Journal
SYSTEMATIC BIOLOGY
Volume 65, Issue 6, Pages 1024-1040Publisher
OXFORD UNIV PRESS
DOI: 10.1093/sysbio/syw044
Keywords
DNA barcoding; gene tree; Lepidoptera; mitochondrial COI; mitochondrial cox1; paraphyly; polyphyly; species delimitation; species monophyly
Categories
Funding
- Government of Canada through Genome Canada
- Ontario Genomics Institute
- Bavarian State Ministry of Education, Culture, Science and the Arts (Barcoding Fauna Bavarica, BFB)
- German Federal Ministry of Education and Research (German Barcode of Life GBOL2: BMBF) [01LI1101B]
- FES grant from Dutch Ministry of Finance
- Kone Foundation
- Finnish Cultural Foundation
- University of Oulu
- Spanish Ministerio de Economia y Competitividad [CGL2010-21226/BOS, CGL2013-48277-P]
- Region Haute-Normandie
- Marie Curie International Outgoing Fellowship within 7th European Community Framework Programme [625997]
- Natural History Museum, University of Oslo
- Norwegian Barcode of Life Network (NorBOL)
- Promotion of Educational Policies, University and Research Department of the Autonomous Province of Bolzano-South Tyrol
- Austrian Federal Ministry of Science, Research and Economics
- regional institutions Tiroler Landesmuseen, inatura and Landesmuseum Karnten
- Stockholm University
- Conseil Regional de Haute-Normandie
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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, non-monophyly 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 non-monophyly 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 similar to 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.
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