1Pairwise sequence alignment (global and local)Multiple sequence pqalignmentlocalglobalSubstitution matricesDatabase searchingBLASTSequence ttitiEvolutionary tree reconstructionRNA structure predictionGene FindingProtein structure predictionstatisticsComputational genomics…Ernst Haeckel(1834-1919)2PhylogenyPhylogeny: An evolutionary tree.Ahypothesisconcerningthe evolutionaryA hypothesis concerningthe evolutionary history of a group of taxaTaxon: a unit of classification–strain, species, individual, gene,p , ,g– also called OTUs(Operational Taxonomic Units)Properties of Trees• Leaf nodes – contemporary taxa•Internal nodes-ancestral taxa•Internal nodes -ancestral taxa• Topology – relationships between species• Branch lengths – degree of changeAAAACTAT3Properties of Trees• If the mutation rate is constant in all lineages (molecular clock hypothesis),lineages (molecular clock hypothesis), the branch lengths are proportional to time.Trees represent the order of branching onlyABC DE†FGFGCDE†AB4One of these trees is not like the othersABCDEABCDEABCDEABCDEABCDEEDCABABCDEVarious types of trees you will seeRRR5ABCDEFABROne of these trees is not like the othersABCDEFRCDEFRABEDCABRFEDCRFPhylogeny reconstructionGiven data observations of contemporary taxa, reconstruct the evolutionarytaxa, reconstruct the evolutionary history.6Data for phylogeny reconstruction•Morphology•Morphology• Behavior• Biochemistry• Molecular and sequence data• Character data: shared characteristics• Distance data: difference between speciesAmerican Scientist7American ScientistSome other examples:•Niche (e g what finches eat)•Niche (e.g., what finches eat)• Biochemistry: serum:anti-serum reactions.• Behavior: Firefly flashing patterns8Multiple Sequence Alignment Glb2;CASgl; ~~~~ALTEKQEALLKQSWEVLKQNIPAHSLRLFALIIEAAPESKYVFSFLKDSGlb2;CASgl; ~~~MALTEKQEALLKQSWEVLKQNIPAHSLRLFALILEAAPESKYVFSFLKDSGlb2;CASgl; ~~~MALTERQEALLKQSWEVLKQNIPGHSLRLFALIIEAAPESKYVFSFLKDSGlb2;CASgl; ~~~~~~~~~~EALLKQSWEVLKQNIPGHSLCLFALIIEAAPESKYVFSFLKDSHUMANMKWVTFISLL FLFSSAYSRG V FRRDA H KSEVAHRFKD LGEENFKALVFour class 2 globins from Casuarina glaucaHUMANMKWVTFISLL FLFSSAYSRG V..FRRDA.H KSEVAHRFKD LGEENFKALVRABIT MKWVTFISLL FLFSSAYSRG V..FRREA.H KSEIAHRFND VGEEHFIGLVPIG ~~WVTFISLL FLFSSAYSRG V..FRRDT.Y KSEIAHRFKD LGEQYFKGLVCHICK MKWVTLISFI FLFSSATSRN LQRFARDAEH KSEIAHRYND LKEETFKAVAAlbumin in four speciesGene Trees vs Species TreesGene sequences can be used to infer the history of speciation–infer the history of speciation– infer the history of gene families9Genes evolve within species17Mouse Rat HumanA species tree represents the evolution of populationsIndividualPopulation18Mouse Rat Human10Allelic variationAllelic variation20Mouse Rat Human21Mouse Rat Human1122Mouse Rat HumanPhylogenetics (usually) assumes that times between species divergences are long enough that allelic variation can be ignored.23Mouse Rat Human12Phylogenetics (usually) assumes that times between species divergences are long enough that allelic variation can be ignored.24Mouse Rat HumanGene Trees vs Species TreesGene sequences can be used to infer the history of speciation–infer the history of speciation– infer the history of gene familiesCaveat emptor: the history of the gene, may not be the same as the history of the organism– gene duplications– horizontal gene transfer13DuplicationA gene tree that doesn’t agree with the species tree.LOSS26G1_FishG2_ChknG1_MouseG2_HumanHuman Mouse Chicken FishLOSSLOSSWhy phylogeny reconstruction?Some applications14Species relationshipsFly Amphioxus Hagfish Lamprey Bony fish MammalsSharkHemoglobin gene family in humanalphaalphaExample: hemoglobinbetabetaα ζ ε γ β δbetaalphaζε αγ αβ, αδtime0 wks 8 wks birthEmbryo Fetus Adult15Character evolutionAmerican Scientist16Bi hBiogeographyFiForensics17Phylogeny reconstruction…atgcaaggagtcgcagagc……atgcgaggtctcgtagtgt…atgggaggtctcccagtgtMdlGiven …atgggaggtctcccagtgt… …atgcgacgtcacgtattgg……atgtgtggtctggcagtga……atgcgacctctcggagaat…Model– Multiple sequence alignment– Model of sequence evolutionfind the (binary) tree that is the best explains the data with respect to the model.Finding the optimal treeGiven k taxa, –Consider all trees withkleaves–Consider all trees with kleaves– Score each tree with respect to chosen evolutionary model.– Select highest scoring tree(s)Phylogeny reconstruction is NP-complete:Except in special cases when the data obeys specific constraints, the only way to find the best tree is to consider all trees.18Character dataPrimitive character:winglessPrimitive character:winglessWingsBees WingsMoths WingsAnts No wingsCentipedes No wingsBeesAntsCentipedesMothsDistance dataMoths Ants CentipedesBees a b cMoths d eAnts fuvBeesAntsCentipedesMothsxyzw19Finding the optimal treeGiven k taxa, –Consider all trees withkleaves–Consider all trees with kleaves¾Score each tree with respect to chosen evolutionary model.– Select highest scoring tree(s)Criteria for evaluating which tree best fits the data:Criteria for evaluating which tree best fits the data:• Maximum parsimony (character data)• Minimum evolution (distance data)• Maximum Likelihood (character data)Multiple Sequence Alignmentas Character Data Each column (or site) is one character.~~~~ALTEKQEALLKQSWEVLKQNIPAHSRLFALIIEAA…~~~MALTEKQEALLKQSWEVLKQNIPAHSRLFALILEAA…~~~MALTERQEALLKQSWEVLKQNIPGHSRLFALIIEAA…~~~~~~~~~~EALLKQSWEVLKQNIPGHSCLFALIIEAA…C1 C2 C3 C4Bees A H S RMoths A H S RAnts G HSRCentipedes G HSC20Multiple Sequence Alignmentas Distance Data HumanRabbitPigChicken~~~~ALTEKQEALLKQSWEVLKQNIPAHSLRLFALIIEAA…~~~MALTEKQEALLKQSWEVLKQNIPAHSLRLFALILEAA…~~~MALTERQEALLKQSWEVLKQNIPGHSLRLFALIIEAA…~~~~~~~~~~EALLKQSWEVLKQNIPGHSLCLFALIIEAA…ChickenPigRabbitHuman HumanRabbitPigChickenHuman 0 3 7 9 Rabbit 0 6 8 Pig 0 6 Chicken 0 Finding the optimal treeGiven k taxa, –Consider all trees withkleaves–Consider all trees with kleaves¾Score each tree with respect to chosen evolutionary model.– Select highest scoring tree(s)Criteria for evaluating which tree best fits the data:Criteria for evaluating which tree best fits the data:¾Maximum parsimony (character data)• Minimum evolution (distance data)• Maximum Likelihood (character data)21Maximum Parsimony: Nature is thriftyThe
View Full Document
Unlocking...