Introduction to Coalescent Theory - Lecture 1

Introduction to Coalescent Theory - Lecture 1

International Centre for Theoretical Sciences via YouTube Direct link

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9 of 40

History

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Introduction to Coalescent Theory - Lecture 1

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

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