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Recoded Aves introduces a lot of fog?



I hope this qualifies as "constructive" criticism... :-)

>       It appears that "Enigmosauria" is not even paraphyletic, but
> polyphyletic.

I'll parrot the question... "why?" If you are going to publish, please tell
us, so that we might shut up in good conscience; if you don't but
nevertheless have evidence, please tell us the evidence then -- it is the
very intention of science that every attempt to burn it down be made (it,
not you, of course); I'll rather not mention the third theoretical
possibility.

>      It is my conclusion that strict parsimony has led them astray, and
that
> they will not discover more accurate avian phylogenetic topologies without
> some form of character weighting (as many of the characters they are using
> are non-independent).

Well. In the molecular world it is possible to weight. It is possible
(though probably pretty expensive) to measure how much more or less likely,
in percent, it is that an A in the 2nd position in a codon mutates into a C
than into a G than into a T. In the morphological world... we'd love to have
such a possibility, wouldn't we?

>      My refined (simplified) definition of Aves is now:    All theropods
> possessing (1) a convex coracoid glenoid, and (2) an enlarged fused
> "semilunate" in adults.

Suppose you find a fossil that would overall fit at the base of your Aves,
has a convex coracoid glenoid, but no Real True Semilunate. You'll say,
fine, that's the sister group to Aves (unlike you expand the definition once
more). Suppose you then find another fossil which would overall fit in the
same position, has a Real True Semilunate, but a beautifully concave
coracoid glenoid. Wouldn't that blow up your definition? I suggest to escape
this problem by using only one character in an apomorphy-based definition
(if at all), like the PhyloCode seems to assume but not to mention
specifically.

> Note:  the first is reversed in at least one genus
> (Phasianus), and the distinctive shape of the second is partially reversed
> in Protarcheopteryx and Caudipteryx.

Reversals, on the other hand, can't endanger an apomorphy-based definition.

> I doubt that Alvarezsaurus will be
> put back in (but it is so scrappy, who knows).

Suddenly it's too scrappy? :->

> Many of the character
> distributions are beginning to make a whole lot more sense.

You still think evolution makes sense? :->

First of all, do I correctly interpret your classification, which seems to
line up badly in places, as the following? I can much more easily think in
images than in number codings:

Aves
|--Troodontidae
|  inc. sed. *Bagaraatan*
`--<Archaeopterygiformes>
    |--+--Dromaeosauridae
    |   `--"'utahraptorid' family"
    `--+--*Pyroraptor*
        `--+--+--*Bambiraptor*
            |     `--Velociraptoridae
            `--+--*Sinornithosaurus*
                |--?*Unenlagia*
                `--+--*Microraptor*
                    `--+--*Rahonavis*
                        `--+--*Archaeopteryx*
                         </Archaeopterygiformes>
                            `--+--*Yandangornis*
                                |--?*Sapeornis*
                                `--+--Mononykiformes
                                    |    |--*Patagonykus*
                                    |    `--+--*Parvicursor*
                                    |        `--*Shuvuuia*
                                    `--+--*Avimimus*
                                        `--+--*Protarchaeopteryx*
                                            `--+--+--*Caudipteryx*
                                                |     `--*Nomingia*
                                                `--+--Caenagnathiformes
                                                    |    |--*Microvenator*
                                                    |
`--+--Caenagnathidae
                                                    |
`--+--Oviraptoridae
                                                    |            `--+--you
forgot *Ingenia* AFAIK
                                                    |               `--great
carnival joke
                                                    |--?*Protopteryx*
                                                    `--+--*Longipteryx*
                                                        `--+--*Jibein_i_a*
                                                           |--?*Hulsanpes*

`--+--+--*Boluochia*
                                                              |
`--Iberomesornithiformes

`--+--+--Enantiornithiformes
                                                                 |
`--Gobipterygiformes
                                                                 `--[well,
Euornithes]

If so, then I'm interested in the following questions:

> CLASS AVEA (AVES)
>   1  Plesion Troodontidae
>   ?  Pl. Bagaraatan

Why *B.* here?

> 1  Dromaeosauridae
>            B  "utahraptorid" family
> 2  Pl. Pyroraptor
> 3  Pl. Bambiraptor
> B  Velociraptoridae

Why do you put *Pyroraptor* here?

> 6  Pl. Rahonavis
> 7  Archaeopterygidae

Now that's odd compared to all what I've seen so far. Why do you think so?

>            8  {{expanded "Metornithes"}}
> _1_ Yandangornithiformes
>   ?  Pl. Sapeornis

Very strange places for both *Yandangornis* and *Sapeornis*. The latter is
almost obviously the sister group of Pygostylia.

>   2  Mononykiformes Kinman, 1994
> 1  Patagonykidae
> 2  Parvicursoridae
>            3  Mononykidae

And where is *Shuvuuia*? Last time I read it was still in a trichotomy:

--+--*Alvarezsaurus*
   `--+--*Patagonykus*
       `--+--*Parvicursor*
           |--*Shuvuuia*
           `--*Mononykus*

How do you code trichotomies, actually?

>   3  Avimimiformes
>   4  Pl. Protarcheopteryx
>   5  Pl. Caudipteryx

*Avimimus* more basal than they all? *P.* and *C.* outside of
Oviraptorosauria?

>   B  Pl. Nomingia
> 6 Caenagnathiformes Cracraft, 1971
>            1  Pl. Microvenator
>            2  Caenagnathidae
>            3  Oviraptoridae

Oviraptorosaurs closer to Pygostylia than dromaeosaurs? I happen to like it,
but *Yandangornis* and *Sapeornis* are anyway closer still, and segnosaurs
are apparently amazingly birdlike.

> ?  Pl. Hulsanpes

Has the same distinctive shape of metatarsal III as Pygostylia, *Sapeornis*
and *Yandangornis*... OK, it's not so distinctive, at least *Sinornithoides*
almost has it likewise, at least in caudal view, but *H.* is certainly not a
troodontid.

> 9  Pl. Boluochia
> B  Iberomesornithiformes
> 10  Enantiornithiformes
> B  Gobipterygiformes

What's the difference between the latter two? What is
Iberomesornithiformes -- just the toothed forms?

> 15  Hesperornithiformes
> 16  Ambiortiformes
> 17  Ichthyornithiformes

Where would *Potamornis* fit? Why are Ambiorti- and Ichthyornithiformes
arranged this way?

Thanks a lot for information!