Ryan Gregory Published online 12 February 2008 Springer Science Business Media LLC 2008 Abstract Charles Darwin sketched his first evolutionary tree in 1837 and trees have remained a central metaphor in evolutionary biology up to the present Today ID: 25122
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Phylogenetictreesarethemostdirect .ThepatternofbranchingknownastheÒtopologyÓofthetreeÑindicatesevolutionaryrelatedness.Forexample,speciesAandBsharearecentcommonancestorthatwasnotsharedbytheotherspeciesandarethereforecalledÒsistertaxa.ÓSimilarly,speciesDandEaresistertaxa.SpeciesFisthemostdistantlyrelatedofthesampleofspeciesandisknownastheÒoutgroup.ÓOutgroupspeciesarenecessarytoÒrootÓanevolutionarytreeÑthatis,toindicatethelastcommon 2005forseveralexamples).Thefollowingsectionsdescribeandseektocorrecttenofthemostcommonlyencounteredmisconcep-tionsaboutevolutionarytrees.Severaloftheseareinterrelatedandthereforeoverlaptoanextent,buteachcanbeillustratedusingdistinctexamples.Learning(andteachingstudents)toavoidthesemisunderstandingsrepre-sentsakeysteptowardthedevelopmentofadequatetreethinkingskills.Misconception#1:HigherandLowerNotionsofaÒGreatChainofBeingÓorscalanaturae(scalesofnature),inwhichlivingspecies(and,insomecases,nonlivingmatterand/orthedivine)arerankedfromlowesttohighestandextendbackatleastasfarasAristotle.AlthoughDarwin(1837)himselfnotedearlyonFig.4Evolutionarytreescanbepresentedinavarietyofways.Thisfigureshowssixcommonapproachestodepictingevolutionaryrelationshipsusingrootedtrees.Thetwomostcommontypes,diagonalandrectangular,areshownatthetop,butanyofthesemaybeencounteredinthescientificliteratureortextbooks.Inallsixtrees, Fig.5 earliestancestorattheroot,fromwhicharedescendedtheinternalnodesand,morerecently,theterminalnodes.Thatistosay,evolutionarytreesindicatethepassageoftimebeginningfromtheroot(oldest)totheterminalnodes(youngest).Timecannotbereadinanyotherdirectiononthetree(forexample,acrossthetips),becauseallterminalnodesrepresentcontemporaryspecies(seeFigs. phylogenyofanimals.Asmanyprominentauthorshavenoted,thereisnoscientificallydefensiblebasisonwhichtoranklivingspeciesinthisway,regardlessofhowinterestingoruniquesomeaspectoftheirbiologymaybetohumanobservers(e.g.,Dawkins1992;Gould1994,1996).Thiserrordoesnotsomuchreflectaspecificmisunderstandingofphylogeneticdiagramspersebutafailuretograsptheveryconceptofcommondescent.Therefore,theadjustmenttobemadeinthiscaseisfromimaginingevolutionasa cshowsthesametree,withanidenticaltopology,inanonladderizedformat.Thiswasdonesimplybyrotatingseveralnodes(Fig.6)sothatmorediversegroupsdonotalwaysappeartotheright(a)orleft(b)oftheinternalnodes.Althoughladderizedtreesappearlesscluttered,theyarenomoreaccuratethannonladderizedones,andinfacttheymaycausereaderstofalselyinterprettheinformationprovidedinthetree(Figs.11 ,meaningthattheterminalnodesarealignedwitheachotherandtheinternalbranchlengthsare TherearenoÒmainlinesÓorÒsidetracksÓinevolution.Undoubtedly,manyreaderswillconsiderthetreedepictedinatoreflectamainlineofevolutionaryprogressfromaprimitiveancestortoanÒadvancedÓspecieslikehumans,withothergroupssuchascartilaginousorbonyfishesappearingassidetracksoffthatline,despitethefactthatroughlyhalfofallvertebratespeciesareteleostfishes(andonly10%aremammals).Notably,thetreeinbisequallyvalidandbythesamefalselogicwouldhaveperchastheendpointofanassumedmainlineandallterrestrialvertebrates,includinghumans,asanapparentsidetrack.Itisimportantthatthepositionsofterminalnodes,allofwhichrepresentcontemporaryspecies,notbemistakenashavingsomesignificance,becausetheydonot(seealsoFig.11).Notealsothathumansaremorecloselyrelatedtobonyfishesthaneitheristosharks.Phylogeneticallyspeaking,ÒfishÓisaninvalidcategoryresultingfromdifferentratesofmorphologicalchangeamonglineagesanddoesnotreflectrealrelationshipsFig.9Someevolutionarytreesincludeinformationabouttimeanddiversity.ashowsanexampleofanevolutionarytreethatincludesnotonlyinformationabouttopologybutalsotimeasgivenintheaxisattheleftandrelativespeciesdiversityasindicatedbythewidthofbranches.Notethatnotallbranchesareofequallengthbecausethe bodysize.Inthiscase,informationisavailableaboutthecommonancestors,anditisclearthatbothdescendantshavebeenlargerthantheirsharedancestorfollowingeverybranchingevent.Onlyhistoricaldataorstatistically Fig.13Evolutionaryrelatednessandphysicalsimilarityarenotnecessarilylinked.Theratesatwhichphysicalfeatureschangecandifferamonglineages(Fig.8),andsuperficiallysimilarmorphologiescanevolveindependentlyinmorethanonelineage.Asaresult,closerelativesmaylookdifferentfromoneanotherordistantrelativesmay Fig.14 2007 diverseassemblageoforganismswithacomplexevolu-tionaryhistory.LookingAheadtoBetterUnderstandingthePastTwopointsareabundantlyclearwhenitcomestophylogeneticliteracy:(1)Itiscrucialforanunderstandingofmodernevolutionaryconcepts,and(2)itisinsufficientlycommon.MisconceptionsaboundregardingevolutionarytreesÑsometimesbecauseof,andsometimescreating,in-correctpreconceptionsabouthow,evolutionoperates.Manyareholdoversofprogressionistorevenpre-evolu-tionarythinkingaboutlifeÕsdiversity.Some,alongwithwidespreadmisunderstandingsofevolutionarymechanismssuchasnaturalselection,undoubtedlycontributetothestaggeringlylowpublicacceptanceoftheprincipleofcommondescentinNorthAmerica(AltersandNelson2002;Milleretal.2006).Thewayforwardonthisissueisunambiguous.Students,membersofthepublic,andothernonspecialistsmustbebettereducatedabouttheinformationthatevolutionarytreesdoanddonotconvey.Tothisend,severalteachingplansandsoftwareexercisesforconstructingand/orusingphylogenetichypotheseshavebecomeavailable(e.g.,BilardelloandValdes1998 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