GENETICS 633 Lecture Notes - Lecture 5: Mutation Rate, Effective Population Size, Spectral Shape Analysis
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Lecture 5: september 22, 2016 mutation and neutral genetic diversity. Author"s note: a lot of these notes require critical thinking, and should be read in conjunction with the lecture slides to help understand them completely. I used notation for the formulas to the best of my ability while keeping up with lecture, but the notation in the slides is much clearer. This assumption gets can be violated when looking at real populations depending on what loci you look at, but this is generally a good approximation. Primary determinants of diversity levels: population mutation rate: effective population size (ne, mutation rate per site per generation per individual (u, population mutation rate: [theta] = 4neu = e(pi) This formula goes more in-depth in the slide from today"s lecture. Nucleotide diversity: how much diversity should we expect: typically, the mutation rate u multiplied by the opportunity for mutation (also is branch length, in the case of two sequences with a single mrca:
