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Re: Lü and Li 2006, a review

1. Well, the choice of the outgroup taxa dooms the base of this study
from the start. Pterosaurs are lizards, not archosaurs as shown by a
cladistic analysis 2 to 14 times larger and more inclusive than any
prior attempt at classifying amniotes.

Your study, on the other hand, is heavily biased towards extant squamates, while failing to include the autapomorphies of extant squamate clades, and at the same time failing to exclude size- and ontogeny-related characters. I'm not saying the outgroup choice of Lü & Li is automatically a good thing -- I'm just saying you can't state as a fact that it's wrong.

Hey, even if you're right, the chosen outgroups are not part of the ingroup clade.

2. 34,000 most parsimonious trees were found and that's because the
limit of the Max Tree was set at 34,000. Wow. That should be a huge
red flag that something is rotten in this tree and more work needs to
be done.

A large number of MPTs* must be expected when there are less than twice as many characters as taxa. This could be a problem.

* BTW, this is not the same as a consensus tree that is phylogenetic grass.

3. As usual, the highly derived pterosaur, Rhamphorhynchus, is shown
to be the sister group to the classic 'Pterodactyloidea' when anyone
with an eyeball would be hard-pressed to find a synopomorphy or two
uniting the two.

Several are published...

In an unpublished cladistic analysis of greater breadth,
Rhamporhynchus is a highly derived dead end leaving no progeny

What? Does this mean you haven't understood the difference between an ancestor and a sister-group? ~:-| _Nobody_ has _ever_ claimed *R.* had any known descendants!!!

5. No tiny pterosaurs (typically known from numbers rather than
names) were included, which also screws up the results royally.

To the contrary. Every single tiny pterosaur I'm aware of is a baby.