Estimation of genetic distance - (Sep/20/2006 )
Dear all,
Can somebody explain these to me
the calculation of genetic diversity foa a lucus is given by:
h= 1- Sigma Xi^2 [n/(n-1)].
i understand this "h= 1- Sigma Xi^2" well. But why we need [n/(n-1)] ?
Best regards
Hi,
If you're calculating Genetic diversity as heterozygosity then for a locus it is calculated as h = 1 − Σ xi2 [n/(n-1)], where:
xi is the frequency of the ith allele at the locus
n is the number of isolates in the sample
n/(n-1) is a correction factor. This is required to allow for normalisation, you can see examples of this in binomial distributions....Durbin et al
Hope this helps
Dear sara,
Thank you for your explaination. I greatful.
I have another question to ask.
- If I have a bacteria collection of 15 isolates
- And it is homogenous for locus A.
Therefore, Xi2 will be = 1.
- n/(n-1) = 15 / (15-1)
= 15/14
= 1.07
- h = 1 − Σ xi2 [n/(n-1)]
= 1 - 1(1.07)
= - 0.07 (negative value)
This negative value will increase if the n is smaller.
So how to explain heterogenecity which is negative value?
Thank you
The number of isolates that you have is very small and that's why you're getting a negative value. If you have a large number of isolates (say in the region of 50 or so) then h, will be very small anyway. But since you have too little data, your h value is bound to give negatives, making it statistically insignificant.
I think average heterozygosity (h) is generally 0.2 or less but there's a bias introduced by a small sample size. This figure varies in different species. In many lizard species, the average heterozygosity is of the order of 0.06. Therefore, the expected magnitude of the bias when a single individual is sampled from each of the two species to be compared is about 0.03
Have a look at this reference on HETEROZGOSITY AND GENETIC DISTANCE. It's pretty out of date but lays some principal foundations in this area.
Nei, M. 1978. Estimation of average heterozygosity and genetic distance from a small sample of individuals. Genetics 89:583-590
Hope my explanation is satisfactory
Good Luck!
Sara
Dear Sara,
Thank you very much for your clear explaination.
It makes me a lot clearer now.
Best regards