Multiple Loci: Linkage

Question 1

Define linked loci

Answer 1

loci that are physically linked on the same chromosome and are inherited as a “package”
(the closer they are the less recombination occurs)

Question 2

Define linkage equilibrium

Answer 2

genotype at one locus is independent of genotype at second locus, the haplotypes are independent events

Question 3

Define linkage disequilibrium

Answer 3

non-random association between genotype at one locus and genotype at second locus, haplotype events do not occur randomly.
the frequencies are not equal

Question 4

What is coefficient D and how to calculate

Answer 4

D = coefficient of linkage disequilibrium
meaning if 0 = in linkage equilibrium, has max of 0.25 and min of -0.25
D = gABgab - gAbgaB
(g = haplotype/chromosome frequency)

Question 5

What are 3 criteria of linkage equilibrium

Answer 5

1. D = 0
2. frequency of B on A = the same frequency as B on a (ex. BA = 12/15 = 0.8 and Ba = 8/10 = 0.8)
3. frequency of AB = frequency of A x B

Question 6

What are the 3 causes of disequilibrium

Answer 6

1. selection of multilocus genotype
2. genetic drift
3. population admixture

Question 7

Explain how selection of multilocus genotypes causes disequilibrium

Answer 7

different multilocus genotypes are favoured under different conditions
a population can start in linkage equilibrium, but selection can occur against a specific multilocus (ex. ab/ab) and remove it from the population by selection, resulting in linkage disequilibrium

Question 8

Explain how genetic drift causes disequilibrium

Answer 8

a mutation event occurs to create a new haplotype in a finite, small population because in big population would likely have multiple mutations occurring. The new haplotype being present causes Ab to convert to ab and results in linkage disequilibrium

Question 9

Explain how population admixture causes disequilibrium

Answer 9

admixture occurs when two or more previously isolated populations interbreed.
the two isolated populations could be in linkage equilibrium, but the mixing of the two may result in disequilibrium and excess of certain haplotypes over others

Question 10

How can the wahlund effect result in disequilibrium

Answer 10

the wahlund effects causes increase in homozygotes and decrease in heterozygotes, so under HWE would expect 0.25 frequency for all 4 haplotypes, but only 2 haplotypes are present AB = 0.5 and ab = 0.5

Question 11

Crossing over causes

Answer 11

genetic recombination

Question 12

The rate of ____ is proportional to the rate of recombination

Answer 12

decrease in D

Question 13

what is the range of r and why

Answer 13

0-0.5
0.5 is max because only half of a chromosome can even cross over

Question 14

What are 3 reasons to bother with linkage disequilibrium, why do we care?

Answer 14

1. genetic hitchhiking
2. reconstruct gene/allele history
3. identify alleles under positive selection

Question 15

What is genetic hitchhiking

Answer 15

A and B could be in disequilibrium and if selection acts on locus A and we only look at locus A, then likely make some incorrect assumptions if do a single locus experiment and they are actually linked
when one undergoes allele frequency changes not because of itself under natural selection but because its near another gene undergoing selection

Question 16

Explain allele/gene’s history

Question 17

Explain affect of alleles under positive selection in disequilibrium

Answer 17

alleles could be young and rare (high LD, because no time yet to decay disequilibrium and only in a few people), old and rare (low LD, time for decay could be rare or common), or old and common (same as last).
if high LD and common therefore means has been under selection to be common so quickly.
would then expect drift to push loci into LE. the higher LD means higher selection