BIOL 600 Bioinformatics: Population Genetics, Human Disease, and Genetic Drift 

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• Words: 3000

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Part A. The basics of HWE.

Q1. There are two alleles, A and a, at the locus MX2. The ‘A’ allele is dominant to ‘a’. At Duquesne there is a

population of 9,344 students. The frequency of A, p, is 0.75 and the frequency of q is 0.25. Assuming HWE at this gene, what would you predict the number of students is with each of the possible genotypes:

Students at Duquesne with AA: _________

Students at Duquesne with Aa: ___________

Students at Duquesne with aa: ___________

Part B. Applying HWE to estimate carriers for a disease.

Every child born in the US is tested for a disease called Phenylketonuria.

Q2. What is PKU? Provide a brief description of the disease. Why are all babies in the US screened for PKU?

Q3. PKU is inherited in recessive mendelian pattern. This means that individuals born with PKU are a homozygotes for the recessive allele that causes this disorder. If the frequency of PKU in the US is 1:25,000 and we assume this is similar at Duquesne, how many students at Duquesne are potentially carriers for this disease? Show how you solved this.

Part C. Effect of Genetic Drift on Allele Frequencies

Go to the website app that models allele frequencies over generations in HWE. On the lefthand upper part of the page, you are going to use following number of individuals specified in the table below. In each of these, the starting frequency of the alleles is p = 0.5 and q = 0.5. Double click in the number cells and type in the correct number, then hit ‘set up’, then ‘go forever’ to start simulation. Click ‘go forever’ again to = stop the simulation at 500 generations (does not have to be exact, try to get as close to 500 as you can), then in the three tables below record the exact generation you ended on, the frequency of the recessive homozygotes f(aa). if one of the alleles was fixed before 500 generations, look up the number that happened for that run in the allele frequency plot with your mouse.  Finally, calculate both allele frequencies p and q. Repeat simulations 5 times for each population size below.

Total Population Size: 128 individuals

MalesAA: 16, Aa: 32, aa: 16	FemalesAA: 16, Aa: 32, aa: 16	Generations simulation stopped	F(aa)	p	q	If fixation occurred prior to end of run, what generation did that happen
Replicate 1
Replicate 2
Replicate 3
Replicate 4
Replicate 5
	Mean

 

 Total Population Size: 64 individuals

MalesAA: 8, Aa: 16, aa: 8	FemalesAA: 8, Aa: 16, aa: 8	Generations simulation stopped	F(aa)	p	q	If fixation occurred prior to end of run, what generation did that happen
Replicate 1
Replicate 2
Replicate 3
Replicate 4
Replicate 5
	Mean

 

 Total Population Size: 32 individuals

MalesAA: 2, Aa: 4, aa: 2	FemalesAA: 2, Aa: 4, aa: 2	Generations simulation stopped	F(aa)	p	q	If fixation occurred prior to end of run, what generation did that happen
Replicate 1
Replicate 2
Replicate 3
Replicate 4
Replicate 5
	Mean

 

Q4. After watching these simulations, why is the effect of small population size on allele frequencies called ‘genetic drift’?

 

Q5. What is the relationship between population size and how rapidly the allele frequencies change? Where does this come from?

 For REF… Use:#getanswers2002570