1. Models of Molecular Evolution I Level 3 Molecular Evolution and Bioinformatics Jim Provan Page and Holmes: Sections 7.1 – 7.2

2. 600 500 400 300 200 100 Myr ago 1.000.75 0.50 0.25 Dayhoff distance (to humans) Fossil divergence time Molecular divergence time The  -globin molecular clock Baboon Cow Quoll Chicken AlligatorFrog Carp Shark

3. The  -globin molecular clock As relationships between species diverge, number of amino acid differences appear to increase proportionally Assuming the divergence time of one of the points is known (humans and cows diverged 80 Myr ago), other divergence times can be calculated: 17 of 149 amino acids (Dayhoff distance 0.131) differ between humans and cows 47 differences (Dayhoff distance 0.445) between humans and alligators Suggests that humans and alligators diverged 3.4 times as long ago as humans and cows (~270 Myr ago) Fossil record suggests that humans and alligators diverged ~300 Myr ago: a-haemoglobin is behaving like a molecular clock

4. Processes of molecular evolution Why should such a clock exist and how accurate is it? Answer to this question will give insights into how nucleotide and amino acid sequences evolve Since the 1960s there have been two conflicting models of how molecular evolution takes place: One (neutralist) is dominated by the genetic drift of neutral mutations The other (selectionist) states that natural selection of advantageous mutations is more important Knowing which model best explains molecular evolution will ultimately lead to development of more realistic models of DNA substitution and thus allow the construction of more accurate phylogenies

5. The classical and balance schools of population genetics Foundation of the neutralist-selectionist debate was laid in the 1950s in the debate between the classical and balance schools of population genetics: The classical school believed that natural selection was predominantly a purifying force, removing deleterious alleles, and that there would be little genetic variation in populations The balance school claimed that levels of genetic variation were so high that most loci were polymorphic and that individuals were heterozygous at a large number of loci – this scenario was maintained by balancing (overdominant) selection Both schools were agreed that natural selection was the driving force in evolution but there was no evidence for the divisive issue: how much genetic variation existed within and between species?

6. Levels of variation in allozymes 0.000.050.100.150.50.4 0.3 0.2 0.1 0.0 Proportion of polymorphic loci Heterozygosity Mammals Birds Fish All vertebrates Reptiles Plants European humans Amphibians Insects exc. Drosophila All invertebrates Invertebrates exc. insects Drosophila

7. The cost of natural selection and the rise of the neutral theory Technical advances had revealed that the balance school was correct concerning levels of variation These results posed a problem: If natural selection had produced all this diversity, would it not also be true that individuals with inferior alleles would be selectively removed from the population? The population could go extinct with all this “selective death” - this is known as the cost of natural selection Cost of natural selection is part of the overall genetic load – the loss of overall fitness due to deleterious alleles: — Reason why classical school through there was low variation — This would be appropriate for substitutional load

8. Segregational load Occurs when a polymorphism is maintained due to overdominant selection Classic example is human sickle-cell anaemia: Individuals homozygous for Hb A haemoglobin allele produce normal haemoglobin Individuals homozygous for Hb S haemoglobin allele produce mutant haemoglobin (sickle cell-anaemia: 80% fatal) but are much less susceptible to malaria Heterozygous individuals do not suffer from sickle-cell anaemia and are much more resistant to malaria Laws of Mendelian segregation show that individuals who are susceptible to malaria (Hb A /Hb A ) or to sickle-anaemia (Hb S /Hb S ) will still be produced

9. The neutral theory of molecular evolution High levels of genetic variation could be maintained in populations without excessive selective death if natural selection was not the driving force in molecular evolution Neutral mutations could be lost (usually) or fixed (very occasionally) by genetic drift: The neutral theory of molecular evolution suggests that mutation and drift predominate The selectionist school believed that selection was the dominant force Both agree that selection removes deleterious alleles Central dogma of chance vs. necessity

10. Neutralist and selectionist models of molecular evolution Deleterious Neutral AdvantageousNeutralistSelectionist

11. The neutralist-selectionist debate Neutralist theory is not anti-Darwinist: Claims that fixation through selection – the main process of morphological evolution – occurs at low frequency Effectively believes that most genes and proteins are already almost-optimally adapted through selection Current debate centres around four major predictions of the neutral theory: There is an inverse correlation between substitution rate and degree of functional constraint acting on a gene Patterns of base composition and codon usage reflect mutational rather than selective processes There is a constant rate (molecular clock) of sequence evolution Level of within species variation is a product of only population size and mutation rate

12. Functional constraint and amino acid substitution Rates of amino acid substitution are extremely variable: Fibrinopeptides evolve 900 times faster than histones To neutralists, this difference is explainable by differences in selective constraint, rather than positive selection The more functionally constrained a gene is, the higher the chance that a mutation will be deleterious Correlation between functional constraint and substitution rate is proposed as evidence for the neutral theory

13. Functional constraint and amino acid substitution Functionally constrained gene Less functionally constrained gene Non-coding DNA Deleterious Neutral

14. Functional constraint at the nucleotide level Gene Mouse  3 Human  1 Rabbit  2 Goat  x and  z AveragePseudogene5.05.14.14.44.7 Position 1 0.750.750.940.940.85 Position 2 0.680.680.710.710.70 Position 3 2.652.652.022.022.34 Functional genes Rates of nucleotide substitution per site, per year x 10 -9