Population Genetics

Question 1

Evolution:

Answer 1

Change in allele frequency over time

Question 2

175 sheep are genotyped
AA=91
AB=28
BB=56
Calculate the frequency of the genotypes
Calculate the allele frequency

Answer 2

Question 3

Hardy-Weinberg equilibrium equation:

Answer 3

p^2 + 2pq + q^2 = 1

Question 4

What are the assumptions made under Hardy-Weinberg equilibrium

Answer 4

Locus is not under selection
No mutations
No migrants ebetering population
No genetic drift (pop. size is infinite)
Random mating

Question 5

Haplotype:

Answer 5

particular sequence of alleles along a chromosome

Question 6

What is linkage disequilibrium

Answer 6

The fact that markers vary in distance, so inheriting two that are close together has a higher probability. This means that inheriting marker a vs b vs c is not independent

Question 7

If two loci are unlinked, what is r^2

Answer 7

0 because pAB = pApB

Question 8

What causes linkage disequilibrium

Answer 8

New allele “born” on a chromosome
That mutation + nearby variants passed to future generations

Question 9

What does crossing over contribute to linkage disequilibrium?

Answer 9

Nothing!
It erodes it by creating new haplotypes
But, the closer two markers are the less likely they are to be separated (1% chance per Mb)

Question 10

What large-scale event has a major impact on linkage disequilibrium

Answer 10

Bottleneck –> different haplotype frequencies

Question 11

What does GWAS stand for

Answer 11

Genome-wide association study

Question 12

How does LD help with mapping if it is long (millions of bp)

Answer 12

Don’t need as many markers to adequately map genome

Question 13

How does LD help with mapping if it is short (tens of kb)

Answer 13

Increases fine-mapping resolution
Easier to identify the causal mutation