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3) Below are the genotypes at three loci for a sample of 6 individuals

a) What are the allele frequencies for each locus?

Locus 1: Allele D frequency = 1.0 (12/12)

Locus 2: Allele E frequency = 0.83 (10/12); allele e frequency 0.17 (2/12)

Locus 3: Allele F frequency = 0.5 (6/12); allele f frequency = 0.5 (6/12)

b) What are the frequencies of genotypes for each locus?

Locus 1: Genotype DD frequency = 1.0

Locus 2: Genotype EE frequency = 0.67; genotype Ee frequency = 0.33

Locus 3: Genotype FF frequency = 0.33; genotype Ff frequency = 0.33; genotype ff frequency = 0.33

c) What is the percent polymorphism (P) for this population?

Recall that P = # of loci with polymorphism / total # of loci. Because only all alleles 2 and 3 are polymorphic:

P = 2 / 3 = 0.67 or 67%

d) What is the average heterozygosity (H-bar) for this population?

H-bar = Heterozygosity for locus 1 + Heterozygosity for locus 2 + Heterozygosity for locus 3 / total # of loci

H-bar = (0 + 0.33 + 0.33) / 3 = 0.22

H-bar = 0.22

e) What would genotype frequencies be at locus 2 in this population if it were in Hardy-Weinberg equilibrium?

Recall that Hardy-Weinberg equilibrium states that p² + 2pq + q² = 1, and using p and q from part "a" (p = 0.83 and q = 0.17) we know that:

For genotype EE: p² = 0.83² = 0.70

For genotype Ee: 2pq = 2 * 0.82 * 0.17 = 0.28

For genotype ee: q² = 0.17² = 0.02

f) If individuals 1-3 were males and individuals 4-6 were females, what would be the effective population size of this population (all are breeders)?

N_e = 4 * M * F / (M + F)

N_e = 4 * 3 * 3 / (3 + 3) = 6

g) What portion of the genetic variance of this population would be likely to remain after three generations of random genetic drift? (Use the effective population size calculated in the preceding question.)

Because we are calculating the percent heterozygosity lost, we start with 100% heterozygosity (H₀ = 1).

H_t = H₀ (1- 1 / 2N_e)^t

H₃ = 1 (1 - 1 / 2 * 6)³

H₃ = 0.92³ = 0.92 * 0.92 * 0.92

H₃ = 0.78

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