@article {22807, title = {What happens to the traditional taxonomy when a well-known tropical saturniid moth fauna is DNA barcoded?}, journal = {Invertebrate Systematics}, volume = {26}, year = {2012}, month = {2012}, pages = {478-505}, chapter = {478}, abstract = {

\"Biodiversity of tropical Saturniidae, as measured through traditionally described and catalogued species, strongly risks pooling cryptic species under one name. We examined the DNA barcodes, morphology, habitus and ecology of 32 \‘well known\’ species of dry forest saturniid moths from Area de Conservacion Guanacaste (ACG) in north-western Costa Rica and found that they contain as many as 49 biological entities that are probably separate species. The most prominent splitting of traditional species \– Eacles imperialis, Automeris zugana, Automeris tridens, Othorene verana, Hylesia dalina, Dirphia avia, Syssphinx molina, Syssphinx colla, and Syssphinx quadrilineata \– is where one species was believed to breed in dry forest and rain forest, but is found to be two biological entities variously distinguishable by DNA barcodes and morphology, habitus, and/or microecological distribution. This implies that \‘standard\’ biological information about each traditional species may be an unconscious mix of interspecific information, and begs renewed DNA barcoding, closer attention to so-called intraspecific variation, and increased museum collection and curation of specimens from more individual and ecologically characterised sites \– as well as eventually more species descriptions. Simultaneously, this inclusion of sibling species as individual entities in biodiversity studies, rather than pooled under one traditional name, reduces the degree of ecological and evolutionary generalisation perceived by the observer.\"

}, keywords = {ADULT MORPHOLOGY, AUTOMERIS, BARCODE GAP, BARCODING, CAIO, COI, COSTA RICA, DIRPHIA, DNA, EACLES, HYLESIA, MALE GENITALIA, OTHORENE, PERIPHOBA, PTILOSCOLA, SATURNIIDAE, SPECIES DELIMITATION, SYSSPHINX, TAXONOMY}, issn = {1445-5226}, doi = {10.1071/is12038}, url = {http://dx.doi.org/10.1071/is12038}, author = {Janzen, D.H. and Hallwachs, W. and Harvey, D.J. and Darrow, K. and Rougerie, R. and Hajibabaei, M. and Smith, M.A. and Bertrand, C. and Gamboa, I.C. and Espinoza, B. and Sullivan, J.B. and Deca{\"e}ns, T. and Herbin, D. and Chavarria, L.F. and Franco, R. and Cambronero, H. and Rios, S. and Quesada, F. and Pereira, G. and Vargas, J. and Guadamuz, A. and Espinoza, R. and Hernandez, J. and Rios, L. and Cantillano, E. and Moraga, R. and Moraga, C. and Rios, P. and Rios, M. and Calero, R. and Martinez, D. and Brice{\~n}o, D. and Carmona, M. and Apu, E. and Aragon, K. and Uma{\~n}a, C. and Perez, J. and Cordoba, A. and Uma{\~n}a, P. and Sihezar, G. and Espinoza, O. and Cano, C. and Araya, E. and Garcia, D. and Ramirez, H. and Pereira, M. and Cortez, J. and Pereira, M. and Medina, W. and Hebert, P.D.N.} } @article {21422, title = {Mapping global biodiversity connections with DNA barcodes: Lepidoptera of Pakistan}, journal = {PLoS ONE}, volume = {12}, year = {2017}, month = {03/2017}, pages = {e0174749}, chapter = {e0174749}, abstract = {

\"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.\"

}, keywords = {BARCODE INDEX NUMBER, BARCODING, BOMBYCIDAE, BRAHMAEIDAE, COI, DNA, HIPPOTION, HYLES, LASIOCAMPIDAE, PAKISTAN, SATURNIIDAE, SPHINGIDAE}, doi = {10.1371/journal.pone.0174749}, author = {Ashfaq, M. and Akhtar, S. and Rafi, M.A. and Mansoor, S. and Hebert, P.D.N.} } @article {21256, title = {Calibrating the taxonomy of a megadiverse insect family: 3000 DNA barcodes from geometrid type specimens (Lepidoptera, Geometridae)}, journal = {Genome}, volume = {59}, year = {2016}, type = {Early view}, keywords = {BARCODING, COI, DNA, GEOMETRIDAE, TAXONOMY, TYPES}, doi = {10.1139/gen-2015-0197}, url = {http://dx.doi.org/10.1139/gen-2015-0197}, author = {Hausmann, A. and Miller, S.E. and Holloway, J.D. and deWaard, J.R. and Pollock, D. and Prosser, S.W.J. and Hebert, P.D.N.} } @article {21255, title = {Species-level para- and polyphyly in DNA barcode gene trees: strong operational bias in European Lepidoptera}, journal = {Systematic Biology}, year = {2016}, type = {Early view}, abstract = {

\"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.\"

}, keywords = {BARCODE GAP, BARCODING, COI, DNA, EUROPE, GENE TREE, LEPIDOPTERA, MAXIMUM LIKELIHOOD, MONOPHYLIZER, NEIGHBOR-JOINING, PARAPHYLY, POLYPHYLY, SPECIES DELIMITATION, SPECIES MONOPHYLY}, doi = {10.1093/sysbio/syw044}, author = {Mutanen, M. and Kivel{\"a}, S.M. and Vos, R.A. and Doorenweerd, C. and Ratnasingham, S. and Hausmann, A. and Huemer, P. and Dinca, V. and van Nieukerken, E.J. and Lopez-Vaamonde, C. and Vila, R. and Aarvik, L. and Deca{\"e}ns, T. and Efetov, K.A. and Hebert, P.D.N. and Johnsen, A. and Karsholt, O. and Pentinsaari, M. and Rougerie, R. and Segerer, A. and Tarmann, G. and Zahiri, R. and Godfray, H.C.J.} } @article {21242, title = {An annotated checklist of the Macroheterocera of south-eastern Ontario}, journal = {Journal of Research on the Lepidoptera}, volume = {13}, year = {1974}, pages = {23-42}, chapter = {23}, keywords = {CANADA, FOODPLANT, SATURNIIDAE, SPHINGIDAE, WORLDMAP}, author = {Ward, P.S. and Harmsen, R. and Hebert, P.D.N.} } @article {21062, title = {A DNA-based registry for all animal species: the Barcode Index Number (BIN) system}, journal = {PLoS ONE}, volume = {8}, year = {2013}, month = {07/2013}, pages = {e66213}, chapter = {1}, keywords = {BARCODE INDEX NUMBER, BARCODING, COI, DNA, GMYC, RESL, SPECIES DELIMITATION}, doi = {10.1371/journal.pone.0066213}, author = {Ratnasingham, S. and Hebert, P.D.N.} } @article {20769, title = {Australian Sphingidae - DNA barcodes challenge current species boundaries and distributions}, journal = {PLoS ONE}, volume = {9}, year = {2014}, month = {07/2014}, pages = {1-12}, chapter = {1}, keywords = {AGRIUS, AUSTRALIA, BARCODE GAP, BARCODING, BIOGEOGRAPHY, CATALOGUE, COENOTES, DNA, ENDEMISM, EUPANACRA, HIPPOTION, HOPLIOCNEMA, LINNEAN SHORTFALL, NEIGHBOR-JOINING, PSILOGRAMMA, SPHINGIDAE, THERETRA, WALLACEAN SHORTFALL}, author = {Rougerie, R. and Kitching, I.J. and Haxaire, J. and Miller, S. E. and Hausmann, A. and Hebert, P.D.N.} } @article {20549, title = {When species matches are unavailable are DNA barcodes correctly assigned to higher taxa? An assessment using sphingid moths}, journal = {BMC Ecology}, volume = {11}, year = {2011}, month = {2011}, pages = {18}, chapter = {18}, abstract = {

\"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.\"

}, keywords = {BARCODING, DNA, HIGHER CLASSIFICATION, IDENTIFICATION, SPHINGIDAE}, url = {http://www.biomedcentral.com/1472-6785/11/18}, author = {Wilson, J.J. and Rougerie, R. and Schonfeld, J. and Janzen, D.H. and Hallwachs, W. and Hajibabaei, M. and Kitching, I.J. and Haxaire, J. and Hebert, P.D.N.} } @article {18606, title = {Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding}, journal = {Philosophical Transactions of the Royal Society of London}, volume = {360}, year = {2005}, note = {B}, month = {2005}, pages = {1835-1845}, keywords = {BARCODING, BIODIVERSITY, COI, COSTA RICA, CRYPTIC SPECIES, DNA, HESPERIIDAE, SATURNIIDAE, SPHINGIDAE, TAXONOMY}, doi = {10.1098/rstb.2005.1715}, author = {Janzen, D.H. and Hajibabaei, M. and Burns, J.M. and Hallwachs, W. and Remigio, E. and Hebert, P.D.N.} } @article {18201, title = {DNA barcodes distinguish species of tropical Lepidoptera}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, year = {2006}, month = {01/2006}, pages = {968-971}, chapter = {968}, keywords = {BARCODING, CLASSIFICATION, COI, COSTA RICA, HESPERIIDAE, LEPIDOPTERA, SATURNIIDAE, SPHINGIDAE}, url = {https://www.pnas.org/doi/epdf/10.1073/pnas.0510466103}, author = {Hajibabaei, M. and Janzen, D.H. and Burns, J.M. and Hallwachs, W. and Hebert, P.D.N.} }