1Bio1B Evolution 2Last lecture:• Introduction to Craig & lecture outline• Foundations– Pre-Darwinian background– Darwin: early influences, Beagle voyage– WallaceToday• Natural selection - principles, lines of evidence in the “Origin”• Descent with modification• Estimation & interpretation of phylogeny• Some major insights about the “Tree of Life”– 3 kingdoms: Archaea, Bacteria, Eukarya– Assembling the eukaryote cell– Metazoan origins & relationshipsOn-line resources:Understanding Evolution (UCMP): http://evolution.berkeley.edu/Tree of life: www.tolweb.org/tree/2The Darwin-Wallace principleof Natural selection• Individuals within a population vary for one ormore characteristics (traits)• Traits are (to some extent) inherited byoffspring from their parents• More offspring are produced than can survive=> those with traits that improvesurvival/reproduction leave more offspring=> these favorable traits will accumulate in thepopulation over generations3Lines of evidence in the “Origin of the speciesby means of natural selection” (Darwin, 1859)• Artificial selection asanalogy to naturalselection• Biogeography:Nested geographicdistributions• Homology of traitsmodified for differentpurposes• Population pressureFig22.10Fig. 22-17Human Cat WhaleBatHomologous structures: variations on astructure present in a common ancestorFig. 22-18Chick embryo Human embryoPharyngealpouchesPost-analtailAnatomical homologies of embryosPharangealpouchesFish - gillsMammals- ears,throat6Molecular homologies - newinsights invisible to Darwin• Genetic code• Transcription &translationmachinery• Colinearsegmentation(Hox) genes• etc etc.7Descent with modification by naturalselection + extinctiontimePhenotype8The currentview of thephylogenetichierarchy(UnderstandingEvolution web site)cf. Aristotle’sscala naturae9What evidence do we use toestimate the tree of life?General principles:Taxa (species, generaetc.) are grouped byshared-derived traitsTaxa should bemonophyleticmorphologyMolecules[DNA]fossilsextant10Key concepts in tree thinkingJ and K aresister taxaMonophyletic“clade”B is most recentcommon ancestorto D, E, G, Hb->ca->ba, b, c = character states for atrait: c is a shared-derivedstate for D + E; b is a shared-ancestral state for D + E; c* isanalogous, not homologousFrom Figs 26.5,26.10c*Examples of shared-derived traits that group majorlineages of vertebratesFig 26.11Fitting observed patternsof sequence variation athomologous (aligned)sites to a phylogenetichypothesis(see also Fig. 26.8)DNA sequence variationHuman0Mushroom30%0Tulip40%40%HumanMushroom0TulipPercentage differences between sequencesComparison of possible trees15% 15% 20%5% 5%10%15%25%Tree 1: More likely Tree 2: Less likelyMethods forestimatingphylogeny frommolecular data• Parsimony - minimize#changes on tree• Maximum likelihood,Bayesian (data +model of sequenceevolution)– Find tree that is mostprobable given thedataJohn Huelsenbeck,IB & MVZ “curator oftrees”14Estimating divergence times from a phylogeny• Branch lengths areproportional to amountof change (Fig 29.19)• Molecular clock:– Zuckerkandle & Pauling1960s– Some genes evolve atapprox constant rate– Absolute rate can beestimated from fossils at(or near) nodes– This calibration can beused to estimate otherdivergence times in tree– See text for caveats!Figs 26.12, 26.13branchnode15Surprise 1: 3 Domains of lifeFig. 26.21Based initiallyon rRNAgenesequences16Cool stuff - understandingmetazoan origins (Nicole King, MCB)Adhesion genesHox genesSee also Fig. 32.317Surprise 2Eukaryotic cells were assemblevia endosymbiosis -mitochondrial & chloroplasts aremodified symbiotic bacteriaEach has a (small) genomeseparate from the
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