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Re: a closer look at L[ü] and Ji 2006

(Lu and Lü are not pronounced the same.)

keeping the Triassic forms at the base, morphologically
and chronologically where they belong.

I can't judge the morphological part, but... chronologically, it's certainly nice if the Triassic forms are at the base, but do we know whether the fossil record is complete enough that we should expect this?

the various late Jurassic Rhamphorhynchus species

A growth series. JVP 2 or 3 years ago, bone histology: there is such a thing as immature *Rhamphorhynchus* in the fossil record.

When six Dorygnathus are used in a cladogram, instead of one as in
prior works,

Make sure you only use adults, and if most or all of them are, make sure you aren't dealing with a morphologically polymorphic species (that's the difficult part).

you find that the short-toothed Donau specimen is basal
to the more derived wicked-toothed forms,


Off the top of my head, this sounds like the latter are adult...

The Dorygnathus more precisely known as SMNS 50164 has a tiny
pterosaur as its sister taxon, TM 10341. When this pterosaur is included
(which it is not in Lu and Ji 2006) not-so-tiny Beipiaopterus is strongly
attracted to it [...]


Put baby and adult apes in the same cladogram, and it will be screwed up.

What is your criterion for declaring a pterosaur adult?

[...] Angustinaripterus, long touted as a good transitional form between
'rhamphorhynchoids' and 'pterodactyloids' but strangely missing from
this analysis, and as I look back -- all other recent analyses. What
happened to our star quarterback? Put him back into the game and see
what happens!


I agree.

which seems as unlikely as pairing a spoonbill with a woodpecker. 

Galápagos finches... screamers and ducks...

Pterorhynchus is strongly attracted to Sordes, but so far has left no
sister taxa. Where is Pterorhynchus in these latest studies? Nowhere.


Bad.

Again, remember, this doesn't happen in a cladogram with tiny
pterosaur exclusion. In other cladograms you get confusion and 34,000+ MPTs.

That's not because the actively misleading babies are excluded, it is because there are far too few characters in that analysis -- not even twice as many as taxa.

Another sister to No. 9 is No. 12 which has a longer and noticeably
sharper rostrum. It begets all of the sharp-nosed pteros,

Surely you mean it is the sister-group of the clade formed by "all of the sharp-nosed pteros"?

It is difficult for me to understand how Germanodactylus can be so
far removed from (azhdarchids (not including Q. and Co.)) +
(nyctosaurs + pterandons)) + (tapejarids + dsungaripterids), but
that's how Lu and Ji show it.


Well, what autapomorphies does that clade have according to Lü and Ji?

It just takes more taxa and more characters and all the confusion
melts away.

John J. Wiens, Ronald M. Bonnett & Paul T. Chippindale: Ontogeny Discombobulates Phylogeny: Paedomorphosis and Higher-Level Salamander Relationships, Systematic Biology 54(1), 91 -- 110 (2005)

Abstract, all emphasis mine:
"Evolutionary developmental [sic] bioloby ('evo-devo') has revolutionized evolutionary biology but has had relatively little impact on systematics [i. e. phylogenetics]. We show that similar large-scale developmental changes in distantly related lineages can dramatically mislead phylogenetic analyses based on morphological data. Salamanders are important model systems in many fields of bioogy and are of special interest in that many species are paedomorphic and thus never complete metamorphosis. A recent study of higher-level salamander phylogeny placed most paedomorphic families in a single clade based on morphological data. Here, we use new molecular and morphological data to show that this result most likely was caused by the misleading effects of paedomorphosis. We also provide a well-supported estimate of higher-level salamander relationships based on combined molecular and morphological data. Many authors have suggested that paedomorphosis may be problematic in studies of salamander phylogeny, but this hypothesis has never been tested with a rigorous phylogenetic analysis. We find that the misleading effects of paedomorphosis go BEYOND the sharing of homoplastic larval traits by paedomorphic adults, and the problem therefore is NOT solved by simply excluding suspected paedomorphic characters. INSTEAD, two additional factors are critically important in causing paedomorphic species to be phylogenetically 'misplaced': (1) the ABSENCE of clade-specific SYNAPOMORPHIES that develop during metamorphosis in nonpaedomorphic taxa and allow their 'correct' placement and (2) parallel adaptive changes associated with the aquatic habitat of the larval stage. Our results suggest that the effects of paedomorphosis on phylogenetic analyses may be COMPLEX, DIFFICULT TO DETECT, and can lead to results that are BOTH WRONG AND STATISTICALLY WELL SUPPORTED by parsimony and Bayesian analyses."

The last sentence says that the absence of confusion -- such as the finding of a single MPT in an analysis -- is no evidence for the result being correct, not even if it is full of bootstrap support values of 100 %.

As a remedy the authors suggest to code paedomorphic taxa as "?" for _all_ ontogeny-influenced characters, including lots of body proportions and the like. This throws away quite a lot of potential information, but it successfully rids the matrix of (one) false signal.

For pterosaurs, you can most probably ignore problem (2), but problem (1) is there, screaming loudly, and you must either deal with it somehow or get a wrong tree (or both).

Unfortunately I can't help you getting this paper -- I don't have access to the pdf, I only have a photocopy.