BIOL2007 What is molecular evolution? Molecular Evolution • Evolution at the molecular level Kanchon Dasmahapatra [email protected] Modes of molecular evolution Modes of molecular evolution Gene duplication INDELS: insertions and deletions Slippage in tandem repeats 1 Modes of molecular evolution Substitutions GCG ACG GGG GAG • Single base pair changes, substitutions or point mutations GCG ACA GGG GA G • Insertions or deletions, also known as indels 64 triplet codons coding for 20 amino acids • Gene duplications - formation of multigene GT T CG T TGG Tryptophan families and pseudogenes Histidine GT C CG C Proline Cysteine • Slippage – microsatellite length changes GT A TGC GT G • Chromosomal mutations Twofold degenerate Fourfold degenerate NON- SYNONYMOUS SYNONYMOUS SUBSTITUTION SUBSTITUTION (silent substitution) Classical vs. Balance schools Who is right? • Classical school • Data in the form of allozymes showed that lots of – polymorphisms are rare polymorphisms are present. – because selection gets rid of less fit alleles • But .... causes the problem of genetic load • Balance school 30,000 to 50,000 genes in humans – polymorphisms are common If only 1000 are homozygous – because of balancing selection If selective coefficient = 0.01 Fitness per locus = 0.99 Summed over 1000 loci, fitness = (0.99) 1000 = 0.00004 2 The neutral theory Neutralists vs. selectionists • Proposed by Kimura (1968) and King & Jukes Neutralists Selectionists (1969) • Majority of mutations that spread through a Deleterious population have no effect on fitness Neutral Advantageous • Therefore, genetic drift NOT natural selection drives molecular evolution • Mutations fixed by • Mutations fixed by genetic drift selection Kimura’s calculations Predictions from neutral theory µ = mutation rate per gene per generation • Molecular clock N = population size (effective) • rate of substitution ∝ 1 No. of alleles in population = 2N functional constraint on gene No. of new mutations per generation = 2Nµ Probability of fixation = 1 2N Rate of substitution = 2Nµ × 1 = µ 2N Time for neutral mutation to fix by drift = 4N 3 Molecular clock Molecular clock Genes evolve at a constant rate X Y Z t 2t Time Predict that dXZ = 2d XY Estimate evolutionary time from genetic divergence Testing the molecular clock Testing the molecular clock • The relative rate test • The relative rate test Old World New World Gene No. of dXZ – dYZ monkeys Human monkeys bases X Y Z X Y Z Synonymous 3520 2.3±0.6 * sites: 9 genes Φηglobin 1827 1.5±0.4 * pseudogene Three introns 3376 1.0±0.5 • If dXZ = dYZ , then dXZ - dYZ = 0 Two flanking 939 3.1±1.1 * regions – check if dXZ = dYZ 4 Variation in the molecular clock Predictions from neutral theory • Lineage effects • Molecular clock – Generation time hypothesis • Humans vs monkeys • rate of substitution ∝ 1 functional constraint on gene • Primates vs rodents – Metabolic rate hypothesis – DNA repair efficiency hypothesis Functional constraints Functional constraints BETWEEN GENES Less constrained BETWEEN NUCLEOTIDES 4 years Fibrinopeptides 9 Growth hormone 3 Haemoglobin a- chain 2 Prolactin Deleterious Neutral Cytochrome c Functionally constrained 1 Histone H2B 0 Substitutions persite,Substitutions nucleotide per 10 Histone H4 Non- Twofold Fourfold Introns Pseudogenes degenerate degenerate degenerate 0 2 4 6 8 10 sites sites sites Amino acid substitutions per site, per 10 9 years Non-synonymous Synonymous mutations or silent mutations 5 Functional constraints Testing neutrality of mutations • Sequence copies of the gene of interest from a variety of species. • Construct a phylogeny of the species using the sequence or other data. • Identify synonymous and non-synonymous mutations. • Calculate the average synonymous rate of subsititution, dS, the average non-synonymous ω rate of substitution, dN, and the ratio, = dN/d S. Testing neutrality of mutations Evidence for positive selection 4 years 9 • Major histocompatibility complex 3 2 1 0 Substitutions per nucleotide site,Substitutions per per nucleotide 10 Non- Twofold Fourfold Introns Pseudogenes degenerate degenerate degenerate sites sites sites For most genes, ω = dN/dS < 1 indicative of If dN > dS , ω > 1 positive selection 6 Evidence for positive selection Points to take away • HIV surface envelope protein Sooty mangabeys • Evolution at the level of DNA • Lots of polymorphism present at the gene level Macaques • Development of the neutral theory Human • The molecular clock African green monkey • Functional constraint and the rate of substitution Human • Detection of positive selection • Both natural selection and genetic drift determine substitution dynamics Reading • Page, R. D. M. & E. C. Holmes. 1998. Molecular Evolution: a phylogenetic approach. Blackwell Publishing. Ch. 7 – Models of molecular evolution. • Li, W. 1993. So, what about the molecular clock hypothesis? Current Opinion in Genetics and Development 3:896901. 7 Improving detection of positive selection ω = 3.065 ω = 0.911 ω = 0.085 Yang & Bielawski (2000) TREE : 15 1.