TY - JOUR T1 - What happens to the traditional taxonomy when a well-known tropical saturniid moth fauna is DNA barcoded? JF - Invertebrate Systematics Y1 - 2012 DO - 10.1071/is12038 A1 - Janzen, D.H. A1 - Hallwachs, W. A1 - Harvey, D.J. A1 - Darrow, K. A1 - Rougerie, R. A1 - Hajibabaei, M. A1 - Smith, M.A. A1 - Bertrand, C. A1 - Gamboa, I.C. A1 - Espinoza, B. A1 - Sullivan, J.B. A1 - Decaëns, T. A1 - Herbin, D. A1 - Chavarria, L.F. A1 - Franco, R. A1 - Cambronero, H. A1 - Rios, S. A1 - Quesada, F. A1 - Pereira, G. A1 - Vargas, J. A1 - Guadamuz, A. A1 - Espinoza, R. A1 - Hernandez, J. A1 - Rios, L. A1 - Cantillano, E. A1 - Moraga, R. A1 - Moraga, C. A1 - Rios, P. A1 - Rios, M. A1 - Calero, R. A1 - Martinez, D. A1 - Briceño, D. A1 - Carmona, M. A1 - Apu, E. A1 - Aragon, K. A1 - Umaña, C. A1 - Perez, J. A1 - Cordoba, A. A1 - Umaña, P. A1 - Sihezar, G. A1 - Espinoza, O. A1 - Cano, C. A1 - Araya, E. A1 - Garcia, D. A1 - Ramirez, H. A1 - Pereira, M. A1 - Cortez, J. A1 - Pereira, M. A1 - Medina, W. A1 - Hebert, P.D.N. SP - 478 EP - 505 KW - ADULT MORPHOLOGY KW - AUTOMERIS KW - BARCODE GAP KW - BARCODING KW - CAIO KW - COI KW - COSTA RICA KW - DIRPHIA KW - DNA KW - EACLES KW - HYLESIA KW - MALE GENITALIA KW - OTHORENE KW - PERIPHOBA KW - PTILOSCOLA KW - SATURNIIDAE KW - SPECIES DELIMITATION KW - SYSSPHINX KW - TAXONOMY AB -
"Sequences from the DNA barcode region of the mitochondrial COI gene are an effective tool for specimen identification and for the discovery of new species. The Barcode of Life Data Systems (BOLD) (www.boldsystems.org) currently hosts 4.5 million records from animals which have been assigned to more than 490,000 different Barcode Index Numbers (BINs), which serve as a proxy for species. Because a fourth of these BINs derive from Lepidoptera, BOLD has a strong capability to both identify specimens in this order and to support studies of faunal overlap. DNA barcode sequences were obtained from 4503 moths from 329 sites across Pakistan, specimens that represented 981 BINs from 52 families. Among 379 species with a Linnaean name assignment, all were represented by a single BIN excepting five species that showed a BIN split. Less than half (44%) of the 981 BINs had counterparts in other countries; the remaining BINs were unique to Pakistan. Another 218 BINs of Lepidoptera from Pakistan were coupled with the 981 from this study before being compared with all 116,768 BINs for this order. As expected, faunal overlap was highest with India (21%), Sri Lanka (21%), United Arab Emirates (20%) and with other Asian nations (2.1%), but it was very low with other continents including Africa (0.6%), Europe (1.3%), Australia (0.6%), Oceania (1.0%), North America (0.1%), and South America (0.1%). This study indicates the way in which DNA barcoding facilitates measures of faunal overlap even when taxa have not been assigned to a Linnean species."
VL - 12 IS - 3 ER - 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 - An annotated checklist of the Macroheterocera of south-eastern Ontario JF - Journal of Research on the Lepidoptera Y1 - 1974 A1 - Ward, P.S. A1 - Harmsen, R. A1 - Hebert, P.D.N. SP - 23 EP - 42 KW - CANADA KW - FOODPLANT KW - SATURNIIDAE KW - SPHINGIDAE KW - WORLDMAP VL - 13 ER - TY - JOUR T1 - A DNA-based registry for all animal species: the Barcode Index Number (BIN) system JF - PLoS ONE Y1 - 2013 DO - 10.1371/journal.pone.0066213 A1 - Ratnasingham, S. A1 - Hebert, P.D.N. SP - e66213 KW - BARCODE INDEX NUMBER KW - BARCODING KW - COI KW - DNA KW - GMYC KW - RESL KW - SPECIES DELIMITATION VL - 8 IS - 8 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 - TY - JOUR T1 - When species matches are unavailable are DNA barcodes correctly assigned to higher taxa? An assessment using sphingid moths JF - BMC Ecology Y1 - 2011 A1 - Wilson, J.J. A1 - Rougerie, R. A1 - Schonfeld, J. A1 - Janzen, D.H. A1 - Hallwachs, W. A1 - Hajibabaei, M. A1 - Kitching, I.J. A1 - Haxaire, J. A1 - Hebert, P.D.N. SP - 18 KW - BARCODING KW - DNA KW - HIGHER CLASSIFICATION KW - IDENTIFICATION KW - SPHINGIDAE AB -"Background
When a specimen belongs to a species not yet represented in DNA barcode reference libraries there is disagreement over the effectiveness of using sequence comparisons to assign the query accurately to a higher taxon. Library completeness and the assignment criteria used have been proposed as critical factors affecting the accuracy of such assignments but have not been thoroughly investigated. We explored the accuracy of assignments to genus, tribe and subfamily in the Sphingidae, using the almost complete global DNA barcode reference library (1095 species) available for this family. Costa Rican sphingids (118 species), a well-documented, diverse subset of the family, with each of the tribes and subfamilies represented were used as queries. We simulated libraries with different levels of completeness (10-100% of the available species), and recorded assignments (positive or ambiguous) and their accuracy (true or false) under six criteria.
Results
A liberal tree-based criterion assigned 83% of queries accurately to genus, 74% to tribe and 90% to subfamily, compared to a strict tree-based criterion, which assigned 75% of queries accurately to genus, 66% to tribe and 84% to subfamily, with a library containing 100% of available species (but excluding the species of the query). The greater number of true positives delivered by more relaxed criteria was negatively balanced by the occurrence of more false positives. This effect was most sharply observed with libraries of the lowest completeness where, for example at the genus level, 32% of assignments were false positives with the liberal criterion versus < 1% when using the strict. We observed little difference (< 8% using the liberal criterion) however, in the overall accuracy of the assignments between the lowest and highest levels of library completeness at the tribe and subfamily level.
Conclusions
Our results suggest that when using a strict tree-based criterion for higher taxon assignment with DNA barcodes, the likelihood of assigning a query a genus name incorrectly is very low, if a genus name is provided it has a high likelihood of being accurate, and if no genus match is available the query can nevertheless be assigned to a subfamily with high accuracy regardless of library completeness. DNA barcoding often correctly assigned sphingid moths to higher taxa when species matches were unavailable, suggesting that barcode reference libraries can be useful for higher taxon assignments long before they achieve complete species coverage."
VL - 11 UR - http://www.biomedcentral.com/1472-6785/11/18 ER - TY - JOUR T1 - Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding JF - Philosophical Transactions of the Royal Society of London Y1 - 2005 DO - 10.1098/rstb.2005.1715 A1 - Janzen, D.H. A1 - Hajibabaei, M. A1 - Burns, J.M. A1 - Hallwachs, W. A1 - Remigio, E. A1 - Hebert, P.D.N. SP - 1835 EP - 1845 KW - BARCODING KW - BIODIVERSITY KW - COI KW - COSTA RICA KW - CRYPTIC SPECIES KW - DNA KW - HESPERIIDAE KW - SATURNIIDAE KW - SPHINGIDAE KW - TAXONOMY VL - 360 N1 - B ER - TY - JOUR T1 - DNA barcodes distinguish species of tropical Lepidoptera JF - Proceedings of the National Academy of Sciences of the United States of America Y1 - 2006 A1 - Hajibabaei, M. A1 - Janzen, D.H. A1 - Burns, J.M. A1 - Hallwachs, W. A1 - Hebert, P.D.N. SP - 968 EP - 971 KW - BARCODING KW - CLASSIFICATION KW - COI KW - COSTA RICA KW - HESPERIIDAE KW - LEPIDOPTERA KW - SATURNIIDAE KW - SPHINGIDAE VL - 103 UR - https://www.pnas.org/doi/epdf/10.1073/pnas.0510466103 IS - 4 ER -