Friday, January 9, 2015

Dino to bird - off on the wrong foot

The revival of the dino to bird idea began with the work of John Ostrom in the 1970's. But Ostrom misinterpreted the flightless Deinonychus as a land-based transitional between dinosaur and Paraves.
But it is now clear that Deinonychus is a secondarily flightless member of Paraves. It is a secondarily flightless dromaeosaur which is included in Paraves. "Secondarily" means that it descended from a flying ancestor.
The current dino to bird theory revival dates back to Ostrom's misinterpretations in the 1970's.
There is no connection between actual dinosaurs and Paraves.

Relevant links:
With the benefit of hindsight it is easy to see that if fossils of the
small flying dromaeosaurs from China had only been discovered before the larger flightless dromaeosaurs like Deinonychus or Velociraptor were found, the interpretations of the past three decades on how birds are related to dinosaurs would have been significantly different. If it had already been established that dromaeosaurs were birds that could fly, then the most logical interpretation of larger flightless dromaeosaurs found afterwards would have to be that they represented birds, basically like the prehistoric equivalent of an Ostrich, which had lost their ability to fly.
At least two schools of researchers have proposed that dromaeosaurids may actually be descended from flying ancestors.

They even have a category for the flightless members of Dromaeosauridae which are actually secondarily flightless:
Temporal range: Early Cretaceous – Late Cretaceous, 143–66Ma

Eudromaeosauria ("true dromaeosaurs") is a subgroup of terrestrial dromaeosaurid theropod dinosaurs. They were relatively large-bodied, feathered hypercarnivores (with diets consisting almost entirely of other terrestrial vertebrates) that flourished in the Cretaceous Period.
If some maniraptorans were
birds, and if birds were not theropods, similarities
between maniraptorans and theropods could
be readily explained by convergence on a cursorial
morphotype subsequent to the loss of flight.
Even distantly related reptiles could converge
closely, in some cases almost indistinguishably,
on the theropod morphotype through the acquisition
of cursoriality, as the case of Effigia, noted
above, dramatically demonstrates (Nesbitt and
Norell 2006, Nesbitt 2007). If this is the case, some
maniraptorans represent lineages of cryptic birds
whose true phylogenetic relationships have been
obscured by convergence and the loss of flight.
Given the evidence that some maniraptorans
may belong within Aves and that, consequently,
Aves may not belong within Theropoda, this possibility
must be seriously considered.
In the case of Effigia, the trend toward bipedalism produced extreme convergence throughout the cranial and
postcranial skeleton on that of highly cursorial
ornithomimosaurs, with further convergence on
numerous characters of the avemetatarsalian,
dinosaurian, theropod, neotetanurine, and coelurosaurian
skeletons; in some cases, the relevant
characters are identical across taxa (Nesbitt and
Norell 2006, Nesbitt 2007).

The taxa that were originally thought to provide support for a dino to bird theory (eg. Deinonychus) are no longer considered to be related to the purported line from dinosaur to Paraves. Rather they are members of Paraves.
Several years later, Ostrom noted similarities between the forefeet of Deinonychus and that of birds, an observation which led him to revive the hypothesis that birds are descended from dinosaurs.[34]
Saurischian monophyly and the origin of birds
Jacques Gauthier
Ostrom (1976)
This is the original Ostrom article. He notes the similarity of caudal rods.
Page 135:
Of greatest interest, though, is the peculiar elongated form of the zygopophyses
of the last 15 to 16 vertebrae. While not so extreme as in the dromaeosaurids
Deinonychus or Velociruptor, or in the rhamphorhynchoid pterosaurs, their
form is very reminiscent of the condition in struthiomimid theropods.
Similarly, the chevrons behind the seventh caudal are also greatly elongated
antero-posteriorly and severely flattened dorso-ventrally, as in both
struthiomimids and dromaeosaurids.
To the best of my knowledge, these conditions are not known in any pseudosuchian, or in any other reptile other than the theropods cited and rhamphorhynchoids.
Following their discovery, dromaeosaurs
were initially thought to be flightless nonavian
dinosaurs ancestral to actual birds which eventually
evolved the ability to fly; hence, according to this
hypothesis, avian aerodynamic adaptations evolved by
exaptations in earth-bound forms (Sereno 1999). The
dromaeosaurs therefore appeared to represent feathered
dinosaurs which were wingless ancestors of birds that
were not yet capable of flight. However, with the discovery
of fully volant basal dromaeosaurs, the microraptors,
with a four-winged, tetrapteryx bauplan and
avian pennaceous, asymmetric flight remiges, the concept
of a dinosaurian trees-down model was introduced
(Zhou and Zhang 2006; Chatterjee and Templin 2012).
Also interesting:
In 1969, this dinosaur was described and named Deinonychus by John Ostrom of Yale University.[24] The next year, Ostrom redescribed a specimen of Pterodactylus in the Dutch Teyler Museum as another skeleton of Archaeopteryx.[25] The specimen consisted mainly of a single wing and its description made Ostrom aware of the similarities between the wrists of Archaeopteryx and Deinonychus.[26]
The Haarlem [archaeoptyeryx] Specimen (TM 6428/29, also known as the Teyler Specimen) was discovered in 1855 near Riedenburg, Germany, and described as a Pterodactylus crassipes in 1857 by Meyer. It was reclassified in 1970 by John Ostrom and is currently located at the Teylers Museum in Haarlem, Netherlands.
Ostrom's interest in the dinosaur-bird connection started with his study of what is now known as the Haarlem Archaeopteryx. Discovered in 1855, it was actually the first specimen recovered but, incorrectly labeled as Pterodactylus crassipes, it languished in the Teylers Museum in the Netherlandsuntil Ostrom's 1970 paper (and 1972 description) correctly identified it as one of only eight "first birds" (counting the solitary feather).
A hypothesis, credited to Gregory Paul and propounded in his books Predatory Dinosaurs of the World (1988) and Dinosaurs of the Air (2002), suggests that some groups of non-flying carnivorous dinosaurs—especially deinonychosaurs, but perhaps others such as oviraptorosaurs, therizinosaurs, alvarezsaurids and ornithomimosaursactually descend from birds.
Because it displays a number of features common to both birds and non-avian dinosaurs, Archaeopteryx has often been considered a link between them.[11] In the 1970s, John Ostrom, following T. H. Huxley's lead in 1868, argued that birds evolved within theropod dinosaurs and Archaeopteryx was a critical piece of evidence for this argument; it had a number of avian features, such as a wishbone, flight feathers, wings, and a partially reversed first toe along with a number of dinosaur and theropod features. For instance, it has a long ascending process of the ankle bone, interdental plates, anobturator process of the ischium, and long chevrons in the tail. In particular, Ostrom found that Archaeopteryx was remarkably similar to the theropod family Dromaeosauridae.[14][15][16][17][18][19][20][21][22]
Shortly after, Wagner presented a talk at the Bavarian Academy of Sciences, which was later published as an article in 1862. In this talk, Wagner gives a detailed account of the curious combination of avian and saurian features that made the fossil so unique and mysterious. He describes the feather imprints of the fossil to be "those of true birds", and went on to describe other features, like the long tail, that bore "not the least resemblance to that of a bird". He compares the fossil to Rhamphorhynchus, a Solnhofen pterosaur which also possessed a long, bony tail. He regarded the creature as a "mongrel" of bird and reptile, the whole of which was incomprehensible to him.[1][20]

Furthermore, a large distal carpal occupying the same position in the basal neotheropods Syntarsus and Coelophysis has been identified as a compound bone formed by fusion of distal carpals 1 and 2, leading Gauthier to suggest that these distal carpals were also homologous to the ‘semilunate' carpal of non-avian maniraptorans. However, this hypothesis is in conflict with ontogenetic data from both Mesozoic birds and living birds,, which show that the distal carpal proximal to the medialmost metacarpal is absent in birds and the lateralmost carpal is involved in the formation of the transversely convex and trochlear proximal articular surface. This conflict has been repeatedly cited as evidence against the theropod hypothesis of avian origins (e.g., ref.,).
Gauthier was wrong in the first place about this subject. This is one of the reasons why the dinosaur to bird theory started out on the basis of wrong analysis.


2011 study (Xu):
An Archaeopteryx-like theropod from China and the origin of Avialae
Archaeopteryx is widely accepted as being the most basal bird, and accordingly it is regarded as central to understanding avialan origins; however, recent discoveries of derived maniraptorans have weakened the avialan status of Archaeopteryx. Here we report a new Archaeopteryx-like theropod from China. This find further demonstrates that many features formerly regarded as being diagnostic of Avialae, including long and robust forelimbs, actually characterize the more inclusive group Paraves (composed of the avialans and the deinonychosaurs). Notably, adding the new taxon into a comprehensive phylogenetic analysis shifts Archaeopteryx to the Deinonychosauria. Despite only tentative statistical support, this result challenges the centrality ofArchaeopteryx in the transition to birds. If this new phylogenetic hypothesis can be confirmed by further investigation, current assumptions regarding the avialan ancestral condition will need to be re-evaluated.
(Characters 1-363 are from Hu et al. (2009), whereas 364-374 are newly
Deinonychosauria: 29.1, 72.1, 75.1, 82.0, 111.1, 134.1, 171.2, 183.1, 189.0, 199.1, 233.1,
238.0, 255.0, 294.1, 297.1, 302.1, 323.1, 334.1, 335.2, 359.0, 364.0, 365.0, 366.1, 367.0,
368.0, 371.0, and 372.1 
Paraves: 1.1, 10.1, 13.0, 14.0, 15.1, 20.1, 21.1, 28.1, 39.0, 61.1, 65.0, 66.0, 69.0, 79.0, 91.0,
95.0, 96.1, 97.1, 106.0, 109.1, 119.1, 125.0, 127.1, 129.1, 137.1, 138.1, 139.1, 154.0, 155.1,
156.1, 160.1, 166.0, 176.1, 179.1, 180.1, 184.1, 202.1, 221.1, 232.0, 237.1, 262.1, 267.1,
277.2, 292.0, 304.2, 306.1, 319.1, 320.2, 336.1, 354.0, and 362.1
Paraves-Oviraptorosauria-Therizinosauroidea clade: 13.1, 14.1, 28.0, 29.0, 39.1, 41.2, 54.0,
66.2, 79.1, 91.2, 106.1, 116.1, 117.1, 119.0, 121.1, 125.1, 126.1, 127.0, 130.1, 131.1, 136.1,
144.1, 157.2, 166.2, 167.2, 200.1, 238.1, 255.1, 276.1, 284.1, 300.1, 329.1, 351.1, 354.1,
359.1, 363.1, 364.1, 365.1, 367.1, 368.1, and 371.1.

2008 study (Zhang)
A bizarre Jurassic maniraptoran from China with elongate ribbon-like feathers
Characters 361-363 are newly added. Characters 4, 25, 33, 40-42, 65, 67, 69, 82, 85, 91,
99, 106, 110, 115, 116, 121, 122, 136, 138, 142, 146, 148, 151, 153, 163, 165-167,
169, 171, 178, 181, 200-203, 212, 230-360 are from Senter (2007); others are from
Kirkland et al. (2005).

2009 study (Hu, D.Y. et al)
A pre-Archaeopteryx troodontid from China with long feathers on the
metatarsus. Nature 461, 640-643

2009 study (Nesbitt)

2010 study (Xu)
Xu, X., Ma, Q.-Y. & Hu, D.-Y. Pre-Archaeopteryx coelurosaurian dinosaurs and their
implications for understanding avian origins. Chin. Sci. Bull. 55, 3971–3977

2011 study (Nesbitt)
Includes basal pterosaurs (Dimorphodon, Eudimorphodon).

2012 study (Michael S. Y. Lee):

2012 study (Turner et al)
"One step" Figure 75

2012 study (Senter)

2013 study (Pascal Godefroit, Cau): (1,500 characters)


2013 (Andres, Myers)

2010 (Andres, Clark, Xu)


2014 study (Stephen L. Brusatte)
Permutation tests, which assess whether the morphospace means of two groups significantly differ from each other over all axes, find birds to be indistinct from their closest paravian relatives (Tables S1 and S2; Supplemental Experimental Procedures).
Although birds are clearly distinct compared to all other living vertebrates, the avian bauplan isn’t especially distinct relative to other coelurosaurs, particularly their closest relatives.
These results are consistent with many recent phylogenetic studies, ours included (see ‘‘Phylogenetic Analysis’’ in the Results), which find few characters separating Avialae from nonavialan theropods. These results may also help explain why so many alternative phylogenetic analyses have difficulty in placing certain taxa (such as Anchiornis and Archaeopteryx) consistently in either Avialae or among the clades of nonavialan theropods most closely related to birds [7–14].
In general anatomical terms, birds are a continuum of millions of years of theropod evolution. There is no great jump between nonbirds and birds in morphospace. Instead, those features that today combine to set birds apart from other vertebrates—feathers, wishbones, air sacs, and hundreds more—evolved piecemeal in Mesozoic theropods [18]. Therefore, we surmise that a Mesozoic naturalist would make no immediate distinction between a Velociraptor-type animal and an Archaeopteryx-type animal.
The clade consisting of Oviraptorosauria and Paraves is supported by a Bremer value of 1 and a jackknife percentage of less than 50%. Paraves—consisting of dromaeosaurids, troodontids, and avialans—is also poorly supported, as it also has a Bremer value of 1 and a jackknife of less than 50%. 

2001 study (Norell),d.aWw

2004 study (Renesto)
Includes one pterosaur (Eudimorphodon)


2007 study (Senter)

2009 study (Xing Xu)

2015 study (Cau)

The phylogenetic affinities of the bizarre Late Cretaceous Romanian theropod Balaur bondoc (Dinosauria, Maniraptora): dromaeosaurid or flightless bird?
Based on phylogenetic analyses and critique of the various unusual features of this theropod, we argue that Balaur is likely not a dromaeosaurid, but a secondarily flightless bird. If you’re at all aware of the discussion that’s surrounded the possible evolution of flightlessness in non-bird paravians (Paul 1988, 2002), the significance of this won’t be lost on you. Our paper (Cau et al. 2015) is published in the open access journal PeerJ, so is available for free to everyone. (2015)
Over the past two decades of research, one overarching pattern has become clear: many features — such as feathers, wishbones, egg brooding, and perhaps even flight — that are seen only in birds among living animals first evolved in the dinosaurian ancestors of birds (Figures 4 and 5). Other features, such as rapid growth, a keeled sternum, pygostyle, and beak, are absent in the earliest birds and evolved, often multiple times, in more derived birds during the Cretaceous. Therefore, what we think of as the bird ‘blueprint’ was pieced together gradually over many tens of millions of years of evolution, not during one fell swoop (Figure 1) [2,3,19,20].
Discoveries of bird-like theropod dinosaurs and basal avialans in recent decades have helped to put the iconic ‘Urvogel’ Archaeopteryx1 into context23456 and have yielded important new data on the origin and early evolution of feathers7. However, the biological context under which pennaceous feathers evolved is still debated. Here we describe a new specimen of Archaeopteryx with extensive feather preservation, not only on the wings and tail, but also on the body and legs. The new specimen shows that the entire body was covered in pennaceous feathers, and that the hindlimbs had long, symmetrical feathers along the tibiotarsus but short feathers on the tarsometatarsus. Furthermore, the wing plumage demonstrates that several recent interpretations89 are problematic. An analysis of the phylogenetic distribution of pennaceous feathers on the tail, hindlimb and arms of advanced maniraptorans and basal avialans strongly indicates that these structures evolved in a functional context other than flight, most probably in relation to display, as suggested by some previous studies101112. Pennaceous feathers thus represented an exaptation and were later, in several lineages and following different patterns, recruited for aerodynamic functions. This indicates that the origin of flight in avialans was more complex than previously thought and might have involved several convergent achievements of aerial abilities.

Tuesday, January 6, 2015

Dinosaur to bird - implausible rates of change

For the dino to bird theory to be correct, the evolutionary rates must have been up to four times faster. But that would mean that for the dino to bird theory to be correct, it would require rates of evolution comparable to those in the Cambrian Explosion. Not plausible.
Huge meat-eating, land-living dinosaurs evolved into birds by constantly shrinking for over 50 million years, scientists have revealed.
Theropods shrunk 12 times from 163kg to 0.8kg before becoming modern birds.
The researchers found theropods were the only dinosaurs to get continuously smaller.
Their skeletons also changed four times faster than other dinosaurs, helping them to survive.
They found that the dinosaur group directly related to birds shrank rapidly from about 200 million years ago.
It showed a decrease in body mass of 162.2kg (25st 7lb) from the largest average body size to Archaeopteryx, the earliest known bird.
These bird ancestors also evolved new adaptations, including feathers, wishbones and wings, four times faster than other dinosaurs.
Shrinking and new bird-like traits jointly influenced the transition of dinosaurs to birds, researchers say.
The researchers concluded that the evolution of the branch of dinosaurs leading to birds was more innovative than other dinosaur lineages.

Because our results allow us to map the appearance dates of lineages onto the phylogeny, we can see that evolutionary rates across part of the lineage leading to birds occurred much faster than expected compared to the rest of the tree – up to four times faster, in fact (Lee et al. 2014a). This seemingly explains why several groups of tetanuran theropods – allosauroids, tyrannosauroids, compsognathids and others – appear near-simultaneously in the fossil record: it seems that the time intervals between their originations really were very short. Why evolution was occurring so rapidly in these animals remains, of course, an unknown.
According to the dino to bird theory, Paraves appeared "near-simultaneously" with its purported coelurosaur dinosaur ancestor . This is no longer evolution theory. This is creationism.

The study itself:


Full study:

The study Supplementary Material:

Also see here:

Comparison with the Cambrian Explosion
The near-simultaneous appearance of most modern animal body plans (phyla) ~530 million years ago during the Cambrian explosion is strong evidence for a brief interval of rapid phenotypic and genetic innovation, yet the exact speed and nature of this grand adaptive radiation remain debated [1–12]. Crucially, rates of morphological evolution in the past (i.e., in ancestral lineages) can be inferred from phenotypic differences among living organisms—just as molecular evolutionary rates in ancestral lineages can be inferred from genetic divergences [13]. We here employed Bayesian [14] and maximum likelihood [15] phylogenetic clock methods on an extensive anatomical[16]and genomic[17] data set for arthropods, the most diverse phylum in the Cambrian and today. Assuming an Ediacaran origin for arthropods, phenotypic evolution was ~4 times faster, and molecular evolution ~5.5 times faster, during the Cambrian explosion compared to all subsequent parts of the Phanerozoic. These rapid evolutionary rates are robust to assumptions about the precise age of arthropods. Surprisingly,these fast early rates do not change substantially even if the radiation of arthropods is compressed entirely into the Cambrian (~542 mega-annum [Ma]) or telescoped into the Cryogenian (~650 Ma). The fastest inferred rates are still consistent with evolution by natural selection and with data from living organisms, potentially resolving ‘‘Darwin’s dilemma.’’ However, evolution during the Cambrian explosion was unusual (compared to the subsequent Phanerozoic) in that fast rates were present across many lineages.
This means that the dino to bird theory is right up there with the Cambrian Explosion in terms of it being very unusual.
The near-simultaneity and the much faster rates of evolution required by the dino to bird theory are VERY UNUSUAL. As unusual as the Cambrian Explosion.


Thursday, January 1, 2015

How did birds come into being?

How did birds come into being?
First we must distinguish between modern birds on the one hand, and their feathered ancestors called "basal paraves" on the other.
Basal paraves were feathered, long-bony-tailed, flying creatures (eg. scansoriopteryx). No modern birds have long-bony-tails.

So the question becomes, how did basal paraves come into being?
The dinosaur to bird theory suggests that basal paraves evolved from coelurosaur dinosaurs (eg. tyrannosaurs).
The pterosaur to bird theory suggests that basal paraves evolved from pterosaurs (eg. rhamphorhynchids). 
The topic immediately becomes complicated, because there is a set of feathered, long-bony-tailed creatures that did not fly (eg. oviraptors, alvarezsaurids).
The dinosaur to bird theory views these creatures as transitional between ground-based coelurosaur dinosaurs and flying basal paraves. They call them "non-paraves maniraptors".
The pterosaur to bird theory views these creatures as secondarily flightless* members of basal paraves.

It is important to realize that according to the fossil record, all these flightless, feathered creatures came after (closer to today than) the flying members of basal paraves.
This is straightforwardly consistent with them being secondarily flightless. On the other hand, for them to be transitional between dinosaurs and flying basal paraves, requires purported lengthy ghost lineages (up to tens of millions of years in length) and purported exaptations.

* An ostrich is an example of a "secondarily flightless" modern bird.