Recombination and genetic variation – models and inference

1. Recombination and genetic variation – models and inference Simon Myers, Gil McVean Department of Statistics, Oxford

2. What does the basic coalescent miss? • The basic coalescent model is excellent at capturing the great stochasticity underlying genealogical processes in natural populations • It does not, however, capture many biologically important features that we would like to learn about • Recombination • Changes in population size • Geographical structure • Natural selection • We would like to extend the basic model to incorporate these features so that we can • Look for their influence (model testing) • Estimate their importance (parameter estimation)

3. Recombination at fine scales Father Mother Child • Reciprocal cross-over • Gene conversion • Region has two “parental” chromosomes • Always one parent in the basic coalescent

4. Adding recombination • Most genes in most genomes undergo recombination • Reciprocal cross-over • Gene conversion • Transformation • Template-switching • For example, few >200kb stretches of the human genome are free of recombination • The effect of recombination on genealogies is described by the ancestral recombination graph (ARG) • Today we will • Examine the effects of recombination on patterns of genetic diversity • Learn how to incorporate it in the coalescent model • Look at how to learn about recombination from empirical data

5. Recombination influences how we think about gene history

6. Ignoring recombination leads to problems in inference • Many inference procedures assume no recombination • Presence of recombination can give misleading inferences Mismatch distributions Phylogenetic tree reconstruction Schierup and Hein (2000)

7. Recombination is an important evolutionary processes • Recombination brings together multiple beneficial mutations • Fisher/Muller • Recombination brings together multiple deleterious mutations • Muller’s ratchet, Kondrashov’s synergistic deleterious mutations • Recombination allows beneficial mutations to escape from linked deleterious ones • The ruby in the rubbish • Recombination creates novel combinations of mutations • Evasion of pathogens and parasites (Hamilton) • Reduction in sib competition (Bell)

8. Recombination allows us to map genes by association Correlated, linked marker Disease-associated mutation Uncorrelated, unlinked marker Much more about this on Thursday in week 2 (Jonathan Marchini)

9. Recombination gives us greater power in inference • A single non-recombining locus gives us a single ‘draw’ from the underlying genealogical process • Looking at a single locus will only give us a small part of the population’s history • Recombination means that different loci have different ‘draws’ from the genealogical process and therefore have independent information about processes we wish to learn about

10. Human history from the mtDNA and autosomal perspectives • Mitochondrial DNA is highly variable and non-recombining • Phylogenetic trees of mtDNA have been used to make inferences about human history • Out of Africa hypothesis with mtDNA eve about 200,000 years ago • Strong population growth • But is it representative? • Single evolutionary history • Natural selection • Small population size • (Female demography only) • Autosomal sequences • Average TMRCA much older (1MY) • Much less evidence for growth Vigilant et al. (1991)

11. Practical: what does recombination do to genetic variation? • Informally, recombination shuffles up genetic diversity • We can see the effect of recombination in how ‘structured’ genetic variation is Chromosomes Sites Chromosome 22: 1Mb 57 Europeans Lipoprotein Lipase: 10kb 48 African Americans Xq13: 10kb 69 worldwide