When studying population genetics of multiple loci, we need to monitor both alle

Question

When studying population genetics of multiple loci, we need to monitor both allele and haplotype requencies. This is because the various loci under consideration may not show independent segregation, that is: they may be linked. We can use the Hardy-Weinberg equation to predict the genotype frequencies if the loci show independent segregation. If they are linked, however, we certainly expect to see a departure from such prediction. Even when genes are not linked, there could be a statistical bias in the association between certain alleles, known in population genetics as linkage disequilibrium. When this bias does not exist, loci are said to be in linkage equilibrium. 1. Using the information provided in the table below, calculate the coefficient of linkage disequilibrium for a single haplotype in the two populations below and indicate if the population is in linkage equilibrium (no bias) or disequilibrium (bias in the association between alleles) for the haplotype by calculating D (you may want to review the slides in the Powerpoint presentation). Show your work. (2 points for this one) Population I fA= 0.3 and fB= 0.8 hAB = 0.62 Population 2 fA= 0.5 and fB = 0.1 hAB = 0.05 This population is in This population is in 2. This question refers to the total degree of linkage disequilibrium for all haplotypes in a population, not just one as in the question above. In this population the frequency of A is 0.2 and a is 0.8, while the frequency of B is 0.3 and b is 0.7. The haplotype frequencies are: AB=0.02 Ab=0.23 ab = 0.40 Calculate the total coefficient of linkage disequilibrium, D, for these haplotypes. (1) sequilibrium, this suggests a (circle one) low moderate /high level of linkage disequilibrium. (1)

Explanation / Answer

1) Linkage means when two genes are inherited together in the offspring.

Linkage equilibrium means when haplotype frequency similiar to multiplied allele frequency then it is called linkage equilibrium

Linkage disequilibrium denotes non random association between allele at two loci . Haplotype frequency not match with the multiplied allele frequency. Cofficient of disequilibrium measure degree to which allele at two loci are associated.

In population 1 haplotype frequency AB = 0.62

f A = 0.3. And f B = 0.8 allelilic frequencies

So hAB = fA x fB + D

D= hAB - fA fB

D = 0.62 - 0.8 x 0.3

D = 0.38

Population 1 in linkage disequilibrium.

Population 2 hAB = 0.05

FA = 0.5. fB = 0.1

D = hAB - fAfB

D= 0.05 - 0.5x 0.1

D = - 0.45

D is less than 0 means its range -0.45 to 0.38. -0.45 is approx to 0 but this population 2 is also in linkage disequibrium because haplotype value is not matched with multiplied allele frequency.

2) haplotype frequency

AB 0.02. X11

Ab. 0.23. X12

aB. 0.35. X21

ab. 0.40. X22

Allele frequency

A1. 0.2. p1

a2. 0.8. p2

B1. 0.3. q1

b2. 0.7. q2

A1. a2. . Total

B1. X11 = p1q1 +D. X21 = p2 q1 -D q1

b2. X12= p1q1-D. X22 = p2q2 + D q2

Total. p1. p2

D= X11 x X22 - X12 x X21

D= .02 x .40 - .23 x .35

D= .008 - .0805

D= - .072

This represent total cofficient of linkage disequilibrium.

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