Topic 14-Population Genetics

Wikipedia
Dr. Kate St.Onge – Biol 207
 Learning Outcomes

Be able to:
ü Calculate allele and genotype frequency if given observed data
ü Calculate expected genotype frequencies using the Hardy-Weinberg equation
ü List and discuss the assumptions of the Hardy Weinberg Law
ü Calculate heterozygosity
ü Calculate expected genotype frequencies and heterozygosity for loci with
multiple alleles
ü Compare the diversity of two populations or two loci using H

Dr. Kate St.Onge – Biol 207

 Topic 14

• PTC Tasting

Dr. Kate St.Onge – Biol 207

 PTC tasting
• Today we are collecting phenotypic data from all of you!
• TAS2R38 is a bitter taste receptor that give the ability to taste
phenylthiocarbamide.
• PTC tasting maps to chr 7q
• There are two alleles commonly found in humans at this locus:
– PAV
– AVI

Dr. Kate St.Onge – Biol 207

 PTC tasting
• PAV/PAV + PAV/AVI

• AVI/AVI

• What can we do with this data?

Dr. Kate St.Onge – Biol 207

 NOT observed

Using HWE to estimate allele frequencies

• If we assume a population is at or near HW equilibrium with respect
to the locus we are studying, we can estimate allele frequencies
and expected genotype frequencies ….. even if we only have f(aa)

1 locus with 2 alleles

p^2 + 2pq + q^2 = 1 (MEMORIZE)

Dr. Kate St.Onge – Biol 207

 Using HWE to estimate allele frequencies

• If we assume a population is at or near HW equilibrium with respect

to the locus we are studying, we can estimate allele frequencies
and expected genotype frequencies

You: Last term:

Taster homos and hets: 85
Taster homos and hets: 78
Non-taster: 81 Non-taster: 63

p= .301 p=0.332
q= .699 q=0.668

p2 = .0906 p2 =0.110
2pq= .421 2pq=0.443
q2 = .489 q2 =0.447

Dr. Kate St.Onge – Biol 207

 Calculating expected heterozygosity
• Measures the amount of variation within a population
• Calculated based on the totally frequency of heterozygotes for a gene
locus
• If one allele is very high and all others are near zero
– most individuals will be homos

• If most alleles are present at a

similar frequency 0.8
• near 50% hets (maximum)

50%

• As the frequency of the recessive

allele decreases
• relative proportion of recessive alleles found
in hets increases 25 + 25%
0.2
most “a”s found in hets (not homos)
few individuals w/ recessive pheno

Dr. Kate St.Onge – Biol 207

 Calculating expected heterozygosity
The probability that an individual in a population will be a heterozygote
at a locus, i.e. two randomly chosen gametes are different

H observed = n hets / n total from observed data

H expected = 1-(p^2+q^2)
p^2 = f(AA)
q^2 = f(aa)
gives us 2pq

This measure can be used to compare levels of genetic variation

between loci or populations

Often when comparing populations we will look at average expected

heterozygosity over several loci

Dr. Kate St.Onge – Biol 207

 Calculating expected heterozygosity
The probability that an individual in a population will be a heterozygote
at a locus, i.e. two randomly chosen gametes are different

You: Last term:

H = 1-(p^2+q^2) 1-(0.110+0.447)
0.420 =0.443

This measure can be used to compare levels of genetic variation

between loci or populations
two populations similar in diversity at this locus

Often when comparing populations we will look at average expected

heterozygosity over several loci

Dr. Kate St.Onge – Biol 207

 HWE and Heterozygosity with multiple alleles
TABLE 25.1 Extensions of the Hardy–Weinberg law
Situation Allelic Frequencies Genotypic
Frequencies
Three alleles f(A1) = p P1 f(A1A1) = p2
f(A2) = q P2
f(A1A2) = 2pq
f(A3) = r P3 f(A2A2) = q2
f(A1A3) = 2pr
het classes
f(A2A3) = 2qr
f(A3A3) = r2 homo class

X-linked alleles f(X1) = p f(X1X1 female) = p2

f(X2) = q f(X1X2 female) = 2pq
f(X2X2 female) = q2
calculate male / female freq separately f(X1Y male) = p
f(X2Y male) = q
For X-linked female genotypes, the frequencies are the proportions among all females; for
X-linked male genotypes, the frequencies are the proportions among all males.

Dr. Kate St.Onge – Biol 207

 HWE and Heterozygosity with multiple alleles
TABLE 25.1 Extensions of the Hardy–Weinberg law
Situation Allelic Frequencies Genotypic
Frequencies
Three alleles f(A1) = p f(A1A1) = p2
f(A2) = q f(A1A2) = 2pq
f(A3) = r f(A2A2) = q2
f(A1A3) = 2pr
f(A2A3) = 2qr
f(A3A3) = r2

sum of all
homo
frequencies

Dr. Kate St.Onge – Biol 207

 HWE and Heterozygosity with multiple alleles
Worked example:
A population of three-toed sloth are genotyped at 2 microsatellite loci:

Locus 1 observed allele freq Locus 2

Alleles Frequencies Alleles Frequencies
114 0.2 p 65 0.65
116 0.5 q 68 0.25
118 0.3 r 71 0.1

What are the expected genotype frequencies at these loci if the population is at HWE?
Which loci has more genetic diversity? Put pqr into hardy weinberg

Heterozygosity (1-sum of all homos)

Dr. Kate St.Onge – Biol 207

 HWE and Heterozygosity with multiple alleles
Worked example:
A population of three-toed sloth are genotyped at 2 microsatellite loci:

Locus 1 Genotype Expected

Alleles Frequencies frequencies
114 0.2 114/114 p^2 = 0.2 (0.2)
0.04
116 0.5
114/116 2pq = 0.2 (0.5) (2)
118 0.3 0.2
114/118
0.12
H=1-(sum of homos frequencies) 116/116
0.25
116/118
1 - (p^2 + q^2 + r^2) 0.3
118/118
0.09
H=0.62

Dr. Kate St.Onge – Biol 207

Dr. Kate St.Onge – Biol 207