TY - JOUR T1 - Species-level para- and polyphyly in DNA barcode gene trees: strong operational bias in European Lepidoptera JF - Systematic Biology Y1 - 2016 DO - 10.1093/sysbio/syw044 A1 - Marko Mutanen A1 - Sami M. Kivelä A1 - Rutger A. Vos A1 - Camiel Doorenweerd A1 - Sujeevan Ratnasingham A1 - Axel Hausmann A1 - Peter Huemer A1 - Vlad Dincă A1 - Erik J. van Nieukerken A1 - Carlos Lopez-Vaamonde A1 - Roger Vila A1 - Leif Aarvik A1 - Thibaud Decaëns A1 - Konstantin A. Efetov A1 - Paul D. N. Hebert A1 - Arild Johnsen A1 - Ole Karsholt A1 - Mikko Pentinsaari A1 - Rodolphe Rougerie A1 - Andreas Segerer A1 - Gerhard Tarmann A1 - Reza Zahiri A1 - H. Charles J. Godfray SP - 1024 EP - 1040 KW - Lepidoptera AB -

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 from4977 species and 41,583 specimens of European Lepidoptera, the largest data set ofDNAbarcodes analyzed fromthis regard. Particular attention was 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. [DNA barcoding; gene tree; Lepidoptera; mitochondrial COI; mitochondrial cox1; paraphyly; polyphyly; species delimitation; species monophyly.]

VL - 65 UR - http://sysbio.oxfordjournals.org/content/early/2016/06/02/sysbio.syw044.abstract JO - Syst. Biol. ER -