Testing Hardy-Weinberg equilibrium

[@daisukye]

So clearly explained! Can you please put more topics about Genetics? I surely can suggest you some that I want. Our whole college will watch your videos I bet.

[@jonathanr2323]

Life saver! I wish my professors were at least half as good as you are

[@davidbala436]

Very well explained! However, it’ll be nice to explain how the Chi-Square value was derived: perhaps in another video. Thanks!

[@himanshibakshi7304]

Thank you so much. This really helped me understand better!

[@hildamwila9217]

So helpful. Thanks

[@yuralee4953]

so clear!! thanks!

[@mingmingcui8381]

Hi, it's nice to stumble onto your video. It's well explained. I have a question here. In the video, a single gene/allele is considered. How about we have multiple genes and we take the mean p and q values, then how do we perform the significant test for HWE? Since it's mean values, I wonder if we can use a t-test for expected and observed heterozygosity in this situation rather than chi-squared test for expected and observed numbers of genotypes.

[@SciEdSusan]

Hi Mingming, you would need to assume each gene has its own p & q values. Like R and r, and then also T and t: there will be a p value for R and also another p value for T. If you're trying to think about observed and expected values for RRTT individuals vs Rrtt (for example), you'd want to use the Multiplicative Rule - that is, when we want to know the frequency of individuals with RR AND TT genotypes, we multiply the the frequencies together (like p-squared[R] * p-squared[T]). For Rr AND tt genotypes, multiply 2pq[R] * q-squared[t]. Then you would still compare observed vs expected values with a chi-squared test.

[@SciEdSusan]

Might want to check out this video for more info on probability rules: kzbin.info/www/bejne/qKiWmniOmc5ri9E

[@mingmingcui8381]

Thank you for your reply. In my case, I need to deal with thousands of genes. Gene diversity (ie, expected heterozygosity) is one of the most important indices for population genetics. The equation to calculating this index is to calculate 2pq for each gene and takes the mean value over the thousands of genes. Since we have an observed mean heterozygosity and an expected mean heterozygosity, I'm not sure about which statistic test to use.

[@zaidalsaialy6588]

Thanks

[@hopesale5614]

Question: Hardy-Weinberg is asking if the frequency of the alleles are going to change in respects of p and q? So you said that the population is not in HW equilibrium because you get a different number of individuals that are homozygous dominant, heterozygous, and homozygous recessive. But if you find the p and q of the expected number, you still get p= 0.72 and q= 0.28. So wouldn't the population actually be in Hardy-weinberg equilibrium?

[@SciEdSusan]

Hi Hope, good observation! Really, HWE states “genotype frequencies in a population remain constant between generations in the absence of disturbance by outside factors”…so it was inaccurate of me to say that we’re looking for a change in allele frequency (p and q). We’re really looking for a change in p-squared, 2pq, and q-squared. Check out this video for a little more on how to check the difference in genotype frequencies using chi-squared testing: kzbin.info/www/bejne/hJyxYpt6g7N5qdE

[@danielcaley522]

I don't understand where 0.52 and 0.08 come from. Would you not take the square root to solve for p and q?

[@SciEdSusan]

0.52 and 0.08 are the expected homozygous genotype frequencies for RR and rr, given the current allele frequencies p & q. We calculate p-squared (freq of RR) by squaring p (allele freq of R) and q-squared (predicted freq of rr individuals) by squaring q (allele freq of r).

[@RuJoe720]

@@SciEdSusan I'm not sure what I'm missing here but something is just not computing for me :(

[@SciEdSusan]

​@@RuJoe720 There are a couple of questions we can ask using the HWE ideas. A common one is, if you know how many white (homozygous recessive rr) individuals there are in a population, then figure out p & q (the allele frequencies of R & r). In that case, usually you DO just take the square root of rr to get q! Here, we’re asking, given all three genotype frequencies, can we figure out if the population is in HWE? So first we calculate p & q, and since we are NOT assuming this pop is in HWE, we include the heterozygotes in the calculation. (We’re not assuming HWE bc we’re trying to test for HWE!) Then, once you have p & q, now you can calculate the expected or predicted values for each genotype, and compare them with what we already have observed in our population, to see if expected = observed. Hope this helps!

[@honorsenvisci2012]

To do similar problems, would the trait have to have incomplete or codominant alleles? It seems if simple dominance, one would not know if RR or Rr and then cannot continue.

[@SciEdSusan]

Hi Jennifer, the trait doesn’t have to be incomplete or co-dominant - but you do have to know how many of the dominant phenotype individuals are RR and how many are Rr. In real life, it’s relatively easy to do this by sampling the DNA. For practice problems, I say, “Scientists have determined that 90 of the red individuals are RR and 35 of the red individuals are Rr. All 25 of the white individuals are rr.” Hope this helps!