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Re: Clarification of scope of paleoart->uses



 I'd go further. I think it's important to retain
 parsimony-uninformative characters for two reasons.

 The obvious one is that, if someone goes on to build on your matrix,
 the new taxa they add may make the previously uninformative
 characters informative.

That's not a reason to already have them in the matrix.

 [...] The autapomorphies in Wilson's list are of two kinds: those
 that are homoplastic in the phylogenetic analysis, and which are
 therefore autapomorphic only in specific cladograms; and others that
 were not included in the analysis. The appendix's introduction
 doesn't spell it out, but I am guess that many if not all of these
 were discovered as parsimony-uninformative characters.

This, too, is not a reason to keep such characters in the matrix.

Keeping them in has disadvantages. It makes your matrix appear bigger than it is (...impressive as it is, of the 720 characters in the supermatrix by Sigurdsen & Green [2011] only 335 are informative; no surprise, because they only kept those 25 taxa, out of something like 110 or 120, that are represented in all three input matrices...), and it increases the CI. Fine, PAUP* will give you the CI with and without parsimony-uninformative characters, but it seems to be normal to report the former instead of the latter and thus make the trees look more robust than they are. And of course, the bigger a matrix, the more opportunities there are for glitches.