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Genes and Evolution Molecular clocks and phylogenies Adam Price Systematics A definition of taxonomy PhylogeniesCharacters and traits Homology and homoplasty.

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Presentation on theme: "Genes and Evolution Molecular clocks and phylogenies Adam Price Systematics A definition of taxonomy PhylogeniesCharacters and traits Homology and homoplasty."— Presentation transcript:

1 Genes and Evolution Molecular clocks and phylogenies Adam Price Systematics A definition of taxonomy PhylogeniesCharacters and traits Homology and homoplasty Simple Phylogenies Molecular evolution Substitutions Synonymous and nonsynonymous Selection and neutral theory Molecular phylogenies Molecular clocks

2 Defining Systematics and Taxonomy Systematics- the study of the diversity of organisms Taxonomy- the science of classification of organisms taxis = Greek to arrange, classify Why? Explains evolutionary relationships Intrinsically interested Underpins an understanding of biology- e.g. ecology, conservation Important in applications to human life

3 Phylogeny- the history of descent of a group of organisms from a common ancestor from Greek- phylon = tribe, race genesis = source Conventionally represented by a phylogeneic tree Monkey Gorilla Chimpanzee Human Ferns Conifers Peas Rice

4 Phylogenic trees Phylogentic trees are based on comparison of traits individuals with common traits are placed together Traits inherited from a common ancestor are termed homologous Traits that differs from the ancestor are termed derived Phylogenies are trees that best explain the distribution of homologous and derived traits in the organisms studied (the focal group). Character = a feature of the organisms (e.g. flower colour, height) Trait = one form of a character (blue flower colour, short height)

5 Scoring traits to make a simple phylogeny

6 Hagfish Perch Salamander Lizard Crocodile Pigeon Mouse Chimpanzee Jaws Lungs Claws or nails Four-chambered heart Fur, mammary glands Feathers A simple phylogeny Relative evolutionary time Ancient eventsRecent events

7 Monophyletic Paraphyletic Polyphyletic Monophyletic taxa include all descendants of a common ancestor Paraphyletic taxa include some, but not all, descendants of a common ancestor Polyphyletic taxa includes members with more than one recent common ancestor Outgroup Outgroup a lineage closely related to the focal group Phylogenetic trees

8 The problem of homoplastic traits traits that appear similar but are not related through ancestry Convergent 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 developmental the importance of fossils Molecular Protein sequences Genetic markers DNA sequences

10 The advantages of molecular traits Disadvantages ? 1/ They directly reflect the underlying process of evolution- changes in the hereditary material 2/ There are a vast number of potential traits 3/ 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)

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 base PyrimidinesT C C T PurinesA G G A Transversions replace a purine with a pyrimidine or vice versa T A T G C A C G A T A C G T G C Transition mutations are about 2 x more common than transversions A TC G Transition Transversion

12 Mutation in Coding vs Noncoding DNA Mutations in noncoding DNA do not generally effect phenotype and therefore are not subjected to selection A substantial part of the DNA of eukaryotes is noncoding- introns, repetitive sequences, pseudogenes Some mutations in coding regions do not change amino acid sequence because of the degenerate codon system Some 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 Synonymous vs nonsynonymous substitutions Substitutions in Coding regions Synonymous substitutions are those that do not change the amino acid that is specified by the gene There 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 Nonsynonymous substitutions are those that change the amino acid chain specified CUU ----> CUC = Leucine -----> Leucine

14 Miss-sense substitutions Substitutions in Coding regions Miss-sense substitutions are those that prematurely terminate the gene UAU ----> UAG = Tyrosine -----> Stop UUA ----> UAA = Leucine -----> Stop Generally rare since nearly always involved change in protein activity

15 Second Letter First Letter Codon usage

16 Synonymous mutations Nonsynonymous mutations Synonymous mutations are more commonly fixed in evolution

17 Upstream regions Downstream regions Non-degenerate sites Twofold degenerate sites Fourfold degenerate sites Introns Pseudogenes Animal mtDNA Different types of sequence evolve at different rates

18 Comparing amino acid sequences leuargphecysserarg leugapphecysphearg leugapphecysphearg leuarg ile cysserarg leuargilecysserarg leuargphecysserarg ser ala ile Sequence 1 Sequence 2 Sequence 3 Sequence 4 Sequence 5 Sequence 6 leuargphecysserarg leugapphecysserarg ser Sequence 1 Sequence 2 leuargphecysserarg leuphecysserarg ser Sequence 1 Sequence 2

19 leuargphecysserarg leugapphecysphearg leugapphecysphearg leuarg ile cysserarg leuargilecysserarg leuargphecysserarg ser ala ile Sequence 1 Sequence 2 Sequence 3 Sequence 4 Sequence 5 Sequence 6 Sequence Number Differences Similarities Comparing amino acid sequences

20 Cytochrome C- a highly conserved gene Acidic side chainsBasic side chains Hydrophobic side chains

21 Time since divergence (millions of years) Amino acid substitutions (per 100 residues) in cytochrome c Yeast vs mould Angiosperms vs animals Insects vs vertebrates Fish vs land vertebrates Amphibians vs birds and mammals Birds vs mammals Mammals vs reptiles Birds vs reptiles A molecular clock for Cytochrome c

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 drift Consider population of size N with a neutral mutation rate at a locus of mutations per gamete per generation No. of new mutations = x 2N Probability of fixation by genetic drift = frequency, p = 1/2N Number of new mutations per generation that are likely to become fixed by genetic drift = no. of mutations x probability of fixation =

23 The rate of fixation of neutral mutations is equal to the neutral mutation rate Molecular clocks Thus, sequences diverge in evolution at a constant rate Thus, the divergence between two sequences can be used to say when the two organisms diverged from each other But remember Not all mutations are neutral Not all loci change at the same rate Transitions are more common than transversions Rates are strictly based on generations (not years), and reproductive rates vary between species Therefore, all molecular clocks need calibrating

24 600 500 400 300 200 100 0 Million years ago Species Divergence based on molecular clock Divergence based on fossil record Divergence of humans from other species based on -globin molecular clock calibrated on fossil evidence of divergence from cows Calibration of -globin molecular clock Shark Carp Frog Alligator Chicken Quoll Cow Baboon


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