GENETICS 633 Lecture Notes - Lecture 5: Mutation Rate, Effective Population Size, Spectral Shape Analysis

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22 Sep 2016
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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.
- Goals for the lecture
oUnderstand how genealogy and mutation combine to shape DNA sequence variation
oUse levels of sequence variation to estimate the population mutation rate
oPredict frequencies of polymorphisms in sequence data
oParameter [theta] is a product of population size and the mutation rate
- Assumptions for today’s discussion
oNo migration or recombination or selection
oRandom mating
oDiploidy (although this works for other ploidies as well)
oPopulation size is large and constant over time
oOnly one coalescent event per generation
oWright-Fisher model
oMutations hit previously unmutated sites infinite sites model
You don’t expect to see very many variants in sequence data on a typical
timescale – the variable sites model assumes that any site that has been
mutated in a generation was never previously mutated, justified by very low
mutation rates
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
- Coalescence with Mutation creates diversity
- Primary determinants of diversity levels: population mutation rate
oEffective population size (Ne)
oMutation rate per site per generation per individual (u)
oPopulation 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?
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