Re: Clarification of scope of paleoart->uses

[David Marjanovic <david.marjanovic@gmx.at>]

>  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.