AMOVA and Statistical phylogeography

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. We’ll see later that AMOVA can be used very generally to partition variation when there is a distance we can use to describe how different alleles are from one another, but for now, let’s stick with nucleotide sequence data for the moment and think of δij simply as the fraction of nucleotide sites at which two sequences differ.