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Re: Clarification of scope of paleoart->uses



On 16 March 2011 22:37, David Marjanovic <david.marjanovic@gmx.at> wrote:
>>  For my cladistic analysis, i lay out everyone else's matrix and then
>>  toss those characters that, somehow, i determine to be most
>>  unrelable.
>
> Don't.
>
> There's no reason to throw out any characters that aren't
> parsimony-uninformative (and even those don't actually hurt);

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.

The less obvious reason is that one of the ways a character can be
parsimony-uninformative is if it occurs in only a single taxon.  In
this case, it doesn't help you figure out the phylogeny, but it DOES
tell you something that's distinctive about the taxon in question
compared with the next largest clade that it's a member of.  It's part
of the differential diagnosis of that taxon.

One of the reasons that Wilson (2002) is still in many respects a more
useful sauropod phylogeny that than other that have appeared since,
some with far larger matrices, is that it has whole delicious
appendix, on pages 271-276, that lists autapomorphies for all the taxa
in the analysis.  [To be fair, Upchurch et al. (2004) also did this,
but editorial style imposed the unhelpful decision that the
autoapomorphies had to be sprinkled through the text and described in
prose rather than telegraphically.]  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.

So: don't throw data away.