Tuesday, September 16, 2014

Flight without a supracoracoideus

http://books.google.ca/books?id=8QRKV7eSqmIC&pg=PA136&lpg=PA136&dq=dorsal+elevator+feduccia&source=bl&ots=fqR1hQfECg&sig=NAYAvTNh7USVZlO-dFmaLcJsDPQ&hl=en&sa=X&ei=UUUYVIndD8-zyATm3oDgDg&ved=0CCQQ6AEwAQ#v=onepage&q=dorsal%20elevator%20feduccia&f=false
The dorsal elevators, principally the deltoideus major, can effect the recovery stroke by themselves, as they did in Archaeopteryx. The German anatomist Maxheinz J. Sy proved this when he cut the tendons of the supracoracoideus in living crows and pigeons (1936). Sy found that pigeons were capable of normal, sustained flight; the only capacity they lost was the ability to take off from level ground. 
https://repository.si.edu/bitstream/handle/10088/6524/VZ_93_Archaeopteryx.pdf?sequence=1&isAllowed=y
Furthermore, the supracoracoideus muscle,
and hence an ossified sternum, is not necessary to effect the
recovery stroke of the wing. Thus the main evidence for
Archaeopteryx having been a terrestrial, cursorial predator is
invalidated. There is nothing in the structure of the pectoral girdle of Archaeopteryx that would preclude its having been a powered flier. 


Friday, September 12, 2014

Four-winged flyers

An interesting video, which unfortunately is biased to the dino to bird theory.
Especially note from 48:00 to 49:00.


Note that at 48:17 they point to exactly the spot where we find Scansoriopteryx.


MICRORAPTOR

http://en.wikipedia.org/wiki/Microraptor#Wings_and_flight
Microraptor had four wings, one on each of its forelegs and hind legs. The long feathers on the legs of Microraptor were true flight feathers as seen in modern birds, with asymmetrical vanes on the arm, leg, and tail feathers. As in modern bird wings, Microraptor had both primary (anchored to the hand) and secondary (anchored to the arm) flight feathers. This standard wing pattern was mirrored on the hind legs, with flight feathers anchored to the upper foot bones as well as the upper and lower leg. It has been proposed that the animal glided and probably lived mainly in trees, because the hind wings anchored to the feet of Microraptor would have hindered their ability to run on the ground.[9] It had long pennaceous feathers on arms and hands (10–20 centimetres long or 3.9–7.9 in), with legs and feet 11–15 cm long (4.3–5.9 in). Toward the tail end, Microraptor was covered in shorter downy (plumulaceous) feathers, 2–6 cm long (0.79–2.36 in). Though not apparent in most fossils under natural light, due to obstruction from decayed soft tissue, the feather bases extended close to or in contact with the bones, as in modern birds, providing strong anchor points.[10]
When describing specimens originally referred to the distinct species Cryptovolans pauli, paleontologist Stephen Czerkas argued that Microraptor may have been able to fly better than Archaeopteryx, noting the fused sternum and asymmetrical feathers of Microraptor, as well as features of the shoulder girdle that indicate flying ability closer to modern birds than to Archaeopteryx. Czerkas cited the fact that this possibly volant animal is also very clearly a dromaeosaurid, to suggest that the Dromaeosauridae might actually be a basal bird group, and that later, larger, species such as Deinonychus were secondarily flightless. The work of Xu and colleagues also suggested that basal dromaeosaurs were probably small, arboreal, and could at least glide, though later discoveries of even more primitive dromaeosaurids with short forelimbs unsuitable for gliding have cast doubt on this view.[9][11]
Whether or not Microraptor could achieve powered flight or only passive gliding has been controversial. While most researchers have agreed that Microraptor had most of the anatomical characteristics expected in a flying animal, some studies have suggested that the shoulder joint was too primitive to have allowed flapping. The ancestral anatomy of theropod dinosaurs has the shoulder socket facing downward and slightly backward, making it impossible for the animals to raise their arms vertically, a prerequisite for the flapping flight stroke in birds. Some studies of maniraptoran anatomy have suggested that the shoulder socket did not shift into the bird-like position of a high, upward orientation close to the vertebral column until relatively advanced avialans like the enantiornithes appeared.[12] However, other scientists have argued that the shoulder girdle in some paravian theropods, including Microraptor, is curved in such a way that the shoulder joint could only have been positioned high on the back, allowing for a nearly vertical upstroke of the wing. This possibly advanced shoulder anatomy, combined with the presence of a propatagium linking the wrist to the shoulder (which fills the space in front of the flexed wing and may support the wing against drag in modern birds) and an alula or "bastard wing" may indicate that Microraptor was capable of true, powered flight.[13] 
Chatterjee also used computer algorithms that test animal flight capacity to test whether or not Microraptor was capable of true, powered flight, in addition to passive gliding. The resulting data showed that Microraptor did have the requirements to sustain level powered flight, so it is theoretically possible that the animal flew on occasion in addition to gliding.[5]

 SCANSORIOPTERYX

http://en.wikipedia.org/wiki/Scansoriopteryx
One distinctive feature of Scansoriopteryx is its elongated third finger, which is the longest on the hand, nearly twice as long as the second finger (in most theropod dinosaurs, the second finger is the longest). This is unlike the configuration seen in most other theropods, where the second finger is longest. The long wing feathers, or remiges, appear to attach to this long digit instead of the middle digit as in birds and other maniraptorans. Shorter feathers are preserved attached to the second finger.[6]
Scansoriopteryx had a non-perforated hip socket, which is more open in most, but not all, other dinosaurs. It also had a pubis (hip bone) which pointed forward, a primitive trait among theropods, and unlike some maniraptorans more closely related to birds, where the pubis points downward or backward.[6] The legs were short, and preserve small pebbly scales along the upper foot (metatarsus), as well as possible impressions of long feathers in the same area, possibly similar to the "hind wings" of Microraptor and other basal paravians.[6]

http://en.wikipedia.org/wiki/Epidexipteryx
A monophyletic Scansoriopterygidae was recovered by Godefroit et al. (2013); the authors found scansoriopterygids to be basalmost members of Paraves and the sister group to the clade containing Avialae and Deinonychosauria.[8]

ARCHAEOPTERYX

http://archosaurmusings.wordpress.com/2008/10/26/the-changing-legs-of-archaeopteryx/
One final point to add here is that the discovery of the wonderful 4-winged Microraptor gui seemed to come as complete shock to everyone. In hindsight of course it really should not have done so since Archaeopteryx clearly has long flight feathers on the legs.

Sunday, September 7, 2014

Propatagium (video)

Here you can see the extensive propatagium that it inherited from its pterosaur ancestor.

https://www.youtube.com/watch?v=YgNpkfKRQ-k


Wednesday, September 3, 2014

Oviraptors as secondarily flightless

Here is an accumulation of material on the idea that Oviraptors were secondarily flightless:

http://en.wikipedia.org/wiki/Oviraptorosauria
Oviraptorosaurs, like deinonychosaurs, are so bird-like that several scientists consider them to be true birds, more advanced than Archaeopteryx. Gregory S. Paul has written extensively on this possibility, and Teresa Maryańska and colleagues published a technical paper detailing this idea in 2002.[5][15][16] Michael Benton, in his widely-respected text Vertebrate Paleontology, also included oviraptorosaurs as an order within the class Aves.[17] However, a number of researchers have disagreed with this classification, retaining oviraptorosaurs as non-avialan maniraptorans slightly more primitive than the deinonychosaurs.[18]
Analyses like those of Maryanska et al (2002) and Osmólska et al. (2004) suggest that they may represent primitive flightless birds.[5][6]

http://en.wikipedia.org/wiki/Caudipteryx
However, not all scientists agreed that Caudipteryx was unambiguously non-avian, and some of them continued to doubt that general consensus. Paleornithologist Alan Feduccia sees Caudipteryx as a flightless bird evolving from earlier archosaurian dinosaurs rather than from late theropods.[8] Jones et al. (2000) found that Caudipteryx was a bird based on a mathematical comparison of the body proportions of flightless birds and non-avian theropods. Dyke and Norell (2005) criticized this result for flaws in their mathematical methods, and produced results of their own which supported the opposite conclusion.[6][9]Other researchers not normally involved in the debate over bird origins, such as Zhou, acknowledged that the true affinities of Caudipteryx were debatable.[5]

The consensus view, based on several cladistic analyses, is that Caudipteryx is a basal (primitive) member of the Oviraptoridae, and the oviraptorids are nonavian theropod dinosaurs.[9] Incisivosaurus is the only oviraptorid that is more primitive.[10]
Halszka Osmólska et al. (2004) ran a cladistic analysis that came to a different conclusion. They found that the most birdlike features of oviraptorids actually place the whole clade within Aves itself, meaning that Caudipteryx is both an oviraptorid and a bird. In their analysis, birds evolved from more primitive theropods, and one lineage of birds became flightless, re-evolved some primitive features, and gave rise to the oviraptorids. This analyis was persuasive enough to be included in paleontological textbooks like Benton's Vertebrate Paleontology (2005).[11] The view that Caudipteryx was secondarily flightless is also preferred by Gregory S. Paul,[12] Lü et al.,[13] and Maryańska et al.[14]
Others, such as Stephen Czerkas and Larry Martin have concluded that Caudipteryx is not a theropod dinosaur at all.[15] They believe that Caudipteryx, like all maniraptorans, is a flightless bird, and that birds evolved from non-dinosaurian archosaurs.[16]
http://www.ncbi.nlm.nih.gov/pubmed/19800747
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.

NOTE:
Oviraptors were either secondarily flightless birds (avialae) or secondarily flightless basal paraves.
In either case, there is no evidence they developed from dinosaurs. They are not transitional between actual dinosaurs and basal paraves.





Saturday, August 30, 2014

"Non-avian dinosaurs" (2)

As I said in the previous post:
The phrase "non-avian dinosaurs" crops up in many articles. What does it mean? As we see below it means Dinosauria minus Aves. Unfortunately, it lumps in the basal paraves (the primitive flying and secondarily flightless primitive creatures) with the real dinosaurs such as Tyrannosaurus, under the same label - "non-avian dinosaur". In short, it lumps basal paraves in with actual dinosaurs. 
Why is this a problem?

The problem is that when someone makes a statement about "non-avian dinosaurs" we do not know whether they are referring to Paraves or whether they are referring to actual dinosaurs.

For example take a quote like the following:
http://en.wikipedia.org/wiki/Feathered_dinosaur
"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. "
We cannot tell whether the quote refers just to feathered Paraves or whether it refers to actual dinosaurs. The way it is worded it leaves the impression that there were actually feathered dinosaurs.
So when someone claims that there are many feathered dinosaurs found, they are almost always referring to feathered Paraves which are not actually dinosaurs.
That is why the phrase "non-avian dinosaurs" (or "non-avian theropods") is not nearly precise enough. In fact, it is misleading.

Here is another example, where they are talking only about oviraptors and not actual dinosaurs. But they call them "non-avian theropods".
http://en.wikipedia.org/wiki/Caudipteryx
Because Caudipteryx has clear and unambiguously pennaceous feathers, like modern birds, and because several cladistic analyses have consistently recovered it as a nonavian, oviraptorid, dinosaur, it provided, at the time of its description, the clearest and most succinct evidence that birds evolved from dinosaurs. Lawrence Witmer stated: “The presence of unambiguous feathers in an unambiguously nonavian theropod has the rhetorical impact of an atomic bomb, rendering any doubt about the theropod relationships of birds ludicrous.”[3]

And on the other hand:
When someone does explicitly claim that an actual dinosaur had feathers, it turns out they are not feathers but bristles. (That is a separate subject, covered earlier).


Wednesday, August 27, 2014

"Non-avian dinosaurs"

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 secondarily flightless primitive 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 the supplementary material tells a different story:

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.
A claim of anything beyond "type 1" filaments (that are actually just bristles) is beyond the evidence, as confirmed by the supplementary material.

This quote expresses exactly what I am saying:
http://reptilis.net/2014/07/31/new-siberian-ornithischian-and-the-over-feathering-of-dinosaurs-again/
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
  • Paul Spagna1
  •  
    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/
    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 later members of Paraves. 







    http://dinosaur-museum.org/featheredinosaurs/arboreal_maniraptoran.pdf
    Scansoriopteryx heilmanni is the only known
    saurischian, or theropod, which has the third digitof the manus elongated to nearly twice that of the second digit. 

    A comment by Andrea Cau:
    http://scienceblogs.com/tetrapodzoology/2008/10/23/epidexipteryx-at-last/
    In my large-scale analysis of theropods (in preparation), Scansoriopterygidae are placed sligtly more basal than Avialae: they’re basal paravians, sister-group of Eumaniraptora (Avialae+Deinonychosauria). This different position explains more the “incisivosaur-like” skull and the absence of some pelvic features widespread among basal avialans, dromaeosaurids and troodontids (in particular the scapular, ischial and pubic features).
    In my blog, I suggested an alternative and very heterodox interpretation of Scansoriopterygids: given the absence of evidence for remiges in Epidexipteryx, is it possible that the “feather impressions” seen in the forelimb of the “Scansoriopteryx heilmanni specimen” are not feathers, but a different tegument: it is interesting to note that in remige-bearing maniraptorans, the remiges are inserted on the second finger, whereas in Scasoriopteryx these impression are close to the hyper-elongated third finger. This very long lateral finger is similar to the pterosaurian fourth digit. So, it is possible that the “feather impressions” of Scansoriopteryx were remnant of a patagium. In my opinion, the presence of this structure may explain the elongation of the lateral digit in these small theropods better than the Aye-Aye hypothesis.


    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).
    http://en.wikipedia.org/wiki/Scansoriopteryx
    Scansoriopteryx also lacks a fully perforated acetabulum, the hole in the hip socket which is a key characteristic of Dinosauria and has traditionally been used to define the group. 
    http://dinosaur-museum.org/featheredinosaurs/arboreal_maniraptoran.pdf
    Scansoriopteryx is clearly more primitive
    than Archaeopteryx in many respects such as its
    saurischian-style pelvis which has remarkably short
    pubes; elongate and robust ischia; and
    comparatively small pubic peduncles. These
    primitive features further suggest that the nearly
    closed acetabulum is not a reversal, but a true
    plesiomorphic condition.
    Rhamphorhynchid pterosaurs
    Rhamphorhynchid pterosaurs had either a completely closed or partially closed acetabulum.
    Also
    http://en.wikipedia.org/wiki/Pterosaur
    "Pterosaur's hip sockets are oriented facing slightly upwards, and the head of the femur (thigh bone) is only moderately inward facing, suggesting that pterosaurs had a semi-erect stance. It would have been possible to lift the thigh into a horizontal position during flight as gliding lizards do."

    GENERAL

    http://en.wikipedia.org/wiki/Scansoriopterygidae
    Scansoriopteryx (and its likely synonym Epidendrosaurus) was the first non-avian dinosaur found that had clear adaptations to an arboreal or semi-arboreal lifestyle–it is likely that they spent much of their time in trees. Both specimens showed features indicating they were juveniles, which made it difficult to determine their exact relationship to other non-avian dinosaurs and birds. It was not until the description of Epidexipteryx in 2008 that an adult specimen was known.
    The scansoriopterygids would have lived alongside synapsids such as the aquatic Castorocauda and arboreal gliding mammal Volaticotherium, the rhamphorhynchoid pterosaurs Jeholopterus and Pterorhynchus, as well as a diverse range of insect life (including mayflies and beetles) and several species of salamander.[14][15]
    A monophyletic Scansoriopterygidae was recovered by Godefroit et al. (2013); the authors found scansoriopterygids to be basalmost members of Paraves and the sister group to the clade containing Avialae and Deinonychosauria.[9] Agnolín and Novas (2013) recovered scansoriopterygids as non-paravian maniraptorans and the sister group to Oviraptorosauria.[10]

    http://dinosaur-museum.org/featheredinosaurs/arboreal_maniraptoran.pdf
    Scansoriopteryx heilmanni is the only known
    saurischian, or theropod, which has the third digit
    of the manus elongated to nearly twice that of the
    second digit. Scansoriopteryx closely resembles
    Archaeopteryx, but differs in the following: a
    definite contact between an elongate ventral process
    of the postorbital and the ascending process of the
    jugal; the lower jaw is equipped with a large
    fenestra; the tail has a greater development in the
    articulation of the zygapophyses. The pelvis is
    similar to that of Archaeopteryx in having the same
    number of sacrals and general shape of the ilia,
    but
    differs in having a small, unexpanded pubic
    peduncle; a significantly short pubis which is not
    retroverted; longer ischia; and an acetabulum which
    is not entirely perforated.
    Scansoriopteryx is clearly more primitive
    than Archaeopteryx in many respects such as its
    saurischian-style pelvis which has remarkably short
    pubes; elongate and robust ischia; and
    comparatively small pubic peduncles. These
    primitive features further suggest that the nearly
    closed acetabulum is not a reversal, but a true
    plesiomorphic condition.



    Riddle of the Feathered Dragons
    The [Scansoriopteryx] pelvis is still like that of a reptile (as opposed to a theropod) 

    Scansoriopterygidae are basal paraves with flight feathers on the arms and legs.
    Scansoriopterygidae (or a group very much like it) is the ancestor of the later Paraves such as Microraptor, Archaeopteryx etc.
    Rhamphorhynchidae (or a group very much like it) is the ancestor of Scansoriopterygidae.

    Rhamphorhynchidae pycnofibres are homologous to Scansoriopteryx feathers.
    The Rhamphorhynchidae acetabulum is homologous to the Scansoriopteryx acetabulum.
    The Rhamphorhynchidae caudal rods are homologous to the Scansoriopteryx caudal rods.