Blackwell Publishing

The reconstruction of phylogeny - How is molecular evidence used?


The parsimony method

A number of statistical techniques can produce an unrooted tree from a set of molecular sequences. We shall concentrate on the parsimony method. It is done in 3 stages:

1. Align the sequences from the various species. This is actually quite difficult: with sequences of more than 100 nucleotides, regions will usually have been deleted during evolution in some species and added to others, such that the sequences of the different species do not simply align.

2. Given a set of aligned sequences, the principle of parsimony with molecular sequences follows the same procedure as with morphological characters. We write out all the possible phylogenies and count the minimum number of events implied by each.

3. The polarities of the changes are needed to find the root of the unrooted tree. Unlike morphological work, only outgroup comparison can be used with molecular evidence. We therefore look for the sequence in a closely related species and see which branch in the unrooted tree it corresponds most closely to.

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