Wednesday, August 27, 2014

"Non-avian dinosaurs"

Worth repeating:

What does "non-avian dinosaur" mean?

The phrase "non-avian dinosaurs" crops up in many articles. What does it mean? As we see below it means Dinosauria minus Aves. It lumps in the basal paraves, the primitive flying and primitive secondarily flightless birds, with the real dinosaurs such as Tyrannosaurus - all of them under the same label - "non-avian dinosaur". In other words, it lumps in basal paraves with actual dinosaurs. 

"Now consider the group consisting of the non-avian dinosaurs (which is what people usually mean by the informal term ``dinosaurs''). This is a paraphyletic group, because it can't be defined simply as ``this animal plus all its descendants'', but must be described as one clade minus another: in this case, Dinosauria minus AvesThe ``non-avian dinosaurs'' make up a singly paraphyletic group because only one clade need be omitted from its base definition."

"it was not until the early 1990s that clearly nonavian dinosaur fossils were discovered with preserved feathers. Today there are more than twenty genera of dinosaurs with fossil feathers, nearly all of which are theropods. "
"By the 1990s, most paleontologists considered birds to be surviving dinosaurs and referred to 'non-avian dinosaurs' (all extinct), to distinguish them from birds (aves)."

AND notice these variations:

"Recent studies by Varricchio et al. reveal that males cared for the eggs of troodontids and oviraptorids, so-called "non-avian theropods" of the Cretaceous".

"The smallest non-avialan theropod known from adult specimens is the troodontid Anchiornis huxleyi, at 110 grams in weight and 34 centimeters (1 ft) in length.[3] "

I will talk about why this is a problem in the next post. 

Another claimed "feathered dinosaur" (2)

Continuing the analysis of Kulindadromeus:

http://en.wikipedia.org/wiki/Kulindadromeus
The second type is represented by groups of six or seven downwards projecting up to 1.5 centimetres long filaments, together originating from a base plate. These are present on the upper arm and thigh. They resemble the type 3 feathers of theropods. The base plates are ordered in a hexagonal pattern but do not touch each other.
However, a claim of anything beyond "type 1 feathers" (that are actually bristles) is beyond the evidence, as confirmed by the supplementary material.

From the supplementary material:
http://www.sciencemag.org/content/suppl/2014/07/23/345.6195.451.DC1/Godefroit.SM.pdf
We considered attempting to describe the feather morphotypes in Kulindadromeus using the nomenclature of Prum et al. (52, 53) or of Xu et al. (21, 22). However, except for our monofilaments (which correspond well to Type 1 in Xu et al.), we could not assign with confidence the other two feather morphotypes in Kulindadromeus to categories described by Prum et al. or Xu et al. Further, fundamental discrepancies between these two previously published nomenclature systems remain to be resolved. Thus we felt that until new fossil material and a synthesis of existing nomenclature systems are available, interpretations of direct homologies between complex feather-types in Kulindadromeus and in Prum et al. or Xu et al. would be premature.

This quote expresses exactly what I am saying:
http://reptilis.net/2014/07/31/new-siberian-ornithischian-and-the-over-feathering-of-dinosaurs-again/#more-1079
So I find it quite strange and disheartening that Godefroit et al.—despite being fairly objective in their supplementary material—go completely gung-ho in calling these structures feathers.

Tuesday, August 26, 2014

Another claimed "feathered dinosaur"

Let's begin with an accumulation of material about Kulindadromeus:

http://en.wikipedia.org/wiki/Kulindadromeus
Kulindadromeus is a feathered, herbivorous dinosaur, a basal neornithischian from the Jurassic of Russia. Its integument is evidence for the trait being basal to Dinosauria as a whole, rather than just to Coelurosauria, as previously suspected.
Kulindadromeus is significant in that the various specimens show large parts of its integument. This includes imbricated rows of scales on top of its tail and also a covering of scales branching into feather-like structures, which until its discovery were thought to be exclusive to the Theropoda, of the saurischian-line.[5] The feather remains discovered are of three types, adding a level of complexity to the evolution of feathers in dinosaurs.[4] The first type consists of hair-like filaments covering the trunk, neck and head. These are up to three centimetres long and resemble the stage 1 "dino-fuzz" already known from theropods like Sinosauropteryx. The second type is represented by groups of six or seven downwards projecting up to 1.5 centimetres long filaments, together originating from a base plate. These are present on the upper arm and thigh. They resemble the type 3 feathers of theropods. The base plates are ordered in a hexagonal pattern but do not touch each other. The third type is unique. It was found on the upper lower legs and consists of bundles of six or seven ribbon-like structures, up to two centimetres long. Each ribbon is constructed from about ten parallel filaments up to 0.1 millimetres wide.[1]
Godefroit et al. concluded that the filaments earlier reported in Ornithischia, with Psittacosaurus and Tianyulong, could be homologous to the "protofeathers" found in non-avian theropods. With known feather-like structures in pterosaurs, there is evidence for it being basal to Ornithodira.

http://www.sciencemag.org/content/345/6195/451.abstract
A Jurassic ornithischian dinosaur from Siberia with both feathers and scales
Middle Jurassic to Early Cretaceous deposits from northeastern China have yielded varied theropod dinosaurs bearing feathers. Filamentous integumentary structures have also been described in ornithischian dinosaurs, but whether these filaments can be regarded as part of the evolutionary lineage toward feathers remains controversial. Here we describe a new basal neornithischian dinosaur from the Jurassic of Siberia with small scales around the distal hindlimb, larger imbricated scales around the tail, monofilaments around the head and the thorax, and more complex featherlike structures around the humerus, the femur, and the tibia. The discovery of these branched integumentary structures outside theropods suggests that featherlike structures coexisted with scales and were potentially widespread among the entire dinosaur clade; feathers may thus have been present in the earliest dinosaurs.
http://news.nationalgeographic.com/news/2014/07/140724-feathered-siberia-dinosaur-scales-science/
The scales on Kulindadromeus resemble the scaly skin seen on some birds, the study says, which also argues for a deep genetic root linking dinosaurs to birds.
Two earlier ornithischian dinosaur discoveries, both from China, had hinted that featherlike bristles had covered dinosaurs, notes paleontologist Stephen Brusatte of the United Kingdom's University of Edinburgh.
"But the new Siberian fossils are the best example yet that some ornithischian [beaked] dinosaurs had feathers, so it wasn't only the theropods that had downy coats," Brusatte says.
"This does mean that we can now be very confident that feathers weren't just an invention of birds and their closest relatives, but evolved much deeper in dinosaur history," he adds. "I think that the common ancestor of dinosaurs probably had feathers, and that all dinosaurs had some type of feather, just like all mammals have some type of hair."

http://palaeo.gly.bris.ac.uk/melanosomes/Kulindaimages.html

http://www.ncbi.nlm.nih.gov/pubmed/19295609

http://en.wikipedia.org/wiki/Tianyulong

http://link.springer.com/article/10.1007%2Fs00114-002-0339-6

http://en.wikipedia.org/wiki/Psittacosaurus

http://www.theguardian.com/world/2014/jul/24/dinosaur-feathers-siberia-fossil-discovery-herbivore

http://www.walkingwithdinosaurs.com/news/post/did-triceratops-have-feathers-or-quills/

http://pterosaurnet.blogspot.ca/2014/01/helpful-background.html

http://flyingdinosaurs.net/a-z-of-feathered-dinosaurs/


For reference:
Stage 1:




From the supplementary material:
http://www.sciencemag.org/content/suppl/2014/07/23/345.6195.451.DC1/Godefroit.SM.pdf
We considered attempting to describe the feather morphotypes in Kulindadromeus using the nomenclature of Prum et al. (52, 53) or of Xu et al. (21, 22). However, except for our monofilaments (which correspond well to Type 1 in Xu et al.), we could not assign with confidence the other two feather morphotypes in Kulindadromeus to categories described by Prum et al. or Xu et al. Further, fundamental discrepancies between these two previously published nomenclature systems remain to be resolved. Thus we felt that until new fossil material and a synthesis of existing nomenclature systems are available, interpretations of direct homologies between complex feather-types in Kulindadromeus and in Prum et al. or Xu et al. would be premature.

http://whyevolutionistrue.wordpress.com/2014/07/27/a-new-feathered-dinosaur-suggests-that-most-dinosaurs-had-feathers/
The fact that feathers appear to be growing out of scale-like features suggests, as biologists have long assumed, that feathers actually evolved from scales, though the authors suggest that the “scales” on birds’ legs and feet are not persistent scales derived from their reptilian ancestors, but evolved back from feathers! Since scales certainly preceded feathers in the fossil record, this shows that truly new structures, certainly involving new genetic information, can evolve (and then be lost, reverting on birds’ feet to scales). That belies the common creationist criticism that new genetic information can’t evolve (we saw that from one commenter earlier today).
 http://www.bbc.com/news/science-environment-28407381
But Dr Paul Barrett of the Natural History Museum in London, has doubts.
"Most feathers have a branching structure," he told BBC News.
"Instead these look like little streamers coming from a central plate. No bird has that structure in any part of its plumage and none of the developmental models that biologists use to understand the evolution of feathers includes a stage that has anything like that kind of anatomy."
http://news.nationalgeographic.com/news/2014/07/140724-feathered-siberia-dinosaur-scales-science/
Kulindadromeus adds a whole new dimension to understanding feather evolution, Vinther says, pointing to the fact that the three feather types found as imprints with the fossils are different from ones found on feathered dinosaurs or modern birds.
What exactly did all these different feathers do? "I don't know; nobody knows for sure," Godefroit says. "These animals couldn't fly, that's all we can tell you."
http://reptilis.net/2014/07/31/new-siberian-ornithischian-and-the-over-feathering-of-dinosaurs-again/#more-1079
So I find it quite strange and disheartening that Godefroit et al.—despite being fairly objective in their supplementary material—go completely gung-ho in calling these structures feathers.

Wednesday, August 6, 2014

Hand Transition

There is a group of researchers and academics (eg. Feduccia et al) that makes a very strong case that birds did not evolve from dinosaurs.

One important aspect of their argument is the discrepancy in digits (fingers) between dinosaurs and modern birds. The evidence indicates that birds have digits II-III-IV while dinosaurs have I-II-III.

I agree with the researchers and academics that birds did not evolve from dinosaurs.
I go a step further and suggest that the ancestors were pterosaurs.
Pterosaur hands and basal paraves hands are such that a very straightforward transition is possible.

Here is the proposed transition:

2-3-4-5-x Pterosaur
x-2-3-4-x Basal Paraves 
x-2-3-4-x Basal eumaniraptora
x-1-2-1-x Modern bird

Summary of Changes:
The first step occurs in pterosaur with the loss of the 5th digit (V).
Then in the transition to basal paraves:
The first finger was lost. 
The second finger lost one phalanx. 
The third finger lost one phalanx. 
The fourth finger was shortened and lost one phalanx. 

Note that the pterosaur to bird theory is also consistent with a frameshift, which also produces the same pattern as above.

Wednesday, July 30, 2014

Pterosaur fingers

In the transition from pterosaur to basal paraves, the 1st finger (I) was lost and the 4th finger (IV) was shortened a great deal.


Pterosaur

Basal Paraves

I am working with the following hypothesis of the transitions of fingers and phalanges:

2-3-4-5-x Pterosaur
x-2-3-4-x Basal Paraves 
x-2-3-4-x Basal eumaniraptora
x-1-2-1-x Modern bird

Numbers represent the number of phalanges. For example, this shows 3 phalanges in the third finger (III) of basal paraves. Roman numerals represent digits (fingers).

Summary of Changes:
The first step occurs in pterosaur with the loss of the 5th digit (V).
Then in the transition to basal paraves:
The first finger was lost. 
The second finger lost one phalanx. 
The third finger lost one phalanx. 
The fourth finger was shortened and lost one phalanx.


For comparison, the dinosaur pattern is 2-3-4-x-x.


What I am suggesting is supported by these references:

http://www.cell.com/current-biology/fulltext/S0960-9822(13)00512-5
The ‘pyramid reduction hypothesis’ assumes II-III-IV identities for neornithine manual digits and postulates the existence of a conservative five-digit pattern with a gradual, bilateral reduction of phalanges and metacarpals in avian evolution [9]. One proposed mechanism postulates that an elevation in peripheral BMPs, signaling factors that modulate cell survival and proliferation [60, 61], drove bilateral medial and lateral digital reduction [9]. This hypothesis is developmentally plausible, and is also consistent with the phalangeal reduction pattern seen in basal birds [9, 23]. However, it predicts that the direct avian ancestor had a five-fingered hand with dominant digits II, III, and IV [9], which is inconsistent with the digital reduction data from basal theropods (e.g., all known basal theropods, including ceratosaurs, have a vestigial digit IV) [5, 62, 63, 64]. In fact, the pyramid reduction hypothesis implies that either birds are not descended from theropod dinosaurs, or that some as yet to be discovered basal theropods were five-fingered with dominant digits II, III, and IV.

http://www.ncbi.nlm.nih.gov/pubmed/12210116?dopt=Abstract
We report herein that a pentadactyl developmental pattern is evident in early wing morphogenesis of Gallus (chicken) and Struthio (ostrich). Five avascular zones (spatially predestined locations of contiguous metacarpal and phalangeal aggregation) and four interdigital vascular spaces are established by the regression patterns of autopodial vasculature. Transient vestiges of the first and fifth metacarpals are confirmed histologically and histochemically. They lie within the preaxial-most and postaxial-most avascular zones, respectively.
These observations reveal conservative patterning of the avian hand and corroborate a II-III-IV metacarpal interpretation, argue for II-III-IV identity of ossified digits in birds, and favour a simple reduction rather than a homeotic shift in terms of the phenotype expressed by Hox genes in the phylogeny of the avian manus. 
We suggest that gradual, bilateral reduction of phalanges and metacarpals, via apoptosis mediated by BMP, occurred during the evolution of birds (Pyramid Reduction Hypothesis). This is congruent with the establishment of a central wing axis that became co-opted for coordinated movements.
On the basis of evidence presented here, the direct avian ancestor is predicted to have been five-fingered with dominant digits (+ metacarpals) as follow: II, III, IV. 
 http://onlinelibrary.wiley.com/enhanced/doi/10.1002/jez.b.22545/#jezb22545-bib-0065
In the initial presentation of the concept, Kundrát et al. (2002) also suggested a mechanism that would be able to derive the Archaeopteryx phalangeal formula from the archosaur one. While the archosaur ground state is thought to be DI(2)–DII(3)–DIII(4)–DIV(5)–DV(3), Archaeopteryx could have DI(2)–DII(3)–DIII(4)–DV(0)–DV(0), but could also be interpreted as DI(0)–DII(2)–DIII(3)–DIV(4)–DV(0). Experiments with molecular signaling pathways in early limb development have shown that modulating interdigital bmp signaling (Dahn and Fallon, 2000) or blocking bmp with a dominant negative receptor (Zou and Niswander, 1996) is able to remove one phalanx from each digit, and therefore a mechanism like that could have caused the archosaur central digits to resemble the Archaeopteryx ones with regard to their phalangeal numbers.

Alternately a frameshift explanation:

http://onlinelibrary.wiley.com/doi/10.1002/jez.b.22545/full
Thumbs down: a molecular-morphogenetic approach to avian digit homologyDaniel Čapek1,2,†, Brian D. Metscher1 andGerd B. Müller1,*Article first published online: 29 OCT 2013
Avian forelimb digit homology remains one of the standard themes in comparative biology and EvoDevo research. In order to resolve the apparent contradictions between embryological and paleontological evidence a variety of hypotheses have been presented in recent years. The proposals range from excluding birds from the dinosaur clade, to assignments of homology by different criteria, or even assuming a hexadactyl tetrapod limb ground state. At present two approaches prevail: the frame shift hypothesis and the pyramid reduction hypothesis. While the former postulates a homeotic shift of digit identities, the latter argues for a gradual bilateral reduction of phalanges and digits. 

http://onlinelibrary.wiley.com/doi/10.1002/jez.b.22545/full
the change of the phalangeal formula (as in the PRH) is actually caused by the change of the transcriptome (as in the FSH), which in turn is directly caused by the loss of digit I (probably shh and hoxD mediated).
At the point when digit I is lost completely, the topological and morphogenetic effect causes the remaining digits to grow more toward anterior and therefore to adopt different phenotypic fates (e.g., Deinonychus; A).

Arguments against a frameshift:

http://en.wikipedia.org/wiki/Bilateral_Digit_Reduction#Digit_homology
However, such frame shifts are rare in amniotes and—to be consistent with the theropod origin of birds—would have had to occur solely in the bird-theropod lineage forelimbs and not the hindlimbs (a condition unknown in any animal).[136] This is called Lateral Digit Reduction (LDR) versus Bilateral Digit Reduction (BDR) (see also Limusaurus[137])
http://www.pnas.org/content/96/9/5111.full.pdf
Once this happened, we postulate a frame shift—a homeotic transformation—
in the developmental identity of the initial condensations:
Condensation CII developed into digit DI, CIII developed
into DII, and CIV developed into DIII (Fig. 6C), thus
conserving a functionally significant mature form within the
confines of a morphogenetic constraint.
We are not aware of any other case in which such a conflict between a developmental and a functional constraint in digit reduction existed.

http://onlinelibrary.wiley.com/doi/10.1002/jez.b.22545/full
it argues that a (partial) homeotic anterior shift took place and that digit IV was completely re-evolved, following in both points the FSH.

http://www.cell.com/current-biology/pdf/S0960-9822(13)00512-5.pdf
Shh levels regulate digit pattern to shift their expression domains
for the developing hand and the re-emergence of a fully
functional digit in position 4

http://www.dinosauria.org/docs/oryctos/07_03_campbell.pdf
Even more revealing is the fact that in the Eichstätt specimen it can be seen that the ginglymoid joint at the end of Metacarpal II is rotated almost 90 degrees, such that in dorsal view it is clear that flexion/extension of Phalanx 1 of Digit II was primarily in the anterior/posterior plane
Significantly, an anteroposterior flexion/extension of Digit II, even with a sizable ventral component, would have made it the first avian alula, albeit a very primitive one. 
The basal paraves 2nd digit is basically at right angles to the other two digits. It forms a "primitive alula". It has a quite different structure and function than the dinosaur 1st digit.


 GENERAL:

http://www.nature.com/nature/journal/v500/n7463/full/nature12336.html
Digit loss is defined as the complete loss of all phalanges and the
metapodial bone; it should be distinguished from digit reduction, in
which only phalanges are lost3. Digit loss can be adaptive. It reduces the
mass of the distal limb, and therefore its moment of inertia; this conserves
energy during running and flying12–14. 


http://onlinelibrary.wiley.com/doi/10.1002/dvdy.22595/full




http://onlinelibrary.wiley.com/enhanced/doi/10.1002/jez.b.22545/




Figure 2. Schematic overview of the major digit reduction hypotheses for the avian lineage. Squares mark positional features (topological identity), and circles compositional features (phenotypic appearance) of digits. Crosses designate reduced digits, asterisks mark strongly derived phenotypes, diagonal arrows indicate hypothetical frame shifts. The bottom row shows the ancestral archosaur condition. The middle rows show the theropod trend, (e.g., HerrerasaurusEoraptorCoelophysis). The top row shows the final tetanuran condition, which includes birds (e.g.,DeinonychusGallus). The pyramid reduction hypothesis (PRH) argues that initially digit I was lost in the theropod linage, leaving the four posterior digits (e.g., Coelophysis), then digit V is reduced, and the three central digits remain. The frame shift hypothesis (FSH1) assumes the loss of both posterior digits, followed by a shift that caused the anterior digits to be formed from the central positions. After the discovery ofLimusaurus with its strong reduced digit I, the shift was predated to the four digit state (FSH2). After the shift, position V would be lost again, this time actually deleting digit IV. The hexadactyl origin hypothesis (HOH) argues that originally a first digit existed that already was a vestige in the archosaur ground state, then the posterior-most digit is lost (digit V from position VI) followed by the adjacent one (digit IV from position V). Modified after Welten et al. (2005). 


https://www.academia.edu/1486957/Transcriptomic_analysis_of_avian_digits_reveals_conserved_and_derived_digit_identities_in_birds
To discover genes that specifically contribute to the second and third wing digit identities, we performed differential expression analysis of the mRNA-seq data between samples LFb and LFc. We found two genes, Tbx3 and Socs2, with high expression in sample LFc (Supplementary Fig. 9 and Fig. 3a). To our knowledge no studies have been published indicating a role for Socs2 in limb development. ISH confirms its strong expression in the third forelimb digit to the exclusion of all other digits in forelimb and hindlimb(Fig.3b–g). Recently it has been shown that the third forelimb digit has a unique mode of development in birds8. This, combined with our gene expression survey, supports the idea that the third wing digit has a unique derived identity in birds.

http://onlinelibrary.wiley.com/doi/10.1002/dvdy.22595/full


Other references:
http://www.researchgate.net/publication/222677306_An_old_controversy_solved_bird_embryos_have_five_fingers
AND
http://www2.gwu.edu/~newsctr/newscenter/research/dinosaur/clark.pdf
AND
http://blogs.discovermagazine.com/loom/2009/06/17/of-birds-and-thumbs/#.U-Okefnlp1Y
AND
http://genomebiology.com/content/pdf/gb-2011-12-10-130.pdf
AND
http://www.sciencedaily.com/releases/2011/09/110904140359.htm
AND
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3333764/


This may well be what the pterosaur hand looked like:
https://imaginosaurus.wordpress.com/tag/hands/



Friday, July 25, 2014

Scansoriopteryx

Scansoriopteryx looks like an excellent example of a transitional on the lineage from pterosaur to primitive bird.  It is a member of basal Paraves. 

ELONGATE OUTER FINGER

Jurassic archosaur is a non-dinosaurian bird
Stephen A. CzerkasAlan Feduccia
Re-examination utilizing Keyence 3D digital microscopy and low angled illumination of the fossil Scansoriopteryx, a problematic sparrow-size pre-Archaeopteryx specimen from the Jurassic Daohugou Biotas, provides new evidence which challenges the widely accepted hypothesis that birds are derived from dinosaurs in which avian flight originated from cursorial forms. Contrary to previous interpretations in which Scansoriopteryx was considered to be a coelurosaurian theropod dinosaur, the absence of fundamental dinosaurian characteristics demonstrates that it was not derived from a dinosaurian ancestry and should not be considered as a theropod dinosaur. Furthermore, the combination in which highly plesiomorphic non-dinosaurian traits are retained along with highly derived features, yet only the beginnings of salient birdlike characteristics, indicates that the basal origins of Aves stemmed from outside the Dinosauria and further back to basal archosaurs. Impressions of primitive elongate feathers on the forelimbs and hindlimbs suggest that Scansoriopteryx represents a basal form of “tetrapteryx” in which incipient aerodynamics involving parachuting or gliding was possible. Along with unique adaptations for an arboreal lifestyle, Scansoriopteryx fulfills predictions from the early twentieth century that the ancestors of birds did not evolve from dinosaurs, and instead were derived from earlier arboreal archosaurs which originated flight according to the traditional trees-down scenario.

The most unusual feature is the extremely elongate outer finger, considered here to be digit IV as in Aves (Capek et al. 2013). It is the longest manual digit whereas the middle digit in theropods is the longest.
The Scansoriopteryx outer finger is intermediate between pterosaur and derived members of Paraves. 







http://www.labnews.co.uk/news/new-finding-challenges-belief-dinosaurs-evolved-from-birds
The investigations – published in Journal of Ornithology – found a combination of plesiomorphic or ancestral non-dinosaurian traits along with highly derived unambiguous birdlike features. The researchers specifically note the primitive elongated feathers on the fore- and hind limbs, suggesting Scansoriopteryx is an ancestral form of early birds that had mastered basic aerodynamic manoeuvres of parachuting or gliding from trees.
These findings fulfil a prediction first made in the 1900s that the ancestors of birds didn’t evolve from dinosaurs, but instead from earlier arboreal archosaurs which originated flight according to the tree-down scenario. These small tree-dwelling archosaurs had improved ability to fly, with feathers that enabled them to at least glide. This ‘tree-down’ view is in contrast with the ‘ground-up’ view many palaeontologists side with.
“Instead of regarding birds as deriving from dinosaurs, Scansoriopteryx reinstates the validity of regarding them as a separate class uniquely avian and non-dinosaurian,” said Alan Feduccia.
Pterosaur fingers: 
http://www.reptileevolution.com/pterosaur-wings.htm




CAUDAL RODS

 http://www.sci-news.com/paleontology/science-scansoriopteryx-hypothesis-birds-evolved-dinosaurs-02059.html
The techniques made it possible to interpret the natural contours of the bones. Many aspects of the [Scansoriopteryx] fossil’s pelvis, forelimbs, hind limbs, and tail were confirmed, while it was discovered that it had elongated tendons along its tail vertebrae similar to Velociraptor.
http://onlinelibrary.wiley.com/doi/10.1111/1755-6724.12009/abstract

In the tails of dromaeosaurids dinosaurs and rhamphorhynchid pterosaurs, elongate osteological rods extend anteriorly from the chevrons and the prezygapophyses. These caudal rods are positioned in parallel and are stacked dorsoventrally.

http://pterosaur-net.blogspot.ca/2013/01/guest-post-dragon-tails-what-pterosaurs.html
The tail of Deinonychus and its raptor relatives is bizarre, but it is not (as Professor Ostrom himself realized) unique. Among all known vertebrates, a similar tail anatomy has evolved in one other group [rhamphorhynchid pterosaurs]. . .
Consider the below images of a tail of a Bambiraptor and of a Velociraptor. Both are dromaeosaurids with caudal-rod bearing tails and both are fully articulated.

ACETABULUM

http://www.aou.org/auk/content/130/1/0001-0013.pdf
A partially closed acetabulum is seen in basal archosaurs and
is characteristic of the scansoriopterids and Jurassic feathered
forms such as Anchiornis
initially described as near Aves by Xu et al. (2009).

Rhamphorhynchid pterosaurs had either a completely closed or partially closed acetabulum.

Monday, July 21, 2014

Consensus

https://www.cfa.harvard.edu/~scranmer/SPD/crichton.html
I want to pause here and talk about this notion of consensus, and the rise of what has been called consensus science. I regard consensus science as an extremely pernicious development that ought to be stopped cold in its tracks. Historically, the claim of consensus has been the first refuge of scoundrels; it is a way to avoid debate by claiming that the matter is already settled. Whenever you hear the consensus of scientists agrees on something or other, reach for your wallet, because you're being had.
Let's be clear: the work of science has nothing whatever to do with consensus. Consensus is the business of politics. Science, on the contrary, requires only one investigator who happens to be right, which means that he or she has results that are verifiable by reference to the real world. In science consensus is irrelevant. What is relevant is reproducible results. The greatest scientists in history are great precisely because they broke with the consensus.
There is no such thing as consensus science. If it's consensus, it isn't science. If it's science, it isn't consensus. Period.
In addition, let me remind you that the track record of the consensus is nothing to be proud of. 
A lecture by Michael Crichton Caltech Michelin Lecture January 17, 2003

Saturday, May 24, 2014

Brainpower

The dino to bird theory postulates that "non-paraves maniraptors" were transitional between basal coelurosaurs and basal Paraves. One problem with this idea (one of many), is the enlarged brains these "non-paraves maniraptors" had, that they did not use for flight.

According to the dino to bird theory this "brainpower needed for flight" existed "long before" it was needed for flight. Not only that, but it existed "multiple times".

The more credible explanation is that they were not transitionals, but rather secondarily flightless paravians. In other words they developed from (and came after) basal paraves.

http://www.bbc.com/news/science-environment-23514985
Several ancient dinosaurs [maniraptors] evolved the brainpower needed for flight long before they could take to the skies, scientists say.
Bird brains tend to be more enlarged compared to their body size than reptiles, vital for providing the vision and coordination needed for flight.
Scientists using high-resolution CT scans have now found that these "hyper-inflated" brains were present in many ancient dinosaurs [maniraptors], and had the neurological hardwiring needed to take to the skies. This included several bird-like oviraptorosaurs and the troodontids Zanabazar junior, which had larger brains relative to body size than that of Archaeopteryx.
http://www.nature.com/nature/journal/v501/n7465/full/nature12424.html
Our new data indicate that the relative size of the cranial cavity of Archaeopteryx is reflective of a more generalized maniraptoran volumetric signature and in several instances is actually smaller than that of other non-avian dinosaurs. Thus, bird-like indices evolved multiple times, supporting the conclusion that if Archaeopteryx had the neurological capabilities required of flight, so did at least some other non-avian maniraptorans. This is congruent with recent findings that avialans were not unique among maniraptorans in their ability to fly in some form.
ALSO

http://www.ncbi.nlm.nih.gov/pubmed/19800747
Quote:
Secondarily flightless birds or Cretaceous non-avian theropods?
Kavanau JL.

Quote:
Recent studies by Varricchio et al. reveal that males cared for the eggs of troodontids and oviraptorids, so-called "non-avian theropods" of the Cretaceous, just as do those of most Paleognathic birds (ratites and tinamous) today. Further, the clutches of both groups have large relative volumes, and consist of many eggs of relatively large size. By comparison, clutch care by most extant birds is biparental and the clutches are of small relative volume, and consist of but few small eggs. Varricchio et al. propose that troodontids and oviraptorids were pre-avian and that paternal egg care preceded the origin of birds. On the contrary, unmentioned by them is that abundant paleontological evidence has led several workers to conclude that troodontids and oviraptorids were secondary flightless birds. This evidence ranges from bird-like bodies and bone designs, adapted for climbing, perching, gliding, and ultimately flight, to relatively large, highly developed brains, poor sense of smell, and their feeding habits. Because ratites also are secondarily flightless and tinamous are reluctant, clumsy fliers, the new evidence strengthens the view that troodontids and oviraptorids were secondarily flightless. Although secondary flightlessness apparently favors paternal care of clutches of large, abundant eggs, such care is not likely to have been primitive. There are a suite of previously unknown independent findings that point to the evolution of, first, maternal, followed by biparental egg care in earliest ancestors of birds. This follows from the discovery of remarkable relict avian reproductive behaviors preserved by virtue of the highly conservative nature of vertebrate brain evolution. These behaviors can be elicited readily by exposing breeding birds to appropriate conditions, both environmental and with respect to their eggs and chicks. They give significant new clues for a coherent theory of avian origin and early evolution.

Thursday, May 15, 2014

Characters

Here is an accumulation of information related to characters analyzed in Nesbitt (2011) and Nesbitt et al (2009).
These support the pterosaur to bird theory and contradict the dino to bird theory.

NESBITT (2011) 

Nesbitt characters 212, 213, 214, 223, 230, 231 and 370.

212. Forelimb–hind limb, length ratio: (0) more than 0.55; (1) less than 0.55 (Gauthier,
1984; Sereno, 1991a; Juul, 1994; Benton, 1999).
Humerus + radius [forelimb] : Femur + tibia [hindlimb]

SEE REFERENCE IN DINOSAURIA (page 204):
Dromaeosaurid forelimbs are among the longest in theropods, the ratio of forelimb length to hindlimb length being about 65% in Velociraptor, 70% in Deinonychus and 80% in Sinornithosaurus.


213. Clavicles: (0) present and unfused; (1) fused into a furcula (modified from Gauthier, 1986; Sereno, 1991a; Benton, 1999; Benton and Walker, 2002). Clavicles are present in non-archosaurian archosauriforms and basal crocodylian-line archosaurs. Clavicles are not present in crocodylomorphs (e.g., Hesperosuchus ‘‘agilis,’’ CM 29894; Protosuchus richardsoni, AMNH FR 3024) and, therefore, they are scored as inapplicable. Like the interclavicle, the clavicles of the pterosaur Eudimorphodon are separate ossifications in a small specimen and incorporated into the sternum (Wild, 1993). All other pterosaurs seem to lack distinct ossifications of the clavicles. Within Dinosauria, clavicles are present, but do not contact in some ornithischians (e.g., Psittacosaurus) and are unossified in others (Butler et al., 2008a). The clavicles of some nonsauropod sauropodomorphs (e.g., Massospondylus) may contact each other at the midline, but do not fuse (Yates and Vasconcelos, 2005). A furcula (fused clavicles) is present in nearly all theropods known from complete skeletons including Coelophysis bauri (AMNH FR 30647; Rinehart et al., 2007; Nesbitt et al., 2009d) and Allosaurus fragilis (UUVP 6102; Chure and Madsen, 1996). This character has been employed by various datasets exploring theropod relationships (e.g., Norell et al., 2001; Clarke, 2004).

Pterosaurs have clavicles and an interclavicle that are fused into the sternum.



214. Interclavicle: (0) present; (1) absent
(fig. 30) (Gauthier, 1986; Sereno, 1991a; Juul,
1994; Benton, 1999).
The interclavicle is present in archosauriforms
plesiomorphically (Sereno, 1991a) and
persists through Pseudosuchia. In Pterosauria,
an interclavicle appears to be present
in young individuals of Eudimorphodon
(MCSNB 8950), but fuse to the pectoral
elements in larger individuals (Wild, 1993). A
distinct interclavicle is not present in all other
pterosaurs. Ornithischians and saurischians
lack an interclavicle. However, the pectoral
girdles in the successive sister taxa to
Dinosauria (Silesaurus, Marasuchus, Lagerpeton)
do not have the pectoral region
completely preserved. As a result, the optimization
of this character within Dinosauromorpha
is not clear.

SEE REFERENCE IN DINOSAURIA (page 204)

The evolutionary transformation of the furcula
from separate clavicles is nicely illustrated in
archosaurs and their close relatives. Euparkeria
capensis and early pseudosuchians retain both the
interclavicle and clavicles. The interclavicle is lost
at the dinosaur node or at an unknown node
among early dinosauromorphs.
 From there, the origin
of the furcula is well understood with the
addition of the work on basal sauropodomorphs of
Yates and Vasconcelos (2005) and the discovery of
furculae in early coelophysoid theropods (Tykoski
et al., 2002; Rinehart et al., 2007). Some ornithischians
have two small clavicles that do not
contact each other (Osborn, 1924a; Brown and
Schlaikjer, 1940; Sternberg, 1951; Chinnery and
Weishampel, 1998). In contrast, saurischians
retain clavicles with the clavicles contacting at the
midline.

Birds and pterosaurs have an interclavicle. Dinosaurs do not.



223. Coracoid, postglenoid process: (0) short; (1) elongate and expanded posteriorly only 

The significance of this is that a longer coracoid allows the bird scapula (attached to the coracoid) to be positioned high enough on the body (horizontally), to allow flapping (by the wings being raised high enough up).



230. Humerus, apex of deltopectoral crest situated at a point corresponding to: (0) less than 30% down the length of the humerus; (1) more than 30% down the length of the humerus (fig. 31) (modified from Bakker and Galton, 1974; Benton, 1990a; Juul, 1994; Novas, 1996; Benton, 1999).
Langer and Benton (2006) thoroughly discussed the distribution of the character states of this character and find that state (1) is restricted to dinosaurs within Archosauria. Here, I follow the conclusions and scorings of Langer and Benton (2006). 

The pterosaur deltopectoral crest is like birds. The dinosaur deltopectoral crest is not like birds. (See details below).



231. Humerus, length: (0) longer than or
subequal to 0.6 of the length of the femur; (1)
shorter than 0.6 of the length of the femur
(modified from Novas, 1996; Langer and
Benton, 2006).
Langer and Benton (2006) thoroughly
discussed the distribution of the character
states and find that state (1) is restricted to
Herrerasaurus (PVSJ 373), Eoraptor (PVSJ
512), and neotheropods.

Humerus length compared to femur length is similar for pterosaurs to birds but different than dinosaurs.



370. Astragalus-calcaneum, articulation:
(0) free; (1) coossified (fig. 46) (Sereno and
Arcucci, 1994a; Irmis et al., 2007a).
In most archosauriforms, save avians and
close relatives
, the astragalus and calcaneum
are separate elements. In pterosaurs (e.g.,
Dimorphodon, YPM 9182), Lagerpeton (PVL
4619), and Dromomeron romeri (GR 223), the
astragalus and calcaneum are coossified.
Among basal dinosaurs, the proximal tarsals
are coossified in Heterodontosaurus (SAMPK-
1332) and coelophysoids (Rowe and
Gauthier, 1990; Tykoski, 2005b).




More info on the deltopectoral crest.

http://pterosaurheresies.wordpress.com/category/pterosaur-evolution
"Both tiny birds and tiny pterosaurs dispensed with their long stiff tail. In birds it became a pygostyle. In pterosaurs the long stiff tail became a reduced, string-like tail with bead-like verts. Note the similarities in the pectoral girdles. Both could stand with their toes beneath their shoulder glenoids. Both had retroverted pedal digits but of two distinct designs. The anterior ilium of both taxa supported large thigh muscles. A large deltopectoral crest supported large flight adductors anchored to the sternum."
Deltopectoral crest: a longitudinal ridge or crest on the (proximal) humerus. Cursorial forms typically do not have a large crest. It is typically an important attachment point for adductors, rather than retractors.
 http://en.wikipedia.org/wiki/Evolution_of_dinosaurs
Dinosaurs evolved within a single lineage of archosaurs 232-234 Ma (million years ago) in the Ladinian age, the latter part of the middle Triassic. Dinosauria is a well-supported clade, present in 98% of bootstraps. It is diagnosed by many features including loss of the postfrontal on the skull and an ELONGATE deltopectoral crest on the humerus.[1]

The Dinosauria: Second Edition:

The humerus is slender and twisted. It has a caudally deflected proximal end and a moderately developed deltopectoral crest that is restricted to the PROXIMAL third of the humerus in Deinonychus and to the PROXIMAL quarter in Velociraptor.

http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37652009000400017&lng=es&nrm=iso&tlng=es

Pterosaur humerus:


Description: The specimen MB.R. 2828 (Fig. 2; Table I) has a slightly dorso-ventral compression, showing several fractures. It possesses the characteristic saddle-shaped proximal articular head, common to the pterosaur humeri. The deltopectoral crest is well developed and inclined proximoventrally. It is tongue-shaped with a rounded distal end. In lateral view the proximal margin of the deltopectoral crest is markedly concave, while the distal margin is straight. There is an elongated ridge on the medial side of the crest running from the distal to the proximal edge, and is likely an attachment of a flight muscle (m. pectoralis, see Bennett 2003). There is an elongated concavity on the medial side, close to the distal margin, whose function is unknown. The ulnar crest is blunt and slightly crushed laterally. The dorsal margin shows a well developed pneumatic foramen, located close to the lateral side.

http://courses.washington.edu/chordate/453photos/skeleton_photos/bird-humeri.jpg
Miscellaneous bird humeri (proximal heads to the left). The top 2 face anteriorly & the bottom 3 face posteriorly.

Notice the bird deltopectoral crest is basically confined to the proximal end as in pterosaurs.


http://en.wikipedia.org/wiki/Dinosaur#Distinguishing_anatomical_features
apex of deltopectoral crest (a projection on which the deltopectoral muscles attach) located at or more than 30% down the length of the humerus (upper arm bone)
Notice the dinosaur deltopectoral crest is not confined to the proximal end as in birds and pterosaurs.



NESBITT (2009) 

11. Furcula shape in anterior view: asymmetrical
(0) or symmetrical/nearly symmetrical (1).
The furculae of most nonparavian theropods
are markedly asymmetrical (e.g., Allosaurus,
Citipati). The furculae of paravians, with the
exception of Buitreraptor, are nearly symmetrical.

It is unclear if the asymmetry of the furcula
of Buitreraptor was the result of taphonomy
or represents morphological asymmetry.
We see that the dinosaur furcula is not like the Paravian furcula.
That supports the conclusion that they are not related.

Also see (page 77)
http://books.google.ca/books?id=8QRKV7eSqmIC&pg=PA77&lpg=PA77&dq=oviraptor+furcula&source=bl&ots=fqQ1dMcCAm&sig=Mh6VWAuDyk92AmCENy_FFdCRvn0&hl=en&sa=X&ei=g-t4U96CENKdyASEzYDYAw&ved=0CGAQ6AEwCQ#v=onepage&q=oviraptor%20furcula&f=false