Sex and molecular evolution

1. Sex and molecular evolution Brian Charlesworth Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh

2. Sex is the most prevalent mode of reproduction among the great division of life (the eukaryotes) that includes the animals, green plants, algae, fungi and protozoa. • All mammals and all birds reproduce sexually, and there are only a few dozen examples of asexually reproducing species among reptiles, amphibia and fish. • Only about 0.1% of the over 300,000 species of flowering plants are thought to reproduce asexually.

3. An exception to the recent origin of asexual species The Bdelloid rotifer Philodina roseola (Meselson laboratory)

4. A regular cycle of sexual reproduction is absent from the other division of life (prokaryotes: bacteria and viruses). • There is, however, often detectable exchange of pieces of genetic information between individuals within prokaryote populations, involving a variety of processes that act as a substitute for sex.

5. The essence of sexual reproduction is the reshuffling of genetic information derived from the two parents of an individual (genetic recombination). To understand the evolutionary significance of sex, we need to understand the significance of recombination.

7. Structure of DNA

11. How evolution works • Evolution involves the transformation of variation between members of a population into differences between ancestral and descendant populations • At the level of DNA sequences, this variation can be studied by comparing the sequences of the same region of the genome in different individuals

12. The gene for glucose-6-phosphate dehydrogenase The set of basepairs for a given DNA sequence is known as a haplotype

13. The most general description of the state of a population would thus be a list of the frequencies of all possible haplotypes. • We could then characterise evolutionary change in terms of the rates of change of the frequency of each haplotype, xi , where xi is the frequency of the ith haplotype. • In practice, we usually collect data on, or model the evolution of, only limited portions of the genome, the simplest level being that of a single basepair.

14. The genetic processes of evolution • Mutation– changes in the sequence of DNA that occur during transmission of a chromosome from parent to offspring. • Natural selection– differences in fitness (survival and reproductive success) between individuals with different genetic make-ups • Recombination– reshuffling of genetic material between the chromosomes derived from different parents • Genetic drift– random fluctuations in the frequencies of genetic variations, caused by the finite size of the population

15. R. A. Fisher Sewall Wright J.B.S. Haldane

16. Mutation rates • The most common type of mutation is a change from one basepair to another, e.g. GC mutates to AT. • Direct estimates have recently been done in several species of animals and plants, and show that probability that a given site in the DNA changes its state is of the order of 10-9 to 10-8 per generation; this is the mutation rate per basepair. • This means that mutation is a very weak force, operating on a timescale of hundreds of millions of generations. • Nevertheless, it is crucial for evolutionary change to happen.

17. 1 1 4 4 6 6 8 8 10 10 12 12 2 2 3 3 5 5 7 7 9 9 11 11 13 13 Measuring the mutation rate Initial isogenic stock x Many separate single-pair mated lines ~ 200 generations to allow mutations to arise DNA extracted and sequenced, or mutations detected by special methods

18. Selection The simplest form of selection is when two alternative variants at a given site in the genome confer differences in fitness on the their carriers. Let one variant be called A1 and the other A2. Let the ratio of the fitnesses of A2 and A1 individuals be 1 – s . The quantity s measures the intensity of selection, and is called the selection coefficient. If q is the frequency of A2, the change in q is q, given approximately by sq(1 – q).

19. The peppered moth Biston betularia, with melanic (dark) and non-melanic forms

20. A1 B1 A2 B2 A2 B1 A1 B2 Genetic recombination A T A G C T T G A C C T A T G Parental combinations of two variants A A A G C C T G A G C T A T A Recombination between A and B sites or between polymorphic sites in a DNA sequence A A A G C C T G A C C T A T G Recombinant haplotypes A T A G C T T G A G C T A T A

21. Genetic drift • The frequencies of genetic variants in one generation are a random draw from the frequencies of the parents in the previous generation. • This cause variant frequencies to experience a “random walk” (genetic drift). • The state of the population must then be charaterised by a probability distribution of variant frequencies, e.g. the probability that variant A2 at a site takes frequency q at time t • The rate at which the scatter of this distribution occurs is measured by the inverse of the effective size of the population, Ne. • The timescale of genetic drift is of the order of Ne generations.

22. Drift in lab populations of the fruitfly Drosophila melanogaster Generations Numbers of copies of the bw eyecolour variant

23. The general equation of evolution (forward diffusion equation) Here, x is the vector of haplotype frequencies, (x, t) is the probability density of x at time t, xi is the deterministic change in the frequency of the ith haplotype, Cij is the covariance between the random changes in frequencies of haplotypes i and j. The Cij are all proportional to 1/Ne; this means that we can multiply both sides by Ne,and work with Net as a time unit and with Ne xi instead of xi.

24. What has all this got to do with the evolution of sex and recombination? • In order to understand how sexual reproduction and genetic recombination influence the evolutionary process, we need to have well-formulated models that can be related to data. • To produce these models, we need to include processes that are likely to be operating in the real world. • Before introducing them, let’s look at some patterns that are revealed by studying DNA sequence variation and evolution. • Differences within different regions of the genome that experience different levels of genetic recombination have proved particularly useful for revealing these patterns.

25. The Drosophila melanogaster genome (heterochromatin in black)

26. Some correlates of low versus high recombination • Regions of the genome with unusually low rates of genetic recombination often seem to have low levels of within-species DNA sequence variability. • Species with low levels of genome-wide recombination, such as largely self-fertilizing plants and animals, also show reduced variability. 3. The level of adaptation at the protein and DNA sequence level is often reduced in non-recombining genomic regions.

27. The fourth/dot chromosome in D. melanogaster 1.2 million basepairs (Mb) / ~80 genes Low recombination: No crossing over under normal lab conditions Characteristics of the dot chromosome: Low silent site variability (about 10% of genomewide mean)

28. Divergence between D. melanogaster and D. yakuba P. Haddrill et al. 2007 Genome Biology 8:R18

29. Drosophila miranda neo-sex chromosomes

31. Polymorphisms on the two neo-sexchromosomes Neo-X Neo-Y Mean silent diversities: neo-X = 0.39% , neo-Y = 0.004%

32. A general feature of low recombination genome regions A lack of recombination among a set of genes in a genome or genomic region means that the evolutionary fates of mutations at different sites are not independent of each other, so that they can interfere with each other’s evolution. This is the Hill-Robertsoneffect. (Hill and Robertson 1966 Genetical Research 8: 269-294)

33. The Hill-Robertson effect A1 B1 Fitness = 0.9 Mutation B1B2 Mutation A1A2 A2 B1 Fitness = 0.95 A1 B2 Fitness = 1 Maximum fitness possible with both advantageous mutations A2 and B2 A2 B2 Fitness = 1.05

34. The effective population size(Ne) of large non-recombining portions of the genome is substantially reduced by such interference among genes subject to selection. • This leads to a reduction in the level of neutral variability in DNA sequences • Genes in low recombination genomic regions are more likely to accumulate deleterious mutations, and less likely to fix selectively advantageous mutations, than genes in regions with normal or high recombination rates, since the chance of spread of mutation with selection coefficient s is determined by the magnitude of Nes.

35. 1 1 2 3 4 5 3 6 7 7 Selection against deleterious mutationswith low recombination (background selection) 10 different sequences 7 different sequences

36. Does background selection have important effects? To answer this, we need to know: • The rate of input of deleterious mutations into the population each generation • The frequency distribution of the sizes of effects of these mutations on fitness (i.e. their selection coefficients)

37. Our previous theoretical work showed that, using estimates of the selection intensities against amino-acid mutations, background selection wildly over-estimates the reduction in neutral variability on the dot chromosome and neo-Y chromosome. (Loewe and Charlesworth 2007 Genetics 175: 1381-1393.) • What is going on?

38. Weak Selection Hill-Robertson Effects These models assumed that selection is sufficiently strong relative to drift that deleterious mutations are mostly held close to their equilibrium values for an infinitely large population. If a large number of sites with low recombination are under selection, this does not hold because of their mutual H-R interference, which means that deleterious variants can drift to intermediate frequencies. This reduces the strength of their HR effects.

39. The Model: • Population of 500 diploid individuals • 2 selected sites alternating with one neutral site • 00101000010100111001011100010101 • 01110100111011000101001001110001 • mutation: 0 → 1 or 1 → 0 (equal rates); red sites are under selection against amino-acid mutations (0 is good, 1 is bad), black sites have no fitness effects • crossing over/gene conversion: • 00110001110000111110010011000111000011000000 • 11110000000101110000001111000000010111111001 • multiplicative effects on fitness of mutations at different sites (Kaiser and Charlesworth 2009, Trends in Genetics 25: 9-12)

40. Results: Compare observed reduction in neutral diversity (π/π0) to expectation under background selection model: → formula overpredicts reduction in π if recombination rates are low and chromosomes long

41. Results: Exponential decline of neutral diversity with chromosome length D. miranda neo-Y Drosophila dot chromosome

44. Conclusions • Many features of variability in the non-recombining regions of the Drosophila genome are captured by models involving mutations at a large number of selected sites, corresponding to the amino-acid coding sites in genes. • This suggests that the reduction in effectiveness of selection resulting from Hill-Robertson interference of this kind may be a major player in the evolutionary significance of recombination and sexual reproduction.

45. ACKNOWLEDGEMENTS • THEORY: Deborah Charlesworth, Isabel Gordo, Vera Kaiser, Laurence Loewe, Martin Morgan, Magnus Nordborg • DATA AND ANALYSES: Andrea Betancourt, Doris Bachtrog, Penny Haddrill, John Welch • MONEY: BBSRC, NSF, Royal Society