Phylogenetic Tree of Life Ernst Haeckel s 1866 Tree of Life Molecular Systematics Macromolecules Morphology and Trees Tree of Life 140 Years Later Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky Ecology Genetics Biogeography Evolution Morphology Taxonomy http tolweb org tree phylogeny html Development Thousands of phylogenetic tests confirm the hypothesis of common ancestry as fact Cytology Placing evolution central in biology Nothing in evolution makes sense except in the light of molecular phylogenetics Molecules vs Morphology How do you best estimate this tree of life Ecology Genetics Biogeography Phylogeny Morphology Development Taxonomy Cytology Placing molecular phylogenetics central in biology Molecules vs Morphology Is the use of morphology suspect Morphology field studies herbarium Macromolecules DNA sequencing genomics Hugh Iltis emeritus Director of Herbarium and maize specialist John Doebley Iltis grad Genetics faculty member and maize specialist Molecules vs Morphology Is the use of morphology suspect CA 4 CO 4 A 4 8 G 4 5 merous Oenothera mutant convergence of unrelated species under similar selection pressure Molecules vs Morphology Is the use of morphology suspect Molecules and Morphology Both approaches have issues and problems Assumptions and issues with molecular data more easily seen Hi CI MOLECULES MORPHOLOGY Platanthera convergence of unrelated species under similar selection pressure divergence of related species under different selection pressure Molecules and Morphology Both approaches have issues and problems Assumptions and issues with molecular data more easily seen few Moderate most morphological many Number of characters Likelihood of correct phylogenetic estimate CI 0 7 0 7 1 0 Low Moderate Consistency index CI of molecular data is higher than that of morphological data Likelihood of correct estimate from molecular data is higher than that from morphological data High most molecular Givnish Sytsma 1997b Low CI MOLECULES MORPHOLOGY Givnish Sytsma 1997a Homoplasy increases with more species sampled Molecules and Morphology Molecular classifications as the backbone Angiosperm Phylogeny Group classification Issues in Molecular Systematics 1 Loss of information as you move away from DNA Issues in Molecular Systematics 1 and redundancy of genetic code convergence not seen selection not at DNA level Active sites in rbcL Conserved sites in rbcL Issues in Molecular Systematics 2 What macromolecule what genome what technique what analysis Protein Genes AA sequencing Serology Duplications DNA DNA DNA hybridization Restriction enzyme digestions DNA sequencing Genome rearrangements Molecular Systematics in brief Extract DNA from plant tissue Polymerase chain reaction PCR to amplify DNA segment Molecular Systematics in brief Molecular Systematics in brief Phylogenetic analysis Sequencing of DNA PCR product Parsimony ACGGTCCA Likelihood Bayesian Alignment of DNA sequence Systematic interpretation Classification Character evolution Biogeography Issues in Molecular Systematics 3 Gene trees Species trees all the time homology issue Sectional relationships of Clarkia Issues in Molecular Systematics 3 Gene trees Species trees all the time homology issue Sectional relationships of Clarkia relationships based on morphology and chromosome structure by Harlan Lewis duplicated pgi protein discovered in some sections in late 1970s by Les Gottlieb Gottlieb argued that duplications are rare and that these 4 sections are related Issues in Molecular Systematics 3 Gene trees Species trees all the time homology issue new phylogeny proposed by Lewis Issues in Molecular Systematics 3 Gene trees Species trees all the time homology issue Modified sectional relationships DNA tree DNA sequences from chloroplast genome say no note sections with single pgi have different molecular weights 59 0 vs 60 4 duplicated pgi protein occurred once but is ancestral loss 60 4 Gottlieb argued that hybridization and chromosomal translocation gave rise to the pgi duplication in early ancestor loss 60 4 loss 59 0 loss 59 0 Issues in Molecular Systematics 3 Gene trees Species trees all the time homology issue confirms this hypothesis multiple losses of one or the other duplicated protein how can this hypothesis be tested Issues in Molecular Systematics 3 Gene trees Species trees all the time homology issue compare orthologous gene copies not paralogous copies big issue in molecular systematics of all organisms but get information from 2 genes Issues in Molecular Systematics 3 Gene trees Species trees all the time Using gene duplications to one s advantage As sequencing costs continue to drop and multiple orthologous genes become easily available for a given set of individuals phylogenetic trees are now commonly inferred from multiple loci at once However trees inferred from different loci are very often incongruent with each other While some of this discordance might be explained by stochastic and technical errors undetected paralogy or model misspecification it has become obvious that biological processes are often at the heart of the discordance including incomplete lineage sorting ILS horizontal gene transfers or hybridization Issues in Molecular Systematics Using gene duplications to one s advantage Bacteria Issues in Molecular Systematics How do you resolve the base of the tree of life What outgroup do you use Issues in Molecular Systematics Using gene duplications to one s advantage each copy acts as the outgroup for the other Gene A1 Where is the root of life Gene A Bacteria Archaea Eukaryota Archaea Gene A2 Bacteria Archaea Eukaryota Eukaryota Issues in Molecular Systematics 4 Hybridization introgression many examples Issues in Molecular Systematics 4 Hybridization introgression P alba P nigra P tristis Eurasian balsam poplar Issues in Molecular Systematics 4 Hybridization introgression nuclear DNA indicates European white and black poplars and Asian balsam P tristis are unrelated Issues in Molecular Systematics 4 Hybridization introgression white balsam black cpDNA indicates European white and black poplars are sister taxa and balsam P tristis is identical to black poplar Distribution of black poplar with general area of white poplar white and Eurasian balsam P tristis green white poplar as the mother hybridized with black poplar as the pollen source sometime ago only way possible today hybrid with white poplar cytoplasm backcrossed repeatedly with black