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FLYTREE: Cooperative Research in Phylogenetics and Bioinformatics

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FLYTREE: Cooperative Research in Phylogenetics and Bioinformatics FLFLYYTRETREEE:: CooperatiCooperativeve ResearchResearch iinn PhyPhyllogogenetieneticscs andand BBiioioinfnformatiormaticscs TowTowardard aa DiDipteranpteran TreeTree ofof LLiiffee Brian Wiegmann, North Carolina SState University, USA Rudolf MMeier, National University oof SSINGAPORE David K.K. YYeates, CSIRO, Entomology, AUSTRALIA Markus Friedrich, Wayne St. University, Detroit Greg Courtney, Iowa SState University F. Christian Thompson, USDA, ARS, Systematic EEntomology LaLab, Washington DC, USA Gail KaKampmeier, Illinois Natural HistoHistory SSurvey, Illinois, USA DIDIPTEPTERARA Lowerer DipDiptereraa BrBraacchycycereraa FFLLIIEESS ((DDIIPTPTEERA)RA):: AA MMajajoror ClCladeade ofof LLiiffee •~125,000 species described (12% of animals) • total species richness at least 2-3 times >> • morphologically exuberant lineage • origins in the late Paleozoic Earliest AAngiospermrms Earliest BrachBrachycera Earlieest DDiptera DDiipptteerarann GeGenomnomeess 1010 AdAddditioitionnalal ddipteripteranan gengenoommeses inin prproogrgress:ess: • DDrosophilarosophila psepseudobscudobscuraura • GGlossinalossina mmorsitansorsitans • AAeededess aeaegygyptipti • 88 spespeccieiess ofof DDrosophilarosophila Anopheles gambiaeiae FFLYTRLYTREEEE -- NNSSFF AToLAToL DiDipptteerara • Cooperative Research iin Phylogenetics and Bioinformatics oof True Flies (Diptera:Insecta) (8 laboratories, 15-20 collaborating dipterists; 5 years) • Large pproject to bbring together major ccontributors to modern sysynthesis of fly phylogeny • Mult-level approach with three main ““tiers” – Tier 1: 42-taxon framework phylogeny covering the entire order. 30 kb of DNA, morphology, full mitochondrial ggenomes. – Tier 2: “Supermatrix” representing data collection for all fly families= >250 taxa, multiple genes, mmorphology – Tier 3: ““Supertree” analyses of Dipteran relationships based on individual analyses of specific phylogenetic groups from within the project and from published analyses. – “Phylogenetic database to distribute biological information on Diptera: ttaxonomy, genetics, development, morphology, behavior, eetc. FLYTREE PIs & Key Collaborators Additional Collaborators TTiieerr 11 • 4422-t-taxonaxon fframerameworkwork pphyhyloglogeenyny • ExeExempmplarlar ttaxaaxa areare “mode“modell orgorganianissmsms”” tthathat rereppreresseentnt allall mmaajojorr lliineneagageess • 3300kb+kb+ ofof nuclenuclearar ggeenominomicc DNDNAA sseeqqueuencence • CompComprerehehensnsiiveve compcomparataratiiveve morpmorphologhologyy sscorecoredd acrosacrosss tthehe ordeorderr • FFullull mimittochondriochondrialal ggeenomenomess fforor allall 4422 ssppeecicieess CCoommparparativeative MoMorrphphoolologygy -- ScScororeded fforor allall liflifee stastaggeses aacrcroossss ththee enentirtiree oorrdederr X Chromosome 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Chromosome 2L 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 Chromosome 2R 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Chromosome 3L 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 Chromosome 3R D. melanogaster, nuclear genome 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 Chromosome 4 MoMoleclecuularlar ddatasetsatasets 101 102 103 104 O’Grady and DeSalle, pers. comm. --fufullll mmiitotocchohonnddrriaiall gengenomomeess aanndd mmuulltiptipllee nnucuclleeaarr ggeenesnes T.bielanensis T.castaneum L.migratoria B.mori 100/100 A.gambiae 100/60 A.quadrimaculatus 100/62 C.capitata C.hominivorax 100/97 99/95 D.melanogaster 100/100 D.yakuba QP JJT-dΓ aa (3586 sites) / QP HKY-dΓ 12+16S (1634 sites) Mitochondrial Nuclear MMoleolecularcular SSyystestematist’smatist’s SStandardtandard AArsersenalnal ofof MMarkarkeersrs Current molecularp hylogenetic arsenal ribosomal genes nuclear coding genes 28S 18S EF-1a DDC Histone III 1 kb PEPCK Opsin Wint-1 Two “new” phylogenetic markers CAD (6.5 kb) GART (3.8 kb) TTiieerr 22 • 250-250-ttaaxoxonn ““ssupermupermaattririx”x” represrepresententiingng aallll ffllyy ffaammiilliieses • 15-15-2020 kkbb ooff nuclnucleaearr DDNANA • CCoommprehensprehensiivvee cocommpapararattiivvee mmoorphorphollooggyy • AnaAnallyysseses undunderer mmululttiiplplee cocondndiittiioonsns reqrequiuiriringng iintntensensiivvee cocommputputaattiioonanall resresoourcesurces • CCoommpaparirissoonn aandnd cocommbbiinanattiioonn ooff ddaattaa papartrtiittiioonsns TTiieerr 33 • SupertSupertreeree aananallyyssiiss ooff recentrecent aandnd newnewllyy oobbttaaiinedned esesttiimmaatteses ooff phyphyllooggenetenetiicc relrelaattiioonsnshihipsps wwiitthihinn ddiiptpteraerann clclaaddeses • MMetetaa aananallyyssiiss ooff pubpublliisshedhed hyhypopotthesheseses • DDetetaaiilleded ssttududiieses ooff kkeyey ddiiptpteraerann clclaaddeses • CCoommprehensprehensiivvee ssumummmaaryry ooff eveviiddenceence oonn phyphyllooggenyeny ffoorr aa llaargrgee ffraractctiioonn ooff ddiiptpteraerann ddiivversersiittyy • 1,1,500500 sspecipecieses SoSommee RecentRecent aandnd OOngngooiingng PPhyhyllooggenetenetiicc StStududiieses ooff DDiiptpteraerann LiLineaneaggeses tthahatt cocontntriribbututee ttoo ttiierer 33 • LLoowerwer DipterDipteraa • TeTephriphrittoideaoidea (‘Nem(‘Nematoatoccerera’)a’) • OestrOestrooiiddeaea • LLoowerwer BBrracachhycycereraa • HHiippppooboscboscooiiddeaea • CCuuliclicooidideaea • SepsidaSepsidaee • ThThererevidevidaeae • CCooeelolopipiddaeae • AcAcrrooccererididaeae • MuMuscsciiddaeae • AsilidAsilidaeae • SaSarrccoopphhaagidagidaee • BBoommbbyliidyliidaeae • PiPipunpuncculidulidaaee • EmEmpidpidooidideaea • RhRhaagiogioniniddaeae • ErErememoonneueurraa • TabaTabannomomoorpharpha • CCalyptralyptrataeatae • SyrpSyrphhididaaee • ScScioiommyzoyzoidideaea • DeDeuteruteroophlebphlebiiiiddaeae Diptera Phylogeny- Current Synthesis Estimated # spp. Ptychopteromorpha 100 Culicomorpha 16,000 Blephariceromorpha 500 Bibionomorpha 9000 Psychodo- + Tipulomorpha 17,000 Tabanomorpha 4000 Xylophagomorpha 100 Stratiomyomorpha 2000 Brachycera Nemestrinoidea 700 Asiloidea 12,000 Muscomorpha Empidoidea 10,000 Lower Cyclorrhapha 10,000 Eremoneura Acalyptratae 25,000 Calyptratae 19,000 Cyclorrhapha Schizophora LOLOWEWERR DDIIPPTERRAA ((NNematatocerocera)a) Tipulomorpha Ptychopteromorpha Bibionomorpha Culicomorpha Blephariceromorpha Blephariceromorpha Axymyiomorpha Bibionomorpha Psychodomorpha Bibionomorpha Axymyiomorpha Brachycera Brachycera Psychodomorpha & Ptychopteromorpha Tipulomorpha Culicomorpha Brachycera Wood & Borkent 1989 Oosterbroek & Courtney 1995 Sinclair 1992 LOLOWEWERR BBRRACCHHYYCCEERRAA ((OOrtthorhorrrhapha)hapha) Lower Diptera Lower Diptera Xylophagomorpha Stratiomyomorpha Tabanomorpha Xyllophagomorpha Stratiomyomorpha Tabanomorpha Nemestrinoidea Nemestrinoidea Asiloidea Asiloidea Empidioidea Empidioidea Cyclorrhapha Cyclorrhapha Sinclair et al 1993 Yeates 2002 Ptychopteromorpha Culicomorpha Blephariceromorpha Bibionomorpha Psychodomorpha Tipuloidea Stratiomyomorpha Xylophaghomorpha Brachycera Tabanomorpha Nemestrinoidea Muscomorpha Asiloidea Empidoidea Eremoneura Aschiza (part) Cyclorrhapha Phoroidea Syrphoidea Hippoboscoidea Muscoidea Oestroidea Schizophora Conopoidea Tephritoidea Nerioidea Diopsoidea Acalyptrata Lauxanioidea Sciomyozoidea Sphaeroceroidea Ephydroidea Carnoidea Opomyzoidea BBioiioinnfformormaattiiccss ofof DDiipptteerraa • DDeveveleloopp ttoooollss ffoorr ddiissssememiinanattiioonn ooff bbiiooddiivversersiittyy iinfnfoormrmaattiioonn oonn fflliieses – FLFLYTREEYTREE webwebsitesite (www.in(www.inhhs.us.uiuiucc.ed.eduu/c/cee/FLee/FLYTREE)YTREE) – BBioiosystemsystematicatic DatabDatabasease ooff WoWorrldld DipterDipteraa (B(BDWD)DWD) – MANDALMANDALAA [[PhPhyloylogengeneticetic/Tax/Taxoonnoommicic ddataata ararcchhiveive anandd ddelivereliveryy – DipterDipteraa WebWeb ((wwwwww..ddipteripteraa.o.orrgg)) – MoMorrphphoolologicgicalal GloGlossarssary,y, IInnterteracactivetive keys,keys, TOLTOL.o.orrg,g, imimageage ddatabatabases,ases, specspeciesies pagespages FLYTREE -- builds on previous and current collaborative projects • PEET - Therevidae - DEB 95-21925 & 99-77958 collecting/specimen database/ monography/ phylogenetics • BSI projects -- Fiji, Thailand, Madagascar • Phylogenomics/Biocomplexity - Drosophilidae (DeSalle and O’Grady) and Deep Arthropod (Cunningham and Regier • Lab cultures/evo-devo/med-vet/ipm What is Mandala? • Cross-platform database system supporting data acquisition & management for systematics & biodiversity studies Specimens Taxonomic Literature Names Illustrations Brief History of Mandala • Begun in 1995 for therevid NSF PEET* project • Currently uses FileMaker® Pro 5/6 – Relational – Works on Macintosh & Windows OS • Extensible, adaptable, & evolving • Fully operational demo available by request *U.S. National Science Foundation Partnerships for Enhancing Expertise in Taxonomy DEB 95-21925 & 99-77958 Serve Species Webpages of Target Taxa from Mandala Existing Mandala Features for FLYTREE • Mandala links GenBank entries to Specimens & Taxa – Record the GenBank accession number – Choose the genetic marker from the editable popup list – URL links the database record to the Genbank website for your sequence when you click on the globe button. Plans for Extending Mandala • Registration system for FLYTREE workers around the world to document work on taxa and genetic markers • Track specimens used in studies • Document taxonomic names • Organize & serve illustrations to web • Upgrade to FileMaker 7 with increased security & web features Expansion of Phylogenetic Infrastructure in Classification- based Web Products • Biosystematic Database of World Diptera • Maddison’sTree of Life Website (Tol.org) • Interactive Key to World Diptera • FLYBASE • FLYTREE Website MANDALA -- FLYTREE Specimens Taxonomic Specimens Literature Names Taxonomic Lineages Names Illustrations Characters .
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