Modes of Molecular Evolution

What is molecular evolution? Modes of molecular evolution

• Evolution at the molecular level • Single base pair changes, substitutions or point mutations Molecular Evolution • Insertions or deletions, also known as indels • Gene duplications - formation of multigene families and pseudogenes Kanchon Dasmahapatra • Slippage – microsatellite length changes

[email protected] • Chromosomal mutations

Substitutions Classical vs. Balance schools Who is right?

GCGACGGGGGAG • Classical school • Data in the form of allozymes show that lots of GCGACAGGGGAG – polymorphisms are rare polymorphisms are present. 64 triplet codons coding for 20 amino acids – because selection gets rid of less fit alleles • But .... causes the problem of genetic load

GTT CGT TGG Tryptophan • Balance school Histidine 30,000 to 50,000 genes in humans GTC CGC Proline Cysteine – polymorphisms are common GTA TGC If only 1000 are homozygous GTG Twofold degenerate – because of balancing selection If selective coefficient = 0.01 Fitness per locus = 0.99 Fourfold degenerate NON- 1000 SYNONYMOUS Summed over 1000 loci, fitness = (0.99) = 0.00004 SYNONYMOUS SUBSTITUTION SUBSTITUTION (silent substitution)

The neutral theory Neutralists vs. selectionists Kimura’s calculations

• Proposed by Kimura (1968) and King & Jukes Neutralists Selectionists µ = mutation rate per gene per generation (1969) N = population size (effective)

No. of alleles in population = 2N • Majority of mutations that spread through a Deleterious µ population have no effect on fitness Neutral No. of new mutations per generation = 2N Advantageous Probability of fixation = 1 2N

• Therefore, genetic drift NOT natural selection Rate of substitution = 2Nµ× 1 = µ drives molecular evolution 2N • Mutations fixed by • Mutations fixed by genetic drift selection

1 Predictions from neutral theory Molecular clock Testing the molecular clock

• Molecular clock • The relative rate test

• rate of substitution ∝ 1 X Y Z functional constraint on gene

–check if dXZ = dYZ

Variation in the molecular clock Predictions from neutral theory Functional constraints

Less constrained • Lineage effects • Molecular clock – Generation time hypothesis Fibrinopeptides ∝ – Metabolic rate hypothesis • rate of substitution 1 Growth hormone functional constraint on gene Haemoglobin a- – DNA repair efficiency hypothesis chain

Prolactin Deleterious Neutral Cytochrome c Functionally constrained

Histone H2B

Histone H4

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Amino acid substitutions per site, per 109 years

Functional constraints Testing neutrality of mutations Evidence for positive selection

4 years 9 • Sequence copies of the gene of interest from a • Major histocompatibility complex

3 variety of species. • Construct a phylogeny of the species using the 2 sequence or other data.

1 • Identify synonymous and non-synonymous mutations.

0 Substitutions per site, nucleotide per 10 • Calculate the average synonymous rate of Non- Twofold Fourfold Introns Pseudogenes degenerate degenerate degenerate sites sites sites subsititution, dS, the average non-synonymous ω rate of substitution, dN, and the ratio, = dN/dS. Non-synonymous Synonymous mutations or silent mutations

2 Improving the detection of positive Evidence for positive selection Points to take away selection • HIV surface envelope protein • Evolution at the level of DNA • Lots of polymorphism present at the gene level Sooty mangabeys • Development of the neutral theory Macaques • The molecular clock Human • Functional constraint and the rate of substitution African green monkey • Detection of positive selection Human • Both natural selection and genetic drift determine substitution dynamics

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