Probability Models for DNA Sequence Evolution

By Rick Durrett, Cornell U.

1. Basic Models

  1. The ATGC's of life
  2. Wright-Fisher model and the coalescent
  3. Ewens sampling formula
  4. Infinite sites model
  5. Finite sites, four nucleotides

2. Neutral Complications

  1. Nonconstant population size
  2. Recombination
  3. Population subdivision: island model
  4. Spatial structure: stepping stone model

3. Natural Selection} 

  1. Directional selection
  2. Balancing selection
  3. Background selection
  4. Hitchhiking

4. Statistical Tests

  1. Tajima's D
  2. Fu and Li's D
  3. Hudson-Kreitman-Aguade
  4. MacDonald-Kreitman

5. Genome Evolution

  1. Inversions
  2. Chromosome size evolution
  3. Translocations
  4. Whole genome duplication