Molecular Systematics. . . Macromolecules,Morphology, and Trees . . .Phylogenetic Tree of LifeErnst Haeckel’s 1866“Tree of Life”Tree of Life 140 Years Later?http://tolweb.org/tree/phylogeny.htmlThousands of phylogenetic“tests” confirm the hypothesisof common ancestry as fact.“Nothing in biology makes sense except in thelight of evolution” Theodosius DobzhanskyEvolutionDevelopmentGeneticsTaxonomyCytologyEcologyBiogeographyMorphologyPlacing evolution central in biologyPhylogenyDevelopmentGeneticsTaxonomyCytologyEcologyBiogeographyMorphology“Nothing in evolution makes sense except inthe light of molecular phylogenetics?”Placing molecular phylogenetics central in biology?Molecules vs. Morphology?How do you best “estimate” this tree of life?Morphology, fieldstudies, herbarium?Hugh Iltis – emeritus Director ofHerbarium and maize specialistMacromolecules – DNAsequencing, genomics?John Doebley– Iltis grad, Geneticsfaculty member and maize specialistMolecules vs. Morphology?Is the use of morphology suspect?5 merous Oenothera mutantCA 4 CO 4 A 4,8 G (4)__• convergence of unrelatedspecies under similarselection pressureMolecules vs. Morphology?Is the use of morphology suspect?• divergence of relatedspecies under differentselection pressure• convergence of unrelatedspecies under similarselection pressureMolecules vs. Morphology?Is the use of morphology suspect?PlatantheraMolecules and MorphologyBoth approaches have issues and problems!Assumptions and issues with molecular data more easily seenConsistency index(CI) of molecular datais higher than that ofmorphological data(Givnish & Sytsma, 1997a)MOLECULESMORPHOLOGYHomoplasy increases with more species sampledHi CILow CIMOLECULESMORPHOLOGYMolecules and MorphologyBoth approaches have issues and problems!Assumptions and issues with molecular data more easily seenLikelihood of correctestimate frommolecular data ishigher than that frommorphological data(Givnish & Sytsma, 1997b)Likelihood of correct phylogenetic estimateNumber of charactersCI< 0.7 0.7 - 1.0fewmanymost molecularmost morphologicalLow ModerateModerate HighMolecules and MorphologyMolecular classifications asthe backbone• Angiosperm PhylogenyGroup classificationIssues in Molecular Systematics1. Loss of information as you move awayfrom DNA . . .Issues in Molecular Systematics1. . . and redundancy of genetic code, convergence notseen, selection not at DNA levelActive sites in rbcLConserved sites in rbcLIssues in Molecular Systematics2. What macromolecule, what genome, what technique,what analysis?• Protein Genes• AA sequencing• Serology• Duplications• DNA• DNA:DNA hybridization• Restriction enzyme digestions• DNA sequencing• Genome rearrangementsPolymerase chain reaction (PCR) to amplify DNA segmentExtract DNA from plant tissueMolecular Systematics - in briefSequencing of DNA PCR productAlignment of DNA sequence. . . ACGGTCCA . . .Molecular Systematics - in briefPhylogenetic analysisParsimonyLikelihoodBayesianMolecular Systematics - in briefSystematic interpretationClassificationCharacter evolutionBiogeography3. “Gene trees” = “Species trees” all the time (homology issue)/Sectional relationships of ClarkiaIssues in Molecular Systematics3. “Gene trees” = “Species trees” all the time (homology issue)/Sectional relationships of Clarkia• relationships based onmorphology and chromosomestructure by Harlan Lewis• duplicated pgi proteindiscovered in some sections inlate 1970s by Les Gottlieb• Gottlieb argued thatduplications are rare and thatthese 4 sections are relatedIssues in Molecular Systematics3. “Gene trees” = “Species trees” all the time (homology issue)/Modified sectional relationships• note: sections with single pgihave different molecularweights (59.0 vs. 60.4)• Gottlieb argued thathybridization andchromosomal translocationgave rise to the pgi duplicationin early ancestorIssues in Molecular Systematics• new phylogeny proposed byLewis3. “Gene trees” = “Species trees” all the time (homology issue)• DNA sequences fromchloroplast genome say no!DNA treeloss 60.4loss 60.4loss 59.0loss 59.0Issues in Molecular Systematics• duplicated pgi proteinoccurred once but is ancestral!• multiple losses of one or theother duplicated protein• how can this hypothesis betested?/3. “Gene trees” = “Species trees” all the time (homology issue)Issues in Molecular Systematicsconfirms this hypothesis!/3. “Gene trees” = “Species trees” all the time (homology issue)•compare “orthologous”gene copies, not“paralogous” copies• big issue in molecularsystematics of allorganisms• but, get informationfrom 2 genes!Issues in Molecular Systematics/3. “Gene trees” = “Species trees” all the timeAs sequencing costs continue to drop and multiple orthologousgenes become easily available for a given set of individuals,phylogenetic trees are now commonly inferred from multiple lociat once. However, trees inferred from different loci are veryoften incongruent with each other. While some of this discordancemight be explained by stochastic and technical errors (undetectedparalogy or model misspecification), it has become obvious thatbiological processes are often at the heart of the discordance,including incomplete lineage sorting (ILS), horizontal gene transfersor hybridization.Issues in Molecular Systematics/Using gene duplications to one’s advantageHow do you resolve the base of the “tree of life”? Whatoutgroup do you use??Issues in Molecular SystematicsBacteriaArchaeaEukaryotaWhere is the root of life?Using gene duplications to one’s advantageIssues in Molecular Systematics???ArchaeaArchaeaBacteriaBacteriaEukaryotaEukaryotaGene AGene A2Gene A1Using gene duplications to one’s advantage: each copy acts as theoutgroup for the other!Issues in Molecular Systematics4. Hybridization/introgression - many examplesP. albaP. nigraP. tristis - Eurasianbalsam poplarIssues in Molecular Systematics4. Hybridization/introgression• nuclear DNA indicates Europeanwhite and black poplars and Asianbalsam P. tristis are unrelatedIssues in Molecular Systematics4. Hybridization/introgression• cpDNA indicates Europeanwhite and black poplars are sistertaxa and balsam P. tristis isidentical to black poplar!Issues in Molecular Systematics4. Hybridization/introgressionDistribution of black poplar withgeneral area of white poplar(white) and Eurasian balsam P.tristis (green)•