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.

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#### Best Answer

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.

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