Allele Frequencies: Changing

John Stanton-Geddes; johnsg@uvm.edu
25 October 2013

www.johnstantongeddes.org

Evolutionary Processes

These forces will change allele frequencies in a population

  • Mutation
  • Migration
  • Non-random Mating
  • Genetic Drift
  • Natural Selection

Mutation

  • source of all genetic variation
  • due to mistakes in DNA replication


What is the mutation rate for humans?

Mutation

mutation rate

Conrad et al. (2011) doi:10.1038/ng.862

Migration

Individuals with specific genotypes move in or out of a population

Source-sink population dynamics

migration

Non-random Mating

assortative mating

A single individual may mate with many females

elephantseals

http://en.wikipedia.org/wiki/Northern_elephant_seal

Genetic Drift

  • random changes in allele frequency
  • nothing to do with selection
  • small populations

surfing

Excoffier and Ray (2008) 10.1016/j.tree.2008.04.004

Genetic Drift

plot of chunk unnamed-chunk-1

Parameters

  • N = 20 diploid individuals
  • p = 20%
  • q = 80%
  • gen = 100

Genetic Drift - Large population size

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Parameters

  • N = 100 diploid individuals
  • p = 20%
  • q = 80%
  • gen = 100

Genetic Drift - 50% allele frequency

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Parameters

  • N = 100 diploid individuals
  • p = 50%
  • q = 50%
  • gen = 100

Genetic Drift model

# Set up parameters
N = 20 # number of diploid individuals
N.chrom = 2*N # number of chromosomes
p = .2; q = 1-p
N.gen = 100 # number of generations
N.sim = 5 # number of simulations

# Simulation
X = array(0, dim=c(N.gen,N.sim))
X[1,] = rep(N.chrom*p,N.sim) # initialize number of A1 alleles in first generation
for(j in 1:N.sim){
  for(i in 2:N.gen){
    X[i,j] = rbinom(1,N.chrom,prob=X[i-1,j]/N.chrom)
    }  
  }
X = data.frame(X/N.chrom)

Selection

Certain phenotypes are more likely to survive or have offspring

  • stabilizing selection

  • diversifying selection

Performance Feedback Revision

Hereditary tyrosinemia

  • metabolic disorder
  • unable to break down the amino acid tyrosine
  • typically fatal in infants
  • high frequency in Quebec

quebec

http://en.wikipedia.org/wiki/Quebec_City

Hereditary tyrosinemia - testing

tyrosinemia report

A Bad Idea

Don't Sleep with Mean People

How strong would selection need to be to remove “meanness” assuming

  • a single locus
  • two alleles
  • recessive allele causes “meanness”