02798nas a2200337 4500008004100000245014500041210006900186260001200255300001500267490000700282520179500289653003102084653001702115653001202132653001502144653001602159653000802175653001802183653001402201653003002215100001902245700002102264700001502285700001902300700002002319700001402339700002502353700001702378700001902395856004602414 2019 eng d00aPhylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives.0 aPhylogenomics resolves major relationships and reveals significa c09/2019 a182 [1-13]0 v193 a

"Background: Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections.
Results: The well-supported tree was overall consistent with prior morphological and molecular studies, although some taxa were misplaced. The bombycid Arotros Schaus was formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths).
Conclusions: Our study establishes a backbone for future evolutionary, comparative, and taxonomic studies of Bombycoidea. We postulate that the rate shifts identified are due to the well-documented bat-moth “arms race”. Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe."

10aANCHORED HYBRID ENRICHMENT10aAPATELODIDAE10aAROTROS10aBOMBYCIDAE10aBOMBYCOIDEA10aDNA10aPHYLOGENOMICS10aPHYLOGENY10aTARGETED SEQUENCE CAPTURE1 aHamilton, C.A.1 aSt Laurent, R.A.1 aDexter, K.1 aKitching, I.J.1 aBreinholt, J.W.1 aZwick, A.1 aTimmermans, M.J.T.N.1 aBarber, J.R.1 aKawahara, A.Y. uhttps://doi.org/10.1186/s12862-019-1505-104045nas a2200421 4500008004100000245022700041210006900268300000800337490000700345520290100352653000903253653000903262653002303271653001003294653000803304653000903312653001003321653001903331653000903350653002303359653001603382653001503398653000803413653000803421653000803429653000803437653000903445653000803454653000803462653001203470653001403482653001403496653000903510100002003519700001603539700001903555856004903574 2017 eng d00aThe influence of molecular markers and methods on inferring the phylogenetic relationships between the representatives of the Arini (parrots, Psittaciformes), determined on the basis of their complete mitochondrial genomes0 ainfluence of molecular markers and methods on inferring the phyl a1660 v173 a

"Background: Conures are a morphologically diverse group of Neotropical parrots classified as members of the tribe Arini, which has recently been subjected to a taxonomic revision. The previously broadly defined Aratinga genus of this tribe has been split into the ‘true’ Aratinga and three additional genera, Eupsittula, Psittacara and Thectocercus. Popular markers used in the reconstruction of the parrots’ phylogenies derive from mitochondrial DNA. However, current phylogenetic analyses seem to indicate conflicting relationships between Aratinga and other conures, and also among other Arini members. Therefore, it is not clear if the mtDNA phylogenies can reliably define the species tree. The inconsistencies may result from the variable evolution rate of the markers used or their weak phylogenetic signal. To resolve these controversies and to assess to what extent the phylogenetic relationships in the tribe Arini can be inferred from mitochondrial genomes, we compared representative Arini mitogenomes as well as examined the usefulness of the individual mitochondrial markers and the efficiency of various phylogenetic methods.

Results: Single molecular markers produced inconsistent tree topologies, while different methods offered various topologies even for the same marker. A significant disagreement in these tree topologies occurred for cytb, nd2 and nd6 genes, which are commonly used in parrot phylogenies. The strongest phylogenetic signal was found in the control region and RNA genes. However, these markers cannot be used alone in inferring Arini phylogenies because they do not provide fully resolved trees. The most reliable phylogeny of the parrots under study is obtained only on the concatenated set of all mitochondrial markers. The analyses established significantly resolved relationships within the former Aratinga representatives and the main genera of the tribe Arini. Such mtDNA phylogeny can be in agreement with the species tree, owing to its match with synapomorphic features in plumage colouration.

Conclusions: Phylogenetic relationships inferred from single mitochondrial markers can be incorrect and contradictory. Therefore, such phylogenies should be considered with caution. Reliable results can be produced by concatenated sets of all or at least the majority of mitochondrial genes and the control region. The results advance a new view on the relationships among the main genera of Arini and resolve the inconsistencies between the taxa that were previously classified as the broadly defined genus Aratinga. Although gene and species trees do not always have to be consistent, the mtDNA phylogenies for Arini can reflect the species tree.

10aATP610aATP810aBAYESIAN INFERENCE10aBIRDS10aCOI10aCOII10aCOIII10aCONTROL REGION10aCYTB10aMAXIMUM LIKELIHOOD10aMETHODOLOGY10aMITOGENOME10aND110aND210aND310aND410aND4L10aND510aND610aPARROTS10aPARSIMONY10aPHYLOGENY10aTRNA1 aUrantowka, A.D.1 aKroczak, A.1 aMackiewicz, P. uhttps://sphingidae.myspecies.info/node/2152703627nas a2200397 4500008004100000245011500041210006900156300000800225490000700233520258300240653002102823653001502844653000802859653000802867653001302875653002102888653001402909653001002923653000802933653002402941653001602965653002302981653000803004653001403012653001403026653001503040653000903055653001503064653001903079100001803098700001603116700001703132700001703149700001403166856004903180 2015 eng d00aElusive ditrysian phylogeny: an account of combining systematized morphology with molecular data (Lepidoptera)0 aElusive ditrysian phylogeny an account of combining systematized a2600 v153 a

"Background: Ditrysia comprise close to 99 % of all butterflies and moths. The evolutionary relationships among the ditrysian superfamilies have received considerable attention in phylogenetic studies based on DNA and transcriptomic data, but the deepest divergences remain for large parts unresolved or contradictory. To obtain complementary insight into the evolutionary history of the clade, and to test previous hypotheses on the subdivision of Ditrysia based on morphology, we examine the morphology of larvae, pupae and adult males and females of 318 taxa representing nearly all ditrysian superfamilies and families. We present the most comprehensive morphological dataset on Ditrysia to date, consisting of over 500 morphological characters. The data are analyzed alone and combined with sequence data (one mitochondrial and seven nuclear protein-coding gene regions, sequenced from 422 taxa). The full dataset consists of 473 exemplar species. Analyses are performed using maximum likelihood methods, and parsimony methods for the morphological dataset. We explore whether combining morphological data and DNA-data can stabilize taxa that are unstable in phylogenetic studies based on genetic data only.

Results: Morphological characters are found phylogenetically informative in resolving apical nodes (superfamilies and families), but characters serving as evidence of relatedness of larger assemblages are few. Results include the recovery of a monophyletic Tineoidea, Sesioidea and Cossoidea, and a stable position for some unstable taxa (e.g. Epipyropidae, Cyclotornidae, Urodoidea + Schreckensteinioidea). Several such taxa, however, remain unstable even though morphological characters indicate a position in the tree (e.g. Immidae). Evidence supporting affinities between clades are suggested, e.g. a novel larval synapomorphy for Tineidae. We also propose the synonymy of Tineodidae with Alucitidae, syn. nov.

Conclusions: The large morphological dataset provides information on the diversity and distribution of morphological traits in Ditrysia, and can be used in future research on the evolution of these traits, in identification keys and in identification of fossil Lepidoptera. The “backbone” of the phylogeny for Ditrysia remains largely unresolved. As previously proposed as an explanation for the scarcity of molecular signal in resolving the deeper nodes, this may be due to the rapid radiation of Ditrysia in the Cretaceous."

10aADULT MORPHOLOGY10aALUCITIDAE10aCAD10aCOI10aDITRYSIA10aDIVERGENCE TIMES10aEF-1ALPHA10aGAPDH10aIDH10aIMMATURE MORPHOLOGY10aLEPIDOPTERA10aMAXIMUM LIKELIHOOD10aMDH10aPARSIMONY10aPHYLOGENY10aROGUE TAXA10aRpS510aTINEODIDAE10aTOTAL EVIDENCE1 aHeikkilä, M.1 aMutanen, M.1 aWahlberg, N.1 aSihvonen, P.1 aKaila, L. uhttps://sphingidae.myspecies.info/node/2151603402nas a2200361 4500008004100000245009100041210006900132260001200201300000800213490000700221520239400228653001402622653000802636653000802644653002602652653001102678653001402689653002302703653002002726653002902746653001902775653002302794653002402817653001602841653001002857653002602867100001902893700002302912700001602935700002702951700001302978856004902991 2016 eng d00aPhylogeography of the Spanish Moon Moth Graellsia isabellae (Lepidoptera, Saturniidae)0 aPhylogeography of the Spanish Moon Moth Graellsia isabellae Lepi c06/2016 a1390 v163 a

"Background: Geographic and demographic factors as well as specialisation to a new host-plant may lead to host-associated differentiation in plant-feeding insects. We explored the phylogeography of a protected moth, Graellsia isabellae, and its two recognised host-plant species (Pinus sylvestris and P. nigra) in order to seek for any concordance useful to disentangle the evolutionary history of this iconic lepidopteran.
Results: DNA variation in one mitochondrial marker and nine nuclear microsatellite loci revealed a strong phylogeographic pattern across 28 populations of G. isabellae studied in Spain and France comprising six groups mostly distributed along different mountain ranges. Reanalysis of a previously published chloroplast microsatellite dataset revealed a three and two-group structure for Spanish P. sylvestris and P. nigra, respectively. Overall, the population groupings of this protected moth did not match the ones of P.  sylvestris and P. nigra.
Conclusions: There was no evidence of host-associated differentiation between populations using P. sylvestris and the ones inhabiting P. nigra. The two major mitochondrial clades of G. isabellae likely diverged before the Last Glacial Maximum and geographically separated the species into a “southern” (Central and Southern Iberian clusters) and a “northern” lineage (Eastern Iberian, Pyrenean and French Alpine clusters). The Eastern Iberian  System, where this insect uses both host-plants, harboured the highest level of genetic diversity. Such a group independently colonised the West and East parts of the Pyrenees. Our results point to a native origin for the French populations occurring in the Alps, genetically related to the Eastern Iberian and Pyrenean sites. The Central Iberian group derived from Southern Iberian ancestors. Secondary contacts were inferred between the Southern/Central Iberian populations and Eastern Iberian cluster as well as between the two Pyrenean ones. The mito-nuclear discordance observed with regard to the Eastern Iberian cluster is congruent with a secondary contact after the evolution of mito-nuclear incompatibilities in geographically isolated areas."

10aCATALOGUE10aCOI10aDNA10aFOODPLANT SPECIFICITY10aFRANCE10aGRAELLSIA10aHAPLOTYPE NETWORKS10aMICROSATELLITES10aMITO-NUCLEAR DISCORDANCE10aPHYLOGEOGRAPHY10aPOPULATION BIOLOGY10aREFUGIUM HYPOTHESIS10aSATURNIIDAE10aSPAIN10aSTATISTICAL PARSIMONY1 aMarí-Mena, N.1 aLopez-Vaamonde, C.1 aNaveira, H.1 aAuger-Rozenberg, M.-A.1 aVila, M. uhttps://sphingidae.myspecies.info/node/2144700850nas a2200277 4500008004100000024001700041245013700058210006900195260000900264300000700273490000700280653000900287653001900296653001800315653002300333653001000356653001000366653002000376653001000396653001100406653001900417653001500436100001600451700002300467856008200490 2013 eng d aPapyrus 215600aMitochondrial lineage sorting in action - historical biogeography of the Hyles euphorbiae complex (Sphingidae, Lepidoptera) in Italy0 aMitochondrial lineage sorting in action historical biogeography  c2013 a830 v1310aADNA10aCLIMATE CHANGE10aGENETIC DRIFT10aHAPLOTYPE NETWORKS10aHYLES10aITALY10aLINEAGE SORTING10aMTDNA10aMUSEUM10aPHYLOGEOGRAPHY10aSPHINGIDAE1 aMende, M.B.1 aHundsdoerfer, A.K. uhttps://bmcecolevol.biomedcentral.com/counter/pdf/10.1186/1471-2148-13-83.pdf