TY - JOUR T1 - Calibrating the taxonomy of a megadiverse insect family: 3000 DNA barcodes from geometrid type specimens (Lepidoptera, Geometridae) JF - Genome Y1 - 2016 DO - 10.1139/gen-2015-0197 A1 - Hausmann, A. A1 - Miller, S.E. A1 - Holloway, J.D. A1 - deWaard, J.R. A1 - Pollock, D. A1 - Prosser, S.W.J. A1 - Hebert, P.D.N. KW - BARCODING KW - COI KW - DNA KW - GEOMETRIDAE KW - TAXONOMY KW - TYPES VL - 59 UR - http://dx.doi.org/10.1139/gen-2015-0197 ER - 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 - Mutanen, M. A1 - Kivelä, S.M. A1 - Vos, R.A. A1 - Doorenweerd, C. A1 - Ratnasingham, S. A1 - Hausmann, A. A1 - Huemer, P. A1 - Dinca, V. A1 - van Nieukerken, E.J. A1 - Lopez-Vaamonde, C. A1 - Vila, R. A1 - Aarvik, L. A1 - Decaëns, T. A1 - Efetov, K.A. A1 - Hebert, P.D.N. A1 - Johnsen, A. A1 - Karsholt, O. A1 - Pentinsaari, M. A1 - Rougerie, R. A1 - Segerer, A. A1 - Tarmann, G. A1 - Zahiri, R. A1 - Godfray, H.C.J. KW - BARCODE GAP KW - BARCODING KW - COI KW - DNA KW - EUROPE KW - GENE TREE KW - LEPIDOPTERA KW - MAXIMUM LIKELIHOOD KW - MONOPHYLIZER KW - NEIGHBOR-JOINING KW - PARAPHYLY KW - POLYPHYLY KW - SPECIES DELIMITATION KW - SPECIES MONOPHYLY 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, 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 of DNA barcodes analyzed from this 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."

ER - TY - JOUR T1 - Australian Sphingidae - DNA barcodes challenge current species boundaries and distributions JF - PLoS ONE Y1 - 2014 A1 - Rougerie, R. A1 - Kitching, I.J. A1 - Haxaire, J. A1 - Miller, S. E. A1 - Hausmann, A. A1 - Hebert, P.D.N. SP - 1 EP - 12 KW - AGRIUS KW - AUSTRALIA KW - BARCODE GAP KW - BARCODING KW - BIOGEOGRAPHY KW - CATALOGUE KW - COENOTES KW - DNA KW - ENDEMISM KW - EUPANACRA KW - HIPPOTION KW - HOPLIOCNEMA KW - LINNEAN SHORTFALL KW - NEIGHBOR-JOINING KW - PSILOGRAMMA KW - SPHINGIDAE KW - THERETRA KW - WALLACEAN SHORTFALL VL - 9 IS - 7, e101108 ER -