Question

Complete the following 10 questions. To get complete credit, you must show your work for calculations and type the correct answers in the yellow highlighted boxes. Round final calculations to two digits. Partial credit will be given for using the correct equations, but getting the wrong answer. Minimal credit (a quarter of possible points) will be given for providing answers with no equations. Even if you only answer a few of the questions, submit the assignment on time. Material covered in this assignment is discussed in chapters 9, 10, and 12 of the Evolution textbook.

Part I
1. In an electrophoretic study of enzyme variation in a species of pelican, you find 77 A1A1, 45 A1A2, and 18 A2A2 individuals at a particular locus in a sample of 140. What are the allele frequencies for the A1 and A2 alleles? Calculate the genotype frequencies for this locus.

Genotypes   A1A1   A1A2   A2A2
Number of individuals   77   45   18
Genotype frequencies          

Frequency of A1 allele  
Frequency of A2 allele  

Show whether these genotype frequencies are in Hardy-Weinberg equilibrium.

2. In the peppered moth (Biston betularia), black individuals may be either homozygous (A1A1) or heterozygous (A1A2), whereas pale gray moths are only homozygous (A2A2). Suppose that in a sample of 250 moths from one locality, 108 are black and 142 are gray.

a) Which allele is dominant?

b) Assuming that the locus is in Hardy-Weinberg equilibrium, what are the allele frequencies? Show your work below:

c) Under this assumption, what proportion of the sample is heterozygous? What is the number of heterozygotes?

d) Under the same assumption, approximately 0.85 of the black moths are heterozygous. Show calculations below for how you arrive at this answer:

e) Why is it necessary to assume Hardy-Weinberg genotype frequencies in order to answer parts b-d?

3. Linkage disequilibrium (LD) occurs when alleles at different loci are nonrandomly associated and are more likely to be inherited together. But how do scientists identify LD? For this question, you will calculate D, the coefficient of linkage disequilibrium to test whether a set of SNPs is in linkage equilibrium or disequilibrium.

Suppose there are two variable sites (SNPs) on two different loci, and we collect sequence data from a sample of 2000 people. At SNP1, the nucleotide in the locus sequence is either a G or a C, while at SNP2, the nucleotide is either an A or a T. All combinations of SNP1 and SNP2 nucleotides are possible, and from the data we see that there are 474 individuals with GA haplotype, 611 with a GT haplotype, 142 with a CA haplotype, and 773 individuals with CT haplotype.

a) What are the haplotype frequencies? Show work below:

b) Now, let’s calculate D. D = (g11 x g22) - (g12 x g21). Show work below. Are these loci in LD?
g11 = frequency of GA
g12 = frequency of GT
g21 = frequency of CA
g22 = frequency of CT

Answer 1

Ans. 1

Genotypes A1A1   A1A2   A2A2
Number of individuals 77 45 18

Genotype frequencies - for genotype A1A1 = (77/140) = 0.55

for genotype A1A2 = (45/140) = 0.321

for genotype A1A2 = (18/140) = 0.128

Frequency of A1 allele = (2*77+45)/280 = 0.71
Frequency of A2 allele = (2*18+45)/280 = 0.29

Ans.2

a) A1 allele is dominant as in heterozygous condition i..e., A1A2, the phenotype is same as A1A1.

b)

genotype frequency for A2A2 = q² = 142/250 = 0.568,

so, allele frequency for A2 allele i.e., q = 0.753 (square root of q²)

Therefore, allele frequency for A1 allele i.e., p = 1 - 0.753 = 0.247

c)

No. of heterozygotes = 2*p*q * 250 = 2*0.247*0.753*250= 93 (approx.)

d)

Total no. of black moths = 108

Heterozygous black moths = 93

so, 93/108 = approximately 0.85 of the black moths are heterozygous.