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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.