Question 1

Which of the following is NOT a force that causes changes in allelic frequencies in populations?

Accepted Answer

Genomic imprinting

Question 2

A population geneticist is studying a population of cattle using a genome-wide SNP panel. What is a potential limitation of this approach compared to whole-genome sequencing?

Accepted Answer

Genome-wide SNP panels may be inherently biased based on the panel used.

Question 3

Principal Component Analysis (PCA) is used in population genetics to:

Accepted Answer

Identify unique factors or patterns describing variation in a dataset

Question 4

In PCA, what does the eigenvalue associated with a principal component represent?

Accepted Answer

The measure of variation within the dataset for that component

Question 5

A scree plot is used in PCA to:

Accepted Answer

Determine the number of principal components to retain for further analysis

Question 6

Which of the following best describes linkage disequilibrium (LD)?

Accepted Answer

Non-random association of alleles at different loci

Question 7

Given the formula for the Pearson correlation coefficient $$R^2 in $$linkage disequilibrium, what does a value of $$R^2 = 1$ indicate?

Accepted Answer

The two loci are in complete linkage disequilibrium

Question 8

In an admixture analysis, what does the K-value represent?

Accepted Answer

The number of populations identified in the dataset

Question 9

A researcher uses cross-validation error to determine the optimal K-value in an admixture analysis. Which K-value should be chosen?

Accepted Answer

The K-value with the smallest cross-validation error

Question 10

Which of the following is a potential source of bias in admixture analysis?

Accepted Answer

Over- or under-representation of a group of similar individuals

Question 11

Which genomic approach is most appropriate for identifying the degree of relatedness between individuals within a population?

Accepted Answer

Identity by Descent (IBD)

Question 12

A population is in linkage equilibrium. What does this imply about the alleles at two loci?

Accepted Answer

All possible combinations of alleles are present at equal frequency

Question 13

Which of the following data types would provide information only about maternal lineage?

Accepted Answer

Mitochondrial DNA (mtDNA)

Question 14

A cattle breed is found to have a high degree of autozygosity. What does this suggest about its genetic history?

Accepted Answer

It has undergone significant inbreeding

Question 15

Which of the following best describes the purpose of using F-statistics in population genetics?

Accepted Answer

To measure the degree of genetic differentiation among populations

Question 16

A researcher observes that two SNPs on the same chromosome are inherited together more often than expected by chance. This is an example of:

Accepted Answer

Linkage disequilibrium

Question 17

Which of the following equations represents the deviation of observed haplotype frequency from expected in linkage disequilibrium?

Accepted Answer

$$D = P_{AB} - p_A p_B$$

Question 18

In a PCA scatterplot of cattle breeds, PC1 separates Bos indicus from Bos taurus. What does this indicate about PC1?

Accepted Answer

PC1 explains the greatest degree of variation related to subspecies differences

Question 19

Which of the following is a real-world application of understanding population structure in animal breeding programs?

Accepted Answer

To inform conservation and management decisions

Population Genetics: Genomic Approaches to Population Structure

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