Slide 1Socrative TestAnti-Evolution ArgumentSlide 4Slide 5Slide 6Slide 7II. Phylogenies – the big pictureSlide 9Slide 10Slide 11Macroevolution = Amount of Change/Time“Evolutionary Time” Can Mean Different ThingsIII. The Basics,Terms and Conventions Used in PhylogeniesThe central concept of phylogenyWhat’s wrong with this Phylogeny?Phylogeny Represents (At Minimum) Levels of AncestrySome Terms to LearnDifferent Ways to Represent a PhylogenyDifferent Ways to Represent a PhylogenyDifferent Ways to Represent a Phylogeny“Ultrametric” PhylogramQuestionIV. Uses for Phylogenetic TreesA. BiogeographyB. Ancestral State ReconstructionExample: Ancestral State of Mammals was to Have HairSome Traits Change More Than Once On a PhylogenyEstimating Ancestral StatesHow Might Traits Have Evolved?Slide 31How Might Traits Have Evolved?How Might Traits Have Evolved?Choose Based on Parsimony (Fewest Changes)Ancestral State EstimationResults in Estimates of Ancestral StatesWhy Reconstruct Ancestral States?i. Number of Origins# of Origins Example Placentas in FishesSome Poeciliopsis speciesSlide 41ii. Why Reconstruct Ancestors? Function of Ancient GenesSlide 43Dinosaur Vision Gene Example BackgroundOpsin GenesOpsin GenesEstimating “Dinosaur” OpsinEstimating “Dinosaur” Opsin2. Create Estimated Sequence in the Labiii. Why Reconstruct Ancestors? Estimate Ancient BehaviorsExample Tungara Frog CallsSonogramAncestral State ReconstructionsAncestral BehaviorsPhonotaxis Experiments with Ancestral CallsUses For Phylogenetic TreesC. Timing of Evolutionary EventsUses For Phylogenetic TreesCorrelated EvolutionPhylogenyUses For Phylogenetic TreesPhylogenetic Distance (PD) as a Measure of BiodiversityUses for biodiversity measuresSummarySlide 65EEMB 102-Lecture 3Intro andUses of Phylogenetic TreesSocrative Test•Name•Perm #http://m.socrative.com OR download the ap. ROOM: eemb102Anti-Evolution Argument•“Evolutionary events happened a long time ago, and cannot be repeated. Therefore, macroevolution is not scientific.”Janice TrahanDr. Richard Schmidt•August 4, 1994. Lafayette, LA.•Jan. 1995 – Trahan diagnosed with HIVPhylogenetic analysis of the RT region; details of the analysis are the same as for Fig. 1.Metzker M L et al. PNAS 2002;99:14292-14297©2002 by National Academy of SciencesI. Historical versus experimentalscience (classroom demonstration)II. Phylogenies – the big pictureThe Primary Use of Phylogenies is to Measure“Evolutionary Time”Macroevolution = Amount of Change/Time•“Change” is measured by comparison–Foot of a chimp compared to foot of a human•Two general ways to measure “evolutionary time”–Fossil/Stratigraphic Record approximates evolutionary time–Phylogeny–Phylogeny and Fossils can be combined“Evolutionary Time” Can Mean Different Things•Chronological Time (years)•Relative Time•Number of Lineage Splits (Speciation Events)•Amount of change in a trait–Genetic•DNA Sequence•Protein Sequence•Expression Pattern–Morphological–Behavioral–Etc.III. The Basics,Terms and Conventions Used in PhylogeniesThe central concept of phylogeny•Darwin recognized the common descent of all of life, the “Tree of Life”•Some species are more closely related than others–i.e. some lineages share a more recent common ancestor than other lineages•Phylogenetic hypotheses are hypotheses of common ancestryWhat’s wrong with this Phylogeny?ButterflyFlyHumanhttp://m.socrative.comWormPhylogeny Represents (At Minimum) Levels of AncestryFrog ToadOak SnakeSome Terms to LearnRootTrichotomyPolytomyTips (or leaves)NodesInternal BranchesSpecies AOTU (OperationalTaxonomic Unit)Different Ways to Represent a PhylogenyFrog ToadOak Snake(Oak, (Snake, (Frog, (Toad))))FrogToadOak Snake==Different Ways to Represent a PhylogenyFrog ToadOak Snake=Frog Toad OakSnakeFrogToadOakSnakeDifferent Ways to Represent a PhylogenyFrog Toad OakSnakeCladogram (branch lengths have no meaning)FrogToadOakSnakePhylogram(Branch lengthsproportional to change)“Ultrametric” PhylogramFrog Toad OakSnake“Ultrametric” Phyologram(branch lengths proportional to change or time. Tips end at same point.)QuestionLizards are as closely related to crocodiles as they are to turtles.a. TRUE because lizards are in between crocodiles and turtles on the top row.b. TRUE because there are the same number of intermediates between lizards and crocodiles (C and P) as between lizards and turtles (C and W).c. FALSE because lizards are more closely related to crocodiles.d. FALSE because lizards are more closely related to turtles.http://m.socrative.com OR download the ap. ROOM: eemb102IV. Uses for Phylogenetic Trees•Biogeography•Ancestral state reconstruction•Assessing the tempo of evolution•Studies of correlation•Biodiversity MetricA. Biogeography•Reconstructing the history of where species have livedB. Ancestral State Reconstruction•Goal: To estimate a trait in a “hypothetical common ancestor”•Species evolve by descent with modification•Any two species will share a common ancestor•Any characteristic of that common ancestor is called an “Ancestral State”Example: Ancestral State of Mammals was to Have HairArtiodactylsCarnivoresBatsInsectivoresRodentsPrimatesMarsupialsBirds/ReptilesOrigin of HairSome Traits Change More Than Once On a PhylogenyTrait PresentTrait AbsentEstimating Ancestral States•Find all ways traits could have evolved to yield present distribution•Choose best explanation–Example: Parsimony criterion–Fewest number of changes during evolution is favored explanationHow Might Traits Have Evolved?Scenario #1Trait PresentTrait AbsentTrait Gained Two TimesTrait PresentTrait AbsentWhat is the MAXIMUM #Of evolutionary changes in the trait?A. 5B. 14C. 15D. None of the abovehttp://m.socrative.com OR download the ap. ROOM: eemb102How Might Traits Have Evolved?Scenario #2Trait PresentTrait AbsentTrait Lost Five TimesHow Might Traits Have Evolved?Scenario #3Trait PresentTrait AbsentTrait Lost Two TimesTrait Gained One TimeChoose Based on Parsimony(Fewest Changes)Scenario 1 – Two StepsScenario 2 – Five StepsScenario 3 – Three StepsAncestral State Estimation•Using parsimony is common•Algorithm exist for finding most parsimonious reconstruction (See Cunningham et al reading)•This is the basis for reconstructing phylogenetic trees themselves•Other ways exist for choosing between trait histories–Maximum likelihood (Uses statistical model of