Dear Nora

The Nei and Shannon-Weaver within population variation indices are reviewed in the following paper.

Hi,

What is important is to have some quantitative estimate of the genetic diversity within a population, in order to be able to compare it with other population(s) or to monitor the diversity in the future. Nei's within-population diversity is easier for interpretation and is more widely used, while Shannon diversity index was "borrowed" from the Information theory and applied to ecology and genetic data. Also, a relatively good measure is the effective allele number (a reciprocal of homozygosity). There is a huge amount of literature and the researcher sometimes gets lost. But again, one does not estimate the within-population diversity per se, but with the aim to compare different populations and to monitor diversity. So, why not using one measure as the main one, and the second - as an additional?

Hi Nora,

Anne Chao did a great work about Information theory and Shannon entropies. You can have a look at her most recent papers:

Article Expected Shannon Entropy and Shannon Differentiation between...

http://www.cell.com/trends/ecology-evolution/pdf/S0169-5347(17)30255-0.pdf

Also, depending on the type of markers you have, you might be interested in comparing measures of alpha genetic diversity from several statistical order, as described here (the paper is also very interesting if you want to take a hierarchical structure into account) :

Article Diversity from genes to ecosystems: A unifying framework to ...

Good luck with your analyses :-)

Neis scale for measure gene diversity

Whar are the benifit to use Neis and Shahon information Index

I think Nei's is more specific for genetic diversity assessment while Shannon is more general and is especially used for ecological diversity.

I think there are two ways to count the genetic diversity of populations, first by Nei's Gst and the second by Fixation Genetic Diversity Fst. By using Fst, we can continue with the AMOVA analysis. On the other hand, Shannon's genetic diversity is somehow used together with Nei's Genetic diversity (Gst) in many papers. Then, I think you can use both (Shannon's and Nei's genetic diversity) in your paper.