibabaei, J. Burns … (2005)

By facilitating bioliteracy, DNA barcoding has the potential to improve the way the world relates to wild biodiversity. Here we describe the early stages of the use of cox1 barcoding to supplement and strengthen the taxonomic platform underpinning the inventory of thousands of sympatric species of caterpillars in tropical dry forest, cloud forest and rain forest in northwestern Costa Rica. The results show that barcoding a biologically complex biota unambiguously distinguishes among 97% of more than 1000 species of reared Lepidoptera. Those few species whose barcodes overlap are closely related and not confused with other species. Barcoding also has revealed a substantial number of cryptic species among morphologically defined species, associated sexes, and reinforced identification of species that are difficult to distinguish morphologically. For barcoding to achieve its full potential, (i) ability to rapidly and cheaply barcode older museum specimens is urgent, (ii) museums need to address the opportunity and responsibility for housing large numbers of barcode voucher specimens, (iii) substantial resources need be mustered to support the taxonomic side of the partnership with barcoding, and (iv) hand-held field-friendly barcorder must emerge as a mutualism with the taxasphere and the barcoding initiative, in a manner such that its use generates a resource base for the taxonomic process as well as a tool for the user.

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Comparative performances of DNA barcoding across insect orders

Massimiliano Virgilio, Thierry Backeljau, Bruno Nevado … (2010)

Background Previous studies on insect DNA barcoding provide contradictory results and suggest not consistent performances across orders. This work aims at providing a general evaluation of insect DNA barcoding and "mini-barcoding" by performing simulations on a large database of 15,948 DNA barcodes. We compared the proportions of correctly identified queries across a) six insect orders (Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera and Orthoptera), b) four identification criteria (Best Match: BM; Best Close Match: BCM; All Species Barcodes: ASB; tree-based identification: NJT), and c) reference databases with different taxon coverage (100, 500, 1,000, 1,500 and 1,995 insect species). Results Analysis of variance revealed highly significant differences among ID criteria and insect orders. A posteriori comparisons of means showed that NJT had always a significantly lower identification success (NJT = 0.656, S.D. = 0.118) compared to both BM and BCM (BM = 0.948, S.D. = 0.026; BCM = 0.946, S.D. = 0.031). NJT showed significant variations among orders, with the highest proportion of correctly identified queries in Hymenoptera and Orthoptera and the lowest in Diptera. Conversely, the proportions of correct matches of BM and BCM were consistent across orders but a progressive increase in false identification was observed when larger reference databases were used. Conclusions Regardless the relatively low proportion of Type I errors (misidentification of queries which are represented in the reference database) of BM and BCM, the lack of reference DNA barcodes for 98% of the known insect species implies that insect DNA barcoding is heavily biased by Type II errors (misidentification of queries without conspecifics in the database). The detrimental effects of Type II errors could be circumvented if insect DNA barcoding is used to verify the lack of correspondence between a query and a list of properly referenced target species (e.g. insect pests). This "negative identification" would only be subjected to Type I errors and could be profitably adopted in insect quarantine procedures.

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Author and article information

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Bernd Schierwater: 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: 2014

Publication date (Electronic): 26 December 2014

Volume: 9

Issue: 12

Electronic Location Identifier: e115774

Affiliations

[1 ]Tiroler Landesmuseen-Betriebsges.m.b.H., Naturwissenschaftliche Sammlungen, Innsbruck, Austria

[2 ]Biodiversity Unit, Department of Biology, University of Oulu, Oulu, Finland

[3 ]University of Graz, Institute of Zoology, Graz, Austria

[4 ]Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada

University of Veterinary Medicine Hanover, Germany

Author notes

* E-mail: p.huemer@ 123456tiroler-landesmuseen.at

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

Conceived and designed the experiments: PH MM KS PDNH. Performed the experiments: PH MM KS PDNH. Analyzed the data: KS PH MM PDNH. Contributed reagents/materials/analysis tools: PH MM KS PDNH. Wrote the paper: PH MM KS PDNH. Provided input on the manuscript: PH MM KS PDNH.

Article

Publisher ID: PONE-D-14-39234

DOI: 10.1371/journal.pone.0115774

PMC ID: 4277373

PubMed ID: 25541991

SO-VID: 3e0bae49-38b3-4033-8dbb-c00f95dffadf

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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 : 3 September 2014

Date accepted : 20 November 2014

Page count

Pages: 21

Funding

This work was supported by Genome Canada (PDNH) ( www.genomecanada.ca/), Ontario Genomics Institute (PDNH) ( www.ontariogenomics.ca/), Ontario Ministry of Research and Innovation (PDNH) ( https://www.ontario.ca/ministry-research-innovation), Kone Foundation (MM) ( www.koneensaatio.fi/en/), Finnish Cultural Foundation (MM) ( https://www.skr.fi/en), and Erlebnis naturschau Dornbirn (PH) ( http://www.inatura.at). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Data Availability The authors confirm that all data underlying the findings are fully available without restriction. All data are available from the BOLD database, DOI: dataset http://dx.doi.org/10.5883/DS-FVLEP. Furthermore all sequences were deposited in Genbank prior to submission, and the accession numbers are provided in S1 Appendix.

Testing DNA Barcode Performance in 1000 Species of European Lepidoptera: Large Geographic Distances Have Small Genetic Impacts

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Most cited references 13

DNA barcodes for 1/1000 of the animal kingdom

Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding.

Comparative performances of DNA barcoding across insect orders

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