Did you keep *Euparkeria* as the outgroup?
Yes, in keeping with Nesbitt/Irmis.
Because that's what the outgroup is in the Nesbitt et al. paper (Irmis is the 2nd author). If you run an analysis where *Allosaurus* and *Huehuecuetzpalli* are part of the ingroup and *Euparkeria* is the outgroup, you have to _expect_ getting random garbage as a result.
Exactly my point. The pterosaurs are ALSO ingroup taxa and, as you suggest, the Nesbitt/Irmis studies are "getting random garbage as a result. "
Especially if there are no characters in the matrix that are informative for large-scale diapsid phylogeny.
I followed Nesbitt/Irmis changing nothing but adding taxa in a TEST of their work.
Remember: if you don't explicitly specify an outgroup, PAUP* uses the first (topmost) OTU as the outgroup.In this case, you'd either have to use *Huehuecuetzpalli* as the outgroup or add a non-crown-diapsid outgroup to the matrix.
Which means you have to KNOW something about the entire spectrum of amniote relations before embarking on making your taxon list. Not just follow the paradigm.
The paradigm needs testing. David Peters St. Louis