Analysis of molecular variance (AMOVA)

ij xixjδij , where xi is the frequency of the ith haplotype and δij is the fraction of nucleotides at which haplotypes i and j differ. It shouldn’t come to any surprise to you that just as there is interest in partitioning diversity within and among populations when we’re dealing with simple allelic variation, i.e., Wright’s F -statistics, there is interest in partitioning diversity within and among populations when we’re dealing with nucleotide sequence or other molecular data. Let’s stick with nucleotide sequence data for the moment.