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1、Ch27_Evo:13937_C05.qxd11/16/094:44PMPage1CHAPTER27PhylogeneticReconstructionPHYLOGENETICTREEISTHEONLYfigureinOntheOriginofSpecies,evidenceofAthecentralimportanceofsuchtreestoevolutionarybiology.AsdiscussedinChapter5,aphylogenetictreeisagraphicalrepresentationoftheevo-lutionaryrelations
2、hipsamongentitiesthatshareacommonancestor.Thoseentitiescanbespecies,genes,genomes,oranyotheroperationaltaxonomicunit(OTU).Morespecifically,aphylogenetictree,withitspatternofbranch-ing,representsthedescentfromacommonancestorintodistinctlineages.Itiscriticaltounderstandthatthebranchingpa
3、tternsandbranchlengthsthatmakeupaphylogenetictreecanrarelybeobserveddirectly,butrathertheymustbeinferredfromotherinformation.Theprincipleunderlyingphylogeneticinferenceisquitesimple:Analysisofthesimilaritiesanddifferencesamongbiologicalentitiescanbeusedtoinfertheevolutionaryhistoryofth
4、oseentities.However,inpractice,takingtheendpointsofevolutionandinferringtheirhistoryisnotstraightforward.Thegoalofthischapteristodiscussboththeprinciplesandmethodsusedinphyloge-neticinferenceaswellassomeofthecomplications.Inthefirstsection,wediscusstheprocessofselectingandgatheringap-p
5、ropriatedatasetsforsubsequentanalysis.Inthenextsection,weexplainthreewidelyusedmethodsofphylogeneticinference:parsimony,distance,andlike-lihoodmethods.Thisisfollowedbyadiscussionofhowthesemethodscanbeevaluatedobjectivelyandhowthereliabilityandaccuracyoftheresultingin-ferencesareassesse
6、d.Wethenraiseseveralproblematicissuesthatmustbecon-sideredwhenusinganyphylogeneticmethod.Finally,weconsiderthefruitsofphylogeneticreconstruction—howtheycanshedlightonpastevolutionaryevents,suchasgeneduplicationsandlateralgenetransfers,aswellashowtheycanbeusedforotherpurposes,suchaspred
7、ictinggenefunctionandresolv-(CourtesyofCambridgeUniversityLibrary.)ingRNAsecondarystructures.ESSENTIALSOFPHYLOGENETICINFERENCETounderstandhowphylogeneticinferenceworks,itisusefultoconsiderthecom-parativelysimplecaseofevolutioninanasexualunicellularorganism.Eachcelldi-vides,yieldingtw
