04047nas a2200973 4500008004100000022001400041024001700055245011000072210006900182260000900251300001200260490000700272520168800279653002101967653001401988653001602002653001402018653000902032653000802041653001502049653001202064653000802076653001102084653001202095653001902107653001302126653001402139653001502153653001602168653002502184653001402209653001302223100001702236700001802253700001702271700001502288700001702303700001902320700001602339700001702355700001702372700001702389700001902406700001702425700001502442700002002457700001502477700001902492700001302511700001602524700001602540700001502556700001702571700001702588700001802605700001302623700001902636700001502655700001502670700001302685700001302698700001502711700001702726700001702743700001602760700001202776700001502788700001502803700001402818700001602832700001502848700001602863700001702879700001302896700001402909700001502923700001602938700001602954700001502970700001602985700001503001700001903016856003803035 2012 eng d a1445-5226 aPapyrus 357300aWhat happens to the traditional taxonomy when a well-known tropical saturniid moth fauna is DNA barcoded?0 aWhat happens to the traditional taxonomy when a wellknown tropic c2012 a478-5050 v263 a
"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."
10aBARCODE INDEX NUMBER10aBARCODING10aBOMBYCIDAE10aBRAHMAEIDAE10aCOI10aDNA10aHIPPOTION10aHYLES10aLASIOCAMPIDAE10aPAKISTAN10aSATURNIIDAE10aSPHINGIDAE1 aAshfaq, M.1 aAkhtar, S.1 aRafi, M.A.1 aMansoor, S.1 aHebert, P.D.N. uhttps://sphingidae.myspecies.info/node/2142200734nas a2200241 4500008004100000245013600041210006900177490000700246653001400253653000800267653000800275653001600283653001300299653001000312100001700322700001700339700001900356700001800375700001600393700002000409700001900429856004400448 2016 eng d00aCalibrating the taxonomy of a megadiverse insect family: 3000 DNA barcodes from geometrid type specimens (Lepidoptera, Geometridae)0 aCalibrating the taxonomy of a megadiverse insect family 3000 DNA0 v5910aBARCODING10aCOI10aDNA10aGEOMETRIDAE10aTAXONOMY10aTYPES1 aHausmann, A.1 aMiller, S.E.1 aHolloway, J.D.1 adeWaard, J.R.1 aPollock, D.1 aProsser, S.W.J.1 aHebert, P.D.N. uhttp://dx.doi.org/10.1139/gen-2015-019704241nas a2200529 4500008004100000245011300041210006900154520281500223653001603038653001403054653000803068653000803076653001103084653001403095653001603109653002303125653001703148653002103165653001403186653001403200653002503214653002203239100001603261700001803277700001403295700002003309700002103329700001703350700001503367700001403382700002503396700002303421700001303444700001503457700001703472700001703489700001903506700001603525700001703541700002003558700001703578700001603595700001603611700001503627700002003642856004903662 2016 eng d00aSpecies-level para- and polyphyly in DNA barcode gene trees: strong operational bias in European Lepidoptera0 aSpecieslevel para and polyphyly in DNA barcode gene trees strong3 a"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."
10aBARCODE GAP10aBARCODING10aCOI10aDNA10aEUROPE10aGENE TREE10aLEPIDOPTERA10aMAXIMUM LIKELIHOOD10aMONOPHYLIZER10aNEIGHBOR-JOINING10aPARAPHYLY10aPOLYPHYLY10aSPECIES DELIMITATION10aSPECIES MONOPHYLY1 aMutanen, M.1 aKivelä, S.M.1 aVos, R.A.1 aDoorenweerd, C.1 aRatnasingham, S.1 aHausmann, A.1 aHuemer, P.1 aDinca, V.1 avan Nieukerken, E.J.1 aLopez-Vaamonde, C.1 aVila, R.1 aAarvik, L.1 aDecaëns, T.1 aEfetov, K.A.1 aHebert, P.D.N.1 aJohnsen, A.1 aKarsholt, O.1 aPentinsaari, M.1 aRougerie, R.1 aSegerer, A.1 aTarmann, G.1 aZahiri, R.1 aGodfray, H.C.J. uhttps://sphingidae.myspecies.info/node/2125500564nas a2200193 4500008004100000245007500041210006900116300001000185490000700195653001100202653001400213653001600227653001500243653001300258100001500271700001600286700001900302856004900321 1974 eng d00aAn annotated checklist of the Macroheterocera of south-eastern Ontario0 aannotated checklist of the Macroheterocera of southeastern Ontar a23-420 v1310aCANADA10aFOODPLANT10aSATURNIIDAE10aSPHINGIDAE10aWORLDMAP1 aWard, P.S.1 aHarmsen, R.1 aHebert, P.D.N. uhttps://sphingidae.myspecies.info/node/2124200631nas a2200217 4500008004100000245008700041210006900128260001200197300001100209490000600220653002500226653001400251653000800265653000800273653000900281653000900290653002500299100002100324700001900345856004900364 2013 eng d00aA DNA-based registry for all animal species: the Barcode Index Number (BIN) system0 aDNAbased registry for all animal species the Barcode Index Numbe c07/2013 ae662130 v810aBARCODE INDEX NUMBER10aBARCODING10aCOI10aDNA10aGMYC10aRESL10aSPECIES DELIMITATION1 aRatnasingham, S.1 aHebert, P.D.N. uhttps://sphingidae.myspecies.info/node/2106201062nas a2200397 4500008004100000245009600041210006900137260001200206300000900218490000600227653001100233653001400244653001600258653001400274653001700288653001400305653001300319653000800332653001300340653001400353653001400367653001600381653002200397653002100419653001600440653001500456653001300471653002400484100001700508700001900525700001600544700001900560700001700579700001900596856004900615 2014 eng d00aAustralian Sphingidae - DNA barcodes challenge current species boundaries and distributions0 aAustralian Sphingidae DNA barcodes challenge current species bou c07/2014 a1-120 v910aAGRIUS10aAUSTRALIA10aBARCODE GAP10aBARCODING10aBIOGEOGRAPHY10aCATALOGUE10aCOENOTES10aDNA10aENDEMISM10aEUPANACRA10aHIPPOTION10aHOPLIOCNEMA10aLINNEAN SHORTFALL10aNEIGHBOR-JOINING10aPSILOGRAMMA10aSPHINGIDAE10aTHERETRA10aWALLACEAN SHORTFALL1 aRougerie, R.1 aKitching, I.J.1 aHaxaire, J.1 aMiller, S., E.1 aHausmann, A.1 aHebert, P.D.N. uhttps://sphingidae.myspecies.info/node/2076903620nas a2200301 4500008004100000024001700041245012800058210006900186260000900255300000700264490000700271520274900278653001403027653000803041653002603049653001903075653001503094100001703109700001703126700001803143700001703161700001803178700001903196700001903215700001603234700001903250856004903269 2011 eng d aPapyrus 872600aWhen species matches are unavailable are DNA barcodes correctly assigned to higher taxa? An assessment using sphingid moths0 aWhen species matches are unavailable are DNA barcodes correctly c2011 a180 v113 a"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."
10aBARCODING10aDNA10aHIGHER CLASSIFICATION10aIDENTIFICATION10aSPHINGIDAE1 aWilson, J.J.1 aRougerie, R.1 aSchonfeld, J.1 aJanzen, D.H.1 aHallwachs, W.1 aHajibabaei, M.1 aKitching, I.J.1 aHaxaire, J.1 aHebert, P.D.N. uhttp://www.biomedcentral.com/1472-6785/11/1800863nas a2200313 4500008004100000024001700041245009500058210006900153260000900222300001400231490000800245653001400253653001700267653000800284653001500292653002000307653000800327653001600335653001600351653001500367653001300382100001700395700001900412700001600431700001800447700001600465700001900481856004900500 2005 eng d aPapyrus 765900aWedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding0 aWedding biodiversity inventory of a large and complex Lepidopter c2005 a1835-18450 v36010aBARCODING10aBIODIVERSITY10aCOI10aCOSTA RICA10aCRYPTIC SPECIES10aDNA10aHESPERIIDAE10aSATURNIIDAE10aSPHINGIDAE10aTAXONOMY1 aJanzen, D.H.1 aHajibabaei, M.1 aBurns, J.M.1 aHallwachs, W.1 aRemigio, E.1 aHebert, P.D.N. uhttps://sphingidae.myspecies.info/node/1860600756nas a2200277 4500008004100000024001700041245006100058210006100119260001200180300001200192490000800204653001400212653001900226653000800245653001500253653001600268653001600284653001600300653001500316100001900331700001700350700001600367700001800383700001900401856005800420 2006 eng d aPapyrus 753200aDNA barcodes distinguish species of tropical Lepidoptera0 aDNA barcodes distinguish species of tropical Lepidoptera c01/2006 a968-9710 v10310aBARCODING10aCLASSIFICATION10aCOI10aCOSTA RICA10aHESPERIIDAE10aLEPIDOPTERA10aSATURNIIDAE10aSPHINGIDAE1 aHajibabaei, M.1 aJanzen, D.H.1 aBurns, J.M.1 aHallwachs, W.1 aHebert, P.D.N. uhttps://www.pnas.org/doi/epdf/10.1073/pnas.0510466103