PhylogeneticsPhylogeneticsThe affinities of all the beings of the same class haveThe affinities of all the beings of the same class havesometimes been represented by sometimes been represented by a great treea great tree . . . As . . . Asbudsbuds give rise by growth to fresh buds, and these if give rise by growth to fresh buds, and these ifvigorous, vigorous, branchbranch out and overtop on all sides many a out and overtop on all sides many afeebler branch, so by generation I believe it has beenfeebler branch, so by generation I believe it has beenwith the great with the great Tree of LifeTree of Life, which fills with its dead, which fills with its deadand broken branches the crust of the earth, and coversand broken branches the crust of the earth, and coversthe surface with its ever branching and beautifulthe surface with its ever branching and beautifulramifications.ramifications.Charles Darwin, 1859Charles Darwin, 1859PhylogeneticsPhylogeneticsWhat exactly is What exactly is phylogeneticsphylogenetics and how is done? and how is done?PhylogeneticsPhylogeneticsBuilding Building ““treestrees”” - showing how - showing how ““branchesbranches”” or or ““cladesclades”” are areconnected to each otherconnected to each otherPhylogeneticsPhylogeneticsBut . . . We only have But . . . We only have extant speciesextant species - the - the ““leavesleaves””PhylogeneticsPhylogenetics - and so we must - and so we must estimateestimate how the how the ““branchesbranches”” once onceconnected the connected the ““leavesleaves””??Thus . . . Phylogenetics is the estimation of theThus . . . Phylogenetics is the estimation of the““treetree”” through through ““timetime”” knowing only the knowing only the ““leavesleaves””PhylogeneticsPhylogeneticsHowever, the However, the ““leavesleaves”” are scattered over are scattered over ““spacespace””. Some. Someareas have related areas have related ““leavesleaves””, others have unrelated , others have unrelated ““leavesleaves””..Thus, phylogenetics is compounded by issues of both Thus, phylogenetics is compounded by issues of both ““timetime””and and ““spacespace””..PhylogeneticsPhylogeneticsAdditionally, many related Additionally, many related ““leavesleaves”” divergediverge in in ““formform””,,while other unrelated while other unrelated ““leavesleaves”” convergeconverge in in ““formform””. Thus,. Thus,phylogenetics is compounded by issues of phylogenetics is compounded by issues of ““timetime”” and and““spacespace”” and and ““formform””..PhylogeneticsPhylogeneticsPhylogeneticsPhylogeneticsIn natural and phylogenetic systems of classification, In natural and phylogenetic systems of classification, characterscharactersare selected are selected a posterioria posteriori for their value in correlating with other for their value in correlating with othercharacterscharacters to form hierarchical structure of groups to form hierarchical structure of groupsPhylogeneticsPhylogeneticsWhat characters are selected or even considered, has been veryWhat characters are selected or even considered, has been verysubjective. Consider Cronquist and Dalghren with mustard oilsubjective. Consider Cronquist and Dalghren with mustard oilfamilies . . .families . . .PhylogeneticsPhylogeneticsDo you rely on morphological or chemical characters or both?Do you rely on morphological or chemical characters or both?PhylogeneticsPhylogeneticsThese first phylogenetic classifications are These first phylogenetic classifications are ““phyleticphyletic”” - involve - involvea a subjective selection of characterssubjective selection of characters for classification for classificationPhylogeneticsPhylogeneticsTwo main groups of systematists became dissatisfied with theTwo main groups of systematists became dissatisfied with thephyletic approach and developed more phyletic approach and developed more objectiveobjective methods: methods:pheneticphenetic and and cladisticcladisticPhylogeneticsPhylogeneticsWith the rise of molecular phylogenetics, additional approachesWith the rise of molecular phylogenetics, additional approachesare now invoked (ML, Bayesian) - far more of a continuum ofare now invoked (ML, Bayesian) - far more of a continuum ofmodels are now seenmodels are now seenPhenetics vs. CladisticsPhenetics vs. CladisticsR. SokalW. HennigPhenetics:Phenetics: ( (Principles ofPrinciples ofNumerical Taxonomy,Numerical Taxonomy,1963) by Peter Sneath1963) by Peter Sneathand Robert Sokaland Robert SokalCladistics:Cladistics:((PhylogeneticPhylogeneticSystematics, Systematics, 1966) by1966) byWilli HennigWilli Hennig. . . all out war in the. . . all out war in the1960s and 1970s!1960s and 1970s!Phenetics vs. CladisticsPhenetics vs. Cladistics•• Phenetics uses Phenetics uses ““overalloverallsimilaritysimilarity”” - all characters- all charactersused! (used! (““distancedistance”” approaches) approaches)Phenetics vs. CladisticsPhenetics vs. Cladistics•• Phenetics uses Phenetics uses ““overalloverallsimilaritysimilarity”” - all characters- all charactersused! (used! (““distancedistance”” approaches) approaches)•• Graphical representation is Graphical representation iscalled a called a phenogram,phenogram,dendrogram, networkdendrogram, networkPhenetics vs. CladisticsPhenetics vs. Cladistics•• Cladistics uses onlyCladistics uses onlyphylogenetically informativephylogenetically informativecharacterscharacters•• Derived state is shared by Derived state is shared by2 but not all taxa - 2 but not all taxa - ““sharedsharedderived character statesderived character states””only informativecladogramcladogramPhenetics vs. CladisticsPhenetics vs. Cladisticscladogramcladogramphenogramphenogram=/PheneticsPheneticsData MatrixData Matrix1. 1. MagnoliaMagnolia2. 2. NymphaeaNymphaea3. 3. RosaRosa4. 4. PrimulaPrimula5. 5. GentianaGentiana6. 6. AsterAstertaxataxaapocarpyapocarpysympetalysympetalyepipetalyepipetalytreestreesepigynyepigynybeetle poll.beetle poll.tepalstepalsheterostylyheterostylybicarpellatebicarpellatevesselsvesselscharacterscharacters++++--++----++--++----++--++--------++--++++----------------++--++----++------++++--++--++--------++++--++--++----++--++statesstates1. 1. MagnoliaMagnolia2. 2. NymphaeaNymphaea3. 3. RosaRosa4.