bsci160 - population genetics

allele

alternative forms of a gene (A or a)

genotype

in diploid organisms, the combination of alleles presents for a gene (AA, Aa, aa)

frequency

a proportion/percentage usually expressed as a decimal fraction (< 1)

• 1/100

• 0.01

• 1%

population

a group of individuals of the same species that live in the same area & interbreed

population genetics

describing the gene pool of a population

• use allelic & genotypic frequencies

  • ex. frequency of the yellow allele is 90% (90% of all alleles are yellow)

allele frequency

the proportion of total alleles composed of a particular allele

• have 2 alleles of every gene

• for diploid (Aa)

  • A = (# A allele) / (# A allele + # a allele)

  • a = (# a allele) / (# A allele + # a allele)

    • should add to 1 → alleles are either one or the other

calculating allele frequency example

genotypic frequency

proportion of the total # of individuals composed of a particular genotype

• AA = (# AA) / (total # individuals)

• Aa = (# Aa) / (total # individuals)

• aa = (# aa) / (total # individuals)

calculating genotypic frequencies example

Hardy-Weinberg Equilibrium (HWB)

used to estimate frequencies using a null model

• allele & genotype frequencies should remain constant unless evolutionary force is acting upon the population

• nonevolving populations

null model

assumes something is not happening

constant frequency

• infinitely large population

• random mating

• no mutation

• no gene flow → isolated from other populations

• no natural selection → all individuals equally likely to survive & reproduce

HWB equilibrium formula

p + q = 1

• p → dominant allele frequency

• q → recessive allele frequency

p² + 2pq + q² = 1

• p² → homozygous dominant genotype frequency

• q² → homozygous recessive genotype frequency

• 2pq → heterozygous genotype frequency

HWB benefits

• can calculate allele frequency if assuming in HWB equilibrium

  • rarely true, but estimate may be close

• can determine if evolutionary agents are acting, provided you know allele frequencies

multiplication rule

the probability of 2 independent events A & B both occurring is:

• P(A and B) = P(A) x P(B)

  • tossing a coin → probability of landing on either side is 50%

    • Probability landing same side 3x in a row is 0.5*0.5*0.5 = 0.125

inheriting allele

• > prob. inheriting more common allele

• prob inheriting allele = frequency of that allele in pop.

  • recessive allele freq. (p) = 0.8 → 80% chance inheriting single allele

  • dominant allele freq. (p) = 0.2 → 20% chance “ “

4 allele combinations

homozygous chances

probability of getting 2 dominant/recessive alleles in a row

heterozygous chances

probability of getting 1 of each allele

• doesn’t matter which from which parent

• 2 heterozygotes for every heterozygote cross

population in HWE?

1. determine allele freq. of pop by hand

2. use allele freq. you calculated to find expected genotype freq. (p² + 2pq + q² =1)

3. compare expected & observed genotype freq.

• if don’t match → not in HWE

determining HWE example

Why might this population not be in HW equilibrium?

• evolutionary forces are at play

  • genetic drift

  • gene flow

  • etc