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Detecting recombination
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Classroom Contents
Introduction to the Coalescent Theory - Lecture 2
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- 1 Third Bangalore School on Population Genetics and Evolution
- 2 Introduction to the coalescent theory
- 3 The coalescent variance
- 4 The coa Review variance
- 5 Robustness of the coalescent
- 6 Example
- 7 Population genetics in and of itself only allows limited inference
- 8 Effective population size
- 9 Variable population size
- 10 In a constant population:
- 11 Exponential growth
- 12 Rule of thumb
- 13 Population structure
- 14 The structured Wright-Fisher model
- 15 This model can equally well be studied backward in time.
- 16 The two-deme model
- 17 Slow migration
- 18 Consequences of slow migration
- 19 Fast migration
- 20 Let 7; be the stationary probability that a lineage is in patch i.
- 21 Source-sink environments
- 22 Is the island model a good model?
- 23 Sex
- 24 Hermaphrodites and self-fertilization
- 25 Males and females
- 26 Stage structure
- 27 Stochastic demography
- 28 Why recombination?
- 29 Recombination backwards in time!
- 30 Recombination makes it possible for linked sites to
- 31 In the The ancestral recombination graph
- 32 In the limit as N - co:
- 33 A walk through tree space
- 34 Simulating data
- 35 How common is recombination?
- 36 Detecting recombination
- 37 It can be shown that a very large fraction of recombination events cannot be detected even with infinite mutation rate.
- 38 Overcoming the evolutionary variance
- 39 The number of SNPs in 20 copies of 10 kb, 1000 runs:
- 40 Same thing, with recombination:
- 41 Linkage disequilibrium LD
- 42 Why "linkage disequilbrium"?
- 43 Where does come from?
- 44 Assuming random mating, we have:
- 45 How does evolve? Well,
- 46 Decay of haplotype sharing
- 47 HapMap Project
