Evolution Exam 3

What is a locus (loci is there is many)?

A specific location of a gene on a chromosome.

What are haplotypes?

Combinations of alleles at different loci on the same chromosome (e.g., AB, Ab, aB, ab).

What is linkage equilibrium?

Alleles at different loci are independent of each other.

How do you recognize linkage equilibrium?

Knowing one allele does NOT help predict the other.

What is linkage disequilibrium?

Alleles are non-randomly associated.

How do you recognize linkage disequilibrium?

Knowing one allele helps predict the other.

What does the disequilibrium coefficient (D) = 0 mean?

No linkage disequilibrium (equilibrium).

What does D (disequilibrium coefficient) ≠ 0 mean?

Linkage disequilibrium is present.

In equilibrium, how do haplotype frequencies behave?

They follow expected proportions (independent combinations).

In disequilibrium, what happens to frequencies?

Some combinations are overrepresented or missing.

What happens to haplotype frequencies in linkage equilibrium under Hardy-Weinberg?

They do not change across generations.

What happens in linkage disequilibrium over generations?

Frequencies change over time.

What is multilocus genotype selection?

Multiple genes together affect survival/fitness.

How does multilocus genotype selection create disequilibrium?

Certain allele combinations are favored or eliminated.

Example for multilocus genotype selection?

Only organisms with ≥3 dominant alleles survive → some genotypes disappear.

What is genetic drift?

Random changes in allele frequencies in small populations.

How does drift cause disequilibrium?

Missing allele combinations due to chance.

Why is population size important?

Small populations = fewer combinations → more imbalance.

What is population admixture?

Mixing of two populations with different allele frequencies.

What happens after mixing in population admixture?

New population shows non-random associations → disequilibrium.

What reduces linkage disequilibrium?

Genetic recombination.

When does recombination occur?

During meiosis (crossing over).

What type of reproduction helps reduce disequilibrium?

Sexual reproduction with random mating.

What happens with high recombination rates?

Faster return to equilibrium.

What happens if recombination rate = 0?

Disequilibrium persists.

Why is linkage disequilibrium important?

Helps detect:

• Natural selection

• Genetic drift

• Population history

• Genetic hitchhiking

What is genetic hitchhiking?

When one allele increases in frequency because it’s linked to a beneficial allele.

What is linkage disequilibrium?

A nonrandom association of alleles at different loci.

What does it mean if two loci are in linkage disequilibrium?

If you know the allele at one locus, you can better predict the allele at the other locus.

What is the evolutionary “goal” regarding linkage disequilibrium?

To reduce it and move back toward equilibrium.

What mainly removes linkage disequilibrium?

Genetic recombination.

During what process does recombination happen?

Meiosis.

What kind of reproduction helps reduce linkage disequilibrium?

Sexual reproduction.

Why does recombination reduce linkage disequilibrium?

It breaks up nonrandom allele combinations.

What does D measure?

The amount of linkage disequilibrium.

What does D = 0 mean?

Linkage equilibrium.

What does D ≠ 0 mean?

Linkage disequilibrium is present.

What happens to linkage disequilibrium when recombination is high?

It decreases faster.

What happens to linkage disequilibrium when genes are close together?

It is more likely to remain because crossing over is less likely to separate them.

What happens to linkage disequilibrium when genes are far apart?

It is less likely because recombination is more likely to separate them.

Why are nearby genes more likely to be in linkage disequilibrium?

They cross over less often.

What organism was used as an example of linkage disequilibrium caused by selection?

Fruit flies.

What trait was being selected for in the fruit fly example?

Insecticide resistance.

What happened to fruit flies sensitive to insecticide?

They were eliminated.

What happened to fruit flies with the beneficial mutation?

They survived and became more common.

What happens to nearby genes when a beneficial gene is strongly selected?

Nearby genes can also increase in frequency even if they do not help directly.

What is genetic hitchhiking?

When nearby alleles increase in frequency because they are linked to a selected allele.

In the fruit fly example, why did nearby genes increase too?

Because they were physically close to the insecticide-resistance gene.

What is the big lesson from the fruit fly example?

Strong selection on one gene can create linkage disequilibrium and pull nearby genes along with it.

What did researchers look for on human chromosome 22?

Linkage disequilibrium.

What did they find on chromosome 22 overall?

Very little linkage disequilibrium overall.

Where on chromosome 22 was linkage disequilibrium more likely to appear?

In regions where genes/loci were physically close together.

Why was linkage disequilibrium stronger between nearby loci on chromosome 22?

Because recombination is less likely to separate nearby loci.

Where in the human genome did researchers find a lot of linkage disequilibrium?

In HLA markers.

What are HLA markers related to?

Immune response.

Why is there a lot of linkage disequilibrium in HLA regions?

Because there is strong selection on immune-related genes.

What kind of selection helped create linkage disequilibrium in HLA regions?

Multilocus selection.

Why would immune genes experience strong selection?

Because of pathogens and disease pressure.

What types of human traits or conditions have been associated with linkage disequilibrium?

Allergies, asthma, fertility-related traits, and disease susceptibility.

What relationship did your professor mention between recombination and allergies?

More recombination was associated with fewer allergies.

Why is linkage disequilibrium useful in humans?

It can help identify disease-associated regions and patterns of inheritance.

What organism was used as an example of self-fertilization and linkage disequilibrium?

Arabidopsis (a plant).

Why did scientists think self-fertilizing plants might show more linkage disequilibrium?

Because self-fertilization reduces mixing between different individuals.

Did linkage disequilibrium exist in the plant example?

Yes.

Did genes farther apart in the plant show less linkage disequilibrium?

Yes.

Did self-fertilization cause a huge increase in linkage disequilibrium overall in that example?

No, not necessarily.

Why did the self-fertilization not cause a huge increase in linkage disequilibrium?

Because meiosis and recombination still occur.

What is the main takeaway from the plant example?

Recombination still matters, even in self-fertilizing organisms.

What tends to create linkage disequilibrium?

Mutation and selection.

What tends to break linkage disequilibrium apart?

Recombination.

What is the basic contrast?

Mutation/selection can build nonrandom associations; recombination breaks them up.

Why is linkage disequilibrium useful in disease studies?

It can help find mutations or nearby genes associated with disease.

What disease was used as an example in linkage disequilibrium?

Crohn’s disease.

What chromosome was mentioned in the Crohn’s disease example?

Chromosome 5.

Did the originally studied mutation directly cause Crohn’s disease?

No, not necessarily.

Why did the mutation seem to associate with Chron’s disease?

Because of linkage disequilibrium with nearby immune-related genes.

What is the key idea from the Crohn’s example?

A mutation may appear linked to a disease because it is close to the true causal gene.

What concept explains that nearby genes were being carried along together?

Genetic hitchhiking / linkage disequilibrium.

What happened when recombination occurred in that region?

Risk of Crohn’s disease was lower because the linked genes could be separated.

What happened when there was no recombination in that region?

The linked disease-associated region stayed together, increasing disease association.

How can linkage disequilibrium help study the history of mutations?

By comparing current disequilibrium to recombination rates, scientists can estimate how long ago a mutation arose.

What happens to linkage disequilibrium over time?

It decays because recombination breaks associations apart.

What does more decay of linkage disequilibrium suggest?

The mutation is older.

What does less decay of linkage disequilibrium suggest?

The mutation is more recent.

Why is using linkage disequilibrium to study history useful?

It helps estimate when a mutation entered a population.

What disease was mentioned as an example of using linkage disequilibrium to study mutation history?

Gaucher disease.

What kind of disorder is Gaucher disease?

A lysosomal disorder.

What body systems/problems were mentioned with Gaucher disease?

Liver, spleen, anemia, and fragile bones.

Why was Gaucher disease useful?

It showed how scientists can estimate when a disease mutation appeared in a population.

What was the general conclusion in the Gaucher disease example?

The mutation could be traced back to roughly about 1,000 years ago in that population.

What mutation related to HIV resistance was mentioned?

CCR5 mutation.

Why was CCR5 discussed in this section?

As another example of tracing the history of a mutation using linkage disequilibrium.

What was the main idea with CCR5?

Linkage disequilibrium can help estimate when a protective mutation arose and spread in a population.

Why is malaria often used in genetics examples?

Because it creates strong natural selection.

What gene was mentioned as being selected in malaria-exposed populations?

G6PD.

What does G6PD affect?

Red blood cells.

Where is G6PD located?

On the X chromosome.

Why is X-linkage important for G6PD?

Males only have one X chromosome, so the mutation affects them more directly.

Why is G6PD common in malaria regions?

Because it provides protection in malaria-prone areas.

What is the downside of G6PD deficiency?

It can cause red blood cell problems and make some treatments dangerous.