Monday, November 16, 2015

The bigger picture

Here is the bigger picture.
We can see the dinosaur branch that simply went extinct, and the pterosaur branch that leads to birds.

Here is a cladistic analysis, which confirms the placement of Oviraptors (eg. Hagryphus, Conchoraptor) and Alvarezsaurids (eg. Mononykus, Shuvuuia) within Paraves:

Here is the TNT input file, which is based on the data from:

A Jurassic ceratosaur from China helps clarify avian digital homologies

517 17

Euparkeria ???0000?0?000???00?0?00000000000000000001??00000000000?0?1000??0


Allosaurus ???0?0100101?0000?000?10?010?0??0??0????11??00000111?0??11001000?


Tyrannosaurus ???100000011101011101100000000001110010?00221000001110??1111010





Gallus 0









Saturday, November 14, 2015


The dino to bird theory requires "remarkable" reversals.
The anklebone (astragalus) of dinosaurs presents a characteristic upward projection, the ‘ascending process’ (ASC). The ASC is present in modern birds, but develops a separate ossification centre, and projects from the calcaneum in most species. These differences have been argued to make it non-comparable to dinosaurs. We studied ASC development in six different orders of birds using traditional techniques and spin–disc microscopy for whole-mount immunofluorescence. Unexpectedly, we found the ASC derives from the embryonic intermedium, an ancient element of the tetrapod ankle. In some birds it comes in contact with the astragalus, and, in others, with the calcaneum. The fact that the intermedium fails to fuse early with the tibiale and develops an ossification centre is unlike any other amniotes, yet resembles basal, amphibian-grade tetrapods. The ASC originated in early dinosaurs along changes to upright posture and locomotion, revealing an intriguing combination of functional innovation and reversion in its evolution.
We confirm the proximal–posterior bone is a pisiform in terms of embryonic position and its development as a sesamoid associated to a tendon. However, the pisiform is absent in bird-like dinosaurs, which are known from several articulated specimens. The combined data provide compelling evidence of a remarkable evolutionary reversal: A large, ossified pisiform re-evolved in the lineage leading to birds, after a period in which it was either absent, nonossified, or very small, consistently escaping fossil preservation.

There is no actual evidence for these reversals. The dino to bird theorists need to imagine they happened so the dino to bird theory does not collapse.

Monday, November 2, 2015

Unjustifiable assumptions of homology
Unjustifiable assumptions of homology incorporated
into data matrices.—The most glaring example of
this problem is the coding of avian and theropod
manual, carpal, and tarsal characters as if they were homologous, despite the ambiguity of the data, and despite the assumption this coding entails that
the BMT ["birds are maniraptor theropods"] hypothesis is correct a priori. 
Because of the above ambiguities, these five
sets of characters [the palate, the basipterygoid process, the carpus, the manus, and the tarsus] cannot be coded for birds and theropods without unjustified assumptions of
homology. They were not included in the primary
analysis of our matrix. This decision is
understood to be especially controversial, so
we have documented our reasoning, which was
based on careful review of the anatomical evidence,
in Appendix 3.

Criticisms of the James and Pourtless study:,d.cWw

James and Pourtless excluded the characteristics that are in dispute. That is impartial.
The critics object to that. The critics want things scored their way.

Tuesday, October 13, 2015

From pterosaur to primitive bird

Here is a draft of the lineage from pterosaur to primitive bird (click to enlarge):

This shows the transition from pterosaur to flying primitive birds and it also shows how the alvarezsaurids and oviraptors fit in as secondarily flightless primitive birds.

Connection of Rhamphorhynchoid pterosaurs to primitive birds:

Oviraptors as secondarily flightless primitive birds:

Connection of Jeholornis and Oviraptors:

If anyone has a comment or a question, please feel free to submit it.

Monday, October 12, 2015

Jeholornis and Oviraptors

I suggest that secondarily flightless oviraptors descended (in both senses) from a flying creature like Jeholornis. Notice the similarities in morphology, time and location.
Jeholornis (meaning "Jehol bird") is a genus of avialans that lived between approximately 122 and 120 million years ago during the early Cretaceous Period in China. Fossil Jeholornis were first discovered in the Jiufotang Formation in Hebei Province, China (in what was previously Rehe Province, also known as Jehol—hence the name) and additional specimens have been found in the older Yixian Formation.[1] Jeholornis had long tails and few small teeth, and were approximately the size of turkeys,[2] making them among the largest avialans known until the Late Cretaceous. Their diet included seeds of cycadsGinkgo or similar plants. Jeholornis were relatively large, primitive avialans, with a maximum adult length of up to 80 cm (2.6 ft).[2] Their skulls were short and high, similar to other primitive avialans like Epidexipteryx and to early oviraptorosaurs like Incisivosaurus.
Avialae is also occasionally defined as an apomorphy-based clade (that is, one based on physical characteristics). Jacques Gauthier, who named Avialae in 1986, re-defined it in 2001 as all dinosaurs that possessed feathered wings used in flapping flight, and the birds that descended from them.[8][9]
Oviraptorosaurs ("egg thief lizards") are a group of feathered maniraptoran dinosaurs from the Cretaceous Period of what are now Asia and North America. They are distinct for their characteristically short, beaked, parrot-like skulls, with or without bony crests atop the head. They ranged in size from Caudipteryx, which was the size of a turkey, to the 8 metre long, 1.4 ton Gigantoraptor.[4] The group (along with all maniraptoran dinosaurs) is close to the ancestry of birds. Analyses like those of Maryanska et al (2002) and Osmólska et al. (2004) suggest that they may represent primitive flightless birds.[5][6]
Caudipteridae is a family of oviraptorosaurian dinosaurs known from the Early Cretaceous of China. Found in the Yixian and Jiufotang Formations, the group existed between 125-120 million years ago.
Protarchaeopteryx (meaning "before Archaeopteryx") is a genus of turkey-sized feathered theropod dinosaur from China.[1] Known from the Jianshangou bed of the Yixian Formation, it lived during the early Aptian age of the Early Cretaceous, approximately 124.6 million years ago.[2]



"Maniraptors" were either secondarily flightless avialae or secondarily flightless non-avialae paraves.
In either case, they descended from flying ancestors. They are not transitional between dinosaurs and Paraves.

Sunday, October 11, 2015


There are many problems with the analyses of the dino to bird theory. Here is one of them:
Also, the use of bipedal coelurosaurian
outgroups, as in the analysis by Clark et
al. (2002), may be contributing to a potentially
misleading topology. Outgroup choice determines
the polarity of character states, including
ancestral reconstructions for entire clades (Nixon
and Carpenter 1993). In this case, using bipedal
cursors as outgroups may obscure phylogenetic
signal by wrongly treating characters indicating
flight loss as plesiomorphy.
The "maniraptors" such as oviraptors and ornithomimosaurs were flightless. They lived on the ground. The question is whether their ancestor was a ground-living creature (such as a dinosaur) or whether their ancestor was a flying, primitive bird.
When a cladistic analysis uses a ground-based dinosaur (eg. allosaurus) as the outgroup it takes the flightlessness of the "maniraptors" as being inherited from a dinosaur lineage, when in fact they actually descended (in both senses) from a flying primitive bird ancestor.

Sunday, October 4, 2015


The ancestor of primitive birds was a rhamphorhynchoid pterosaur much like Jeholopterus or Pterorhynchus.
The earliest primitive birds were the feathered, flying creatures with long-bony-tails, such as the scansoriopterygids.
The scansoriopterygids would have lived alongside synapsids such as the aquatic Castorocauda and arboreal gliding mammal Volaticotheriumthe 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]
The [Epidendrosaurus] material described in this paper was collected from a new locality, Daohugou, in east Nei Mongol, northeast China, which is west of Liaoning Province. Many salamanders(Wang 2000), plants and insects (Zhang 2002)have recently been discovered from this new locality. It is notable that an anurognathid rhamphorhynchoid pterosaur [Jeholopterus] with beautiful hair [pycnofibers] covering the whole body has also been reported from this locality (Wang et al. 2002). The estimated age of the deposit at this locality is very controversial and ranges from the Middle Jurassic or the Early Cretaceous according to various authors (Wang etal. 2000; Zhang 2002); however, most workers currently regard it as being Late Jurassic.
Two other Chinese specimens were reported with integumental covering, coming from the same stratum (the Daohugou Bed) as Jeholopterus. So far we have not had the opportunity to examine this material. The first one is a small unnamed anurognathid with extensive preservation of soft tissue, including fibres that have been interpreted as protofeathers (Ji & Yuan 2002). The published pictures show that the soft tissue interpreted as protofeathers is of the same nature as the pycnofibres of Jeholopterus.
At least some pterosaurs had hair-like filaments known as pycnofibres on the head and body, similar to, but not homologous (sharing a common structure) with, mammalian hair. Though a fuzzy "integument" (natural covering/outer coat) "was first reported in 1831" by Goldfuss,[29] recent pterosaur finds and the technology for histological and ultraviolet examination of pterosaur specimens have provided incontrovertible proof: pterosaurs had pycnofibre coats. Pycnofibres were not true hair as seen in mammals, but a unique structure that developed a similar appearance. Although, in some cases, actinofibrils (internal structural fibres) in the wing membrane have been mistaken for pycnofibres or true hair, some fossils such as those of Sordes pilosus (which translates as "hairy demon") and Jeholopterus ninchengensis do show the unmistakable imprints of pycnofibres on the head and body, not unlike modern-day bats, another example of convergent evolution.[21] The head-coats do not cover the pterosaur's large jaws in many of the specimens found so far.[29]
Jeholopterus was a small anurognathid pterosaur from the Middle to Late Jurassic[1] Daohugou Beds of the Tiaojishan Formation of Inner MongoliaChina , preserved with hair-like pycnofibres and skin remains.
We report a new and nearly completely articulated rhamphorhynchoid pterosaur, Jeholopterus ningchengensis gen. et sp. nov., with excellently preserved fibres in the wing membrane and “hairs” [pycnofibers] in the neck, body and tail regions. Many of its characteristics such as a short neck, short metacarpals and distinctively long fifth pedal digit are characteristic of rhamphorhynchoids. The new species can be further referred to the ‘strange’ short-tailed rhamphorhynchoid family Anurognathidae. It is much more complete than the other known members of the family, namely, Anurognathus from Solnhofen, Germany, Batrachognathus from Karatau, Kazakhstan, and Dendrorhynchoides from Beipiao, Liaoning Province, China. The new pterosaur also shows that the wing membrane is attached to the ankle of the hind limb. The pedal digits are webbed. Furthermore, the “hair” of Jeholopterus bears some resemblance to the hair-like integumental structures of the feathered dinosaur Sinosauropteryx although there is yet no direct evidence to argue for or against their homology.
A new rhamphorhynchoid [Pterorhynchus] is described with a headcrest that is unprecedented among the long-tailed pterosaurs. The preservation of the headcrest presents significant implications regarding the physical appearance and aerodynamics of all pterosaurs. Also, "hair-like" integumentary structures of this pterosaur are shown to be complex multi-strand structures which presents evidence on the origin of feathers and the possibility of a remarkably early ancestral relationship between pterosaurs and birds.
Pterorhynchus was a genus of rhamphorhynchid "rhamphorhynchoid" pterosaur from the Middle or Late Jurassic-age Daohugou Formation[1] of Inner Mongolia,China.
This type specimen consists of an articulated, nearly complete skeleton with remains of the integument. These included the wing membrane, hair-like structures, a long version of the vane found at the end of "rhamphorhynchoid" tails, and a head crest with both a low bony base and a large keratin extension; the latter feature is unusual in "rhamphorhynchoids" (i.e. basal pterosaurs), the fossils of which do not often show head crests.
The hairs (pycnofibers) were originally described as pinnate, with many strands arising from a single base (calamus), and seen as corresponding to the hypothetical Stage II in the evolution of feathers.
The only known Yi qi fossil was found in rocks assigned to the Tiaojishan Formation, dating to the Callovian-Oxfordian age of the Middle-Late Jurassic,[1] dated to between 165 and 153 million years ago.[3] This is the same formation (and around the same age) as the other known scansoriopterygids Epidexipteryx and Scansoriopteryx.
Darwinopterus (meaning "Darwin's wing") is a genus of pterosaur, discovered in China and named after biologist Charles Darwin. Between 30 and 40 fossil specimens have been identified,[1] all collected from the Tiaojishan Formation, which dates to the middle Jurassic period, 161-160.5 Ma ago.[2] The type species, D. modularis, was described in February 2010.[3] D. modularis was the first known pterosaur to display features of both long-tailed ('rhamphorhynchoid') and short-tailed (pterodactyloid) pterosaurs, and was described as a transitional fossil between the two groups.[4] Two additional species, D. linglongtaensis and D. robustodens, were described from the same fossil beds in December 2010 and June 2011, respectively.[5][6]
Darwinopterus, like its closest relatives, is characterized by its unique combination of basal and derived pterosaurian features. While it had a long tail and other features characteristic of the 'rhamphorhynchoids', it also had distinct pterodactyloid features, such as long vertebrae in the neck and a single skull opening in front of the eyes, the  (in most 'rhamphorhynchoids', the antorbital fenestra and the nasal opening are separate).[5]
Turner et al 2012.

For reference:
The Rhamphorhynchoidea forms one of the two suborders of pterosaurs and represent an evolutionary grade of primitive members of this group of flying reptiles. This suborder is paraphyletic in relation to the Pterodactyloidea, which arose from within the Rhamphorhynchoidea, not from a more distant common ancestor.
Plieninger, 1901
Included groups




Sunday, August 9, 2015

Primitive Birds

Here is a partial list of primitive (feathered, long-bony-tailed) flying and secondarily flightless birds.

Scansoriopterygids (Temporal range: Late Jurassic, 165–156 Ma)
Anchiornis (Temporal range: Late Jurassic, 161–160.5 Ma)
Aurornis (Temporal range: Late Jurassic, 160 Ma)
Xiaotingia (Temporal range: Late Jurassic, 160 Ma)
Zhongornis (Temporal range: Early Cretaceous, 122 Ma)
Oviraptors (secondarily flightless)

Eosinopteryx? (Temporal range: Late Jurassic, 160 Ma)
Pedopenna? (Temporal range: Middle or Late Jurassic, 164 Ma)

The flying primitive (feathered, long-bony-tailed) birds evolved from pterosaurs.
The secondarily flightless primitive birds evolved from the flying primitive birds. 

Monday, July 20, 2015

Basalmost Paraves

There is a set of 4-winged, flying, primitive birds (eg. Anchiornis, Aurornis, Xiaotingia etc.) that at times have been classified as avialans and sometimes as dromaeosaurids. They actually belong to the basalmost Paraves. 
They are the Tetrapterygidae and the Scansoriopterygids.
I suggest that these flying primitive birds evolved from pterosaurs.
Later, some of these primitive birds settled on the ground and became secondarily flightless (eg. eudromaeosaurids, oviraptors etc).
the work of Xu et al. (2003), (2005) and Hu et al. (2009) provide examples of basal and early paravians with four wings,[10][11][12] adapted to an arboreal lifestyle who would only lose their hindwings when some adapted to a life on the ground and when avialans evolved powered flight.[13] Newer research also indicates that gliding, flapping and parachuting was another ancestral trait of Paraves, while true powered flight only evolved once, in the lineage leading to modern birds.[14]
Tetrapterygidae (meaning "four-wings") is a group of four-winged dinosaurs proposed by Sankar Chatterjee in the second edition of his book The Rise of Birds: 225 Million Years of Evolution, where he included Microraptor, XiaotingiaAurornis, and Anchiornis.[1] The group was named after the characteristically long flight feathers on the legs of all included species, as well as the theory that the evolution of bird flight may have gone through a four-winged (or "tetrapteryx") stage, first proposed by naturalist William Beebe in 1915.[2] Chatterjee suggested that all dinosaurs with four wings formed a natural group exclusive of other paravians, and that this family was the sister taxon to the group Avialae, although most phylogenetic analyses have placed the animals of his Tetrapterygidae elsewhere in Paraves, such as Xiaotingia, Aurornis, and Anchiornis being placed in Avialae.[3]


Zhenyuanlong  is a secondarily flightless member of Paraves. (2015)
A large, short-armed, winged dromaeosaurid (Dinosauria: Theropoda) from the Early Cretaceous of China and its implications for feather evolution
Regardless of the precise phylogenetic relationships of dromaeosaurids, Zhenyuanlong provides the first glimpse of feather morphologies in a short-armed dromaeosaurid. Feathers are not preserved on the holotype of Tianyuraptor, and the shortness of the forearm in this taxon led to the suggestion that its arms lacked aerodynamic function15. Although the arms of Zhenyuanlong are short, they supported large and complex wings comprised of pennaceous coverts, primaries, and secondaries, some of which are asymmetric. Whether these wings served any type of aerodynamic function is a separate question that can only be answered with biomechanical analysis, but the wings of Zhenyuanlong are strikingly similar to those of Microraptor in general size, morphology, and composition, albeit they are supported by much smaller arms.
The integumentary similarities between Zhenyuanlong and Microraptor-type animals could suggest one of several explanations. First, the large short-armed dromaeosaurids may have had some volant abilities, unrecognized previously because Tianyuraptor was preserved without feathers and its small arms were assumed to be un-flightworthy15. Perhaps there was not a large functional and behavioural gap between animals like Microraptor and Zhenyuanlong. We find this unlikely, however, given the striking differences in body size between them, and the incredibly short arms of Zhenyuanlong which do not appear optimized for flight (although we reiterate that biomechanical modelling is needed to properly test this). Alternatively, the integumentary similarities between small and clearly volant dromaeosaurids7 and larger and presumably non-volant dromaeosaurids could suggest that the larger and short-armed Zhenyuanlong evolved from more volant ancestors and maintained a many aspects of the integument through the inertia of common descent or for other selective reasons, not because it needed them for flight. It may be that such large wings comprised of multiple layers of feathers were useful for display purposes40, and possibly even evolved for this reason and not for flight, and this is one reason why they may have been retained in paravians that did not fly.

Sunday, July 5, 2015

Primitive birds flying

Primitive birds (basalmost paraves) flapped their wings and flew using the same set of muscles as their pterosaur ancestors.
At times people have argued that a flying pterosaur would not devolve into a gliding primitive bird. I would agree. But this is not an issue, because the evidence indicates that flying pterosaurs evolved into flying primitive birds, not into gliding primitive birds.

At one stage, it was thought that the flight muscles of
pterosaurs were very [modern] birdlike, with the arm lifted by
a muscle, m. supracoracoideus, anchoring on the sternum
rather than the shoulders. In birds, this muscle
arcs over the glenoid to attach on the dorsal surface
of the humerus, elevating the wing with a pulley-like
system (e.g., Kripp 1943; Padian 1983a; Wellnhofer
1991a). Detailed reconstruction of the proximal arm
musculature of pterosaurs shows that this is not
the case, however, and that the [pterosaur] arm was more likely lifted by large muscles anchored on the scapula and
back, and lowered by those attached to the sternum
and coracoid
 (fig. 5.8; Bennett 2003a). Unlike [modern] birds,
where two vastly expanded muscles are mainly used
to power flight, it appears that pterosaurs used several
muscle groups to form their flapping strokes.

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.

Concerning the lack of asymmetric feathers in flying basalmost paraves, the following seems relevant:

The basal deinonychosaur Anchiornis [a primitive bird] might offer a possible explanation. It had symmetrical feathers, but they were arranged in an unique away; in species with asymmetrical feathers, the most distally attached wing feathers are the longest ones. In Anchiornis, the longest are anchored near the wrist, making the center of the wing the broadest area. This is not an unusual profile among flightless maniraptors – oviraptors like Caudipteryx have this sort of arrangement as well. Anchiornis, however, differs in that the feathers at the front (as in, anchored more distally) of the longest feather decrease rapidly in size as they are closer to the end of the supporting digit; this results in a rounded, yet slightly pointy wing shape.
It is possible that this arrangement could had been an early adaptation to the demands of powered flight, before true asymmetrical feathers evolved. If so, it is possible that Anchiornis did engage in powered flight, or even a method of escape akin to rudimentary WAIR. So far, no tests have been conducted to examine the aerodynamic capacities of it’s wings.
In Anchiornis, the entire wing forms the airfoil.
Primitive bird:
In modern birds (Neornithes), the wing is composed of a layer of long, asymmetrical flight feathers overlain by short covert feathers [1-3]. It has generally been assumed that wing feathers in the Jurassic bird Archaeopteryx [4-9] and Cretaceous feathered dinosaurs [10, 11] had the same arrangement. Here, we redescribe the wings of the archaic bird Archaeopteryx lithographica [3-5] and the dinosaur Anchiornis huxleyi [12, 13] and show that their wings differ from those of Neornithes in being composed of multiple layers of feathers. In Archaeopteryx, primaries are overlapped by long dorsal and ventral coverts. Anchiornis has a similar configuration but is more primitive in having short, slender, symmetrical remiges. Archaeopteryx and Anchiornis therefore appear to represent early experiments in the evolution of the wing. This primitive configuration has important functional implications: although the slender feather shafts of Archaeopteryx [14] and Anchiornis [12] make individual feathers weak, layering of the wing feathers may have produced a strong airfoil. Furthermore, the layered arrangement may have prevented the feathers from forming a slotted tip or separating to reduce drag on the upstroke. The wings of early birds therefore may have lacked the range of functions seen in Neornithes, limiting their flight ability.
Longrich NR, Vinther J, Meng Q, Li Q, Russell AP.

Elliptical wings are short and rounded, having a low aspect ratio, allowing for tight maneuvering in confined spaces such as might be found in dense vegetation. As such they are common in forest raptors (such as Accipiter hawks), and many passerines, particularly non-migratory ones (migratory species have longer wings). They are also common in species that use a rapid take off to evade predators, such as pheasants and partridges.

Altogether we have a picture of a flying, feathered, 4 winged, arboreal, primitive bird with a long bony tail, that flew like a pterosaur. With elliptical wings and symmetric feathers

Here are the aspects related to flight capability:
  • muscles used 
  • keeled or not keeled sternum 
  • flight feathers (asymmetric or not) 
  • feathered hindlimbs

Thursday, July 2, 2015

Fingers - Quick Summary
There is a debate between embryologists and paleontologists whether the hands of theropod dinosaurs and birds are essentially different, based on phalangeal counts, a count of the number of phalanges (fingers) in the hand. This is an important and fiercely debated area of research because its results may challenge the consensus that birds are descendants of dinosaurs.
Dinosaurs have hands with digits 2-3-4-x-x. (Roman numerals represent fingers, numbers represent phalanges).
But primitive birds (basal paraves) have hands with digits x-2-3-4-x.
This is a problem for the dino to bird theory.
To overcome this problem, the dino to bird folk propose changes that include the following:
  • the loss of digit I 
  • the reappearance of the lost digit IV
  • digits II-III-IV adopting the phalangeal count and characteristics of earlier digits I-II-III (via a frame shift) resulting in x-2-3-4-x with digit III the longest.  

The pterosaur transition (from 2-3-4-5-x) would be:
  • the loss of digit I
  • digits II-III-IV lose one phalange each, resulting in x-2-3-4-x with digit IV the longest (as in scansoriopterids). 
Note: The dino to bird folk do not consider scansoriopterids to be on the line leading to birds.

Frame shift
Thus the change of the phalangeal formula (as in the PRH) is actually caused by the change of the transcriptome (as in the FSH [frame shift hypothesis]), which in turn is directly caused by the loss of digit I (probably shh and hoxD mediated).
Dinosaur to bird (notice the original loss of digit IV and its re-appearance)
In the diagram, Neotheropoda ( 1 ), basal tetanurae ( 2 ), a coelurosaurian ( 3 ), the bird (?)Archaeopteryx ( 4 ) and modern bird ( 5 ).

If scansoriopterygids are the basalmost members of paraves, then the very first paraves were (or were very similar to) the scansoriopterygids, which have x-2-3-4-x with digit IV being the longest.
Which is consistent with a pterosaur ancestry and contrary to a dino ancestry.

See here for more details: