Molecular Evolution? Molecular Evolution • Evolution at the Molecular Level

BIOL2007 What is molecular evolution? Molecular Evolution • Evolution at the molecular level

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

= 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 = 2N Probability of fixation = 1 2N

Rate of substitution = 2N × 1 = 2N

Time for neutral mutation to fix by drift = 4N

3 Molecular clock Molecular clock

Genes evolve at a constant rate

X Y Z

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 Nonsynonymous 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 nonsynonymous mutations. • Calculate the average synonymous rate of

subsititution, dS, the average nonsynonymous 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

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