God Fearing Atheist

Might as well talk about this inbetween commercial breaks.

It's nice to suggest troodontids might be "post urvogels", but its another thing to actually posit a phylogenetic hypothesis, test it, and have your hypothesis corroborated by the character data. So far as I know, none of these things have every been done by Paul (or Larry Martin), and as im sure you're aware, there are a moutain of studies that, without exception, place them basal to birds.

So for me or anyone else to take this suggestion seriously, I need an explicit phylogenetic hypothesis, a test of this hypothesis, and for it to fare better than other hypotheses (that is, be more parsimonious).

Urvogel Reverie

And here we run into fundamental differences between us in philosophy of systematics that are never going to be resolved. I will comment however that Paul has very robustly demonstrated that cladistics will be of limited usefulness in determining patterns of secondary flightlessness in these taxa and there is nothing besides naive belief in the untrammelled perspicacity of cladistics, to suggest that it might. The fact that a strict cladistic interpretation of birds such as Caudipteryx would have it as an animal with no flighted ancestry should well illustrate the point. I have seen the type of Caudipteryx in person and find its morphology entirely consistent with it being a secondarily flightless bird.

Even given these considerations, it is entirely inaccurate to say that there have never been any cladistic analyses of this very problem. What do you call Maryanska et al. (2002)? Moreover, it borders on the disingenuous to assert that only a cladogram-underwritten analysis can be an explicit scientific hypothesis for understanding evolution. Paul's work is explicit, prediction generating, based upon hard morphological data, and is in no way unscientific. Cladists have merey defined the problem raised by Paul's work out of existence in their narrow, assinine dogma, so as to not have to deal with it. They can stick their heads in the sand as does our proverbial ostrich, but the morphological evidence still exists and must be dealt with, and that data is in at least several cases, strongly indicative of secondarily flightless status for several theropod clades. While cladists stick their fingers in their ears and close their eyes and ignore it, the real scientists will be analyzing Paul's arguments and taking a more critical look at our concepts of theropod and bird phylogenesis.

Urvogel Reverie

God Fearing Atheist

Secondary flightlessness can never be established solely through cladistic methodologies, and im unaware of anyone who has ever claimed otherwise. Character distributions are content-neutral when it comes to functional hypotheses.

In any case, my concern was not the "secondarily flightless" in "secondarily flightless post-urvogel bird", but the post-urvogel part. Their being secondarily flightless is a matter distinct from their being more derived than Archaeopteryx.

I see no strong case for this.

I call it irrelevant to what was at issue; Maryanska et al., ignoring problems both at the time of publication (taxon sampling) and since (Incisivosaurus), didnt even include a single troodontid OTU.

To the contrary, Paul's work seems to have all the scientific content of the Feducciary "thecodont hypothesis". To me, there is absolutely no difference between claiming birds are the sister group to some unknown basal archosauromorph/archosaur and Paul claiming maniraptorans on the whole (or some clades in particular) are the sister group to some unknown bird(s). Neither of these are science.

Phylogenetic hypotheses are corroborated and falsified only by synapomorphies, as im sure you'll agree. When your "hypothesis" fails to propose an actual sister group or appeals one that is "currently unknown", it becomes impossible to do either.

On the same subject, I found your statement that "the very behavior described herein may offer corroborative evidence of the Paulian argument that Troodon is a flightless bird" a very strange one. At best, monoautochronic ovulation is a synapomorphy of Oviraptor/Troodon + birds, but coupled with the two functional oviducts in the former, show they're both basal to those birds we have similar reproductive info on.

Urvogel Reverie

I am too tired tonight to put in a decent reply to such an impressive list of cladistic fundamentalist generated bloviation, but tomorrow I'll post something. Congrats (assuming he was rooting for them) on the Sox victory, Sean.

Urvogel Reverie

God Fearing Atheist

But of course. I mock New York and their inferior team.

Jet Black

do you two agree on anything?

Urvogel Reverie

We both vehemently hate creationism and support the veracity of evolutionary biology. We also hate Gould, passionately. And we apparently both like the Sox.

Urvogel Reverie

Urvogel Reverie

I agree and did not intend to regard them as linked in this usage.

There is an abundance of data from the morphology of Caudipteryx which are very difficult to reconcile with any hypothesis that this animals lacks flighted ancestry. First and foremost, let us consider the general morphology of the taxon. With its greatly shortened forelimbs, elongated hindlimbs, and severely abbreviated tail, short, blunt cranium and herbivorous diet, it at least superficially approaches the condition we observe in extant ratite birds (e.g., Struthio). Naturally one would object that this hardly shows Caudipteryx to be secondarily flightless, but it it is worth noting that this distribution of general proportional and morphometric characters is at the same time, concordant with what would be expected if Caudipteryx were a flightless bird.

Upon more detailed consideration of the morphological evidence, the resemblance between Caudipteryx and secondarily flightless, cursorial crown birds such ratites is indisputable. Jones et al. (2000) demonstrated that the hindlimb proportions of Caudipteryx and the center of gravity therein are similar to those in extant ratites. This is in marked contrast to the severe abbreviation of the forelimbs, which renders their explanation as "protowings" (the only feasible explanation if one is to argue that there is no flight ancestry in the phylogenetic history of Caudipteryx) at best problematic (Feduccia 1999, Paul 2002). The presence of fairly robust sternal plates in Caudipteryx combined with the abbreviation of the forelimbs, presence of symmetrical, pinnate feathers, and evidence for a non-arboreal habitus and herbivory, is most plausibly accounted for by flighted ancestry for caudipterygians. Sereno (1999a) argued that as the glenoid is caudoventrally directed, it is unlikely that Caudipteryx is secondarily flightless. However, as Paul (2002) has noted, the glenoid in Caudipteryx is most likely laterally oriented and regardless, there are secondarily flightless birds, which lack lateral glenoid fossae. Thus, Sereno’s objections in this regard must be considered highly dubious.

The minor digit is severely reduced to a splint-like structure supporting the robust and straightened major digit, in a condition more derived than that seen in archaic birds (e.g., Archaeopteryx). An adaptive explanation for such a structure in a form lacking flighted ancestry is practically inconceivable. The tail is reduced in length with but 22 caudal vertebrae. Feduccia (1999), Martin & Czerkas (2000), Zhou et al. (2000) and Paul (2002) all reported a retroverted hallux in Caudipteryx, thus contrary to Chiappe & Dyke (2002) several studies have found such a structure to be present in Caudipteryx. My observation of the Caudipteryx specimens was unable to verify this, although it should be noted that the Caudipteryx material I had the opportunity to inspect was not that reported on by Zhou et al. (2000). The femur is strikingly avian in lacking utterly the fourth trochanter and thus almost certainly Caudipteryx possessed at best a rudimentary caudofemoralis musculature. This pattern is consistent with that observed in secondarily flightless birds, but disparate form that seen in theropods.

The cranium is particularly avian. The foramen magnum opens ventrally (Feduccia 1999, Geist & Feduccia 2000), the contact between the quadratojugal and quadrate is ligamentous (Geist & Feduccia 2000, Ruben & Jones 2000) and the quadratojugal/squamosal contact has been lost (Geist & Feduccia 2000, Ruben & Jones 2000). Chiappe & Dyke (2002) insisted that all of these characters are at best ambiguous and uncertain, but with the possible exception of the, my observation of Caudipteryx confirmed as much. The palate of Caudipteryx includes a rostral secondary palate formed by the premaxillary and maxillary shelves and generally resembles the highly apomorphic bony palate of Oviraptorosauria. The teeth are distinctly avian in morphology.

It is worth further elaborating on the evidence offered by the controversial study of Jones et al. (2000), which has been severely criticized by Chiappe & Dyke (2002). These authors insisted that the theropod material incorporated into the analysis by Jones et al. (2000) is too poorly preserved to permit accurate measurement of postcranial element for morphometric analysis. However, contrary to the sense engendered by these authors, this is not the case for all the taxa used in the analysis offered by Jones et al. (2000) and for e.g., I question the relevance towards the actual argument stressed by Jones et al. that Carnotaurus, is not adequately represented to justify the measurements offered for it. Consider the question: if we removed Carnotaurus would it destroy the conclusion reached by Jones et al? Of course not. I think Sean, you put it as such (paraphrasing): Hardly the Jones et al. killer. The problems with the central data set merely illustrate the need for more accurate and precise analysis of the morphometric data in question; they do not invalidate the conclusion reached by Jones et al. in 2000, they at best render it provisional.

Morevoer Chiappe & Dyke's (2002) review of the arguments adduced in favor of secondarily flightless status for Caudipteryx seems in my opinion to fundamentally miss or deliberately confuse the central point of the paper in question: that both the gross morphology and detailed morphometrics of Caudipteryx are congruent with those of extant secondarily flightless birds. What remains indeterminate is if such data are also congruent with "normal" cursorial theropods. Of course Chiappe & Dyke (2002) utterly fail to mention this, if even to recognize but then dismiss this conclusion upon faith that more accurate and precise morphometric analysis of theropod pelvic limbs will illustrate that Caudipteryx is equally similar thereto.

To demonstrate convincingly that Caudipteryx is not a secondarily flightless bird, or a post-urvogel in the phylogenetic sense, a plausible adpative scenario to explain the non-flight related acquisition of a number of characters and character complexes must be presented. These include the structure of the manus, and the digits therein, the loss of the fourth trochanter and the subsequent drastic reduction in the caudofemoralis musculature, the drastic abbreviation of the tail and pectoral limb, and the retroverted hallux. Until this has been accomplished, the most logical and parsimonious conclusion is that Caudipteryx is a secondarily flightless bird displaying manual and cranial characters which suggest it is more derived than is Archaeopteryx.

What, however, of the immediate objection and favorite refrain of those who would contest this assessment: that Caudipteryx finds itself placed squarely amongst Oviraptorosauria? This leads us to:

I see this as merely convenient dismissal of a perfectly decent cladistic analysis. I seriously question your hostility thereto if Maryanska et al. (2002) had tested the secondarily flightless hypothesis vis-a-vis Oviraptorosauria, and even with these flaws, failed to recover such a topology. Moreover, to maintain which you may or may not be implicitly doing, that the case for oviraptorosaur secondarily flightless (and post-urvogel) status rests solely upon this singular study is absolutely specious.

Paul is not a scientist? This is odd, in that just a few posts before you were quoting him in defense of your statements pertaining to theropod physiology. If he isn't a scientist, you know, you really probably ought not to advance his opinions in defense of your own. Such matters aside however, I want the readers of this thread to take a very close look at the parsed structure of Sean's statement here. When you have done so, it amounts to the statement that anything which is not cladistics, is not science (at least in terms of understanding evolutionary history).

Needless to say such a demarcation criterion never has been and never will be the norm amongst those not deluded by the Sectarian excesses of Hennigian fundamentalism. The failure to engage in rigid cladistic methodology is not sufficient grounds for rendering a hypothesis unscientific. Rather the inability to test a hypothesis has been regarded as the principal and most logical method of demarcating science from philosophy since the work of Popper.

In order to demonstrate that Paul's work, or anyone else's for that matter, is fundamentally not scientific Sean must illustrate that the hypothesis generates no testable predictions which may be falsified or corroborated by new data. Until he has done so, any assertion that the hypothesis in question is not scientific displays nothing more than juvenile redefinition of demarcation criteria to promulgate and defend a narrow, delusional, naive dogma pertaining to the practical applications of researching phylogeny. It can be summarily dismissed as wanting of even the slightest substantiation or meaning until that time.

Moreover it is interesting to note that Sean's statements here seem to indicate the conception that one can only assess shared derived morphological characters within the framework of a cladistic analysis, in that only such a framework can reveal these characters. Such a framework may be helpful, generally speaking and ignoring a number of potential difficulties, in elucidating those patterns but they exist, are discoverable and can be objectively analyzed indepedent of such a framework. For instance, Ostrom at length illustrated what he perceived to be a number of shared derived characters between theropods and birds independent of any cladistic framework, and his research in turn was the foundation of Gauthier's celebrated 1986 recycling of his 1984 thesis. Sean's statements herein reiterate what I stated in an earlier post, that cladists by remaining dogmatically and myopically entrenched within their view of phylogenetic research, can effectively cocoon themselves from any data which question their preconceived hypotheses and the veracity of the cladogram.

Urvogel Reverie

Urvogel Reverie

To demonstrate the point that one can quite contrary to the ridiculous make-believe of Sean, offer shared derived characteristics with which to unite any given taxon to another, I present what seem defensible synapomorphic characters underwriting two potential levels of avian relationship for Troodontidae:

If troodontids are the sister group of all other birds:

1. Teeth with expanded roots.
2. Constriction between tooth crown and root.
3. Oval resorption pit on lingual aspect of root surrounding developing tooth crown and ventrally sealed.
4. Interdental plates absent.

Since multiple aspects of troodontid morphology suggest a more derived position within Aves than that just postulated, it seems best to regard these characters as plesiomorphic and retained from the common ancestor of the sister group of all other birds, and all its descendants (not assumed by default to be Archaeopteryx herein). Rather, the following traits suggest that troodontids are nested well within Aves:

1. Quadrate articulating with braincase.
2. Width of foramen magnum exceeds that of occipital condyle.
3. Trigeminal subdivided within prootic, with accessory foramina present.
4. Contralateral communication of rostral and caudal tympanic diverticulae.
5. Hypoglossal with three distinct foramina in caudolateral braincase floor.
6. Opthalmic branch of the trigeminal with separate exit on rostral surface of laterosphenoid.
7. Supraoccipital hollow.
8. Vagus and and spinal branch of the accessory nerve issue from shared ganglion within a deep pit on the internal surface of the braincase.
9. Metotic laterally sealed forming a veritcal slit.
10. Grooves for the glossopharyngeal vein and nerve pass across the metotic strut.
11. Basisphenoidal recess absent.
12. Secondary foramen for protractor nerve present lateral to foramen for opthalmic branch of the trigeminal within the laterosphenoid.
13. Pneumatic recesses within basisphenoid/parasphenoid caudoventral to pituitary fossa.
14. Olfactory tract severely reduced

These characters are shared with at the very least pygostylian birds, and thus strongly argue for the post-urvogel status of Troodontidae. The most favorably comparisons come with Enaliornis and Hesperornis. Given that such a preponderance of character data render convergence an unlikely explanation, it seems most parsimonious to argue that troodontids are secondarily flightless birds, occupying a level within the standard topology of the class Aves well beyond that of Archaeopteryx, as the urvogel lacks most if not all (the interpretation of some in Archaeopteryx remains contentious) of these characters. Alternative arguments for the non-avian status of Troodontidae would require the parallel acquisition of these characters, for which it is difficult to envision any credible scenario accounting for their convergent appearance.

Urvogel Reverie

God Fearing Atheist

You're going to need to quantify each of those pieces of "general morphology" for me, and tell me what clade they're supposed to be synapomorphic of (again, my concern is their "post-urvogel" status, not their secondary flightlessness).

No they didnt. More on this below.

Quantify this, and tell me what clade its supposed to be synapomorphic of.

Huh? Their sternal plates are unfused, lacking carinae, and smaller than the coracoids.

This seems question begging, as Chiappe & Dyke point out. Also, asymmetry is predicted to be derived in Prum's model.

Isnt a "non-arboreal habitus" symplesiomorphic in theropods?

Like in other oviraptorsaurs, therizinosaurids and ornithomimosaurs?

Synapomorphic of what clade?

Synapomorphic of what? Caudipteryx + Pygostylia?

Caudipteryx does not show the MT I torsion associated with hallucal retroversion. Even if it was preserved on the posterior of the other metatarsals (which I see no evidence for), this would have been achieved postmortem.

Absence or reduction of the fourth trochanter is known in troodontids, dromaeosaurids, and oviraptorosaurs as well.

The braincase isnt sufficently preserved to make that call.

The preservation is not sufficent to tell, but it wouldnt matter anyway (a loose suture is known in dromaeosaurids, and ligamentous contact was described in other oviraptorosaurs).

Refered specimens (e.g. Zhou & Wang 2000) show this to be false.

Hows that? What clade are these dental characters synapomorphic of?

Its not just Carnotarsus (though it is very strange to give measurments for a part of the body that we have no data on). Afrovenator doesnt have an MT III. Yangchuanosaurus and Staurikosaurus dont have metatarsi at all. Its chock full of inaccurate measurments taken from models, illustrations or photographs (tibial lengths of Velociraptor and Dilophosaurus are way off, for example), redundancy (the Albertosaurus of Jones et al. is actually a specimen of Gorgosaurus, and Gorgosaurus is included as well), rejection of potentially problematic specimens (Sinornithoides and Bambiraptor) on grounds of ontogeny, but the inclusion of others with similar "problems" (e.g. their Ceratosaurus). We also have to take into account recent finds, like Sinornithosaurus and Microraptor.

Lets also not forget Christiansen and Bonde's 2004 reexamination of their paper, which, by using accurate measurments from real specimens, came to exactly the opposite conclusion. To quote myself:

No. Phylogenetic hypothesis are not dependent on how convincing one finds a particular exaptive or adaptive scenerio. Phylogenies -- Caudipteryx's "post-urvogel" status -- depend on synapomorphies and synapomorphies only.

More later...when im up to it.