[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index][Subject Index][Author Index]

Re: smallest pteros

David Marjanovic wrote-

> Warning!!! I don't know about MacClade, but PAUP* automatically interprets
> "-" as a gap -- as a deletion in a molecular sequence (respectively as an
> insertion in the other taxa). _Never_ put this symbol into a purely
> morphological data matrix!!! You will get bogus results.

Is that so?  Does PAUP treat a gap as a state that can group taxa together?
Because I've been using '-' as 'inapplicable' in my coelurosaur analysis
this whole time.  Let's see what replacing it with '?' does to the tree.

> Which means that the tree published in the description of *Junggarsuchus*
> _is_ bogus. OK, it's probably not, but the tree length is probably wrong,
> should be all support values and indices.

And the Theropod Working Group's matrices, which recently have used '-' for
'unknown' in some taxa as well.  Holtz's (2000) analysis only used '?', so
seems fine.

Jaime Headden wrote-

> >   This is why I am skeptical of find only one single tree, because even
> > with only 1% missing data in a 70 taxon, 175 character tree (making
> > data fields, 1% of these as missing is going to result in over a 120
> > "unknown" conditions for the whole, and that WILL influence the tree
> > structure with every variation the program attempts to find for all

True, but one coded character _can_ be enough to place a taxon unambiguously
in PAUP.  So there's no assurance x% of unknown data will lead to x many

Mickey Mortimer
Undergraduate, Earth and Space Sciences
University of Washington
The Theropod Database - http://students.washington.edu/eoraptor/Home.html