利用DNA序列构建系统树的方法

HEREDITAS(Beijing)26(2):205210,2004:2002-12-30;:2004-01-29:(40172005)[SupportedbyNationalNatureScienceFoundationofChina(No.40172005)]:(1980-),,,:Tel:[phone],E2mail:[e-mail]:(1964-),,,,:,Tel:[phone],E2mail:[e-mail]1,1,2(11,430074;21,200433):DNA,,,,,,:;;;;:Q349:A:0253-9772(2004)02-0205-06TheMethodsofConstructingPhylogeneticTreeswithDNAsequencesLITao1,LAIXu2Long1,ZHONGYang2(11FacultyofEarthSciences,ChinaUniversityofGeosciences,Wuhan430074,China;21SchoolofLifeSciences,FudanUniversity,Shanghai200433,China)Abstract:Constructionofphylogenetictreesisakeymeansinmolecularevolutionarystudies.Themethodsofconstructingphylogenetictreesincludethedistance2basedmethods,parsimony,maximumlikelihood,andBayesianinferencemethods.Toresolveaspecialproblemaboutphylogeny,severalnoticesarenecessary:first,toselectthereasonabledataatlessbiasaspossible;second,tochoosethepropermethodtoreconstructphylogenetictree;third,toevaluatetheconclusionsandexplainthemonthefieldofevolution.Thepresentpaperprovidesabriefintroductionoftheprinciplesofdataselectionandtree2constructionmethods,anddiscussesabouttheiradvantageanddisadvantagepoints.Keywords:PhylogeneticTree;Distance2basedMethod;Parsimony;MaximumLikelihood;BayesianInference,,,,DNA,DNA,,,,,,,,DNA1,,,:,,?,,,,,[1],;,()[2],,,,,[3],,,,[4],,?Felsenstein,[5]?,Felsenstein,123[6]:211DNA,DNA,,,(JCKimura),,,,,,,4:UPGMAFitch2Margoliash21111UPGMAUPGMA:,(AB),ABC,CAB,C,,D,,21112Fitch2MargoliashFitch2Margoliash(FM):3,AB,C;3,C,AB,A(B)CdAB(dBC)A(B)C1,ABxy,dAB=x+y,dBC=y+z;dAC=x+z,x,y,z;AB,x,y,z,[7]:Rs=ni=1nj=1(dij-^dij)2d2ijn(),dij,^diji,j1,Rs1Fitch2MargoliashFig.1SketchmapofFitch2Margoliashmethod21113(ME)RzhetskyNei[8]:,602HEREDITAS(Beijing)200426Fitch2Margoliash,,RzhetskyNei[8,9]:d__L_,A,,:ijk,a(ij)k1,0,:d_=AL+0V(dij),T=(ATA)-1AT,TiT_i,i(^Li):^Li=Tid_S,,ABSB-SA[9]:0,AB;0,BA;0AB,,2MP,,21114(NJ),X(2),:S0=ni=1LiX=1n-1nijdij,12(3),S12[10]:S12=LXY+L1X+L2X+LXY=12(n-2)ni=3(d1i-d2i)+12d12+1n-2n3ijdij2NJFig.2AstarliketreeinNJmethod,312Fig.3AtreewithOTUs1and2areclustered,,,,,,Fitch2Margoliash[10]212(MP)Occam:,(),[11]:();,,i:AGGGTAACTG;j:ACGAT2TATTA;k:ATAATTGTCT;l:AATGTTGTCG3(4):43Fig.4ThreePossibleUnrootedTreeswithFourOTUs,,:A(0322011113);B(0322012123);C(0321012123),A,479MP,3,,7022:DNA2[11],;,,,MP()[8],,MPLake(EP)MP,[12],14[13],,3,[11]213(ML):;,Felsentein,i,mVm,igi,jPij(v)[14]:Pij(v)=1/4+(1-gi)e-vm(j=i)1/4(1-e-vm)(ji)ijkl,xyz,5(),x,:f(i,j,k,l)=xyzgxPxy(v5)Pyi(v1)Pyj(v2)Pxz(v6)Pzk(v3)Pzl(v4)54MLFig.5ARootedMLtreewithFourOTUs45,,ML:,;,,214:(priorprobability)(posteriorprobability),;,,,[15]n,X,ii(),P(i),P(X|i),:P(i|X)=P(X|i)P(i)B(n)j=1P(X|j)P(j),B(n),B(n)(2n-3)!/[2n-2(n-2)!],B(n)(2n-5)!/[2n-3(n-3)!][16],,,[15],MCMC(MarkovChainMonteCarlo),,,,,,,,,,MetropolisHasting,1,0802HEREDITAS(Beijing)200426,,,,[15,16]3,[17],,,3,,,3,(),1,0,1UPGMA[18],,UPGMA,NJ,,,,,William(GeneralizedNJ),[19],,NJMEFM,,[20][21],,,,,,,,[22],,MP[23],,,[24],,,,,,,,,,,,,[25],MCMC,,,,,,[22],MCMC,,,,,(),,[16],,,,,(References):[1]NaylorGJ,BrownWM.AmphioxusmitochondrialDNA,chrodatephylogenyandthelimitsofinferencebasedoncomparisonsofse29022:DNAquences.SystBiol,1998,47(1):6176.[2]CummingsMP,OttoSP,WakeleyJ.SamplingpropertiesofDNAsequencedatainphylogeneticanalysis.MolBiolEvol,1995,12:814822.[3]KimJ.Generalinconsistencyconditionformaximumparsimony:effectsofbranchlengthsandincreasingnumberoftaxa.SystBi2ol,1996,45:363374.[4]FelsensteinJ.Casesinwhichparsimonyandcompatibilitymethodswillbepositivelymisleadind.SystZool,1978,27:401410.[5]HulsenbeckJP,KirkpatrickM.Dophylogeneticmethodsproducetreeswithbiasedshape?.Evolution,1996,50:14181424.[6]LaBao2Zhong.Constructingmolecularevolutionarytrees.ZoolRe2search,1993,14(2):186193...,1993,14(2):186193.[7]FitchWM,MargoliashE.Constructionofphylogenetictrees.Science,1967,155:279284.[8][America]NeiM,KumarS.MolecularEvolutionandPhyloge2netics.LaBao2Zhong,ZHONGYang,GAOLi2Pingtranslate,ZHAOShou2Yuan,ZHANGJian2Zhicollect.HigherEducationPress,Beijing,2002,76163.[],(,,,,)..:,2002,76163.[9]RzhetskyA,NeiM.Asimplemethodforestimatingandtestingminimum2evolutiontrees.MolBiolEvol,1992,9:945967.[10]SaitouN,NeiM.Theneighbor2joiningmethod:anewmethodforreconstructingphylogenetictrees.MolBiolEvol,1987,4:406425.[11]ZHONGYang,ZHANGLiang,ZHAOQiong.AnIntroductiontoBioinformatics.HigherEducationPress,Beijing,2001,116149.,,..:,2001,116149.[12]LakeJA.Arate2independenttechniqueforanalysisofnucleicacidsequence:evolutionparsimony.MolBiolEvol,1987,4(2):167191.[13]JinL,NeiM.Limitationoftheevolutionparsimonymethodofphylogeneticanalysis.MolBiolEvol,1990,7(1):82102.[14]FelesensteinJ.EvolutionarytreesfromDNAsequences:Amaximumlikelihoodapproach.JMolEvol,1981,17(6):368376.[15]HuelsenbeckJP,RonquistF,NielsenR,BollbackJP.Bayesianin2ferenceofphylogenyanditsimpactonevolutionarybiology.Science,2001,294(5550):23102314.[16]HuelsenbeckJP,LargetB,MillerRE,RonquistF.PotentialapplicationsandpitfallsofBayesianinferenceofphylogeny.SystBiol,2002,51(5):673688.[17]SaitouN,ImanishiT.RelativeEfficienciesoftheFitch2Margo2liash,Maximum2Parsimony,Maximum2Likel