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Lecture 13

BIOL299 Lecture Notes - Lecture 13: Allele Frequency, Genetic Drift, Population Genetics

Biology (Biological Sciences)
Course Code
Darren De Lorey

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Lec13 BIOL207
A. Population Genetics
a. Population defined: a large group of individuals of the same species who
are capable of mating with each other (means live near each other, etc…)
b. Main question: what is the frequency of a given allele in a population and
how does it change? Can use this information to e.g.
i. Calculate disease risks (medicine/public health, agriculture)
ii. Follow migration patterns (current, historical anthropology;
ecology and conservation)
iii. Monitor populations (conservation biology, public health,
agriculture & foresty)
iv. Follow evolution (selective pressure changes allele frequency)
c. Changes in allele frequency (deviations from expected frequencies); these
indicate something is happening with the population (e.g. migration,
disease, selection)
B. Calculating allele frequency
a. How do we calculate the observed genotypic frequency?
i. Can be easily inferred with co-dominant (or semi-dominant)
alleles. Because of this, molecular markers are heavily used in
population genetics
b. p = frequency of one allele (most common allele; usually dominant)
c. q = frequency of the other allele (rarer allele; usually recessive)
d. p + q = 1, e.g. 0.5 + 0.5 = 1; or 0.9 + 0.1 = 1, etc.
e. calculating p, q
i. by observation of genotypes (may be inferred from phenotype)
e.g. AA 1125 individuals
Aa 750 individuals
aa 125 individuals
TOTAL 2000 individuals
p= 2(AA) + 1(Aa) / 2(total individuals)
q= 2(aa) + 1(Aa) / 2(total individuals)
p= 2(1125) + 1(750) / 2(2000)
p = 0.75
q=2(125) + 1 (750) / 2(2000)
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f. Note !!! Knowing allele frequencies alone does not tell you anything about
the population structure, or fitness advantage/disadvantage of various
e.g. each of these populations each has p=0.8, q=0.2
#1 #2 #3
AA 640 800 700
Aa 320 0 200
aa 40 200 100
For p=0.8, q=0.2 and 1000 individuals,
HWE is AA =640 , Aa= 320, aa=40, so only #1 is in HWE
g. Given p, q the only way to predict genotypic frequencies is to use HW
formula, but if predictions do not match observations, then we suspect a
change is happening in the population i.e. population is not in HW
C. Hardy-Weinberg Equilibrium
a. HWE: p,q and genotypic frequency are stable from generation to
b. HW Equilibrium requires certain conditions
i. random mating –
1. most mating (e.g. humans) is non-random i.e. assortative
ii. no new alleles (no gene flow)
1. no migration
2. no mutation
iii. no natural selection
1. neither allele can confer a fitness advantage
iv. large population size
1. no genetic drift: loss (or fixation) of one allele due to
random sampling (fixation means frequency goes to 1; loss
means frequency goes to 0)
b. does genetic drift impact evolution?
2. no founder effects or population bottlenecks
a. founder effect -- result of migration of a small
b. bottleneck -- result of a disaster that reduces the
population size
D. What happens to allele frequencies over time?
a. Can calculate expected frequency of genotypes (AA, Aa, aa) in a
population using the Hardy-Weinberg formula:
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