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Introduction to Coalescent Theory - Lecture 1
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- 1 Third Bangalore School on Population Genetics and Evolution
- 2 Introduction to the coalescent theory
- 3 The Gregor Mendel Institute
- 4 The Coming of Data
- 5 "We cranked the handle and nothing came genome chromosome 21
- 6 Example: Polymorphism in the human genome chromosome 21
- 7 Making sense of sequence data
- 8 The neutral model
- 9 History
- 10 Importance
- 11 Three insights
- 12 Some English
- 13 The neutral Wright-Fisher model
- 14 The Wright-Fisher model
- 15 Summary
- 16 The coalescent and classical population genetics
- 17 Implications for how we should view polymorphism data
- 18 Example: mitochondrial Eve
- 19 The coalescent
- 20 Topology & branch lengths
- 21 Distribution of the branch lengths
- 22 Scale time so that one unit of scaled time corresponds to N generations.
- 23 Let Tk be the
- 24 Summary
- 25 What do coalescence trees look like?
- 26 Deep branches often dominate
- 27 Example: How big a sample is needed to include the MRCA of everyone?
- 28 What do larger coalescence trees look like?
- 29 Distribution of the topology
- 30 Example: ancient Neanderthal mtDNA
- 31 The mutation rate
- 32 The probability of "identity by descent"
- 33 Superimposing mutations
- 34 The expected number of mutations is:
- 35 Note that
- 36 Mutation models
- 37 Estimating 0 under the infinite-sites model
- 38 segregating polymorphic sites, S.:
- 39 Both are unbiased, however,
- 40 How do we detect deviations from the standard model e.g., growth?
