question 1 In the remaining small population of red wolves which consist of 35 m
ID: 48703 • Letter: Q
Question
question 1
In the remaining small population of red wolves which consist of 35 males and 65 females today, using Coalescent Theory, calculate the equilibrium heterozygosity of a neutral locus if the mutation rate is 10-7. Assume no other forces are acting on this locus other than neutral processes
QUESTION 2
The gene SLC24A5 is a key part of the melanin expression pathway, which contributes to skin and hair pigmentation. A SNP that is strongly associated with lighter skin pigment in Europe (and therefore has been under selection) is rs1426654. The SNP has two alleles, A and G, with G being associated with light skin, at a frequency of 100% in Utah European-Americans. The SNP varies in frequency in populations in the Americas with mixed African and American Indian ancestry. A sample in Mexico had 38% A and 62% G; in Puerto Rico the frequencies were 59% A and 41% G, and a sample of African-Americans from Charleston had 19% A with 81% G. What is the HT in at this locus across the Mexico, Puerto Rico and Charleston populations?
QUESTION 3
The gene SLC24A5 is a key part of the melanin expression pathway, which contributes to skin and hair pigmentation. A SNP that is strongly associated with lighter skin pigment in Europe (and therefore has been under selection) is rs1426654. The SNP has two alleles, A and G, with G being associated with light skin, at a frequency of 100% in Utah European-Americans. The SNP varies in frequency in populations in the Americas with mixed African and American Indian ancestry. A sample in Mexico had 38% A and 62% G; in Puerto Rico the frequencies were 59% A and 41% G, and a sample of African-Americans from Charleston had 19% A with 81% G. What is the HS in the Charleston populations?
QUESTION 4
The gene SLC24A5 is a key part of the melanin expression pathway, which contributes to skin and hair pigmentation. A SNP that is strongly associated with lighter skin pigment in Europe (and therefore has been under selection) is rs1426654. The SNP has two alleles, A and G, with G being associated with light skin, at a frequency of 100% in Utah European-Americans. The SNP varies in frequency in populations in the Americas with mixed African and American Indian ancestry. A sample in Mexico had 38% A and 62% G; in Puerto Rico the frequencies were 59% A and 41% G, and a sample of African-Americans from Charleston had 19% A with 81% G. What is the FST in at this locus across the Mexico, Puerto Rico and Charleston populations?
Hint: To estimate FST, take the following steps:
Find the allele frequencies for each subpopulation (given in this problem).
Find the average allele frequencies for each allele for the total population (all three subpopulations combined).
Calculate the heterozygosity (2pq) for each subpopulation.
Calculate the average of these subpopulation heterozygosities. This is HS.
Calculate the total heterozygosity based on the averaged total population allele frequencies. This is HT.
Finally, calculate FST=(HT-HS)/HT.
QUESTION 5
Using the Continent-Island model, calculate the change in allele frequency for a biallelic locus if 29 birds migrated to a small island with 123 native individuals. The native birds had a frequency of p=.36 prior to the migration event. The migrants had an allele frequency of p=.72.
QUESTION 6
Calculate the genetic distance (using Nei's 1972 formula) between the Mexico and Puerto Rico populations at the melanin synthesis gene, SLC2485. As in the previous questions, Mexico had 38% A and 62% G in a population of 324 people; in Puerto Rico the frequencies were 59% A and 41% G in the same size population.
QUESTION 7
Select all statements that are true about the STRUCTURE plot for three populations of birds above.
The three populations are genetically distinct
A small amount of gene flow is occurring between the blue and green populations
Genetic drift is strongest in population 1
Populations were defined a priori using STRUCTURE
Assuming equal population sizes, population 3 most likely has the greatest genetic diversity
Population 3 is located between populations 1 and 2 geographically
QUESTION 8
Which of the following does not support Neutral Theory?
The rate of synonymous nucleotide substitutions is generally greater than the rate of nonsynonymous nucleotide substitutions.
The 3rd codon position generally shows a higher substitution rate than the first or second codon positions.
The rate of substitution in non-coding DNA is approximately equal to the mutation rate.
Most nucleotide substitutions in coding regions cause a different amino acid to be made upon translation.
The three populations are genetically distinct
A small amount of gene flow is occurring between the blue and green populations
Genetic drift is strongest in population 1
Populations were defined a priori using STRUCTURE
Assuming equal population sizes, population 3 most likely has the greatest genetic diversity
Population 3 is located between populations 1 and 2 geographically
Explanation / Answer
7. Population 3 is located between populations 1 and 2 geographically .
Assuming equal population sizes, population 3 most likely has the greatest genetic diversity.
8. Most nucleotide substitutions in coding regions cause a different amino acid to be made upon translation.
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