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Re: bat origins - the smoking gun: guidelines



As I've said in previous and future papers, the key to finding the
ancestor to any taxon ? or to nest enigma taxa ? is to remember these
three things:

1. PAUP nests everything. So you're going to get an answer. It may not
be the right answer or the best answer because some taxa have, in the
past, been nested by default. But that can be avoided as much as is
currently feasible by having a broad spectrum taxon list.

2. Taxon selection is everything. PAUP not only needs taxa to work with
in order to provide suitable sister taxa, it also needs slots to place
questionable/enigma/ancestral taxa into. A larger spectrum of taxa
brings greater assurance that you've covered all the bases and provided
a sufficient spectrum of slots. New discoveries should drop be able to
drop right in without affecting the branching sequence. New disoveries,
in this case, will certainly add resolution.

I say 'taxon selection is everything', but that is really true only
after a certain minimum number of characters are employed from every
corner of the body,  I found that 150 will get you 95% there and 225
will provide well.

3. Avoid suprageneric taxa like the plague. Essentially this either
creates chimaera taxa in an attempt to fill matrix boxes or it ignores
and overlooks important variations within. It also presumes monophyly
where none or only some may really exist. Try to stay with species or
specimens if possible. Put the labels on after the analysis is complete
and all sister taxa bear familial resemblances.

The study of the ancestry of bats has suffered from all of the above.

If you do all these things, not only will you get the best known sister
taxon to a particular taxon, but you will see the series leading up to
it.

David Peters
St. Louis