Introduction

We've already encountered $\pi$, the nucleotide diversity in a population, namely

$$\pi = \sum_{ij} x_ix_j \delta_{ij} \quad ,$$

where $x_i$ is the frequency of the $i$th haplotype and $\delta_{ij}$ 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.