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Process Data Supertree Jon Hill1, Katie E. Davis2, Jaime Tovar2, Matthew A. Wills2 1. Environment Department, University of York, York, UK, 2. Department of Biology and Biochemistry, University of Bath, Bath, UK [email protected] @S_Toolkit Tinamidae Anseriformes Opisthocomidae Glaucidium gnoma Musophagidae Pastor roseus Glaucidium hardyi Sagittariidae Creatophora cinerea Cathartidae Acridotheres albocinctus Glaucidium nanum Falconidae Glaucidium brasilianum%2 Accipitridae Acridotheres cristatellus Strigidae Acridotheres grandis Glaucidium peruanum Tytonidae Acridotheres javanicus%1 Glaucidium brasilianum%1 Psittacidae Pseudasturidae Acridotheres fuscus Glaucidium tucumanum Acridotheres cinereus Sandcoleidae Acridotheres javanicus%2 Glaucidium bolivianum Coliidae Glaucidium jardinii Passeriformes Acridotheres melanopterus Primoscenidae Acridotheres burmannicus Glaucidium passerinum Trogonidae Acridotheres ginginianus Glaucidium tephronotum Cuculidae Acridotheres tristis Trochilidae Poliopsar sericeus Vireolanius leucotis Apodidae Poliopsar cineraceus Pteruthius rufiventer Hemiprocnidae Temenuchus sinensis Pteruthius annamensis Aegothelidae Pteruthius validirostris Caprimulgidae Temenuchus pagodarum Pteruthius ricketti Nyctibiidae Temenuchus malabaricus Pteruthius aeralatus Pteruthius schauenseei Steatornithidae Temenuchus erythropygius Pteruthius robinsoni Leptosomidae Leucopsar rothschildi Pteruthius cameranoi Podargidae Sturnornis albofrontata Pteruthius ripleyi Brachypteraciidae Pteruthius flaviscapis Gracupica nigricollis Pteruthius aenobarbus Coraciidae Gracupica contra Pteruthius intermedius Alcedinidae Pteruthius aenobarbulus Meropidae Agropsar philippensis Pteruthius melanotis Todidae Agropsar sturninus Pteruthius tahanensis Momotidae Sturnus unicolor Pteruthius hybrida Pteruthius pallidus Pici Sturnus vulgaris Pteruthius xanthochlorus Galbulae Pteruthius occidentalis Bucerotidae Vireo cassinii Upupidae Hylophilus ochraceiceps Phoeniculidae Cyclarhis gujanensis Erpornis zantholeuca Messelirrisoridae Pitta sordida Psarisomus dalhousiae Formicarius analis Furnarius leucopus Deconychura longicauda Conopophaga peruviana Thamnophilus caerulescens Myiarchus cinerascens Pipra coronata Procnias nudicollis Porphyrolaema porphyrolaema Entomyzon cyanotis Passer montanus Passer domesticus Motacilla alba Carduelis carduelis Carduelis spinus Coccothraustes coccothraustes Fringilla coelebs Passerella iliaca Emberiza citrinella Thraupis episcopus Ploceus vitellinus Dinemellia dinemelli Vidua macroura Emblema pictum Lonchura cantans Estrilda nonnula Mandingoa nitidula Uraeginthus ianthinogaster Prunella modularis Chloropsis sonnerati Irena puella + Nectarinia cuprea Muscicapa striata Ficedula hypoleuca Erithacus rubecula Luscinia svecica Phoenicurus ochruros Turdus philomelos Turdus merula Catharus guttatus Zoothera naevia Cinclus cinclus Mimus polyglottos Sturnus vulgaris = Troglodytes troglodytes Certhia brachydactyla Sitta europaea Bombycilla garrulus Regulus regulus Sylvia atricapilla Sylvia communis Sylvia nisoria Zosterops senegalensis Garrulax sannio Hypsipetes philippinus Pycnonotus leucogenys Pycnonotus xanthopygos Phylloscopus trochilus Delichon urbica All trees and meta-data from the Locustella naevia Hippolais icterina Acrocephalus dumetorum Alauda arvensis Parus palustris Parus caeruleus Parus major literature is entered into the STK Parus cristatus Chaetops aurantius Picathartes oreas Picathartes gymnocephalus Oriolus chinensis Vireo cassinii Gymnorhina tibicen Manucodia keraudrenii via a GUI. The data is stored as Cyanocitta stelleri Pica pica Corvus corax Corvus corone an XML file (Phyml) and is ready All trees in the literature are digitised for processing. Source trees are collected from the literature. Any tree can be used, regardless of the data used to create it. Process data A Taxa Equivalents Status Artemia_franciscana Artemia_franciscana green Pastor roseus G Creatophora cinerea Acridotheres grandis Drosophila_pseudoobscura Drosophila_pseudoobscura green Acridotheres cristatellus E Acridotheres albocinctus Euphausia_americana Euphausia_americana green Acridotheres javanicus%1 AcridotheresPastor fuscus roseus Euphausia_australis Euphausia_australis red F AcridotheresCreatophora cinereus cinerea AcridotheresAcridotheres javanicus%2 albocinctus Euphausia_brevis_Atlantic Euphausia_brevis_Atlantic red AcridotheresAcridotheres melanopterus cristatellus D AcridotheresAcridotheres burmannicus grandis Euphausia_brevis_Pacific Euphausia_brevis_Pacific red AcridotheresAcridotheres ginginianus javanicus%1 H AcridotheresAcridotheres tristis fuscus Euphausia_crsytallorophias Euphausia_crsytallorophias red Poliopsar sericeusAcridotheresPastor cinereus roseus + Poliopsar cineraceusAcridotheresCreatophora javanicus%2 cinerea Euphausia_crystallorophias Euphausia_crystallorophias green TemenuchusAcridotheres sinensisAcridotheres melanopterus albocinctus TemenuchusAcridotheres pagodarumAcridotheres burmannicus cristatellus Euphausia_diomedea Euphausia_diomedea red TemenuchusAcridotheres malabaricusAcridotheres ginginianus grandis TemenuchusAcridotheres erythropygiusAcridotheres tristis javanicus%1 Euphausia_distinguenda Euphausia_distinguenda green Leucopsar PoliopsarrothschildiAcridotheres sericeus fuscus G Sturnornis PoliopsaralbofrontataAcridotheres cineraceus cinereus Euphausia_eximia Euphausia_eximia green Gracupica nigricollisTemenuchusAcridotheres sinensis javanicus%2 Gracupica contraTemenuchusAcridotheres pagodarum melanopterus Euphausia_frigida Euphausia_frigida green A Agropsar philippensisTemenuchusAcridotheres malabaricus burmannicus A trees Permute Agropsar sturninusTemenuchusAcridotheres erythropygius ginginianus Euphausia_gibboides Euphausia_gibboides green Sturnus unicolorLeucopsarAcridotheres rothschildi tristis E Sturnus vulgarisSturnornisPoliopsar albofrontata sericeus Euphausia_hemigibba Euphausia_hemigibba green GracupicaPoliopsar nigricollis cineraceus E%1 GracupicaTemenuchus contra sinensis Euphausia_krohni Euphausia_krohni green F AgropsarTemenuchus philippensis pagodarum AgropsarTemenuchus sturninus malabaricus Sturnus Temenuchusunicolor erythropygius Euphausia_lamelligera Euphausia_lamelligera green G%1 D Sturnus Leucopsarvulgaris rothschildi Sturnornis albofrontata Euphausia_longirostris Euphausia_longirostris green Gracupica nigricollis G%2 H Gracupica contra Euphausia_lucens Euphausia_lucens green Agropsar philippensis Agropsar sturninus Euphausia_mutica Euphausia_mutica green Sturnus unicolor E%2 Sturnus vulgaris Euphausia_pacifica Euphausia_pacifica green E Euphausia_sibogae Euphausia_sibogae green F Pastor roseus Euphausia_similis Euphausia_similis green Creatophora cinerea A Acridotheres albocinctus Euphausia_superba Euphausia_superba green Acridotheres cristatellus Acridotheres grandis Euphausia_tenera Euphausia_tenera green D G Acridotheres javanicus%1 Acridotheres fuscus Euphausia_triacantha Euphausia_triacantha green Acridotheres cinereus H F Acridotheres javanicus%2 Euphausia_tricantha Euphausia_tricantha green Acridotheres melanopterus Acridotheres burmannicus Euphausia_vallentini Euphausia_vallentini green D Acridotheres ginginianus E%3 Acridotheres tristis Gonodactylus_sp Gonodactylus_sp. yellow Poliopsar sericeus Poliopsar cineraceus H Temenuchus sinensis Gonodactylus_viridus Gonodactylus_viridis;Gonodactylinus_viridis yellow Temenuchus pagodarum Temenuchus malabaricus Kempina_mikado Kempina_mikado green Temenuchus erythropygius Leucopsar rothschildi Litopenaeus_vannamei Litopenaeus_vannamei green Sturnornis albofrontata Gracupica nigricollis Meganyctiphanes_norvegica Meganyctiphanes_norvegica green Gracupica contra Agropsar philippensis A Agropsar sturninus Sturnus unicolor E Sturnus vulgaris G F D H OTUs in the source data need to have Source trees need to have at least two Non-monophyletic taxa (such as sub-species) need to All source trees included in the final supertree consistant nomenclature. Synonyms, higher- OTUs in common with another source tree be removed. All permutations of possible positions are must be independant of each other. The taxa and level taxa need to replaced and names to be included in the supertree analysis. calculated and a mini-supertree representing the characters used to create the source trees are standardised. We use online resources to do The red circles and the two unconnected uncertianty can be used as a source tree instead. examined and duplicates and overlaps can be this as automatically as possible discarded circles above should be removed. Supertree Anomura 847 OTUs 60 source trees Brachynauphoeta foulpointeensis Gromphadorhina oblongonota Gromphadorhina grandidieri Gromphadorhina portentosa Henschoutedenia flexivitta Princisia vanwaerebeki Leozehntnera maxima Heminauphoeta sp. 1 Diploptera punctata Elliptorhina chopardi Aeluropoda insignis Pseudocalolampra Rhyparobia maderae Henschoutedenia sp. B Pseudomops oblongata Nauphoeta cinerea Elliptorhina sp. l Pseudomops sp. 2 Xestoblatta cavicola Pseudomops sp. 1 Panchlora viridis Panchlora nivea a Nauphoeta sp. Paratemnopteryx couloniana Xestoblatta sp. 1 Ischnoptera sp. 2 Blattella germanicaIschnoptera sp. 3 t Ischnoptera sp. 1 Loboptera decipiensBlattella Blattellalituricollis asahinai t Paratemnopteryx sp. Symploce yayeyamana Princisaria Paraprincisaria Alloblatta Gyna capucina Gyna lurida Gyna caffrorum Neorhicnoda Lobopterella dimidiatipes Diplopterinae a Panchlora sp. 1 Hyporhicnoda Panchlora azteca Paradicta rotunda Blattella vaga Blaptica dubia Blaptica sp. Symploce pallens Monachoda Petasodes Byrsotria fumigata
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