1: Population genetic tests for selection

Question 1

What is a Haplotype?

Answer 1

A specific combination of alleles (genetic variants) along a single chromosome that are inherited together from a single parent

Question 2

Under strong selection of a beneficial variant, what is expected to happen to genetic variation?

Answer 2

Genetic variation is reduced, especially around the site under selection

Question 3

Describe Haplotype homozygosity

Answer 3

Individual carries 2 identical copies of a haplotype in a particular region of their genome

Question 4

Describe the site frequency spectrum (SFS)

Answer 4

• Shows the distribution of allele frequencies at polymorphic sites within a pop.
• Provides a snapshot of genetic diversity by categorising the frequencies of different alleles across the population

Question 5

Describe Tajima’s D

Answer 5

Statistical test used to assess deviations from the neutral theory
- (Neutral theory = most genetic variation comes from random drift/mutation, rather than natural selection)
- If D + = excess of intermediate-frequency alleles (due to balancing selection)
- If D - = excess of rare alleles (due to positive selection)

Question 6

Whats the difference between ancestral and derived alleles?

Answer 6

Ancestral:
- Present in common ancestor of a group of species
- Original variant that existed before mutations occured

Derived:
- Newer variant that’s arised through mutation, AFTER the divergence of species from common ancestor
- Not shared between other related species

Question 7

Under positive selection we expect an increase in ——- variants

Answer 7

Derived

Question 8

Describe Fay & Wu’s H

Answer 8

• Statistical test used to detect deviations from neutrality in DNA sequence
• Positive H = excess of high-frequency of derived alleles (due to positive selection or selection sweep)
• Negative H = excess of low frequency derived alleles (due to balancing selection)