被子植物系统发育

被子植物系统发育第一页，共二十二页，编辑于2023年，星期五一、前言背景二、材料与方法三、结果四、讨论第二页，共二十二页，编辑于2023年，星期五一、前言背景Premiseofthestudy:Recentanalysesemployinguptofivegeneshaveprovidednumerousinsightsintoangiospermphylogeny,butmanyrelationshipshaveremainedunresolvedorpoorlysupported.Inthehopeofimprovingourunderstandingofangiospermphylogeny,weexpandedsamplingoftaxaandgenesbeyondpreviousanalyses.Soltisetal.,1999,2000——the567-taxon,three-gene(rbcL,atpB,and18SrDNA)

第三页，共二十二页，编辑于2023年，星期五Hiluetal.(2003)——conductedabroadanalysisofangiospermsbasedonmatKsequences,withresultsthatagreedcloselywiththethree-genetopologyDaviesetal.(2004)——constructedasupertreeforangiosperms.Soltisetal.(2007)——undertookaBayesiananalysisofthe567-taxon,three-genedatasetandobtainedatopologynearlyidenticaltothatobtainedwithparsimony.Belletal.(2010)——usedaBayesianrelaxedclockmodeltoanalyzethissamethree-genedatasetandfoundresultssimilartoSoltisetal.(2007).第四页，共二十二页，编辑于2023年，星期五Burleighetal.(2009)——usedfivegenesforthesame567taxaanalyzedinSoltisetal.Thefive-genematrixhadsignificantlymoremissingdata(27.5%)thanthethree-genematrix(2.9%),butthefive-geneanalysisresultedinhigherlevelsofbootstrapsupportacrossthetree.第五页，共二十二页，编辑于2023年，星期五Thevalueofconstructingdatasetsofmanygenesemployednearlycompleteplastidgenomesequencedata(e.g.,Leebens-Macketal.,2005)limitedinsamplingtofewerthan100taxabasedonmanygenesbutfocusedonlyonmajorangiospermcladesThevalue——withverylargeamountsofdata(i.e.,13to83genes),many,ifnotmost,deep-levelquestionsofangiospermphylogenycanberesolved.(e.g.,Schönenbergeretal.,2005;Jianetal.,2008;H.Wangetal.,2009;Brockingtonetal.,2010;TankandDonoghue,2010）第六页，共二十二页，编辑于2023年，星期五Thegoal:assembleadatasethavingbothbroadtaxonomiccoverageandnumerousgenes.1、Thethree-andfive-geneanalysesof567taxahavebroadtaxonomiccoverage,supportformanyportionsoftheframeworkofangiospermphylogenyislowinthesestudies.2、Conversely,studiesemployingcompleteplastidgenomesequenceshavedeepgenecoverageandstronginternalsupport,buttaxonomiccoverageisoftensparse.第七页，共二十二页，编辑于2023年，星期五Inthistext:1、usinggenesthatrepresentallthreeplantgenomiccompartments：nucleus,plastid,andmitochondrion2、constructinga17-genedatasetfor640speciesrepresenting640genera,330families,and58of59orders(sensuAPGIII,2009)).第八页，共二十二页，编辑于2023年，星期五二、材料与方法1、DNAsamplesextracted:fromeitherfreshorsilica-driedmaterialfollowingthegeneralmethodofDoyleandDoyle(1987)ormodificationsthereofthatemployliquidnitrogenandhigherCTABconcentrations(e.g.,Soltisetal.,1991;Sytsma,1994)第九页，共二十二页，编辑于2023年，星期五MultipleSpecies2、UsethesamespeciesandDNAsamples[ManyoftheseDNAsampleshavebeenusedinearlieranalyses(e.g.,Chaseetal.,1993;Soltisetal.,2000).]acrossallofthegenesanalyzedhere,althoughmultiplespeciesweresometimesusedasnecessaryplaceholderstoreducemissingdata.

第十页，共二十二页，编辑于2023年，星期五Theoutgroup3、Extantgymnosperms:Cycas,Ginkgo,Gnetum,Metasequoia,Pinus,Podocarpus,Welwitschia,andZamia.第十一页，共二十二页，编辑于2023年，星期五ConstructedTowDataSetsGiventhepotentialproblemsinherentinphylogenyreconstructionusingmtDNAsequences.ConstructedadatasetwithoutthemtDNAdata,resultinginamatrixof13genes.第十二页，共二十二页，编辑于2023年，星期五TheselectionoftaxonsamplingWithpoorlyresolvedclades(e.g.,Malpighiales,Saxifragales)targetedfordensertaxonsampling.Avoidedparasiticclades:cancreateanalyticalproblemsduetogeneloss,acceleratedmolecularevolution,andhorizontalgenetransfer.第十三页，共二十二页，编辑于2023年，星期五The17GenesFromthenucleargenome—18Sand26SrDNA;Fromtheplastidgenome—atpB,matK,ndhF,psbBTNH(fourcontiguousgenesheretreated

asoneregion),rbcL,rpoC2,rps16,andrps4;Fromthemitochondrialgenome—atp1，matR,nad5,andrps3第十四页，共二十二页，编辑于2023年，星期五The17-genematrixwas25260bpandrepresentallthreeplantgenomesThe13-genematrixwas19846bpandrepresentonlythenucleusandplastid.Thepercentageofmissingdataforthefulldatasetwas41%andforthedatasetwithoutmtDNAdatawas42%.第十五页，共二十二页，编辑于2023年，星期五AlignmentandphylogeneticanalysesAllsequencedatawerestoredandmanagedin

TOLKIN—awebapplication,distancecollaborationaspartoftheAngiospermTreeofLifeproject,thatallowsuserstoaccessandsharedatainrealtime,aswellasautomaticallygenerateFASTAfilesandlinktootherrelevantinformationandresources.AlignmentsofcombinedsequencesweregeneratedwiththeprogramMAFFTattheDNAlevelusingthel-ins-ialgorithmanddefaultalignmentparameters.第十六页，共二十二页，编辑于2023年，星期五Adjustmentsweremadebyeyewhentherewereobviousalignmenterrorsduetoparticularlydivergentor“gappy”sequences.第十七页，共二十二页，编辑于2023年，星期五DataSite:1、Theindividualgeneregionsvariedintheamountofmissingdatapersite:18SrDNA(6%),26SrDNA(15%),atpB(5%),atp1(1%),matK(13%),matR(3%),nad5(4%),ndhF(20%),psbBTNH(19%),rbcL(4%),rpoC2(21%),rps16(26%),rps3(10%),andrps4(50%).2、Individualgeneregionsalsovariedinthenumberoftaxawithdatainthecombinedanalyses:18SrDNA(78%),26SrDNA(57%),atpB(88%),atp1(59%),matK(92%),matR(76%),nad5(59%),ndhF(80%),psbBTNH(54%),rbcL(98%),rpoC2(63%),rps16(35%),rps3(62%),andrps4(58%).第十八页，共二十二页，编辑于2023年，星期五3、Morethan50%missingdatawereremovedwiththeprogramPhyutilitytoavoidregionsofpotentiallyproblematicambiguousalignmentcausedbysuchbroadsampling.第十九页，共二十二页，编辑于2023年，星期五analyses—RAxMLandMP