W11 pop genomics

Question 1

What are the approaches to finding genes responsible for adaptation?

Answer 1

Top down–> Phenotype to genotype

Bottom up–> Genotype to phenotype

Question 2

What is the top down approach?

Answer 2

1. Identify important trait then find loci associated to the trait
2. QTL association mapping

Question 3

What is the bottom up approach?

Answer 3

1. Identify loci under selection, then find trait associated with loci
2. Population genetics
3. Benefits:
   - Does not require knowledge of the selection pressure of the phenotype

Question 4

What are the types of selection?

Answer 4

1. Directional/ positive- best allele sweep to fixation, loss of variation
2. Balancing- maintains variation otherwise lost to drift

Question 5

What causes low levels of genetic variation?

Answer 5

1. Positive selection
2. Low mutation rate
3. Drift (small population size)
4. Purifying selection (background selection

Question 6

What is hitchhiking?

Answer 6

• Nearby (neutral) variation are also swept with the beneficial mutation and become fixed

Question 7

what methods are used to measure variation in sequence data?

Answer 7

1. Segregating sites – two alleles at each polymorphic site
2. Nucleotide Polymorphisms – θ
3. Nucleotide Diversity – Π

Question 8

Tajimas D

Answer 8

Quantifying Differences in the Site Frequency Spectrum

• Examines the frequency distribution of segregating sites at a locus
• D will be negative when there are lots of rare alleles in the sequences
• Indicating selection or recent population expansion

Question 9

Detecting Selection: Site Frequency Spectrum (SFS) Approaches

Answer 9

Involves counting the times a site is found with a different base in X number of sequences

1. After a selective sweep there is likely to be an excess of rare or common polymorphisms
2. Population size expansion after a bottleneck and introgression/gene flow can also mimic the pattern of selective sweeps
3. Tajima’s D – Quantifying Differences in the Site Frequency Spectrum