... reasonable.¹

For those of you who are familiar with molecular phylogenetics as it is usually applied, there's another important difference. Not only are these parsimony networks. They are networks in which some haplotypes are regarded as ancestral to others, i.e., haplotypes appear not only at the tips of a tree, but also at the nodes.

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...Templeton-2004.²

It continues to produce networks in which some haplotypes are ancestral to others, but in this context, such an approach is reasonable. Ask me about it if you're interested in why it's reasonable.

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... challenges.³

When we talk about statistical phylogeography, you'll see an alternative approach to addressing the concerns NCA was intended to address, and for the final project in the course, you'll have a chance to examine a recent debate between proponents of the different approaches and decide which you would apply to your own data.

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... 619).⁴

Makes you wonder a little about why it's called statistical parsimony if some of the reconstructed cladograms aren't parsimonious, doesn't it?

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... substituion.⁵

If you're interested, you can find the formula for restriction site differences in equation (1), p. 620.

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