Monday, November 2, 2015

Unjustifiable assumptions of homology
Unjustifiable assumptions of homology incorporated
into data matrices.—The most glaring example of
this problem is the coding of avian and theropod
manual, carpal, and tarsal characters as if they were homologous, despite the ambiguity of the data, and despite the assumption this coding entails that
the BMT [birds are maniraptor theropods] hypothesis is correct a priori. 
Because of the above ambiguities, these five
sets of characters [the palate, the basipterygoid process, the carpus, the manus, and the tarsus] cannot be coded for birds and theropods without unjustified assumptions of
homology. They were not included in the primary
analysis of our matrix. This decision is
understood to be especially controversial, so
we have documented our reasoning, which was
based on careful review of the anatomical evidence,
in Appendix 3.

Criticisms of the James and Pourtless study:,d.cWw

James and Pourtless excluded the characteristics that are in dispute. That is impartial.
The critics object to that. The critics want things scored their way.



    280. Ossified carpals: (0) absent; (1) present (Personal observation, but may appear in some ceratosaur matrices) 281. Lateral proximal carpal (ulnare?) (Kirkland et al, character #145; certain taxa scored from character 231 of Smith et al 2007 supplementary info): (0) quadrangular; (1) triangular in proximal view 282. "Semilunate" distal carpal (Modified from Rauhut 2003, character #146): (0) absent (same as state (0) for Rauhut 2003 #146): (1) present (code as (1) for Rauhut 2003 #146: states (1), (2) or (3)) 283. Two distal carpals (Kirkland et al, character #146; certain taxa scored from character 232 of Smith et al 2007 supplementary info): (0) in contact with metacarpals, one covering the base of Mc I (and perhaps contacting Mc II) , the other covering the base of Mc II; (1) two distal carpals not present, single distal carpal capping Mc I and II 284. Distal carpals (Kirkland et al, character #147): (0) not fused to metacarpals; (1) fused to metacarpals, forming carpometacarpus

  2. Ascending process

    361. Bracing for ascending process of astragalus on anterior side of distal tibia (Rauhut, 2003, character #207): (0) distinct 'step' running obliquely from mediodistal to lateroproximal; (1) bluntly rounded vertical ridge on medial side; (2) anterior side of tibia flat
    367. Astragalus and calcaneum (Kirkland et al, character #191): (0) condyles indistinct or poorly separated; (1) distinct condyles separated by prominent vertical tendinal groove on anterior surface 368. Astragalus and calcaneum*2 (Kirkland et al, character #195; Sereno et al 1996; certain taxa scored from character 327 of Smith et al 2007 supplementary info ): (0) separate from tibia; (1) fused to each other and to the tibia in late ontogeny 369. Fibular facet on astragalus (Rauhut 2003, character #213): (0) large and facing partially proximally; (1) reduced and facing laterally or absent 370. (ordered) Height of ascending process of the astragalus (Rauhut, 2003 #215; certain taxa scored from character321 of Smith et al 2007 supplementary info): (0) lower than astragalar body; (1) higher than astragalar body; (2) more than twice the height of astragalar body 371. Shape of ascending process of the astragalus (Kirkland et al, 2005 #193): (0) tall and broad, covering most of anterior surface of distal end of tibia; (1) short and slender, covering only lateral half of anterior surface of tibia; (2) tall with a medial notch that restricts it to lateral side of anterior face of distal tibia 372. Ascending process of astragalus (Rauhut, 2003, character #216; also Kirkland et al, character #194; certain taxa scored from character 322 of Smith et al 2007 supplementary info; Originally from Welles and Long 1974): (0) confluent or only slightly offset from astragalar body; (1) offset from astragalar body by a pronounced groove

    1. 375. Calcaneum (Rauhut 2003, character #219 ): (0) without facet for tibia; (1) well-developed facet for tibia present

  3. J&B:
    Excluded from the primary analysis of our matrix were elements of
    the palate, the basipterygoid process, the carpus,
    the manus, and the tarsus, together accounting for
    the exclusion of 18 characters (characters 12–15,
    63–65, 148–156, and 196–197) used in the CNM

  4. J&B:
    A total of 21 characters were turned on for the alternative
    analysis: 1 character for the basipterygoid
    process, 5 characters of the palate, 14 characters
    of the carpus and manus, and 1 character of the

    "The structure of the avian tarsus has recently been cited as evidence for the derivation of birds from theropod dinosaurs. Although birds and theropods have a long triangular ossification in front of the tibia and attached to the proximal tarsals, the morphological relationships of this bone are fundamentally different in the two groups. In modern birds and in all Mesozoic birds, this "pretibial" bone is a high, narrow structure associated primarily with the calcaneum, but independently ossified. The corresponding structure in dinosaurs is a broad extension [ascending process] of the astragalus" [The astragalus is also called the talus bone].
    (L.D. Martin et al)

  6. Basipterygoid

    12. Basipterygoid processes ventral or anteroventrally projecting (0) or lateroventrally
    projecting (1).
    13. Basipterygoid processes well developed, extending as a distinct process from the base of
    the basisphenoid (0) or processes abbreviated or absent (1).
    14. Basipterygoid processes solid (0) or processes hollow (1).
    15. Basipterygoid recesses on dorsolateral surfaces of basipterygoid processes absent (0) or
    present (1).

    381. Shape of pterygoid articulation with basipterygoid process (Carrano and Sampson, 2008, #54): 0 tab-like 1 acuminate

  7. J&B:
    A structure homologous with the true basipterygoid
    process of reptiles is apparently absent
    in both modern birds and crocodylomorphs,
    though the underlying cartilages from which a
    true basipterygoid process would develop are
    present, which complicates assessments of homology
    (McDowell 1978, Walker 1990).

  8. Martin et al 1980

    Just above the tarsus of Archaeopteryx, a thin sheet of bone is closely appressed
    to the tibial shaft. Ostrom has described this bone as an "ascending process of the
    astragalus"a nd homologizedi t with a correspondings tructurei n the theropod ankle.
    Although there has been some recent speculation that this process is a calcite deposit
    on the Archaeopteryx slabs, there can be little doubt that this structure is bone (it
    glows under ultraviolet light, while the calcite does not) and that it is present in the
    same position in at least the London, Berlin, and Eichsfiitt specimens. In modern
    birds this process appears rather late in development, after the fusion of the proximal
    tarsals, as a long triangular cartilage in front of the lateral side of the distal end of
    the tibia and just above the calcaneum( Fig. 1F, I). After ossification,i t fusesw ith
    the proximal tarsus, the distal end of the tibiotarsus. A brief description of this bone
    is given by Morse (1872: 12-16) and Wyman (in Morse 1872: 11-12), who termed
    it the "pretibial" bone. Subsequent workers, familiar with the similar structure in
    dinosaurs, termed it the "astragalar process" (Baur 1883; Osborn 1900; Heilman
    1926; Ostrom 1975a, 1976a).

    We think that the pretibial bone of birds and the ascending process of the theropod
    dinosaur astragalusa re nonhomologousI.n theropodst he processi s a broad extension
    of the astragalus, which covers much of the anterior face of the tibia (Fig. 1D).
    In contrast, the pretibial bone of birds is a separate ossification on the lateral side
    of the tibia. When it fuses to a joint-forming tarsal, it always fuses to the calcaneum
    (outer condyle), although some contact may be made with the more medial astragalus.
    It is the last tarsal cartilage to appear in the developing embryo. The pretibial
    bone can be clearly seen in the tibiotarsus of the Lower Cretaceous Enaliornis
    (where it may not completely fuse to the tibia, even in adults) and in the Upper
    Cretaceous toothed birds Hesperornis and Baptornis (Fig. 1H). In these birds, in
    contrast to the astragalus of theropod dinosaurs, it is a high, narrow ossification
    associated primarily with the calcaneum. These differences in placement and its late
    appearance during development suggest that it is a uniquely derived character for
    birds and is properly termed a pretibial bone, rather than an astragalar process.
    Ostrom (1976a) has described the tarsus of Archaeopteryx as identical with that

  9. 2009 study
    364. Skull roof dorsoventral thickness (Carrano and Sampson, 2008, #18): 0 thin, relatively flat 1 thickened 365. Skull roof ornamentation (Carrano and Sampson, 2008, #19)(ordered): 0 none

  10. J&B:
    223. Palatine: without elongate maxillary process
    (0); with elongate maxillary process (1).
    224. Palatine: without “hook-shaped” process
    enclosing choana (0); with process (1).
    225. Palatine: without broad pterygoid wing (0);
    with broad pterygoid wing (1).
    226. Palatine: tetraradiate with jugal process (0);
    triradiate without jugal process (1).
    227. Pterygoid: without basal process (0); with
    basal process (1).
    52. Vomers: not fused (0); fused anteriorly (1).
    Gauthier (1986).
    53. Palatal teeth: present (0); absent (1). Benton
    54. “Secondary palate”: no distinct “secondary
    palate” (0); “secondary palate” short (1);
    “secondary palate” extensive (2).
    55. Maxilla, palatal shelf: flat (0); with midline
    ventral tooth-like projection (1). Clark et al.
    56. Posterior maxillary sinus cup shaped: absent
    (0); present (1). Modified from Chiappe
    57. E ctopterygoid: present with no jugal “hook”
    (0); attached to jugal by a distinctly “hooklike”
    process (1); present but not attached
    to jugal (2); absent (3). Modified from Elzanowski
    58. E ctopterygoid, position: ventral to or level
    with transverse flange of pterygoid (0);
    dorsal to transverse flange of pterygoid (1).
    Modified from Sereno and Novas (1993).
    59. E ctopterygoid: no fossa on ventral surface
    (0); fossa on ventral surface (1). Modified
    from Clark et al. (2002).
    60. E ctopterygoid: no fossa on dorsal surface (0);
    fossa on dorsal surface (1). Clark et al. (2002).

  11. Xu Xing
    we identify the three manual digits of Xiaotingia
    and other maniraptorans as II-III-IV, rather than as I-II-III as in
    many other studies8

    Well, what methods and tests are the anti-theropod critics using? Not cladistics: they do not use cladistics, because every time someone does a cladistic analysis, birds come out most closely related to theropod dmosaurs. The critics often admit their aversion to cladistics, but even when they do not, their papers speak for them: not a single real cladogram has appeared in any of their works.


  14. Generally speaking there are the following areas:
    Outgroup selection
    Alternate interpretations of characters
    "Maniraptors" as SECONDARILY flightless members of PARAVES

    "Now this is a complication for evolution. We have three-fingered dinosaurs, and three-fingered birds, but it looks like they aren’t the same fingers. Bird ancestors would have had to resurrect their discarded Digit IV, then eliminate Digit I, all before fusing the whole assemblage into a bony gemisch anyway. It’s not parsimonious at all."

    "The answer is that there are two developmental processes going on. The first is the formation of the condensations, CI through CV. This process partitions the terminal region into an appropriate number of chunks, but doesn’t actually specify the identity of the digits. The second process takes each of those chunks and assigns a digit identity to them, and this process is to some degree independent of the first and uses a different set of signals. Wolpert et al. have noticed this in modern embryos:"

  17. Excellent summary chart (Xu Xing)

  18. A Jurassic ceratosaur from China helps clarify avian digital homologies

    Published 13 November 2015
    The anklebone (astragalus) of dinosaurs presents a characteristic upward projection, the ‘ascending process’ (ASC). The ASC is present in modern birds, but develops a separate ossification centre, and projects from the calcaneum in most species. These differences have been argued to make it non-comparable to dinosaurs. We studied ASC development in six different orders of birds using traditional techniques and spin–disc microscopy for whole-mount immunofluorescence. Unexpectedly, we found the ASC derives from the embryonic intermedium, an ancient element of the tetrapod ankle. In some birds it comes in contact with the astragalus, and, in others, with the calcaneum. The fact that the intermedium fails to fuse early with the tibiale and develops an ossification centre is unlike any other amniotes, yet resembles basal, amphibian-grade tetrapods. The ASC originated in early dinosaurs along changes to upright posture and locomotion, revealing an intriguing combination of functional innovation and reversion in its evolution.

    Rather, it is part of the late fusion events leading to the composite tibiotarsus of birds.


    Page 75
    Further complicating the issue, tibiotarsi of a variety of pterosaurs are even more bird-like and have been frequently misidentified as bird fossils.

  22. Carpus
    "The combined data provide compelling evidence of a remarkable evolutionary reversal: A large, ossified pisiform re-evolved in the lineage leading to birds, after a period in which it was either absent, nonossified, or very small, consistently escaping fossil preservation. The bird wrist provides a modern example of how developmental and paleontological data illuminate each other. "