Pitfalls of Character-Based Phylogeny
In “Character-Based Phylogeny”, we asked for the construction of an unrooted binary tree from a consistent character table. However, the assumption of consistency is often inaccurate, as many character collections derived from real data are inconsistent, owing to the fact that the reinforcement of mutations by evolution can cause species to lose features over time, evolve to produce the same character on different evolutionary paths, or revert to a past character. This issue arises even when using genetic characters taken from SNPs, as point mutations can be undone.
As an example of why using characters can lead us astray, let's return to our first example of a character introduced in “Character-Based Phylogeny”. There, we learned that dinosaurs may be divided into the two Orders Saurischia and Ornithischia depending on hip-bone shape: the former have "lizard hips," whereas the latter have "bird hips." Adding to this information the fact that birds are widely believed to descend from dinosaurs, we would guess that birds derive from ornithischians. Yet this is not the case: birds derive from theropods, a suborder of the saurischians! The shared hip bone shape with ornithischians is either simply coincidence or caused by the "convergence" of bird hip shape with that of ornithischians along their different evolutionary paths.
Another example of a character that would be ill-suited for phylogenetic analysis is the presence or absence of wings in insects. Many wingless modern species have evolved from wildly differing ancestors that lost their wings independently of each other.
If we divided a collection of taxa based on either of these characters, many different taxa would be lumped together when they do not in fact share a recent common ancestor, which could have disastrous consequences when trying to assign characters to the splits of a phylogeny.
The moral is that we must select our characters carefully, although the Catch-22 is that we don't know in advance which characters are the most appropriate to use until we actually start constructing phylogenies. At the same time, if we err on the side of caution, then using too few characters might not provide us with enough splits to generate an unrooted binary tree, thus inducing an enormous number of possible phylogenies (recall “Counting Unrooted Binary Trees” and how quickly the total number of trees grows with the number of taxa).
A submatrix of a matrix
Given: An inconsistent character table
Return: A submatrix of
100001 000110 111000 100111
000110 100001 100111