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 feathered basal paraves 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 feathered 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 lumps in the basal paraves (the feathered 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) goes 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. (See here for details). 



    NEW
    Alternative based on Yi qi:
    2-3-4-5-x Pterosaur
    2-3-4-x-x Yi qi (the rod-like bone is the 4th finger metacarpal)
    2-3-4-x-x Scansoriopteryx 
    2-3-4-x-x Basal eumaniraptora
    1-2-1-x-x Modern bird

    Note that David Peters make an interesting case for the idea that the Yi qi "styliform element" is a displaced radius and ulna.
    https://pterosaurheresies.wordpress.com/2015/05/03/no-styliform-element-on-yi-qi-thats-just-a-displaced-radius/
    https://pterosaurheresies.wordpress.com/2015/05/04/yi-qi-and-occams-razor/



    Dinosaur hand transition reference:
    https://www.google.ca/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&cad=rja&uact=8&ved=0CCsQFjAC&url=http%3A%2F%2Fwww.researchgate.net%2Fprofile%2FXing_Xu%2Fpublication%2F240308509_Tracing_the_Evolution_of_Avian_Wing_Digits%2Flinks%2F02e7e537560ae766a3000000.pdf&ei=CZxGVaugLNalyAS1nIDgAg&usg=AFQjCNFdcg3bgYQxu_mVRcztatgns_d_fQ&sig2=PauK8RYVATPAVZvHO0sFwA&bvm=bv.92291466,d.aWw

    Also see the July 30 post.

    http://www.sciencedirect.com/science/article/pii/S0169534702000186
    New studies by Larsson and Wager, and by Feduccia and Nowicki of the embryogenesis of birds undisputedly show Anlagen for five fingers. This has important implications. First, the early presence of digit I, and its later disappearance, indicate that the evolutionary reduction of digits occurred via developmental arrest followed by degeneration. Second, it shows that the digits in the wings of birds develop from Anlagen II–IV. This suggests that the hypothesized descent of birds from theropods might be problematic, because theropods are assumed to have digits I–III.