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An AMOVA example

Excoffier et al. [1] illustrate the approach by presenting an analysis of restriction haplotypes in human mtDNA. They analyze a sample of 672 mitochondrial genomes representing two populations in each of five regional groups (Figure 2). They identified 56 haplotypes in that sample. A minimum spanning tree illustrating the relationships and the relative frequency of each haplotype is presented in Figure 3.

Figure 2: Locations of human mtDNA samples used in the example analysis (from [1]).
\resizebox{!}{6cm}{\includegraphics{amova-sample-locations.eps}}

Figure 3: Minimum spanning network of human mtDNA samples in the example. The size of each circle is proportional to its frequency (from [1]).
\resizebox{!}{6cm}{\includegraphics{amova-haplotypes.eps}}

It's apparent from the figure that haplotype 1 is very common. In fact, it is present in substantial frequency in every sampled population. An AMOVA using the minimum spanning network in Figure 3 to measure distance produces the results shown in Table 1. Notice that there is relatively little differentiation among populations within the same geographical region ( $\Phi_{SC} = 0.044$). There is, however, substantial differentiation among regions ( $\Phi_{CT} = 0.220$). In fact, differences among populations in different regions is responsible for nearly all of the differences among populations ( $\Phi_{ST} = 0.246$). Notice also that $\Phi$-statistics follow the same rules as Wright's $F$-statistics, namely

\begin{eqnarray*}
1 - \Phi_{ST} &=& (1 - \Phi_{SC})(1 - \Phi_{CT}) \\
0.754 &=& (0.956)(0.78) \quad ,
\end{eqnarray*}

within the bounds of rounding error.3


Table 1: AMOVA results for the human mtDNA sample (from [1]).
Component of differentiation $\Phi$-statistics
Among regions $\Phi_{CT} = 0.220$
Among populations within regions $\Phi_{SC} = 0.044$
Among all populations $\Phi_{ST} = 0.246$



next up previous
Next: An extension Up: Analysis of molecular variance Previous: Analysis of molecular variation
Kent Holsinger 2010-12-13