Good source of information about AMOVA I'm looking for a good source of information about Analysis of Molecular Variance (AMOVA), a kind of statistical analysis used in population genetics. Especially how are the $\phi$-statistics calculated and what is the difference compare to F-statistics (fixation index) in measuring the level of differentiation among diffrent population divisions. 
 A: I know you didn't ask for an implementation of it, but the fact that a free one exists in package ade4 for R must be helpful.  The help file references 
Excoffier, L., Smouse, P.E. and Quattro, J.M. (1992) "Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data." Genetics, 131, 479–491.
Which is also cited by Wikipedia and I would guess (not my area) is the definitive reference.
A: There is a nice tutorial on Analysis of Molecular Variance, by Peter Werner, which discusses the use of $F$- or $\phi$-statistics. You may also want to take a closer look at the following paper, for a more complete overview:

Meirmans PG. Using the AMOVA framework to estimate a standardized
  genetic differentiation measure. Evolution. 2006
  60(11):2399-402.

To add to Peter's response, there's a nice "add-on" to ade4 for genetic data: adegenet, and AMOVA is also available in the pegas R package. 
A: I was interested in the same problem and here is link for the best sourse I found then. There is also nice example, what is missing in many other sources about AMOVA.
