CHAPTER 20A

Population Genetics and Evolution

Introduction to Population Genetics and Evolution

Population genetics studies the distribution and change of allele frequencies under the influence of evolutionary processes. Evolution is defined as the change in genetic variation, such as allele frequencies, within a population over time.

• Evolution is not the improvement of species toward an optimum, adaptation toward an ideal form, or changes that an individual organism experiences.

• Key processes include random mating, genetic drift, natural selection, migration, and mutation.

Evolutionary Genetics

Evolutionary genetics focuses on how genetic variation is inherited and changes over generations.

• Allele frequency: The proportion of a specific allele among all alleles at a genetic locus in a population.

• Genotype frequency: The proportion of a specific genotype among all individuals in a population.

• Calculating allele frequencies from genotype frequencies and vice versa is fundamental, especially under Hardy-Weinberg equilibrium.

• Phylogenetic trees represent genetic relationships between individuals and species.

Random Mating and Hardy-Weinberg Equilibrium

Random mating is a key assumption of Hardy-Weinberg equilibrium, which predicts genotype frequencies from allele frequencies in a population.

• Random mating does not change allele frequencies.

• Genotype frequencies can be predicted using Hardy-Weinberg equations:

Hardy-Weinberg Equations:

• For two alleles, p and q:

$p + q = 1$

$p^2 + 2pq + q^2 = 1$

• p: frequency of allele G

• q: frequency of allele g

• p2: frequency of GG genotype

• 2pq: frequency of Gg genotype

• q2: frequency of gg genotype

Example Calculation

Given 100 individuals: 36 GG, 48 Gg, 16 gg

• Frequency of G: $F(G) = [2(36) + 48]/200 = 0.6$

• Frequency of g: $F(g) = [2(16) + 48]/200 = 0.4$

Conditions for Hardy-Weinberg Equilibrium

• Random mating

• Infinite population size

• No natural selection

• No migration

• No mutation

If these conditions are met, allele frequencies remain constant and genotype frequencies can be predicted.

Calculating Allele and Genotype Frequencies

Allele and Genotype Frequencies in Human Populations

Genotype and allele frequencies can be calculated from observed counts in a population.

Genotype	Observed Counts	Observed Frequencies	Expected Frequencies
MM	342	0.332	0.331
MN	500	0.486	0.489
NN	187	0.182	0.180

• Allele frequencies: $F(M) = 0.575$, $F(N) = 0.425$

• Genotype frequencies sum to 1.

• Chi-square test ($rac{ ext{observed} - ext{expected}}{ ext{expected}}$) can be used to test for Hardy-Weinberg equilibrium.

Estimating Allele Frequencies with Complete Dominance

When dominance is complete, carrier frequencies can be estimated using Hardy-Weinberg equilibrium.

Genotype	Phenotype	Observed Counts	Expected Frequencies
FF	healthy	1999	0.9558
Ff	healthy	1	0.0437
ff	cystic fibrosis	1	0.0005

• Allele frequency of f: $q = 1/2000 = 0.0005$

• Carrier frequency: $2pq = 2(0.022)(0.978) = 0.0437$

Extending Hardy-Weinberg to Multiple Alleles

For loci with more than two alleles, genotype frequencies are calculated using the sum of allele frequencies.

Blood Type	Genotype	Expected Frequency
A	AA	0.053
A	Ai	0.313
B	BB	0.008
B	Bi	0.122
AB	AB	0.041
O	ii	0.462

• Allele frequencies: $p = 0.23$, $q = 0.09$, $r = 0.68$

• $p + q + r = 1$

Hardy-Weinberg Equilibrium for X-linked Genes

Reaching equilibrium for X-linked genes takes longer due to differences in allele transmission between males and females.

• Allele frequencies fluctuate more in early generations before stabilizing.

Non-Random Mating

Types of Non-Random Mating

Non-random mating affects genotype frequencies but not allele frequencies.

• Inbreeding: Mating between relatives increases homozygosity.

• Assortative mating: Mating based on similarity (positive) or difference (negative) in traits.

Inbreeding

Self-fertilization is the most extreme form of inbreeding, rapidly increasing homozygosity.

Generation	A1A1	A1A2	A2A2
1	0.250	0.500	0.250
2	0.375	0.250	0.375
3	0.437	0.125	0.437
4	0.468	0.063	0.468

• Allele frequencies remain unchanged, but homozygosity increases.

Quantifying Inbreeding

The inbreeding coefficient (F) measures the probability that two alleles are identical by descent (IBD).

• For first cousins: $F = 2 imes ( rac{1}{4})^4 = rac{1}{16}$

• Inbreeding increases the risk of recessive genetic diseases.

Assortative Mating

• Positive assortative mating: Increases homozygosity for specific traits.

• Negative assortative mating: Increases heterozygosity for specific traits.

Genetic Drift in Finite Populations

Genetic Drift

Genetic drift is the change in allele frequencies due to random sampling in finite populations.

• Effects are stronger in small populations.

• Can lead to fixation or loss of alleles.

Founder Events

Founder events occur when a new population is established by a small number of individuals, leading to non-representative sampling of alleles.

• Example: Ellis-van Creveld syndrome in isolated populations.

Population Bottlenecks

Bottlenecks occur when a population's size is drastically reduced, decreasing genetic variation and altering allele frequencies.

• Example: Kinked tail in cheetahs due to reduced genetic diversity.

Summary Table: Effects of Evolutionary Forces on Allele Frequencies

Force	Effect on Allele Frequency	Effect on Genotype Frequency
Random Mating	No change	Predictable (HWE)
Non-Random Mating	No change	Altered (increased homozygosity)
Genetic Drift	Change (random)	Change
Natural Selection	Change (directional)	Change
Migration	Change	Change
Mutation	Minimal change	Change

Additional info: These notes expand on the provided slides by including definitions, formulas, and examples for key concepts in population genetics and evolution, suitable for exam preparation and deeper understanding.