1. Models of Molecular Evolution III Level 3 Molecular Evolution and Bioinformatics Jim Provan Page and Holmes: Sections 7.5 – 7.8

2. The nearly neutral theory Variable rates of nucleotide substitution Variable rates of nucleotide substitution Variable mutation rates (generation time, metabolic rate, DNA repair) Nearly neutral mutations (population size and weak selection)

3. Development of the nearly neutral theory By the early 1970s it was becoming clear that: Some amino acid substitution rates were inconsistent with a Poisson clock Levels of heterozygosity were not as high as expected in natural populations Tomoko Ohta suggested that most non-synonymous changes were not perfectly neutral Deleterious Advantageous Neutral Slightly deleterious Slightly advantageous

4. Development of the nearly neutral theory Nearly neutral mutations are those where the product of the population size and the selection coefficient is near zero i.e. Ns  0 These changes are subject to weak natural selection as well as genetic drift Rate of substitution (per year) for nearly neutral mutations will depend on population size, selective coefficient and mutation rate, set to generation time Mutations at non-coding and synonymous sites are still neutral Relative importance of selection or genetic drift and hence probability of fixation depends on population size

5. The nearly neutral theory and real time molecular clocks Long generation time (lower mutation rate) Small population size (higher probability of fixation) + Short generation time (higher mutation rate) Large population size (lower probability of fixation) + ~ Real time molecular clock ~ Real time molecular clock

6. The nearly neutral theory and real time molecular clocks A study of 20 mammalian genes showed that R(t) values were generally well over 1.0, rejecting the Poisson clock After correcting for generation time and lineage effects: Average R(t) for synonymous sites dropped from 14.4 to 4.6 Average R(t) for non-synonymous sites only dropped from 8.26 to 6.95 Most variation in synonymous sites is due to lineage effects Non-synonymous rates are less generation time dependent than synonymous sites

7. Testing the neutral theory within species Neutral theory makes two very important predictions about levels of genetic variation within species: Extent of polymorphism is a function only of the population size (N) and the mutation rate (  ) Levels of polymorphism are correlated with amount of variation between species i.e. genes that evolve slowly between species also exhibit low variation within a species Original allozyme studies cast doubt on these predictions: Levels of heterozygosity were found to be too low Difficult to draw firm conclusions, since N and  are hard to quantify, and allozymes underestimate diversity levels Best to test theories at the DNA level

8. Testing the neutral theory within species Important assessment of the neutral theory is to test proposed correlation between levels of within species polymorphism and between species divergence: If synonymous and non-synonymous substitutions are neutral then ratio of both types of change will be the same within and between species because they result from the same neutral mutation process Positive natural selection would alter this ratio because an advantageous non-synonymous mutation would be fixed quicker by natural selection i.e. be a polymorphism for less time, leading to less within-species non-synonymous variation than expected given levels detected between species

9. Patterns of substitution at the Adh locus in Drosophila D. melanogaster D. simulans D. yakuba 2/140/110/17 1/21/05/15 SynonymousNon-synonymousFixed177Polymorphic422 G = 7.43 P = 0.006

10. Recombination and DNA polymorphism in Drosophila Most dramatic example of incompatibility between levels of variation between and within a species occurs in regions of the Drosophila genome where recombination rates are low: Distal tip of the X chromosome Small chromosome IV Neutralist explanation is that these regions have either lower mutation rates or are under selective constraint If this is the case, these regions should also show reduced levels of variation between species

11. Recombination and DNA polymorphism in Drosophila The yellow-achaete (y, ac) region on the X chromosome of D. melanogaster has a reduced level of polymorphism Extent of divergence in this region between D. melanogaster and D. simulans (5.4%) is similar to that observed in other genes (average 4.7%) – this contradicts the neutral theory Natural selection can explain this discrepancy through the dual action of selective sweeps and genetic hitchhiking

12. Hitchhiking and selective sweeps Time t1t1t1t1 t2t2t2t2 t3t3t3t3 t4t4t4t4

13. Can we resolve the neutralist- selectionist debate? Most support for neutral theory has come from comparisons of genes across distantly related species Natural selection is more apparent over shorter time scales As time proceeds, fixation due to selection may be obscured by neutral mutations Majority of original selection events in adaptive radiations e.g. mammals Overall, it seems reasonable to conclude that both selection and drift shape evolutionary fate of mutations: Majority of substitutions do not affect fitness (neutralist) The “footprints” of natural selection are still evident in more recently evolved levels, particularly at non-synonymous sites