University of Oulu

Marko Mutanen, Sami M. Kivelä, Rutger A. Vos, Camiel Doorenweerd, Sujeevan Ratnasingham, Axel Hausmann, Peter Huemer, Vlad Dincă, Erik J. van Nieukerken, Carlos Lopez-Vaamonde, Roger Vila, Leif Aarvik, Thibaud Decaëns, Konstantin A. Efetov, Paul D. N. Hebert, Arild Johnsen, Ole Karsholt, Mikko Pentinsaari, Rodolphe Rougerie, Andreas Segerer, Gerhard Tarmann, Reza Zahiri, and H. Charles J. Godfray Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera Syst Biol (2016) 65 (6): 1024-1040 first published online June 10, 2016 doi:10.1093/sysbio/syw044

Species-level para- and polyphyly in DNA barcode gene trees : strong operational bias in European Lepidoptera

Saved in:
Author: Mutanen, Marko1; Kivelä, Sami M.2; Vos, Rutger A.3;
Organizations: 1Department of Genetics and Physiology, University of Oulu, Finland
2Department of Ecology, University of Oulu, Finland
3Naturalis Biodiversity Center, Leiden, The Netherlands
4Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Canada
5SNSB – Bavarian State Collection of Zoology, Munich, Germany
6Tiroler Landesmuseen-Betriebsgesellschaft m.b.H., Innsbruck, Austria
7Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
8INRA, UR633 Zoologie Forestière, 45075 Orléans, France
9Institut de Recherche sur la Biologie de l’Insecte, CNRS UMR 7261, Université François-Rabelais de Tours, UFR Sciences et Techniques, 37200 Tours, France
10Natural History Museum University of Oslo, Norway
11Centre d’Écologie Fonctionnelle et Évolutive, UMR 5175 CNRS / University of Montpellier / University of Montpellier 3 / EPHE / SupAgro Montpellier / INRA / IRD, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
12Crimean Federal University, Simferopol, Crimea
13Zoologisk Museum, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
14Département Systématique et Evolution, Muséum National d’Histoire Naturelle, Institut de Systématique, Evolution, Biodiversité, ISYEB–UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Paris, France
15Ottawa Plant Laboratory, Canadian Food Inspection Agency, Canada
16Department of Zoology, University of Oxford, UK
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 0.8 MB)
Persistent link:
Language: English
Published: Oxford University Press, 2016
Publish Date: 2016-12-14


The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, nonmonophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service “Monophylizer” to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species nonmonophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set ofDNAbarcodes analyzed fromthis regard. Particular attentionwas paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore,we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric—conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.

see all

Series: Systematic biology
ISSN: 1063-5157
ISSN-E: 1076-836X
ISSN-L: 1063-5157
Volume: 65
Issue: 6
Pages: 1024 - 1040
DOI: 10.1093/sysbio/syw044
Type of Publication: A1 Journal article – refereed
Field of Science: 1181 Ecology, evolutionary biology
Dataset Reference: Data available from the Dryad Digital Repository:
Copyright information: This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (, which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact