Presentation on theme: "Molecular clocks and phylogenies"— Presentation transcript:
1 Molecular clocks and phylogenies Genes and EvolutionMolecular clocks and phylogeniesSystematics A definition of taxonomyPhylogenies Characters and traitsHomology and homoplastySimple PhylogeniesMolecular evolutionSubstitutionsSynonymous and nonsynonymousSelection and neutral theoryMolecular phylogeniesMolecular clocksAdam Price
2 Defining Systematics and Taxonomy Systematics- the study of the diversity of organismsTaxonomy- the science of classification of organismstaxis = Greek to arrange, classifyWhy?Explains evolutionary relationshipsIntrinsically interestedUnderpins an understanding of biology- e.g. ecology, conservationImportant in applications to human life
3 from Greek- phylon = tribe, race genesis = source Phylogeny- the history of descent of a group of organisms from a common ancestorfrom Greek- phylon = tribe, race genesis = sourceConventionally represented by a phylogeneic treeMonkeyGorillaChimpanzeeHumanFernsConifersPeasRice
4 Phylogenic trees Phylogentic trees are based on comparison of traits individuals with common traits are placed togetherCharacter = a feature of the organisms (e.g. flower colour, height)Trait = one form of a character (blue flower colour, short height)Traits inherited from a common ancestor are termed homologousTraits that differs from the ancestor are termed derivedPhylogenies are trees that best explain the distribution of homologous and derived traits in the organisms studied (the focal group).
6 A simple phylogeny Relative evolutionary time Ancient events HagfishPerchSalamanderLizardCrocodilePigeonMouseChimpanzeeLungsJawsClaws ornailsFour-chamberedheartFeathersFur, mammaryglandsRelative evolutionary timeAncient eventsRecent events
7 Phylogenetic trees Outgroup Paraphyletic Polyphyletic Monophyletic Monophyletic taxa include all descendants of a common ancestorParaphyletic taxa include some, but not all, descendants of a common ancestorPolyphyletic taxa includes members with more than one recent common ancestorOutgroup a lineage closely related to the focal group
8 The problem of homoplastic traits traits that appear similar but are not related through ancestryConvergent evolution- independent evolution of similar traits due to similar selection pressure (e.g. wings in birds and bats)Parallel evolution- independent evolution of common traits in organisms sharing distant relatives (e.g. patterns of butterfly wings).Evolutionary reversals- the loss of a derived trait (e.g. limbs of snakes, teeth of frogs).
9 Traits used in phylogenetics Morphology and developmentalthe importance of fossilsMolecularProtein sequencesGenetic markersDNA sequences
10 The advantages of molecular traits 1/ They directly reflect the underlying process of evolution- changes in the hereditary material2/ There are a vast number of potential traits3/ They can detect difference between very closely related organism (even those that show no phenotypic difference)4/ They are not effected by the environment (unlike some morphological traits)5/ Since mutations generally occur as random events with specific probabilities, the number of mutations can be used to calibrate evolutionary time (molecular clocks)Disadvantages ?
11 Transitions and Transversions in nucleotide substitutions Transitions replace a purine base with the other purine base, or a pyrimidine base with the other pyrimidine basePyrimidines T C C TPurines A G G ATransversions replace a purine with apyrimidine or vice versaT A T G C A C GA T A C G T G CATCGTransitionTransversionTransition mutations are about 2 x more common than transversions
12 Mutation in Coding vs Noncoding DNA A substantial part of the DNA of eukaryotes is noncoding- introns, repetitive sequences, pseudogenesMutations in noncoding DNA do not generally effect phenotype and therefore are not subjected to selectionSome mutations in coding regions do not change amino acid sequence because of the degenerate codon systemSome mutations in coding regions change amino acid sequence to a similar type of amino acid, therefore having little or no effect on protein function
13 Substitutions in Coding regions Synonymous vs nonsynonymous substitutionsSynonymous substitutions are those that do not change the amino acid that is specified by the geneCUU ----> CUC = Leucine -----> LeucineNonsynonymous substitutions are those that change the amino acid chain specifiedThere are various degrees of nonsynonymous mutations depending on there effect on protein function. When the mutation changes the amino acid to a similar type then function may be little effected. Some amino acids of proteins are more important than others- active sites for example.CUU ----> AUU = Leucine -----> Isoleucine
14 Substitutions in Coding regions Miss-sense substitutionsMiss-sense substitutions are those that prematurely terminate the geneUAU ----> UAG = Tyrosine -----> StopUUA ----> UAA = Leucine -----> StopGenerally rare since nearly always involved change in protein activity
20 Cytochrome C- a highly conserved gene Hydrophobic sidechainsAcidic side chainsBasic side chains
21 A molecular clock for Cytochrome c Angiosperms vs animalsYeast vs mouldInsects vs vertebratesMammalsvs reptiles(per 100 residues) in cytochrome cAmino acid substitutionsBirds vsreptilesFish vs land vertebratesAmphibians vs birds and mammalsBirds vs mammalsTime since divergence (millions of years)
22 The Neutral Theory of molecular evolution Most mutations are either selectively neutral or nearly so.Thus, the genetic variation within species results from random genetic driftConsider population of size N with a neutral mutation rate at a locus of mutations per gamete per generationNo. of new mutations = x 2NProbability of fixation by genetic drift = frequency, p = 1/2NNumber of new mutations per generation that are likely to become fixed by genetic drift = no. of mutations x probability of fixation=
23 Molecular clocksThe rate of fixation of neutral mutations is equal to the neutral mutation rateThus, sequences diverge in evolution at a constant rateThus, the divergence between two sequences can be used to say when the two organisms diverged from each otherBut rememberNot all mutations are neutralNot all loci change at the same rateTransitions are more common than transversionsRates are strictly based on generations (not years), and reproductive rates vary between speciesTherefore, all molecular clocks need calibrating
24 Calibration of -globin molecular clock Divergence of humans from other species based on -globin molecular clock calibrated on fossil evidence of divergence from cowsShark600Carp500Frog400Million yearsagoChickenAlligator300200CowQuoll100BaboonSpeciesDivergence based on molecular clockDivergence based on fossil record