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Re: was ... Jaime. Now: M. Baeker has a problem with phylogenetic analysis

----- Original Message -----
From: "David Peters" <davidrpeters@earthlink.net>
Sent: Monday, June 19, 2006 7:03 PM

If you find it too difficult to come up with an adult/juvenile pterosaur
pairing, go to the literature and see what forms Wellnhofer and Bennett
have promoted as adults and parents of the same genotype. Then expand
the universe of taxa to include all pterosaurs and you'll find that
rather than matching parents, the so-called 'juveniles' actually form
series that fill phylogenetic gaps between taxa. It's not an isolated
incident. Happens about six times.

I still don't understand why you act as if PAUP* could tell you if an OTU is adult or juvenile. It can't.

As you are fond of saying, PAUP* nests everything. If you would put "Archaeoraptor" into a theropod matrix, it _would_ come out somewhere. I can't predict if it would find itself in a polytomy with *Microraptor* and Euornithes, but I bet it would not turn the entire tree into phylogenetic grass. Probably it would come out close to *Yanornis* with the tail as a reversal -- would be great if someone with a bit of time on their hands could test this.

> Fledglings usually *do not* look like parents.

In pterosaurs they do, as embryos tell us.

The features necessary for flight indeed do: the ratio of wing finger length to wingspan does not change in ontogeny, the ratio of hindlimb length to wingspan does not change in ontogeny, and the pterosaurs in the eggs have wing loadings that fall into the range of adult pterosaurs. (Source for all: Unwin's talks last week.)

But that's not all. It is completely inevitable that small pterosaurs have relatively larger eyes and brains than big ones; this is a relationship that holds throughout at least the vertebrates (where eyes are present) and can very easily be explained by the way vertebrate ontogeny works. The ossification of tarsals and small phalanges is delayed compared to the flight apparatus. Then there's bone histology -- only adults have an external fundamental system.

Chiappe and Co. told us one embryo was Pterodaustro because
it was found with and looked like adult Pterodaustro.

Not precisely, though.

More details revealed it to be an anurognathid.

On the third day of the congress we had excursions to the natural history museum and the geology museum. There I saw most of the feathered dinosaur specimens I knew from the literature (and then some -- there are apparently unpublished specimens of *Sinornithosaurus* on display). It turns out that despite the good photos in National Geographic I had got some 3D relationships wrong. Do you remember how I lamented that the middle portion of the tail feathers of *Protarchaeopteryx* had not been prepared and was still lying under rock? Nonsense. The white patch is not the overlying but the underlying layer. The tip of the bony tail of *P.* is, if anywhere, on the counterslab, which is not on display (let's hope it still exists). Do you remember how I lamented that the feathers on the snout tip of NGMC 91 had not been prepared free? Again the feathers are a layer above, not below, the rest of the slab; if there were feathers on the tip of the snout, they are on the counterslab, to which the same comments apply. The same holds for the snout of the holotype of *Sinosauropteryx*.

Lesson: To claim anything based on a photo requires even more care than I had thought.

Take-home message: I don't see the slightest reason to believe your tracing that "revealed it to be an anurognathid".

>> Just include all pterosaurs and let PAUP find the relationships.
> It can't if you plug in units (specimen or species) *that differ in
> more than just phylogeny*.

Example please.

Well, it _can_, but only by chance, that is, if you happen not to have too many size- or ontogeny-dependent characters in your matrix.

Example: *Iberomesornis*. Sure you remember all the cladograms from the 1990s that had

    `--Euornithes (not named yet)

based on several convincing features, like the presence of only 5 sacral vertebrae in *I.* (like in Archie) vs 8 in Enantiornithes and 9 upwards in Euornithes, or the lack of fusion in its metatarsi. Then came Sereno and showed (long paper, badly accessible journal) the specimen was a juvenile enantiornithean. Oopsie. Guess why I will never put *Liaoxiornis*, or "*Cathayornis caudatus*", into my bird matrix, even after having seen 2 or 3 specimens in museums.

Phylogeny is easier than you think.

Phylogenetics is more complicated than you think.