Arlequin35

Copyright©1995-2015LaurentExcoffier.AllrightsreservedManualArlequinver3.521ARLEQUINVER3.5.2USERMANUALAnIntegratedSoftwarePackageforPopulationGeneticsDataAnalysisAuthors:LaurentExcoffierandHeidiLischerComputationalandMolecularPopulationGeneticsLab(CMPG)InstituteofEcologyandEvolutionUniversityofBerneBaltzerstrasse63012BernSwitzerlandSwissInstituteofBioinformaticsE-mail:[e-mail]:(optional)304.2.2.2Distancematrix(optional)314.2.2.3Samples324.2.2.4Geneticstructure344.2.2.5Manteltestsettings354.3Exampleofaninputfile394.4Automaticallycreatingtheoutlineofaprojectfile414.5Conversionofdatafiles414.6Arlequinbatchfiles425Examplesofinputfiles445.1Exampleofallelefrequencydata445.2Exampleofstandarddata(Genotypicdata,unknowngameticphase,recessivealleles)445.3ExampleofDNAsequencedata(Haplotypic)455.4Exampleofmicrosatellitedata(Genotypic)465.5ExampleofRFLPdata(Haplotypic)475.6Exampleofstandarddata(Genotypicdata,knowngameticphase)496Arlequininterface516.1Menus516.1.1FileMenu516.1.2ViewMenu526.1.3OptionsMenu526.1.4HelpMenu536.2Toolbar536.3Tabdialogs546.3.1Openproject566.3.2Handlingofunphasedgenotypicdata576.3.3ArlequinConfiguration586.3.4ProjectWizard606.3.5Importdata616.3.6LoadedProject626.3.7Batchfiles646.3.8CalculationSettings666.3.8.1GeneralSettings676.3.8.2Diversityindices696.3.8.3Mismatchdistribution716.3.8.4Haplotypeinference736.3.8.4.1Haplotypicdata,orgenotypic(diploid)datawithknowngameticphase736.3.8.4.2Genotypicdatawithunknowngameticphase746.3.8.5Linkagedisequilibrium796.3.8.5.1Linkagedisequilibriumbetweenpairsofloci796.3.8.5.2Hardy-Weinbergequilibrium826.3.8.6Neutralitytests83ManualArlequinver3.5.2Tableofcontents56.3.8.7Geneticstructure866.3.8.7.1AMOVA866.3.8.7.2Detectionoflociunderselection896.3.8.7.3Populationcomparison926.3.8.7.4Populationdifferentiation946.3.8.8Genotypeassignment956.3.8.9Manteltest967Outputfiles977.1Resultfiles977.2Arlequinlogfile977.3Linkagedisequilibriumresultfile977.4Allelefrequencies977.5Detectionofoutlierloci987.6SiteFrequencySpectrum(SFS)987.7ViewresultsinyourHTMLbrowser987.8XMLoutputfile997.8.1PotentialXMLformattingproblemwithFirefoxver3.x1007.8.2Includegraphicsintothexmloutputfile1007.8.3WhyuseRtomakegraphs?1017.8.4ExampleofR-lequingraphicaloutputs1017.8.4.1Geneticdiversity1027.8.4.1.1Numberofallelesperlocus1027.8.4.1.2Expectedheterozygosity1027.8.4.1.3Thetavalues1037.8.4.1.4Theta(H)formicrosatellitedata1047.8.4.1.5Allelesizerangeatdifferentloci(microsatellitedata)1047.8.4.1.6Garza-Williamsonindex(microsatellitedata)1047.8.4.1.7ModifiedGarza-Williamsonindex(microsatellitedata)1057.8.4.2Geneticdistancesbetweenpopulations1057.8.4.2.1MatrixofpairwiseFST’s1057.8.4.2.2MatrixofReynold’scoancestrycoefficient1067.8.4.2.3Slatkin’slinearizedFST’s1067.8.4.2.4Averagenumberofpairwisedifferenceswithinandbetweenpopulations1077.8.4.2.5Modelofpopulationdivergenceallowingforunequalderivedpopulationsize1087.8.4.3Matrixofmoleculardistancebetweenhaplotypes1097.8.4.4Matrixofmoleculardistancesbetweengenecopieswithinandbetweenpopulations(phaseknownonly)1097.8.4.5Matrixofmoleculardistancesbetweenhaplotypeswithinpopulations1117.8.4.6Haplotypefrequencieswithinpopulation1117.8.4.7Haplotypefrequenciesinpopulations1127.8.4.8Mismatchdistribution1127.8.4.8.1Demographicexpansion1127.8.4.8.2Spatialexpansion1137.8.4.9Populationassignmenttest1147.8.4.10Detectionoflociunderselection115ManualArlequinver3.5.2Tableofcontents68Methodologicaloutlines1168.1Intra-populationlevelmethods1178.1.1Standarddiversityindices1178.1.1.1Genediversity1178.1.1.2Ex