PCB 3063 Lecture 9 population genetics

What is population genetics?

The branch of genetics studying group genetic makeup and changes over time.

What is a gene pool?

The total collection of genes and alleles in a population at a specific time.

Why do populations evolve over time?

Due to changes occurring within their gene pool.

What type of organisms do population geneticists usually focus on?

Interbreeding, sexually reproducing individuals sharing a common allele set.

What is genotypic frequency?

The proportion of a specific genotype present within a population.

What is the formula for f(AA)?

f(AA) = (number of AA individuals) / N

What must the sum of all genotypic frequencies equal?

f(AA) + f(Aa) + f(aa) = 1

Why calculate allelic frequencies instead of genotypic frequencies?

To measure the overall abundance of individual alleles rather than diploid combinations.

How is allele frequency p calculated without genotypic frequencies?

p = (2nAA + nAa) / 2N

How is allele frequency q calculated without genotypic frequencies?

q = (2naa + nAa) / 2N

What rule always applies to the sum of two allele frequencies p and q?

p + q = 1

In the MN blood group, what genotype corresponds to phenotype MM?

LMLM

In the MN blood group, what genotype corresponds to phenotype MN?

LMLN

In the MN blood group, what genotype corresponds to phenotype NN?

LNLN

Given 182 MM, 172 MN, 44 NN, what is p = f(LM)?

p = [2(182) + 172] / 796 = 0.673

Given 182 MM, 172 MN, 44 NN, what is q = f(LN)?

q = [2(44) + 172] / 796 = 0.327

How is allele frequency p calculated from known genotypic frequencies?

p = f(AA) + ½ f(Aa)

How is allele frequency q calculated from known genotypic frequencies?

q = f(aa) + ½ f(Aa)

What is the formula for allele frequency p (A1) in a 3-allele system?

p = f(A1A1) + ½ f(A1A2) + ½ f(A1A3)

What is the formula for allele frequency q (A2) in a 3-allele system?

q = f(A2A2) + ½ f(A1A2) + ½ f(A2A3)

What is the formula for allele frequency r (A3) in a 3-allele system?

r = f(A3A3) + ½ f(A1A3) + ½ f(A2A3)

What is the sum rule for a 3-allele system (p, q, r)?

p + q + r = 1

What central question led to the Hardy-Weinberg law?

Whether a rare dominant allele increases in frequency over time solely through reproduction.

What process alone does the Hardy-Weinberg law evaluate?

The effect of reproduction alone on allele and genotype frequencies.

What is Assumption 1 of the Hardy-Weinberg law?

No natural selection (equal survival and reproductive success for all genotypes).

What is Assumption 2 of the Hardy-Weinberg law?

No mutation (no creation or alteration of alleles).

What is Assumption 3 of the Hardy-Weinberg law?

No migration into or out of the population.

What is Assumption 4 of the Hardy-Weinberg law?

Infinitely large population size (sampling errors are negligible).

What is Assumption 5 of the Hardy-Weinberg law?

Random mating across the population.

What does random mating mean mathematically?

Each genotype mates in proportion to its frequency in the population.

Does the Hardy-Weinberg law apply to the whole genome at once?

No, it applies to a single locus at a time.

What is Prediction 1 of the Hardy-Weinberg law?

Allele frequencies do not change from generation to generation.

What is Prediction 2 of the Hardy-Weinberg law?

Genotypic frequencies stabilize after one generation of random mating in p², 2pq, q².

In Hardy-Weinberg equilibrium, what formula represents heterozygote frequency?

2pq

In Hardy-Weinberg equilibrium, what formula represents homozygous dominant frequency?

p²

In Hardy-Weinberg equilibrium, what formula represents homozygous recessive frequency?

q²

Does reproduction alone cause evolutionary change?

No, reproduction alone recombines alleles without altering overall frequencies.

Can evolution occur if a population is at Hardy-Weinberg equilibrium?

No, evolutionary forces like mutation or selection are required.

What is the first application of the Hardy-Weinberg law?

Determining whether a population is at genetic equilibrium.

What is the second application of the Hardy-Weinberg law?

Identifying evolutionary forces acting on non-equilibrium populations.

What is the third application of the Hardy-Weinberg law?

Estimating genotypic frequencies when only one phenotype/genotype is observed.

Given A1A1=135, A1A2=44, A2A2=11 (N=190), what is allele frequency p?

p = [2(135) + 44] / 380 = 0.826

Given p = 0.826 in a two-allele system, what is q?

q = 1 - 0.826 = 0.174

Expected number of A1A1 individuals out of 190 if p = 0.826?

(0.826)² × 190 ≈ 129.8

Expected number of A1A2 individuals out of 190 if p=0.826 and q=0.174?

2(0.826)(0.174) × 190 ≈ 54.5

Expected number of A2A2 individuals out of 190 if q = 0.174?

(0.174)² × 190 ≈ 5.7

What statistical test determines if observed genotype counts match HW equilibrium?

Chi-square test for goodness of fit.

If observed genotype counts differ significantly from HW expectations, what is concluded?

The population is not at Hardy-Weinberg equilibrium; assumptions are violated.

If cystic fibrosis affects 1 in 2,000 people (0.0005), what is q²?

q² = 0.0005

If q² = 0.0005 for cystic fibrosis, what is q?

q = √0.0005 ≈ 0.02

If q = 0.02, what is p?

p = 1 - 0.02 = 0.98

If p = 0.98, what proportion of the population is homozygous normal (p²)?

(0.98)² = 0.96 (approx 96%)

If p = 0.98 and q = 0.02, what proportion of the population are carriers (2pq)?

2(0.98)(0.02) = 0.0392 (approx 4%)

Does nonrandom mating alone change allele frequencies?

No, nonrandom mating reshuffles alleles, altering genotypic but not allelic frequencies.

What are the two major classes of nonrandom mating?

Positive assortative mating and negative assortative mating.

What is positive assortative mating?

The preference for mating between individuals with similar phenotypes.

Give an example of positive assortative mating in humans.

Mating preferences based on height (tall with tall, short with short).

What is negative assortative mating?

The preference for mating between individuals with dissimilar phenotypes.

What is inbreeding?

Preferential mating between closely related individuals.

How does inbreeding differ from trait-based positive assortative mating?

Inbreeding affects all genes across the genome, not just trait-specific loci.

How does inbreeding alter genotypic proportions?

It increases homozygosity and decreases heterozygosity.

What parameter quantifies the degree of inbreeding?

Inbreeding coefficient (F).

What does the inbreeding coefficient (F) measure?

Probability that two alleles are identical by descent from a common ancestor.

What is the numerical range of the inbreeding coefficient (F)?

0 to 1

What does F = 0 signify?

Random mating with no alleles identical by descent.

What does F = 1 signify?

Complete inbreeding where all alleles are identical by descent.

Why is inbreeding frequently harmful?

It exposes deleterious recessive alleles in homozygous state.

What is inbreeding depression?

The reduced fitness and appearance of harmful traits due to inbreeding.

What was observed regarding mean IQ in the Schull and Neel study?

Mean IQ dropped by 6 points for every 10% increase in F.

How does child mortality change among offspring of first cousins?

Child mortality is ~40% higher compared to children of unrelated parents.

What was the survival rate of inbred mice (F = 0.25) released into the wild?

56% of the survival rate of non-inbred mice.

How can controlled inbreeding be useful in agriculture/breeding?

It fixes desirable traits while allowing weeding out of harmful recessive traits.

Name the four evolutionary processes that alter allele frequencies.

Mutation, migration, genetic drift, and natural selection.

What is the only mechanism that creates entirely NEW alleles?

Mutation

Do mutations occur to satisfy the adaptive needs of an organism?

No, mutations occur randomly regardless of benefit or harm.

What determines the rate of change in allele frequency due to mutation?

The mutation rate and the difference in frequency between alleles.

When does mutation reach equilibrium between forward (p→q) and reverse (q→p) rates?

When forward and reverse mutation rates produce equal numbers of converted alleles.

What non-biological process operates similarly to mutation rate equilibrium?

Chemical reaction equilibrium or diffusion.

What is migration (gene flow)?

Movement of genes or alleles into or out of a population.

How does migration affect genetic differences between two populations?

It reduces genetic divergence, making populations more similar.

How does migration affect genetic variation within a recipient population?

It increases genetic variation within the recipient population.

What primary factor determines allele frequency change in migration?

Extent of migration and initial allele frequency differences between populations.

When does gene flow cause zero net change in recipient allele frequencies?

When source and recipient populations already share identical allele frequencies.

What is genetic drift?

Random fluctuations in allele frequencies due to chance events in finite populations.

What size of population is most susceptible to genetic drift?

Small populations.

What is sampling error in population genetics?

Deviation of a sample allele frequency from the true parent population frequency.

What analogy illustrates sampling error in small populations?

Flipping a coin 10 times versus 1,000 times.

What is the Founder Effect?

Genetic drift occurring when a small group establishes a new population.

Why do founder populations differ genetically from source populations?

The founders carry only a small, non-representative sample of original alleles.

What is a genetic bottleneck?

Drastic population reduction caused by environmental events or catastrophes.

How does a bottleneck affect gene pool composition?

Surviving alleles randomly represent only a fraction of original genetic diversity.

Are allele frequency changes caused by genetic drift directional or random?

Random; frequencies are equally likely to increase or decrease.

How does genetic drift impact variation WITHIN a single population over time?

It reduces overall genetic variation by causing allele loss or fixation.

What does it mean when an allele becomes 'fixed'?

Its frequency reaches 1.0 (100%), eliminating alternative alleles at that locus.

Which alleles are most likely to reach fixation during genetic drift?

Alleles with higher initial starting frequencies.

How does genetic drift impact differences BETWEEN isolated populations over time?

It causes isolated populations to diverge genetically from one another.

What is natural selection?

Differential reproduction and survival of genotypes due to adaptive advantages.

What happens over time to alleles that confer higher reproductive fitness?

Their frequencies gradually increase within the population.

What is fitness (W) in evolutionary genetics?

The relative reproductive success of a genotype compared to others.

What is the numerical range for relative fitness (W)?

0 to 1