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Re: Pterosaur.net

 What was especially problematic about Hone and Benton (2008) is that
 their matrix contains repeated taxa.  For instance, Lepidosauromorpha
 is an OTU, but so are Gephyrosaurus, Sphenodontia and Squamata (which
 ARE Lepidosauromorpha).  Similarly, Choristodera is an OTU, but so
 are Champsosaurus, Laz[a]russuchus and Cteniogenys (which ARE
 Choristodera).  By itself, this only indicates laziness or taxonomic
 unfamiliarity on the authors' part, but what's disturbing is that the
 lepidosauromorphs do not clade with Lepidosauromorpha, and the
 choristoderes do not clade with Choristodera.  Instead, choristoderes
 form a clade which is closer to other archosauromorphs than
 Choristodera (with 100% bootstrap support).  Similarly,
 lepidosauromorphs form a clade two nodes more derived than
 Lepidosauromorpha (with Youngin[...]a in between them, both nodes
 supported with 100% bootstrap values).  So if the supermatrix
 couldn't get lizards to clade with themselves, what's the liklihood
 it got pterosaurs to clade with their real sister taxon?

What the vertical gene transfer.

I haven't read the paper (the JSP isn't easy to get, it's too expensive for most libraries), so I better not make any categorical statements... but... if the above is the whole story, the paper is a stomach-cramping, gut-wrenching failure of peer-review. I must have missed _something_. Please, someone set me straight. Please.