Hardy Weinberg

Weidii

Hey, I've been having trouble sorting this question out and I'm wondering if anyone can point me to a website that explains how do do it...

"In an experimentla population of Drosophilia, a sample of males and virgin females includes 66 A1A1, 86 A1A2 and 28 A2A2 flies. Each genotype is represented equally in both sexes and each can be distinguished by eye colour. Determine the allele and genotype frequencies and whether or not the locus is in Hardy-Weinberg equilibrium"

I understand the Hardy Weinberg principal, but I'm not sure how to determine the allele and genotype.

Weidii

In a study of individual oysters (Crassostrea gigas) that were homozygous and
heterozygous for the Sod 1 and Sod 2 alleles of the superdismutase locus, the
following results were obtained.

Genotype Sod1Sod1 Sod1Sod2 Sod2Sod2

Numbers of individuals 60 331 129

(I stuck the colours in to make it easier to see the corresponding numbers)

a. What are the frequencies of the three genotypes?
b. What are the frequencies of p and q?
c. What is the value of the χ2 test statistic?
d. Are the oysters in Hardy-Weinberg equilibrium?
e. What is the probability of getting the value of the test statistic that you
calculated by random chance if the population is in Hardy-Weinberg

equilibrium?


There's a similar one that I'm having trouble with. Any advice would be great.

adamski8

i would have been able to answers these questions easily a few years ago but now ive forgotten. they arent hard if you get shown it a few times. Any genetics book would show examples of these problems if you can get access from a college library

liberal

Weidii wrote: »

In a study of individual oysters (

Crassostrea gigas) that were homozygous and
heterozygous for the Sod 1 and Sod 2 alleles of the superdismutase locus, the
following results were obtained.

Genotype Sod1Sod1 Sod1Sod2 Sod2Sod2

Numbers of individuals 60 331 129

(I stuck the colours in to make it easier to see the corresponding numbers)

a. What are the frequencies of the three genotypes?
b. What are the frequencies of p and q?
c. What is the value of the

χ2 test statistic?
d. Are the oysters in Hardy-Weinberg equilibrium?
e. What is the probability of getting the value of the test statistic that you
calculated by random chance if the population is in Hardy-Weinberg

equilibrium?


There's a similar one that I'm having trouble with. Any advice would be great.

right so ted,

p2+2pq+q2= 1 (p2= p squared, q2= q squared)

A.

Total oysters = 60 +331 + 129 = 520


Frequency of S1S1 = 60/520 = 0.115

Frequency of S1S2 = 331/520 = 0.637

Frequency of S2S2 = 129/520 = 0.248


B.

Now you know the following

p2 = 0.115 and q2 = 0.248

so p = the square root of 0.115 = 0.335

and q = the square root of 0.248 = 0.498

C. I can't answer

D.

put in the figures you've calculated into the equation!

p2+2pq+q2=1

(0.115)+2(0.335)(0.498)+(0.248) = 0.696

that's not close enough to 1, they oyster population does not satisfy the HW equation.

E. I can't answer


Hopefully some one will check my answers

Weidii

Thanks so much, that's a great help.

darjeeling

Weidii wrote: »

In a study of individual oysters (

Crassostrea gigas) that were homozygous and
heterozygous for the Sod 1 and Sod 2 alleles of the superdismutase locus, the
following results were obtained.

Genotype Sod1Sod1 Sod1Sod2 Sod2Sod2

Numbers of individuals 60 331 129

(I stuck the colours in to make it easier to see the corresponding numbers)

a. What are the frequencies of the three genotypes?
b. What are the frequencies of p and q?
c. What is the value of the

χ2 test statistic?
d. Are the oysters in Hardy-Weinberg equilibrium?
e. What is the probability of getting the value of the test statistic that you
calculated by random chance if the population is in Hardy-Weinberg

equilibrium?


There's a similar one that I'm having trouble with. Any advice would be great.

For (C), you take the p and q frequencies calculated in (B), and work out the expected genotype counts in a population of 520 individuals if there were completely random mating. The counts will be given by (p^2) * 520, 2pq * 520 and (q^2) * 520. You then use a chi squared test to compare the observed and expected counts and come up with the value of the chi statistic.

For (D) and (E), I'd compare the chi statistic from (C) with the chi distribution under the number of degrees of freedom you have (1 in this case). If there's less than a 5% chance of getting a Chi stat as large as the one seen, then you reject HWE. You can go on to find the exact probability of getting an HWE chi statistic as large as your observed one.

This wikipedia page actually shows you the whole calculation, including the calculation of the chi test statistic.


Edit:

I've just had a look over the answer above for (B).

To calculate p and q, you can't just use the HW formula (p^2 + 2pq + q^2 = 1) and take the square root of each homozygote frequency, as this is assuming that the population is in HW proportions - the very thing we want to test. Assuming that p = sqrt (freq(S1S1)) and q = sqrt (freq(S2S2)) gives you values of p=0.34 and q = 0.5. Clearly these don't add to 1, as p and q must.

Instead, you have to calculate p by knowing that each S1S1 oyster has 2 S1 alleles, each S1S2 oyster has 1 and each S2S2 oyster has 0.

Doing this:
p = ( 2*count(S1S1) + 1*count(S1S2) + 0*count(S2S2) ) / 2* (total oysters) =( (2*60) + 331 ) / (2*520) = 0.434.

Similarly, q = 0.566.

And now p + q = 1

Weidii

Thanks for your time, much appreciated. I've scoured a few web pages on this too and I think I am getting the hang of it.

Kevster

C. gigas? I used to crack open those bad boys by the hundred last summer in my job at the Marine Institute. 'Shucking', I believe it's caklled.

flynny51

I think For the chisq and probability you need to use R.

What is the probability of getting the value of the test statistic that you
calculated by random chance if the population is in Hardy-Weinberg equilibrium?

http://www.r-project.org/