01809nas a2200229 4500008004100000245010500041210006900146300001100215490000700226520115300233653000801386653001301394653002301407653001501430653001401445100001801459700001401477700001801491700001501509700001701524856003801541 2022 eng d00aThe (non) accuracy of mitochondrial genomes for family-level phylogenetics in Erebidae (Lepidoptera)0 anon accuracy of mitochondrial genomes for familylevel phylogenet a[1-13]0 vXX3 a
"The use of molecular data to study the evolutionary history of organisms has revolutionized the field of systematics. Now with the appearance of high throughput sequencing (HTS) technologies, more and more genetic sequence data are available. One of the important sources of genetic data for phylogenetic analyses has been mitochondrial DNA. The limitations of mitochondrial DNA for the study of phylogenetic relationships have been thoroughly explored in the age of single locus phylogenetic studies. Now with the appearance of genomic scale data, increasing number of mitochondrial genomes are available, leading to an increasing number of mitophylogenomic studies. Here, we assemble 47 mitochondrial genomes using whole genome Illumina short reads from representatives of the family Erebidae (Lepidoptera), in order to evaluate the accuracy of mitochondrial genome application in resolving deep phylogenetic relationships. We find that mitogenomes are inadequate for resolving subfamily-level relationships in Erebidae, but given good taxon sampling, we see its potential in resolving lower level phylogenetic relationships."
10aDNA10aEREBIDAE10aMAXIMUM LIKELIHOOD10aMITOGENOME10aPHYLOGENY1 aGhanavi, H.R.1 aTwort, V.1 aHartman, T.J.1 aZahiri, R.1 aWahlberg, N. uhttps://doi.org/10.1111/zsc.1255904241nas 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/2125500656nas a2200205 4500008004100000024001700041245014500058210006900203260000900272300001200281490000700293653001600300653000900316653001600325653001500341653001400356100001600370700001500386856004900401 2011 eng d aPapyrus 189900aResults of a lepidopterological expedition to north and northwest Iran in summer 2007 with new records for Iran (Lepidoptera) (plates 19-22)0 aResults of a lepidopterological expedition to north and northwes c2011 a135-1650 v1610aBRAHMAEIDAE10aIRAN10aSATURNIIDAE10aSPHINGIDAE10aWORLDMAP11 aLehmann, L.1 aZahiri, R. uhttps://sphingidae.myspecies.info/node/1895400643nas a2200205 4500008004100000245012100041210006900162260000900231300001000240490000900250653001400259653000900273653001900282653001500301653002200316653001400338100002100352700001500373856004900388 2007 eng d00aTaxonomic notes and new records of the genus {ISphingonaepiopsis} Wallengren, 1858 (Lepidoptera: Sphingidae) in Iran0 aTaxonomic notes and new records of the genus ISphingonaepiopsis c2007 a41-520 v161010aCATALOGUE10aIRAN10aMALE GENITALIA10aSPHINGIDAE10aSPHINGONAEPIOPSIS10aWORLDMAP11 aKitching, I., J.1 aZahiri, R. uhttps://sphingidae.myspecies.info/node/18796