群体遗传学研究中的数据处理方法

1、Ⅰ.RAPDAMOVA张富民　葛　颂＊(,　　100093):,RAPDAMOVA。,RAPD,AMOVARAPDistance,RAPDAMOVA。AMOVA,DCFARAPDistance,DCFAWINAMOVA,RAPDAMOVA。,8(Oryzarufipogon),RAPDAMOVA,AMOVA。AMOVA,4AMOVA,AMOVANEI-LI,JACCARDAMOVA。:,RAPDistance,DCFA,:Q347　　　:A　　　:1005-0094(2002)04-0438-07Dataanalysisinpopulationgenetics.I.analysisofRAPDdatawithAMO-VAZHANGFu-Min,GESong＊LaboratoryofSystematicandEvolutionaryBotany,InstituteofBotany,ChineseAcademyofSci-ences,Beijing100093Abstract:RandomAmplifiedPolymorphicDNA(RAPD)datahavebeenincreasin。

2、glyusedinstudiesonpopulationandconservationgenetics.Analysisofmolecularvariance(AMOVA)hasbecomeoneoftheimportantmethodsutilizedinanalysisofpopulationgeneticstructure.Currently,WINAMOVAisthemostpopularsoftwarethatisusedforAMOVAanalysis,andoftenrunstogetherwithRAPDis-tance,asoftwaretocalculategeneticdistances.However,cautionsshouldbetakenwhenAMOVAanalysisisusedtoprocesstheRAPDdatabecauseofthedominantcharacteristicofRAPDmarkerandthelimitationofRAPDistance.Inthispaper,webrieflyintroducetheprinciplea。

3、ndalgorithmofAMOVAanalysisanddescribeanewprogram,DCFA,thatsubstitutesforRAPDistance.Wealsoil-lustratetheprocessesofrunningtheprogramsDCFAandWINAMOVA.Inaddition,weanalyzeeightOryzarufipogonpopulationsasanexampletodemonstratehowtoprocessRAPDdatawithAMOVA,anddiscusstheresultsinlightofpopulationgeneticstructure.Finally,basedonthecomparisonoffourcommonlyuseddistancecoefficients,wesuggestthatthecoefficientsofEuclideansquareddistanceandNEI-LIratherthanJACCARDaresuitableforanalysisofmolecularvariance.Ke。

4、ywords:populationgeneticstructure,RAPDistance,DCFA,evolutionarydistance:“973”(G2000046805)(30025005):2002-05-20;:2002-09-29:,,1968,,。＊Authorforcorrespondence.E-mail:gesong@ns.ibcas.ac.cn　2002,10(4):438～444　　　　　　　BiodiversityScience　　,、(Hamrick&Loveless,1989)。,(、、)、、、、(Slatkin,1987;,1997;Schaaletal.,1998)。,、,、(Hamrick,1983;,1994,1997)。(,1997;,,2002)。,Wright(1951,1965)F-statistics(Weir,1990;Rousset,1996)。Wright(1951,1965)F-statis-tics(Weir&Cockerham,1984;Long,1986),、。WrightF-statisticsF-statistics。

5、(Cockerham,1969,1973;Nei,1977;Weir&Cock-erham,1984;Long,1986;Hartl&Clark,1997)。DNA,F-statisticsDNA,SSR、ISSR、RAPD、AFLP,ISSR、RAPD、AFLP,F-statistics(Lynch&Milligan,1994;Apostoletal.,1996;,,2001)。,F-statistics,(),。,(Takahata&Palumbi,1985;Lynch&Crease1990),。,Excoffieretal.(1992)(AnalysisofMolecularVariance,AMOVA),(),,F-statisticsΥ-statistics。AMOVA,RAPD(Huffetal.,1993)。AMOVA,,,WINAMOVA(Excoffier,1993),(Shim&Jorgensen,2000;Hapkeetal.,2001;Parduccietal.,2001),RAPD、ISSR、AFLP,AMOVA(Geetal.,1999;Nebauereta。

6、l.,1999;,,2001;Li&Ge,2001;Qianetal.,2001;Ro-manetal.,2001;Salesetal.,2001)。AMOVARPAD,:(1)、NEI-LIJACCARDRAPD,Ny-bom&Bartish(2000),3AMOVA,;(2)AMOVA,WINAMOVA1.55(Excoffier,1993)RAPDistance(Armstrongetal.,1996)V1.04100、20、210RAPD,(DOS),WINAMOVA;(3)WINAMOVA255()RAPD。Arlequin2.000(Schneideretal.,2000),1000,(pro-jectfile),。,AMOVA,RAPDistanceDCFA1.1,WINAMOVAArlequin。,(Oryzarufipogon)RAPD(Geetal.,1999),AMOVA。RAPDAMOVA,AMOVA,。1　AMOVA4:(I)———RAPDAMOVA439　　:(haplotype),(genotype)(Schneideretal.,2000)。,、cpDN。

7、AmtDNA;(),:,,,(RAPD、AFLP、IS-SR)。AMOVA,。1.1　,kji()xijk:xijk=x+ak+bjk+cijk。xxijk,a(),b,c()。、、,s2a、s2b、s2c。(nestedanalysisofmolecularvariance)(AmongGroups,AG)、/(AmongPopula-tions/WithinGroups,AP/WG)、(With-inPopulation,WP)σ2a、σ2b、σ2c,σ2(σ2=σ2a+σ2b+σ2c)。Υ-statistics:ΥST=σ2a+σ2bσ2　ΥCT=σ2aσ2　ΥSC=σ2bσ2b+σ2cΥST、ΥCT、ΥSC、、。1.2　1.2.1　AMOVA(evolutionarydis-tance)(,)(δ2),。。AMOVA,AMOVAANOVA。1.2.2　GPN:SSD(TOTAL)=12N∑Nj=1∑Nk=1δ2jkN,N,22。:SSD(WP)=∑Gg=1∑Igi=1∑Nigj=1∑Nigk=1δ2jk2NigIgI,Niggi。SSD(AP/WG)=∑{∑Igi=1∑Iigj。

8、=1∑Igi'=1∑Ni'gk=1δ2jk∑Igi=12Nig-∑Igi=1∑Nigj=1∑Nigk=1δ2jk2Nig}SSD(AG)=SSD(TOTAL)-(SSD(WP)+SSD(AP/WG))s2a、s2b、s2c:(degreeoffreedom,:d.f.):d.f.(AG):G-1;　d.f.(AP/WG):P-G;d.f.(WP):N-P:s2a=SSD(AG)/(G-1)、s2b=SSD(AP/WG)/(P-G)、s2c=SSD(WP)/(N-P)1.2.3　,n,:SG=∑Gg=1∑gp=1N2pNg;　n=N-SGP-Gn′=SG=∑Pp=1N2pNG-1;　n″=N-∑GgN2gNG-1SGn,Ngg,Npp。σ2a=n″s2a+n′s2b+s2c　σ2b=ns2b+s2c　σ2c=s2cσ2(σ2=σ2a+σ2b+σ2c),()、/、。1.2.4　Υ-satisticsDNA(),Υ-satistics,。1.2.5　,AMOVA:440　　　　BiodiversityScience10、,σ2cΥST;,σ2bΥSC;,σ2aΥCT。(、/、)。1.2.6　。

9、DNA(),ΥST,:D=-log(1-ΥST)(Reynoldsetal.,1983)D=ΥST/(1-ΥST)(Slatkin,1995),Nei's(1972,1978)。,。2　AMOVARAPDRAPD,,,F-statistics,BIOSYS-1(Swofford&Se-lander,1981)POPGENE(Yehetal.,1997)。AMO-VARAPD(Huffetal.,1993;Geetal.,1999;,,2001),RAPD,。DCFA1.1WINAMOVA1.55RAPDAMOVA。2.1　RAPDRAPD(Williamsetal.,1990)。,1(),0()。(RAPD)(01),,RAPD,。。RAPD,WINAMOVA(1)。2.2　DCFA1.1WINAMOVAWINAMOVA1.55(Excoffier,1993),(.dis)。WINAMOVARAPDistance(Armstrongetal.,1996)(DOS),100()×210(),,。,Visualc++(MFC)MSWindowsDCFA1.1,RAPD,,RAPD,16。,。

10、,,WINAMOVA。,,WINAMOVA1.55RAPD,255()。DCFA1.11　WINAMOVA1.55(,)Table1　ExamplesofthefilesforprogramWINAMOVA1.55.TheunderlinedwordscanbeeditedwithoutlimitationFiletypeDistancefileGroupfilePopulationfileFilenamerice.disrice.grprice1.popFormat123450.002.000.001.003.000.001.001.002.000.001.003.002.002.000.002groups1234567811individuals143542Interpretation5RAPDThematrixofdistancesamong5RAPDphenotypes82,11、2、34;2Eightpopulationsaredividedinto2groups.Group1includespopula-tions1,2,3and4.Group2in-cludestherem。