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:
http://theropoddatabase.blogspot.ca/2015/01/bandit-cladogram-evaluated-james-and.html
http://dml.cmnh.org/2009Apr/msg00230.html
http://dml.cmnh.org/2009Apr/msg00236.html
http://scienceblogs.com/tetrapodzoology/2009/06/08/birds-come-first-hypothesis/#comment-12898
https://www.google.ca/url?sa=t&rct=j&q=&esrc=s&source=web&cd=15&cad=rja&uact=8&ved=0CC4QFjAEOApqFQoTCPHX39mS-MgCFUxWHgod3RMGig&url=http%3A%2F%2Fwww4.ncsu.edu%2F~mhschwei%2FResearch_files%2FMakovicky___Zanno_2011_theropod_diversity_and_avian_characteristics-1.pdf&usg=AFQjCNFFUYs0N4rfq2F8aGPuSQSnEumwdw&sig2=cKMU3Gu8JjB9YDNvGjDDFQ&bvm=bv.106674449,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.
CARPUS
ReplyDeletehttp://www.nature.com/articles/nature08124.epdf?referrer_access_token=1LIOYM249T2ALXmHhUVXQtRgN0jAjWel9jnR3ZoTv0NAxxXDTxDgb7tt7vNCs5i7CDx_p1E8pIL0dPMGIw0CIZ1LRnUZIDT1a3FIDY_UW4FRwpODRDVwWg-KbK448VK63yIXiGAa_H8fA42yVK8TsNhr_ASjWKKTbM-PJCMVzpKKElR4FEstewHl9DZGaHr9&tracking_referrer=www.nature.com
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
Ascending process
ReplyDeletehttp://www.nature.com/articles/nature08124.epdf?referrer_access_token=1LIOYM249T2ALXmHhUVXQtRgN0jAjWel9jnR3ZoTv0NAxxXDTxDgb7tt7vNCs5i7CDx_p1E8pIL0dPMGIw0CIZ1LRnUZIDT1a3FIDY_UW4FRwpODRDVwWg-KbK448VK63yIXiGAa_H8fA42yVK8TsNhr_ASjWKKTbM-PJCMVzpKKElR4FEstewHl9DZGaHr9&tracking_referrer=www.nature.com
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
375. Calcaneum (Rauhut 2003, character #219 ): (0) without facet for tibia; (1) well-developed facet for tibia present
DeleteJ&B:
ReplyDeleteExcluded 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
matrix.
J&B:
ReplyDeleteA 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
tarsus
http://www.jstor.org/pss/4085810
ReplyDelete"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)
Basipterygoid
ReplyDelete12. 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).
http://www.nature.com/articles/nature08124.epdf?referrer_access_token=1LIOYM249T2ALXmHhUVXQtRgN0jAjWel9jnR3ZoTv0NAxxXDTxDgb7tt7vNCs5i7CDx_p1E8pIL0dPMGIw0CIZ1LRnUZIDT1a3FIDY_UW4FRwpODRDVwWg-KbK448VK63yIXiGAa_H8fA42yVK8TsNhr_ASjWKKTbM-PJCMVzpKKElR4FEstewHl9DZGaHr9&tracking_referrer=www.nature.com
381. Shape of pterygoid articulation with basipterygoid process (Carrano and Sampson, 2008, #54): 0 tab-like 1 acuminate
J&B:
ReplyDeleteA 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).
Martin et al 1980
ReplyDeletehttps://sora.unm.edu/sites/default/files/journals/auk/v097n01/p0086-p0093.pdf
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
2009 study
ReplyDeletePalate
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
J&B:
ReplyDeletePalate:
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
(1999).
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.
(2002).
56. Posterior maxillary sinus cup shaped: absent
(0); present (1). Modified from Chiappe
(2002a).
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
(1999).
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).
Xu Xing
ReplyDeletehttp://www.ivpp.cas.cn/qt/papers/201403/P020140314389417822583.pdf
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
http://www.indiana.edu/~ensiweb/din.bird.html
ReplyDeleteWell, 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.
http://figshare.com/articles/Reweaving_the_Tapestry_A_Supertree_of_Birds/976113
ReplyDeleteGenerally speaking there are the following areas:
ReplyDeleteOutgroup selection
Alternate interpretations of characters
"Maniraptors" as SECONDARILY flightless members of PARAVES
http://www.talkorigins.org/faqs/dinosaur/bird_and_frog_development.html
ReplyDelete"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."
http://www.talkorigins.org/faqs/dinosaur/bird_and_frog_development.html
ReplyDelete"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:"
Excellent summary chart (Xu Xing)
ReplyDeletehttp://ars.els-cdn.com/content/image/1-s2.0-S0960982213005125-gr2.jpg
A Jurassic ceratosaur from China helps clarify avian digital homologies
ReplyDeletehttp://www.nature.com/articles/nature08124.epdf?referrer_access_token=1LIOYM249T2ALXmHhUVXQtRgN0jAjWel9jnR3ZoTv0NAxxXDTxDgb7tt7vNCs5i7CDx_p1E8pIL0dPMGIw0CIZ1LRnUZIDT1a3FIDY_UW4FRwpODRDVwWg-KbK448VK63yIXiGAa_H8fA42yVK8TsNhr_ASjWKKTbM-PJCMVzpKKElR4FEstewHl9DZGaHr9&tracking_referrer=www.nature.com
http://www.nature.com/ncomms/2015/151113/ncomms9902/full/ncomms9902.html#ref23
ReplyDeletePublished 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.
http://www.nature.com/ncomms/2015/151113/ncomms9902/full/ncomms9902.html#ref-link-65
ReplyDeleteRather, it is part of the late fusion events leading to the composite tibiotarsus of birds.
ReplyDeletehttp://books.google.ca/books?id=8QRKV7eSqmIC&pg=PA75&lpg=PA75&dq=pretibial+pterosaur&source=bl&ots=fqR5hPhEFg&sig=xdj1IoSLh3AX8At1DunGPoPXYQ8&hl=en&sa=X&ei=Ly9VVMjZDdGeyASIy4LABQ&ved=0CC0Q6AEwBA#v=snippet&q=pterosaurs%20are%20even%20more%20bird-like%20and%20have%20frequently&f=false
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.
Carpus
ReplyDeletehttp://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001957
"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. "