Wednesday, January 6, 2016

Primitive Birds

1. Introduction

The current mainstream theory is that birds evolved from coelurosaur dinosaurs and that ground-dwelling Oviraptors and Alvarezsaurids were on lines that branched from that lineage, as shown here:


However recent analyses show a different placement of Oviraptors and Alvarezsaurids.
This article will present those recent analyses and show where the Oviraptors and Alvarezsaurids are located. We will then look at the significance of the recently discovered pennaceous-feathered, four-winged primitive birds.
Altogether, a new picture arises.


2. Euparaves 

To analyze this subject, it is necessary to identify a new clade, Euparaves.
Euparaves (node-based) definition:
The last common ancestor of Epidendrosaurus ninchengensis (Scansoriopterygidae) and Passer domesticus (the house sparrow) and all descendants thereof.


3. Where are oviraptors and alvarezsaurids placed?

Here are recent analyses that shed new light on the placement of the Oviraptors and Alvarezsaurids.
From these recent analyses, we can see that Oviraptors and Alvarezsaurids are WITHIN Euparaves. They are not successive outgroups (sister-groups) between dinosaurs and Euparaves.


3.1 Brusatte et al (2014)
Shows Oviraptors and Pedopenna within Euparaves.





3.2 Xu et al (2009)
Shows Alvarezsaurids (eg. Patagonykus etc.) within Euparaves.


Figure S7

3.3 Agnolin and Novas (2011)
http://www.scielo.br/img/revistas/aabc/v83n1/a08fig01m.jpg  Figure 1(B)
Shows Alvarezsaurids (eg. Patagonykus etc.) within Euparaves




3.4 Agnolin and Novas (2013)
Shows both Oviraptors and Alvarezsaurids within Euparaves



3.5 O'Connor and Sullivan (2014)
Shows Zhongornis and Oviraptors (eg. Caudipteryx etc.) within Euparaves.


3.6  Here is a new cladistic analysis based on the core set of dinosaurs, scansoriopterygids, oviraptors and alvarezsaurids, from the Xu et al (2009) study. (For details see Appendix 4).
Shows both Oviraptors (eg. Conchoraptor etc.) and Alvarezsaurids (eg. Mononykus etc.) within Euparaves.

Notice that this is very similar to the Agnolin and Novas (2013) finding above.


Conclusion
From these recent analyses, we can conclude that the ground-dwelling Oviraptors and Alvarezsaurids were WITHIN Euparaves. 
This is a good start. Now we need to look more deeply into the basal Euparaves.


4. What were the basal Euparaves like?

From the cladograms, we can see that the membership of basal Euparaves includes at least Scansoriopterygidae, Anchiornis, Aurornis, Xiaotingia, Pedopenna, Zhongornis.

In the Brusatte et al study (2014), Pedopenna is included with Scansoriopterygidae as a basal Euparaves and the Tetrapterygidae members XiaotingiaAurornis, and Anchiornis (along with Eosinopteryx) are grouped as basal Euparaves. 
In the O'Connor and Sullivan study (2014), Zhongornis is shown as a basal Euparaves.
All the studies above show Scansoriopterygidae as basal Euparaves. 

These basal Euparaves are all recently discovered, pennaceous-feathered, arboreal, long-bony-tailed, four-winged primitive birds. 

Tetrapteryx (4 winged)

It has been hypothesized that bird flight went through a four-winged ("tetrapteryx") stage.


Pascal Godefroit1 , Andrea Cau2 , Hu Dong-Yu3,4, François Escuillie´5 , Wu Wenhao6 & Gareth Dyke7 (2013a)
Epidendrosaurus, Epidexipteryx and Eosinopteryx, also from the Middle–Late Jurassic of northeastern China, are here regarded as basal, non-eumaniraptoran paravians. Thus our phylogeny is entirely consistent with the presence of a tetrapterygian condition (= four winged) and elongated rectrices in basal eumaniraptorans.

Xing Xu , Fucheng Zhang (2005)
The unusual presence of long pennaceous feathers on the feet of basal dromaeosaurid dinosaurs has recently been presented as strong evidence in support of the arboreal–gliding hypothesis for the origin of bird flight, but it could be a unique feature of dromaeosaurids and thus irrelevant to the theropod–bird transition. Here, we report a new eumaniraptoran theropod [Pedopenna] from China, with avian affinities, which also has long pennaceous feathers on its feet. This suggests that such morphology might represent a primitive adaptation close to the theropod–bird transition. The long metatarsus feathers are likely primitive for Eumaniraptora and might have played an important role in the origin of avian flight.

Dongyu Hu1, Lianhai Hou1,2, Lijun Zhang1,3 & Xing Xu1,2  (2009)
The early evolution of the major groups of derived non-avialan theropods is still not well understood, mainly because of their poor fossil record in the Jurassic. Here we report on an exceptionally well-preserved small theropod specimen [Anchiornis] collected from the earliest Late Jurassic Tiaojishan Formation of western Liaoning, China2. The specimen is referable to the Troodontidae, which are among the theropods most closely related to birds. .... the extensive feathering of this specimen, particularly the attachment of long pennaceous feathers to the pes, sheds new light on the early evolution of feathers and demonstrates the complex distribution of skeletal and integumentary features close to the dinosaur–bird transition.
Large pennaceous feathers are now known to occur on the lower leg and particularly the metatarsus of at least one basal member of each of the three major paravian groups, namely the basal troodontid Anchiornis, the basal avialan Pedopenna and the basal dromaeosaurid Microraptor13,16. Furthermore, many basal avians have proportionally large pennaceous feathers on the lower leg13,17, which are reduced in more derived birds. This suggests that large pennaceous feathers first evolved distally on the hindlimbs, as on the forelimbs and tail. This distal-first development led to a four-winged condition at the base of the Paraves. Whereas the large feathers of the forewing developed further in subsequent avian evolution, the large hindwing feathers were reduced and even lost12. This suggests that extensive feathering of the pes was a critical modification in the transition to birds and that the pedal scales of extant birds might be secondarily derived structures, a possibility also supported by some developmental studies18
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 MicroraptorXiaotingiaAurornis, 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 Avialaealthough most phylogenetic analyses have placed the animals of his Tetrapterygidae elsewhere in Paraves, such as XiaotingiaAurornis, and Anchiornis being placed in Avialae.[3]


Could the basal Euparaves fly (powered flight)?

As we shall see, the basal Euparaves could indeed fly. We need to consider forewings, hindwings, airfoil, sternum, propatagium and semilunate carpal. (Also see Appendices 1, 2 and 3).


4.1 Forewings

It is sometimes thought that the primitive birds could not fly because they did not have the needed shoulder mechanism for powered flight. It is true that the lack of a derived supracoracoideus precluded takeoff from the ground. But takeoff from tree branches was possible.

https://en.wikipedia.org/wiki/Microraptor

Chatterjee and Templin also ruled out the possibility of a ground-based takeoff. Microraptor lacked the necessary adaptations in its shoulder joint to lift its front wings high enough vertically to generate lift from the ground, and the authors argued that a ground-based takeoff would have damaged flight feathers on the feet. This leaves only the possibility of launching from an elevated perch, and the authors noted that even modern birds do not need to use excess power when launching from trees, but use the downward-swooping technique they found in Microraptor.

Feduccia (1999)
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. 

4.2 Hindwings


The hindwings generated lift.

Xiaoting Zheng,1,2* Zhonghe Zhou,3 Xiaoli Wang,1 Fucheng Zhang,3 Xiaomei Zhang,2 Yan Wang,1 Guangjin Wei,1 Shuo Wang,3,4 Xing Xu1,3* (2013)
In Microraptor, the metatarsal feathers are proportionally large with highly asymmetrical vanes (1), whereas in Pedopenna, Anchiornis, and Sapeornis they are proportionally smaller and have nearly symmetrical vanes (2, 3). In all cases, however, the metatarsal feathers are similar in general arrangement (nearly perpendicular to the metatarsus, forming a large flat surface) and in having stiff vanes and curved rachises. These features suggest that the metatarsal feathers were aerodynamic in function (12), providing lift, creating drag, and/or enhancing maneuverability, and thus played a role in flight (1–7, 24, 25). The presence of metatarsal feathers with a probable aerodynamic function in both deinonychosaurians and avialans strongly supports the interpretation that leg feathers were an important factor in the origin of avialan flight, although the nature of their biomechanical contribution to flight ability in taxa that possessed them is debated (1–7, 24–26).

1,2 Justin T. Hall, 1,2 Michael B. Habib, 4 David W. E. Hone and 2 Luis M. Chiappe  (2012)
The evolution of powered flight in birds remains a contentious issue in vertebrate paleontology. The diminutive predatory dinosaur Microraptor gui preserves evidence of extensive, lift-generating feathers on each manus and forearm, but also preserves evidence of lift-generating feathers associated with the hindlimbs, effectively forming a pair of “hindwings”.

4.3 Airfoil

It is sometimes thought that the primitive birds could not fly because they did not have asymmetric flight feathers and thus lacked an airfoil. It is true that they did not have asymmetric flight feathers. But that does not necessarily preclude flapping flight.

Nicholas R. Longrich et al (2012)
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.

Teresa J. Feo, Daniel J. Field, Richard O. Prum (2015)
The elongated wing feathers of Mesozoic Paraves exhibit small barb angles in cutting-edge leading vanes that are comparable with those of modern flying birds (figure 4b). This suggests that the leading vanes of these Mesozoic feathers are functionally similar to those of modern birds, and were similarly capable of withstanding aerodynamic forces in airflow. Furthermore, our observations document that the outer hindwing feathers of the four-winged dromaeosaurid Microraptor were similar in vane structure to the primary feathers of two-winged Mesozoic taxa, corroborating previous interpretations of their aerodynamic function [33]. The presence of small cutting-edge barb angles, in conjunction with sufficient vane asymmetry for feather pitch stability, support the conclusion that some form of aerial locomotion was plesiomorphic for the most exclusive clade including Microraptor and modern birds."

4.4 Sternum

It is sometimes thought that the primitive birds could not fly because some did not have an ossified sternum. It is true that some did not have an ossified sternum. But that does not necessarily preclude flapping flight.


STORRS L. OLSON ALAN FEDUCCIA (1979)
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. 

O'Connor and Sullivan (2014)
Ossified sternal plates (present and fused in all living birds) are known in basal dromaeosaurids, oviraptorosaurs, and scansoriopterygids (forming a fully fused sternum in some individuals of the first two clades), but are absent in troodontids and in the basal birds Archaeopteryx and Sapeornis (Clark et al., 1999; Norell and Makovicky, 1999; Wellnhofer and Tischlinger, 2004; Xu and Norell, 2004; Zhou and Zhang, 2003). 

4.5 Propatagium

The lift generating effect of the propatagium must also be considered.

Richard E. Brown* and Allen C. Cogley (1998)
Through flight experiments with live birds and computer modeling we define the aerodynamic contributions of the propatagium in avian flight. From flight trials we found that in House Sparrows, with all flight feathers removed except for the distal six primaries, the loss of approximately 50% of the propatagium's projected area and its cambered profile produced a significant reduction in the distance a bird was able to cover in flight. Removal of the secondary feathers, leaving six distal primaries and an intact propatagium, did not have a noticeable affect upon flight. From the computer model which is representative of the bird wing's mid-antebrachial chord (cambered propatagium, symmetrical musculoskeletal elements, and flat secondary flight feathers), we found that the propatagium: (1) produced the majority of the lift; (2) had a higher (relative to secondary feathers) production of lift in relation to its angle of attack, i.e., steeper lift-curve slope; and (3) produced more lift with a chord only 1/5 that of the feather subsection. We conclude that the cambered propatagium is the major lift generating component of the wing proximal to the wrist.

4.6 Semilunate carpal

https://en.wikipedia.org/wiki/Scansoriopterygidae
Scansoriopterygids had a semilunate carpal (half-moon shaped wrist bone) that allowed for bird-like folding motion in the hand.
Mark N Puttick,1,2 Gavin H Thomas,3 Michael J Benton,1 and P David Polly (2014)
The origin of birds (Aves) is one of the great evolutionary transitions. Fossils show that many unique morphological features of modern birds, such as feathers, reduction in body size, and the semilunate carpal, long preceded the origin of clade Aves
 https://www.geol.umd.edu/~tholtz/dinoappendix/
The grouping of Oviraptorsauria plus Dromaeosauridae plus Troodontidae plus Avialae now has a name: Pennaraptora. A new detailed analysis of the evolution of the wrists of dinosaurs shows that the origin of the half-moon shaped wrist bone (semilunate carpal) is a pennaraptoran trait.

XU Xing1† , ZHAO Qi1 , NORELL Mark2 , SULLIVAN Corwin1 , HONE David1 , ERICKSON Gregory2,3, WANG XiaoLin1 , HAN FengLu1,4 & GUO Yu1,4 (2008)
With an estimated mass of 110 grams, Anchiornis is the smallest known non-avian theropod dinosaur. It exhibits some wrist features indicative of high mobility, presaging the wing-folding mechanisms seen in more derived birds and suggesting rapid evolution of the carpus.

Apomorphy of Avialae
Also, we can conclude that basal Euparaves were capable of flapping flight because their flight-related characteristics have often caused them to be placed within Avialae:

https://en.wikipedia.org/wiki/Avialae

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].

Conclusion:
Based on the extensive set of flight-related characteristics, we can conclude that these 4 winged primitive birds could fly (powered flight) by flapping their forewings and using their hindwings for additional lift.
They could take off from an elevated perch such as a tree branch. Their shoulder mechanism was such that they could not take off from level ground because they did not yet have a derived supracoracoideus.


5. What was the basalmost Euparaves like?

What was the nature of the basalmost (very first) Euparaves, the common ancestor of scansoriopterygids and oviraptors/alvarezsaurids?
Here is some material on basalmost Paraves that is directly relevant:

Dongyu Hu1, Lianhai Hou1,2, Lijun Zhang1,3 & Xing Xu1,2  (2009)
This distal-first development led to a four-winged condition at the base of the Paraves.

Mark N Puttick,1,2 Gavin H Thomas,3 Michael J Benton,1 and P David Polly (2014)
Before the origin of Aves, on the branch leading to Paraves, high rates of evolution led to a smaller body size and a relatively larger forelimb in Paraves. These changes are on a single branch leading to Paraves, representing a shift to a new smaller size and larger forelimb at this point.
Paraves, rather than Aves alone, shifted to a different evolutionary model relative to other coelurosaurian theropods (Table 2). On all trees and for both femur and forelimb size, the model with a regime shift at Paraves, rather than Aves, is favored (Table S10). We found strong support for a reduction in femur length within Paraves (57.5 mm for Paraves, 147.9 mm for other coelurosaurians) with weaker evidence for a concurrent reduction in evolutionary rates (Table 2). Importantly, the best-fitting paravian regime-shift model for femur length is substantially better than the best-fitting avian regime shift model (ΔAICc = 6.15; Table 1). The paravian forelimb reduced slightly in size (Paraves = 158.4 mm; other taxa = 234.4 mm; Table 2). In contrast, the equivalent model that incorporates a reduction in rate within Aves (Table 2) is an inferior fit (ΔAICc = 2.48).


Daniel T. Ksepka (2014)
Here again, the lineage leading to birds stands out as an exception, with maniraptoran theropods sustaining high rates of size evolution relative to other dinosaur lineages [12]. A third recent study [13] employing likelihood methods capable of detecting branch-specific rate shifts places the shift to higher rates of size evolution on the branch leading to Paraves (the clade uniting birds, dromaeosaurids, and troodontids).

Xing Xu (2012)
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). 
(Also see Appendix 11).


Was the basalmost Euparaves ground-dwelling or was it flying in the trees?

1.  If the common ancestor (the basalmost Euparaves) was ground-dwelling, then the flying nature of scansoriopterygids etc. would have been an adaptation after branching from the ground-dwelling common ancestor. In that case:
  • flight evolved multiple times independently (homoplasy).
  • it requires multiple exaptations 
  • it requires multiple reversals  
  • it requires an implausible rate of evolution 
  • the timing of found fossils is inconsistent with it (stratigraphic incongruence)
  • character optimization does not favor that alternative.

2. If the common ancestor (the basalmost Euparaves) was flying (powered flight), then the ground-dwelling nature of oviraptors/alvarezsaurids/eudromaeosaurs, would indicate that they settled on the ground after branching from the flying common ancestor.
In that case, there were multiple occasions of primitive birds settling on the ground (secondary losses).

Issues with the first option:

5.1  Extensive Homoplasy

Jingmai K. O’CONNOR Corwin SULLIVAN (2014)
As a result of the high amount of homoplasy that characterizes derived maniraptoran evolution, the identity of the avian sister taxon remains debated despite the rapid accumulation of morphological data. 

Xing Xu1,2, Hailu You3 , Kai Du4 & Fenglu Han2 (2011)
Xiaotingia zhengi independently evolved some salient features seen in other maniraptoran taxa, which highlights the extensive homoplasy that exists among maniraptorans.

Xing Xu (2012)
The early history of flight is highly complex. As Longrich and colleagues [8] point out, flight capability is likely to have evolved independently on multiple occasions among Archaeopteryx and its kin. For example, flight feathers with asymmetrical vanes seem to have evolved independently at least twice near the dinosaur-bird transition, once near the base of the Avialae and once in the deinonychosaurs [8].

Pascal Godefroit, Helena Demuynck, Gareth Dyke, Dongyu Hu, François Escuillié & Philippe Claeys (2013b)
Note, however, that this phylogeny remains only weakly supported presumably due to the numerous homoplasies widely distributed across coelurosaurian phylogeny3,17

5.2  Multiple Exaptations
Earlier analyses had placed Alvarezsaurids and Oviraptors earlier than Euparaves which necessitates a great deal of claimed exaptations. Those exaptations are only required due to the misplacement of the oviraptors and alvarezsaurids. (See Appendix 6).

5.3  Multiple Reversals 
Earlier analyses had placed Alvarezsaurids and Oviraptors earlier than Euparaves which necessitates a great deal of claimed "remarkable" reversals. Those reversals are only required due to the misplacement of the oviraptors and alvarezsaurids. (See Appendix 7).

5.4  Implausible Rate of Evolution
Earlier analyses had placed Alvarezsaurids and Oviraptors earlier than Euparaves which necessitates an implausible rate of evolution. That implausible rate of evolution is required due to the misplacement of the oviraptors and alvarezsaurids. (See Appendix 10).

5.5  Stratigraphic Incongruence
Earlier analyses had placed Alvarezsaurids and Oviraptors earlier than Euparaves. However, the Alvarezsaurid and Oviraptor fossils that have been found, are actually tens of millions of years later than Euparaves. So lengthy ghost lineages are required due to the misplacement of the oviraptors and alvarezsaurids. (See Appendix 8).

5.6  Character Optimization
Also see Appendix 9.

Ingi Agnarssona,b* and Jeremy A. Millerc (2008)
Character optimization is the process by which alternative reconstructions of a character on a cladogram are evaluated.
In the absence of compelling evidence to the contrary, ambiguous optimization is better resolved in favour of secondary losses (reversals) over parallel gains of complex structures. This is more consistent with the stronger conjecture of homology based on observable detailed similarity, rather than mere absence (De Pinna, 1991)

Zhonghe Zhou  (2014)
It is possible that an aerodynamic function of pennaceous feathers could have evolved several times in various theropod lineages; however, it is also more likely that flight and aerodynamic functions of the pennaceous feathers could have been lost many times in theropod (including birds) evolution — during evolution, the loss of features is far more common than the evolution of novel features.

Conclusion
From the extensive set of issues related to the first option, we can conclude that the most parsimonious alternative is that the common ancestor, the basalmost Euparaves, was flying (powered flight). 



Oviraptors and Alvarezsaurids: secondarily flightless

It follows from this that oviraptors and alvarezsaurids were secondarily flightless, since they descended from flying ancestral basalmost Euparaves. Which confirms earlier studies. (Also see Appendix 5).

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]

TERESA MARYAŃSKA, HALSZKA OSMÓLSKA, and MIECZYSŁAW WOLSAN (2002) 
Oviraptorosauria is a clade of Cretaceous theropod dinosaurs of uncertain affinities within Maniraptoriformes. All previous phylogenetic analyses placed oviraptorosaurs outside a close relationship to birds (Avialae), recognizing Dromaeosauridae or Troodontidae, or a clade containing these two taxa (Deinonychosauria), as sister taxon to birds. Here we present the results of a phylogenetic analysis using 195 characters scored for four outgroup and 13 maniraptoriform (ingroup) terminal taxa, including new data on oviraptorids. This analysis places Oviraptorosauria within Avialae, in a sister−group relationship with Confuciusornis. Archaeopteryx, Therizinosauria, Dromaeosauridae, and Ornithomimosauria are successively more distant outgroups to the Confuciusornis−oviraptorosaur clade. Avimimus and Caudipteryx are successively more closely related to Oviraptoroidea, which contains the sister taxa Caenagnathidae and Oviraptoridae. Within Oviraptoridae, “Oviraptor” mongoliensis and Oviraptor philoceratops are successively more closely related to the Conchoraptor−Ingenia clade. Oviraptorosaurs are hypothesized to be secondarily flightless. Emended phylogenetic definitions are provided for Oviraptoridae, Caenagnathidae, Oviraptoroidea, Oviraptorosauria, Avialae, Eumaniraptora, Maniraptora, and Maniraptoriformes.



7. Conclusion

The most parsimonious conclusion is that:
  • the basalmost (first) Euparaves was a flying (powered flight) primitive bird living in the trees; 
  • that the basal Euparaves were flying (powered flight) primitive birds living in the trees, that evolved from the basalmost Euparaves; 
  • that Oviraptors and Alvarezsaurids were secondarily-flightless Euparaves primitive birds, living on the ground, that had descended from the flying basal Euparaves.
This means that the very first Euparaves were already flapping fliers (powered flight).
And since the new placement of the Oviraptors and Alvarezsaurids places them within Euparaves, it means that the Oviraptors and Alvarezsaurids did not branch from a hypothesized lineage from dinosaur to primitive bird.

Suggested high level phylogeny:
7. Discussion

The mainstream theory is that Oviraptors and Alvarezsaurids branched from a hypothetical lineage stretching from coelurosaur dinosaur to primitive bird.
But as we have seen, the Oviraptors and Alvarezsaurids are actually secondarily-flightless primitive birds. So they no longer can be considered to be related to such a hypothetical lineage.
So where does that leave us? What remains of that hypothetical lineage, keeping in mind that the basalmost (very first) Euparaves was already a powered flyer?
This is good material for further research.

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Supplementary Information 

Appendix 1


Basal Euparaves could fly

The evidence indicates that basal Euparaves were capable of flapping flight ("powered flight").


Traits associated with Aves evolved before their origin, at high rates, and support the notion that numerous lineages of paravians were experimenting with different modes of flight through the Late Jurassic and Early Cretaceous.

Shoulder mechanism
But early birds, including Archaeopteryx, lacked the shoulder mechanism by which modern birds' wings produce swift, powerful upstrokes
The lack of a morphologically derived SC [supracoracoideus] in Late Jurassic and Early Cretaceous birds precluded a high velocity recovery stroke which undoubtedly limited powered flight in these forms. Subsequent evolution of the derived SC capable of imparting a large rotational force to the humerus about its longitudinal axis was an important step in the evolution of the wing upstroke and in the ability to supinate (circumflex) the manus in early upstroke, a movement fundamental to reducing air resistance during the recovery stroke.

Basal Euparaves could fly even though they did not have asymmetric feathers.
http://www.sciencedirect.com/science/article/pii/S0960982212011943
Primitive Wing Feather Arrangement in Archaeopteryx lithographica and Anchiornis huxleyi
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.

Hindwings provided additional lift


HINDWING FUNCTION IN FOUR-WINGED FEATHERED DINOSAURS  (2012)
The evolution of powered flight in birds remains a contentious issue in vertebrate paleontology. The diminutive predatory dinosaur Microraptor gui preserves evidence of extensive, lift-generating feathers on each manus and forearm, but also preserves evidence of lift-generating feathers associated with the hindlimbs, effectively forming a pair of “hindwings”.
Vertebrate paleontologist Nick Longrich of the University of Bath in the United Kingdom, meanwhile, agrees that the large hindlimb feathers are an interesting discovery, but he suspects they may still have originally had an aerodynamic function. “I think they're airfoils,” he says—the structures on aircraft wings that provide lift. The hindlimb feathers “don't look like insulatory feathers to me: They're really long, they overlap the same way flight feathers do, and the fact that they curve is a characteristic flight feather feature.”

https://www.researchgate.net/publication/236048162_Hind_Wings_in_Basal_Birds_and_the_Evolution_of_Leg_Feathers
Hind Wings in Basal Birds and the Evolution of Leg Feathers 
Xiaoting Zheng,1,2* Zhonghe Zhou,3 Xiaoli Wang,1 Fucheng Zhang,3 Xiaomei Zhang,2 Yan Wang,1 Guangjin Wei,1 Shuo Wang,3,4 Xing Xu1,3* (2013)
Recent discoveries of large leg feathers in some theropods have implications for our understanding of the evolution of integumentary features on the avialan leg, and particularly of their relevance for the origin of avialan flight. Here we report 11 basal avialan specimens that will greatly improve our knowledge of leg integumentary features among early birds. In particular, they provide solid evidence for the existence of enlarged leg feathers on a variety of basal birds, suggest that extensively scaled feet might have appeared secondarily at an early stage in ornithuromorph evolution, and demonstrate a distal-to-proximal reduction pattern for leg feathers in avialan evolution.
The specimens described here collectively provide important new information about avialan hindlimb integumentary features, particularly in that they confirm the presence of a four-winged condition in basal birds. Large metatarsal feathers were first discovered in the basal dromaeosaurids Microraptor and Sinornithosaurus (1, 20–22), were subsequently reported in the enigmatic Pedopenna and the basal deinonychosaurians Anchiornis and Xiaotingia (2–4, 23), and can now also be definitively said to occur in the basal avialan Sapeornis. The morphology of the metatarsal feathers shows considerable variation among taxa known to possess these structures.
In Microraptor, the metatarsal feathers are proportionally large with highly asymmetrical vanes (1), whereas in Pedopenna, Anchiornis, and Sapeornis they are proportionally smaller and have nearly symmetrical vanes (2, 3). In all cases, however, the metatarsal feathers are similar in general arrangement (nearly perpendicular to the metatarsus, forming a large flat surface) and in having stiff vanes and curved rachises. These features suggest that the metatarsal feathers were aerodynamic in function (12), providing lift, creating drag, and/or enhancing maneuverability, and thus played a role in flight (1–7, 24, 25). The presence of metatarsal feathers with a probable aerodynamic function in both deinonychosaurians and avialans strongly supports the interpretation that leg feathers were an important factor in the origin of avialan flight, although the nature of their biomechanical contribution to flight ability in taxa that possessed them is debated (1–7, 24–26).

 Propatagium 

  1. Richard E. Brown* and
  2. Allen C. Cogley (
  3. 1998
  4. )
Journal of Experimental Zoology
Contributions of the propatagium to avian flight
Through flight experiments with live birds and computer modeling we define the aerodynamic contributions of the propatagium in avian flight. From flight trials we found that in House Sparrows, with all flight feathers removed except for the distal six primaries, the loss of approximately 50% of the propatagium's projected area and its cambered profile produced a significant reduction in the distance a bird was able to cover in flight. Removal of the secondary feathers, leaving six distal primaries and an intact propatagium, did not have a noticeable affect upon flight. From the computer model which is representative of the bird wing's mid-antebrachial chord (cambered propatagium, symmetrical musculoskeletal elements, and flat secondary flight feathers), we found that the propatagium: (1) produced the majority of the lift; (2) had a higher (relative to secondary feathers) production of lift in relation to its angle of attack, i.e., steeper lift-curve slope; and (3) produced more lift with a chord only 1/5 that of the feather subsection. We conclude that the cambered propatagium is the major lift generating component of the wing proximal to the wrist.
Cambered:
a. A slightly arched surface, as of a road, a ship's deck, an airfoil, or a snow ski.b. The condition of having an arched surface.

It would appear that the ability to take off from the ground began with Euavialae.
https://en.wikipedia.org/wiki/Euavialae
Euavialae (meaning "true winged birds") is a group of birds which includes all avialan species more closely related to modern birds, than to the primitive, long-tailed birds Archaeopteryx and Jeholornis.[1]

Anchiornis, Aurornis, Pedopenna, Xiaotingia and Zhongornis

These are all basal Euparaves. They could fly. They have been placed in different spots in different analyses by different researchers. We can conclude that they were capable of flapping flight because of their flight-related characteristics, which have often caused them to be placed within Avialae. 

ANCHIORNIS
Anchiornis huxleyi was a small, paravian dinosaur with a triangular skull bearing several details in common with dromaeosaurids and troodontids.
Anchiornis is notable for its proportionally long forelimbs, which measured 80% of the total length of the hind limbs. This is similar to the condition in early avians such as Archaeopteryx, and the authors pointed out that long forelimbs are necessary for flight. Anchiornis also had a more avian wrist than other non-avialan theropods. The authors initially speculated that it would have been possible for Anchiornis to fly or glide. However, further finds showed that the wings of Anchiornis, while well-developed, were short when compared to later species like Microraptor, with relatively short primary feathers that had rounded, symmetrical tips, unlike the pointed, aerodynamically proportioned feathers of Microraptor.[2]
https://en.wikipedia.org/wiki/Aurornis
phylogenetic analysis of Aurornis published in 2013 found that it belongs in the bird lineage, in a more basal position than Archaeopteryx.[2] The analysis was based on "almost 1,500 [anatomical] characteristics."[6] On the other hand, a phylogenetic analysis conducted by Brusatte et al. (2014) [see above] recovered Aurornis outside Avialae; it was recovered as a troodontid closely related to AnchiornisXiaotingia and Eosinopteryx.[7]
Aurornis.jpg
Pedopenna was originally classified as a paravian, the group of maniraptoran dinosaurs that includes both deinonychosaurs and avialans (the lineage including modern birds), but some scientists have classified it as a true avialan more closely related to modern birds than to deinonychosaurs.[3]
The bird-like characteristics of Pedopenna are further evidence of the dinosaur-bird evolutionary relationship. Apart from having a very bird-like skeletal structure in its legs, Pedopenna was remarkable due to the presence of long pennaceous feathers on the metatarsus (foot). Some deinonychosaurs are also known to have these 'hind wings', but those of Pedopenna differ from those of animals like MicroraptorPedopenna hind wings were smaller and more rounded in shape. The longest feathers were slightly shorter than the metatarsus, at about 55 mm (2 in) long. Additionally, the feathers of Pedopenna were symmetrical, unlike the asymmetrical feathers of some deinonychosaurs and birds. Since asymmetrical feathers are typical of animals adapted to flying, it is likely that Pedopenna represents an early stage in the development of these structures. While many of the feather impressions in the fossil are weak, it is clear that each possessed a rachis and barbs, and while the exact number of foot feathers is uncertain, they are more numerous than in the hind-wings of MicroraptorPedopenna also shows evidence of shorter feathers overlying the long foot feathers, evidence for the presence of coverts as seen in modern birds. Since the feathers show fewer aerodynamic adaptations than the similar hind wings of Microraptor, and appear to be less stiff, suggests that if they did have some kind of aerodynamic function, it was much weaker than in deinonychosaurs and birds. Xu and Zhang, in their 2005 description of Pedopenna, suggested that the feathers could be ornamental, or even vestigial. It is possible that a hind wing was present in the ancestors of deinonychosaurs and birds, and later lost in the bird lineage, with Pedopenna representing an intermediate stage where the hind wings are being reduced from a functional gliding apparatus to a display or insulatory function.[2]
The initial analysis by Xu et al. showed that Xiaotingia formed a clade with ArchaeopteryxDromaeosauridae and Troodontidae to the exclusion of other groups traditionally seen as birds. Xu et al  therefore (re)defined the concepts of Deinonychosauria and Avialae to the extent that Archaeopteryx and Xiaotingia belonged to the Deinonychosauria in the clade Archaeopterygidae.[1] This led to popular reports that "Archaeopteryx is no longer a bird",[2] although Xu et al noted that there are several competing definitions of the clade Aves currently in use, pointing out that their definitions are compatible with a traditional Aves with Archaeopteryx as a specifier.[1] This was challenged by an analysis using different methods published several months later however, in which Archaeopteryx was again recovered as an avialan, while Xiaotingia remained closely allied to Anchiornis within the Troodontidae.[3] In 2012, an expanded and revised version of the initial analysis also found Archaeopteryx to be avialan and Anchiornis to be troodontid, but recovered Xiaotingia as the most primitive member of the clade Dromaeosauridae rather than a close relative of Anchiornis within Troodontidae.[4]

Zhongornis (meaning "intermediate bird"[1]) is a genus of primitive birds that lived during the Early Cretaceous.
Reinterpretation of the Early Cretaceous maniraptoran (Dinosauria: Theropoda) Zhongornis haoae as a scansoriopterygid-like non-avian, and morphological resemblances between scansoriopterygids and basal oviraptorosaurs
Jingmai K. O’CONNOR Corwin SULLIVAN
Revised anatomical interpretation of the tail and more detailed comparisons with non-avian dinosaurs strongly suggest that Zhongornis haoae is not a bird but a member or close relative of the enigmatic maniraptoran clade Scansoriopterygidae. Although the poor preservation and immature ontogenetic status of all known specimens of this clade prevent detailed comparisons, proportions of the hand support a close affinity with Zhongornis, while at the same time revealing significant differences between this genus and known basal birds. Zhongornis also bears some similarity to basal oviraptorosaurs, supporting the hypothesis that the Jurassic scansoriopterygids may be stem-group relatives of the Cretaceous Oviraptorosauria. This suggests that the Aves + Scansoriopterygidae clade, as resolved here including Zhongornis, may be an artifact of homoplasy and the currently limited information available for scansoriopterygids. Although we consider Zhongornis too poorly preserved and the current information too limited to definitively reassign this taxon to Scansoriopterygidae, we consider that there is ample evidence to strongly question the previous assignment of this taxon to Aves.

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 MicroraptorXiaotingiaAurornis, 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]


Pascal Godefroit1 , Andrea Cau2 , Hu Dong-Yu3,4, François Escuillie´5 , Wu Wenhao6 & Gareth Dyke7 (2013a)
A Jurassic avialan dinosaur from China resolves the early phylogenetic history of birds
Epidendrosaurus, Epidexipteryx and Eosinopteryx, also from the Middle–Late Jurassic of northeastern China, are here regarded as basal, non-eumaniraptoran paravians. Thus our phylogeny is entirely consistent with the presence of a tetrapterygian condition (= four winged) and elongated rectrices in basal eumaniraptorans. We also postulate a single origin for typical forewing-powered flight, generally inferred to be present only in more derived birds5,24; shifting Archaeopteryx into deinonychosaurs3,4 minimally implies two origins (in Archaeopteryx and in ‘true’ birds) or a much more complex situation, with an earlier origin close to the base of Paraves for forewing-driven flight and subsequent modifications to the tetrapterygian condition in various deinonychosaurs5 . These relationships are also consistent with the recent discovery of potentially fourwinged flight surfaces in a range of Mesozoic basal birds25. 
This new comprehensive phylogeny shows that basal avialans (Aurornis, Anchiornis, Xiaotingia) were already diversified in northern China during the Middle–Late Jurassic. 


Scansoriopterygidae

We can conclude that Scansoriopterygids were capable of flapping flight because their flight-related characteristics have often caused them to be placed within Avialae. 

https://en.wikipedia.org/wiki/Scansoriopteryx
Scansoriopteryx ("climbing wing") is a genus of avialan dinosaur. Described from only a single juvenile fossil specimen found in LiaoningChinaScansoriopteryx is a sparrow-sized animal that shows adaptations in the foot indicating an arboreal (tree-dwelling) lifestyle. It possessed an unusual, elongated third finger. The type specimen of Scansoriopteryx also contains the fossilized impression of feathers.[1]
Scansoriopteryx lent its name to the family Scansoriopterygidae. Studies of dinosaur relationships have found Scansoriopteryx to be a close relative of true birds and a member of the clade Avialae.[11]
Scansoriopteryx heilmanni (and its likely synonym Epidendrosaurus ninchengensis) 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.
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.[10] Agnolín and Novas (2013) recovered scansoriopterygids as non-paravian maniraptorans and the sister group to Oviraptorosauria.[11]
Both juvenile scansoriopterygid specimens preserve impressions of simple, down-like feathers, especially around the hand and arm. The longer feathers in this region led Czerkas and Yuan to speculate that adult scansoriopterygids may have had reasonably well-developed wing feathers which could have aided in leaping or rudimentary gliding, though they ruled out the possibility that Scansoriopteryx could have achieved powered flight. Like other maniraptorans, scansoriopterygids had a semilunate carpal (half-moon shaped wrist bone) that allowed for bird-like folding motion in the hand. Even if powered flight was not possible, this motion could have aided maneuverability in leaping from branch to branch.[4] 
In a 2007 cladistic analysis of relationships among coelurosaurs, Phil Senter found Scansoriopteryx to be the closest dinosaurian relative of avian birds, and a member of the clade Avialae.[7] This view was supported by a second phylogenetic analysis performed by Zhang et al. in 2008.

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.

Scansoriopteryx




==========================================================

Appendix 2

Tails

Notice the similarities in the tails of the flying basal Euparaves (Anchiornis, Epidendrosarus, Epidexipterx and Zhongornis) and the secondarily-flightless Oviraptors (Caudipteryx and Khaan).

http://www.ivpp.cas.cn/cbw/gjzdwxb/xbwzxz/201401/P020140121386966325113.pdf 
Reinterpretation of the Early Cretaceous maniraptoran (Dinosauria: Theropoda) Zhongornis haoae as a scansoriopterygid-like non-avian, and morphological resemblances between scansoriopterygids and basal oviraptorosaurs (O'Connor and Sullivan 2014)
As is most clearly preserved in the short third free caudal vertebra, the length of a single transverse process of each anterior caudal in Zhongornis is approximately equal to the transverse width of the corresponding vertebral body, as in Caudipteryx, Epidexipteryx, and basal birds (e.g. Archaeopteryx, Confuciusornis, and the enantiornithines Concornis and Rapaxavis). 
As in Caudipteryx and Epidexipteryx, the last few caudals of Zhongornis decrease progressively in size, and the distalmost caudal has a rounded distal margin
Some features of Zhongornis are shared by both scansoriopterygids and basal oviraptorosaurs. The most obvious is the tail, which distinguishes scansoriopterygids and Zhongornis from other paravian theropods (deinonychosaurs and Aves); a reduced tail, lacking distally elongate vertebrae and having an incipient pygostyle, is present in both Epidexipteryx and Caudipteryx. Our new estimate of the number of caudal vertebrae in Zhongornis (approximately 20) is comparable to observations for both scansoriopterygids (16 in Epidexipteryx, 22+ in Epidendrosaurus) and basal oviraptorosaurs (22 in Caudipteryx).

Fig. 7 Tails and pelves of derived maniraptoran theropods (modified from Persons et al., in press) A. Anchiornis (Deinonychosauria: Troodontidae?); B. Archaeopteryx (Aves); C. Jeholornis (Aves); D. Confuciusornis (Aves); E. Gallus (Aves); F. Caudipteryx (Oviraptorosauria); G. Khaan (Oviraptorosauria); H. Epidendrosaurus (Scansoriopterygidae); I. Zhongornis (incertae sedis); J. Epidexipteryx (Scansoriopterygidae) Color key: blue short proximal caudal vertebrae; green transitional caudals; yellow elongate distal caudals; orange partially or fully fused terminal caudals (pygostyle)

-----------------------------------------------------------------------------------------------------

Appendix 3

Oviraptors and Scansoropterygidae

http://www.researchgate.net/publication/225452453_Pre-Archaeopteryx_coelurosaurian_dinosaurs_and_their_implications_for_understanding_avian_origins
Xu, X., Q.Y. Qing, and D.Y. Hu. (2010)
Pre-Archaeopteryx coelurosaurian dinosaurs and their implications for understanding avian orders.
..the scansoriopterygids Epidendrosaurus [53] and Epidexipteryx[54] are more similar to basal birds, such as Jeholornis and Sapeornis [64,65], than to Archaeopteryx in many of their derived features, particularly in a number of derived cranial features. Surprisingly these cranial features are also seen in the oviraptorosaurs [54]. Together, the Jurassic maniraptorans suggest a monophyletic group composed of the scansoriopterygids,
all other birds except Archaeopteryx, and probably also the oviraptorosaurs. This would represent a sister taxon to a monophyletic group containing the troodontids, the dromaeosaurids, and Archaeopteryx (Figure 1). Such a phylogenetic hypothesis would have significant implications for the reconstruction of the theropod-bird transition but it has yet to be tested by quantitative phylogenetic analysis.

http://www.nature.com/nature/journal/v455/n7216/full/nature07447.html
http://www.ivpp.cas.cn/qt/papers/201403/P020140314394563113449.pdf
Fucheng Zhang1, Zhonghe Zhou1, Xing Xu1, Xiaolin Wang1 & Corwin Sullivan1 (2008)
A bizarre Jurassic maniraptoran from China with elongate ribbon-like feathers
Here we report a new basal avialan, Epidexipteryx hui gen. et sp. nov., from the Middle to Late Jurassic of Inner Mongolia, China. This new species is characterized by an unexpected combination of characters seen in several different theropod groups, particularly the Oviraptorosauria. Phylogenetic analysis shows it to be the sister taxon to Epidendrosaurus4, 5, forming a new clade at the base of Avialae6.


https://www.google.ca/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&cad=rja&uact=8&ved=0CDAQFjACahUKEwjigNb1vYHHAhWXG5IKHfNYBPQ&url=http%3A%2F%2Fdocencia.med.uchile.cl%2Fsmg%2Fpdf%2Fdinos2002.pdf&ei=XmC5VeLZDJe3yATzsZGgDw&usg=AFQjCNGlrsCF6bWr-XJndlp0iGVShn9LNg&sig2=IR_l7AMOalggmW_t5g74DQ&bvm=bv.99028883,d.aWw
Jones et al (2000)
Caudipteryx has been described as a feathered dinosaur14,15 and
therefore would be expected to have had a dinosaurian mechanism
of cursoriality. However, relative total hindlimb proportions in
Caudipteryx contrast sharply with those in all other bipedal dinosaurs
and are indistinguishable from those in cursorial birds
(Fig. 1b). Accordingly, based on the tight linkage of hindlimb
proportions to cursorial mechanisms in bipedal archosaurs, we
suggest that Caudipteryx ran using a mechanism more similar to
that of modern cursorial birds than to typical dinosaurs.
 
Significantly, lower leg (tibia + metatarsal) length in Caudipteryx is also the
same as the `effective hindlimb' length of cursorial birds, which is
equivalent to total hindlimb length in theropods (Fig. 1a).

A subsequent phylogenetic analysis conducted by Agnolín and Novas (2011) recovered scansoriopterygids not as avialans, but as basal members of the clade Paraves remaining in unresolved polytomy with alvarezsaurids and the clade Eumaniraptora (containing avialans and deinonychosaurs).[8]Turner, Makovicky and Norell (2012) included only Epidexipteryx hui in their primary phylogenetic analysis, as a full-grown specimen of this species is known; regarding Scansoriopteryx/Epidendrosaurus, the authors were worried that including it in the primary analysis would be problematic, because it is only known from juvenile specimens, which "do not necessarily preserve all the adult morphology needed to accurately place a taxon phylogenetically" (Turner, Makovicky and Norell 2012, p. 89). Epidexipteryx was recovered as basal paravian that didn't belong to Eumaniraptora. The authors did note that its phylogenetic position is unstable; constraining Epidexipteryx hui as a basal avialan required two additional steps compared to the most parsimonious solution, while constraining it as a basal member of Oviraptorosauria required only one additional step. A separate exploratory analysis included Scansoriopteryx/Epidendrosaurus, which was recovered as a basal member of Avialae; the authors noted that it did not clade with Epidexipteryx, which stayed outside Eumaniraptora. Constraining the monophyly of Scansoriopterygidae required four additional steps and moved Epidexipteryx into Avialae.[9]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.[10] Agnolín and Novas (2013) recovered scansoriopterygids as non-paravian maniraptorans and the sister group to Oviraptorosauria.[11]
Constraining Epidexipteryx as a basal oviraptorosaur requires only one additional step in our dataset (fig. 75). Three features support the inclusion of Epidexipteryx in Oviraptorosauria, which are caudal vertebrae without a transition point (char. 115.1), a dentary that has teeth only anteriorly (char. 220.1), and a first premaxillary tooth much larger than the succeeding teeth (char. 251.2). A tail without a transition point is unique to oviraptorosaurs and Epidexipteryx and premaxillary teeth greatly enlarged relative to other premaxillary teeth is unique to Incisivosaurus, Protarchaeopteryx, and Epidexipteryx.
Epidexipteryx resembles basal oviraptorosaurs
in several respects, particularly
in its cranial morphology. Zhang et al. (2008)
noted some of these, drawing attention to
the anteroposteriorly short but dorsoventrally
tall skull, the posterodorsally displaced
naris and anteroposteriorly long parietals.
Likewise, the highly procumbent anterior
dentition and the slightly downturned mandible
compares favorably to basal oviraptorosaurs
like Incisivosaurus, Caudipteryx, and
putatively Protarchaeopteryx.
Constraining Epidexipteryx as a basal oviraptorosaur
requires only one additional step in our dataset (fig. 75).”

The presence of numerous flight features reveal that Caudipteryx, like the extant flightless ratites, originated from volant ancestors (de Beer 1956; Feduccia 2012, 2013), most likely via the evolutionary process of heterochrony, specifically paedomorphosis (arrested development), by which the adult retains the morphology of a younger stage of development (Livesey 1995).


(O'Connor and Sullivan 2014)
Very little is known about the enigmatic scansoriopterygids; only two taxa have been previously assigned to this clade, and the holotype of Epidexipteryx is a subadult while that of Epidendrosaurus is a juvenile. This makes it difficult to put forth strong arguments in support of a relationship between this clade and any other. However, basal oviraptorosaurs like Caudipteryx and Incisivosaurus share several features with scansoriopterygids, including a short and deep skull with robust rostral dentition, unserrated teeth, a distally expanded scapula, and a relatively robust but reduced long boney-tail without a distinct transition point in the caudal vertebrae (Turner et al., 2012). The hand shows similarities in that the length ratio between the alular and major metacarpals is comparable, at 38% in Epidendrosaurus and 39% in Protarchaeopteryx, and the first phalanx of the alular digit is elongate in both Caudipteryx (subequal in length to the major metacarpal) and Epidendrosaurus (longer than the major metacarpal). If the two clades are closely related in some way, their resemblances presumably represent synapomorphies. The differences in their overall proportions might then result from adaptation to contrasting ecological niches, in that known scansoriopterygids are inferred to have been arboreal whereas oviraptorosaurs were cursorial. Alternatively, scansoriopterygids and oviraptorosaurs may not be particularly close relatives, in which case any derived, exclusive similarities between the two clades would be the result of some kind of homoplasy (Xu et al., 2011). Some of the resemblances between oviraptorosaurs, scansoriopterygids, and basal birds other than Archaeopteryx may be ancestral for all derived maniraptorans but secondarily absent in deinonychosaurs (Xu et al., 2011). Another factor that might have produced homoplastic resemblances is dietary similarity, given that several features that unite the two clades (e.g. unserrated dentition) are considered indicators of herbivory (Zanno and Makovicky, 2011). 
The recently described maniraptoran theropod Zhongornis haoae, known from a single juvenile specimen, was originally identified as a bird. However, morphological re-evaluation reveals striking resemblances to both Oviraptorosauria and Scansoriopterygidae. The reduced, but still long, boney tail is reinterpreted as having approximately twenty vertebrae and is reminiscent of the tails of Caudipteryx and Epidexipteryx in its proportions and morphology
Oviraptors





==========================================================

Appendix 4

TNT input file

Here is the TNT input file, which is based on a subset of the data from Xu et al 2009. It contains the core set of dinosaurs, scansoriopterygids, oviraptors and alvarezsaurids.



xread
517 17

Euparkeria ???0000?0?000???00?0?00000000000000000001??00000000000?0?1000??0
??00?00?0?000?00?0000?0?0?0?0?000?0???0??00??0?0?001?0?000????????0030?01?0??000?1
0200?0?10?001?00000100000?0???0?0000?000???0???00?000?0??0??00??0010?00????????0??
???????????0?????0???0??0?00?00?????10?0????0???0???????000?0???????00??00?????00??0?
??00110010???00?0?0?0???0?0???????0?0000??0?00?????????0???0?0??0?0????0???0?0??????
?????????????????????????????????????????????????????????0??????????????????????????????
????????????????????????????????

Marasuchus
????
????????????????????????????????????????????????????????????????????????????????????
????????0000?00--0??001???0?00?0??0?????????????????????????????????????????????0?????
????00000?00?000--?00?00??1??0?0?0?00?20000?0?0??0?0??00000000000??????????0????01?
00?????10?0????????0???????000002-?00?00000000-0?000000-??00000011?4?00-20000-0?000
002?010000000000?00??00000000010000000?0000000?01??????????????????????????????????
????????????????????????????????????????????????????????????????????????????????????????
??????


Allosaurus ???0?0100101?0000?000?10?010?0??0??0????11??00000111?0??11001000?
00??010???0?00010001120?00010??001001100?0011000??011001?10?0000000000010010?1?0
00001010100102000000102000000000102120010000111000101100001001100100300000?00?
0?0110100101010000?1??10??00010110000000000000000100000??01001110000000?0000100
100000000100?1100001000011000000?000101000100011010001012?0?10000001101110?0020
00000?020000000010201111000000111200?100113100000010001110002000104?10?0010001
00000000000???????????????????????0???????????????????????

Compsognathus
0??00100
0???1010?1?0??201000?00?00??0000??000000000010???10110???000?001000??????
?0?????????????0?????1????????????00?????????????00000010010?0?000?1210?1??101001001
10200000000010??1??00?00111?00?????10001??110?023????0?00?0?00?10000010010100???1
???0001010?000000?1???????0?0000?????010100??0???0?0?1???????00?011??0100001000001
0000?0??1?????0000?1???1??0??????0??0?0001??10?0000200?000?0200??0010102??101000??
?1012?1?010113?0000000???0000?10010104?00?0110???0000??????0???????????????????????
0???????????????????????


Tyrannosaurus ???100000011101011101100000000001110010?00221000001110??1111010
0
0001?111
22?010100100103?00001000001001110?00100001101?01?010?02000000000100101
1?0110010101011010001001020000000001021200000001111?0100100001001100000310?00?
10?0?0?0001001111000001??11??00010100000001001001?00100010?1?0?01111100000?0110
10110000001010001100001000001021000?101101001200011010001012?20??0100020110100
0020000100020000000010200111000000111200?0001131002000100010100000001?0?00?101
0?0?02????????0???????????????????????0???????????????????????



Confuciusornis
011?1
?1?0000???????0???0?110???????0????1???1?00??0?????10-??0?0?10??000?????0?00001
?????????0??0?????????????1?????0?????????????00100000010?1?000?0???000?11-????1?????
2??????????????????0?????????0100???1?????0?5????0?21?-?1?????????????011?21?010?0???
??0?11114020????1111???0?11?11?002???0?1?1??????02??100?30-?1???00101????1?211011?1
1????2??1?10???0?1????????01??1??20???11?0?01?10??0?00??000?0-----------------------1?2??1
110?0???020??0-10?1?3??0000?0???11????200?1?4??0-0110???000???120?0?????????????????
??????

Jeholornis
????
??????0????????????????????????0?????????????????????????????????????????????1??0??
????????????????????????????????????10?????00?????????????????????????1?????1????????2?
???????????????????????????0?????2?????3???1???0?2?2???1???????????0???????1?????1??10
11[04]0????????1?1??????110?012?0??0??1?????????????????????????????????????1??1??????
??????????????????????????????????????????????????000?0-----------------------102??01100????
???200-000113?000000???????0003000104??0-0110??????00030000-----------------------


Shuvuuia
???0?011000010101?1010200000?000000000001100-1111-10111011001000-100000100010000
00010-??01?120000021101000100110??100010??110121000010001000001001110??0000?1??0
1??02--210011?1?2010?1121111?1110101010100??01?011?0?502??1120111211100200?11100
10?20??002000-1000000030001011-0001100???1?1?010?2-?111????2??111?000?20-2?1??0000
0?0??-?22000-01??11121?1010011??1???1121??1011122110?0000200102000?001101120-------
----------------1?2??2200?1000101211-1111?3??0200?01?0000???301?1????1-10?10?1000????01
?????????????????????????

Mononykus
?
???
????????????????????????????????????????????????????????????????????????????????????
??????????????????????100??????????1012?0???????????????????????????????????2--?1?0?1??
0????????1?11?0--?101?10101???1?011?0??????11?01?12?1????????????1??20??002000-?00?0
000300010?1-00011?1?1?1?1?0?????0??????????111??00?2????1??00?00?0??-?????0-?1????12
1?101001?101????1?1??1011??21???0000200102000?000101120-----------------------112112200?
1000101?11-1111????0200?01?0000?????1?1????1-10010?1000?????1???????????????????????
??


Gallus 0
110102
10?00??????101????????0??0000?100??0201111?000?1110-100?01?????01?00100?0??
?1??????012??101----0???????100?101??0?1??????????????????????????????????11-----1-----2-
-------11011200111111?0?10111100001101?101701110031?-???????????????001?2111103010-
10011011111010111101110011?1?1101012-00101?01???0210111?30-2--2?10031201011?211??
?1101112--11101010?110121?11???111???101110020011??01?001002--0-----------------------10
2?1121000001010200-02111210000000000000000-3--101-00?011?00?00?000----0----------------
-------


Conchoraptor
??????00
111
0?0?00??1???0?020???????1????1???111?000??12?10-?1000010??001?????000000
0?????????1??1?????????0????1??????00??11?????0212000201?0?0?000?0???101011-????1???
??2????-?????????0????????????1???01??0????????11??0??????1????????????0???????1?11?01
??0??010001??????001????????????010?1?001?1??????0210000?1100?1??20??1???010??000-0
??????11?1010?010?0????????????0????????0?0?00?00??0?0???10000-----------------------102??
1?1000?0?11110?-110113??000000?0?10?00?0010104??0-0010?0?00000?00100-------------------
----


Microraptor
0100?01000??1??????0??00????????00?0????????1??0??????????????????????0???????????????
??????????0??????????????????????????????????0?00010??????01??1??????010???1?01--210?0
000?0????2???011?????????0?100?0?1?00??014???1??10?1?1??1--1-0?1??2011?01101??0????1
??1111011???0??11???00??1100?111?11??1?1??????02011?1?21110?2001131?0?011111010?1
?????11?1111??10?0?????????0?0???01???1000010?11?01?11?010000-----------------------10???
???????0????2?0??0010????????????????????0011???????0????????????0?0-----------------------


Hagryphus
????
????????????????????????????????????????????????????????????????????????????????????
????????????????????????????????????????????????????????????????????????????????????????
????????????????????????????????????????????????????????????????????????????????????????
???????????????0?110???????????????????????????????????????????????????????????????????
??????????????????????????????????????????10000-----------------------1020001100000011010?-
0001131000000100010000?200?104-00-011010100000?00000-----------------------


Dilong
10?100
0?011
?10100110?1000?0001001010000001221000010110?0010001000000000120001?1
0010011??0?????00001001100000???1??1?100??0????????000000100001111111010101?1101?
00100102000000000????1?00??0?1?1??0100?????1?????0101????????????0????1?001????000?
??????0????01000?01??10001???????????????1?1?00000??0?10100100?0?0??11?????????0????
?0??0????11?110001?00??010001?12?201???00020111??0????0?00?0?2?0??000?1?2??1010?00
?011?2???00?1?3??0000?10?010????000?1?4??000010???000???120?????????????????????????
????????????????????????


Epidexipteryx
??-????????????????????????????????0???????????0000???????0?0??00?????01?1???????00?0?
???????????????????????????????????????????1??00??00????1?00??????0????0??11002???011?
1???00??????????0????????0??00?0???0????14????1?20?2????1??2????????10?1?????1?1???0?
100?1002????0000????1??????????0??????????1???????0??00??????0?00102????210?0??1????
????1???????????????0?????1??01???11102????0??0?????001???????????????????????????????
?????????????0??????????????????????????????????????????????????????????????????????????
??

Epidendrosaurus
????????????????????????????????????????????????0100?0
??????1??00?????0????????????????
???????????????????????0???????????????????21000000100?1?00?10???0????????????????1???
?
????????????????????????0?00?0?0?01???13???0??10?1????10?0???1?1????1??????101?????1
?0110?2????00?0?0??1?1?110????0??0?1?????1???????0?000??????0?00??2????2?0?0??1?????
2?2?0100????0??????0???????????????1020??00??0?00??001?0-----------------------102??????0??
??????00-00?103??0?0000?0??0?000000?114?00-0000?0?00?100200?0-----------------------

Sinosauropteryx 
1000
000
001?01??0?0????00000??0?000??0?????????00??00?0???10???????0??00????0??00012
?10??????????0??????????????0??????????????????00?00?100??????????????1??101001001102
000000000????1??01?10111?10?????10?01??2?0??13??????00?0?0??1110?0111101000??????0
0010100100000?00?00???0?0000??110010100??0???0?0?101020?000?111??1??0001000011?00
0?0??1??010001??0??01??01??1??00?0?00?201101000020??00?00200??000010201221001?0?1
112?1?11010300000000???1000?10010104?00?00100?100000000100???????????????????????0
???????????????????????

=======================================================

Appendix 5

Oviraptors as secondarily-flightless 

Here is an accumulation of material that supports the idea that Oviraptors were secondarily-flightless primitive birds. Being "secondarily-flightless" means they evolved from earlier flying primitive birds.

http://en.wikipedia.org/wiki/Oviraptorosauria
Oviraptorosaurs Temporal range: Cretaceous, 130–66 Ma
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
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 analysis 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]


http://agro.icm.edu.pl/agro/element/bwmeta1.element.agro-article-f38bf90a-7c6b-47fc-982a-30d0be44fd5e/c/app47-097.pdf
Avialan status for Oviraptorosauria (2002)
TERESA MARYAŃSKA, HALSZKA OSMÓLSKA, and MIECZYSŁAW WOLSAN
Oviraptorosauria is a clade of Cretaceous theropod dinosaurs of uncertain affinities within Maniraptoriformes. All previous phylogenetic analyses placed oviraptorosaurs outside a close relationship to birds (Avialae), recognizing Dromaeosauridae or Troodontidae, or a clade containing these two taxa (Deinonychosauria), as sister taxon to birds. Here we present the results of a phylogenetic analysis using 195 characters scored for four outgroup and 13 maniraptoriform (ingroup) terminal taxa, including new data on oviraptorids. This analysis places Oviraptorosauria within Avialae, in a sister−group relationship with Confuciusornis. Archaeopteryx, Therizinosauria, Dromaeosauridae, and Ornithomimosauria are successively more distant outgroups to the Confuciusornis−oviraptorosaur clade. Avimimus and Caudipteryx are successively more closely related to Oviraptoroidea, which contains the sister taxa Caenagnathidae and Oviraptoridae. Within Oviraptoridae, “Oviraptor” mongoliensis and Oviraptor philoceratops are successively more closely related to the
Conchoraptor−Ingenia clade. Oviraptorosaurs are hypothesized to be secondarily flightless. Emended phylogenetic definitions are provided for Oviraptoridae, Caenagnathidae, Oviraptoroidea, Oviraptorosauria, Avialae, Eumaniraptora, Maniraptora, and Maniraptoriformes.
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.

https://bio.unc.edu/files/2011/04/FeducciaCzerkas2015.pdf
Testing the neoflightless hypothesis: propatagium reveals flying ancestry of oviraptorosaurs (2015)
Alan Feduccia1• Stephen A. Czerkas2
We focus here on the discovery of an anatomical feature, the propatagium, which argues that Caudipteryx supports the neoflightless hypothesis—that is, it is derived from a flighted ancestry (Paul 2002)—and therefore its highly derived avian anatomy was selected for in an aerodynamic context.
The recognition of avian characters in oviraptorosaurs goes back to Elzanowski (1999, p. 311) who concluded that: ‘‘cranial similarities between oviraptorosaurs and ornithurine birds raise the possibility that oviraptorosaurs are the earliest known flightless birds.’’ We believe evidence now supports the view that many maniraptorans look avian, despite their inability to fly, because they were derived from basal volant birds and had become secondarily flightless (Fig. 1). Highly derived avian characteristics, such as the reduction of the manual digits in Caudipteryx, are so strikingly similar to that in extant birds that to conclude that this resemblance is only an exaptation defies the logical simplicity that it might look avian because it is a bird.
Considerable debate surrounds the numerous
avian-like traits in core maniraptorans (oviraptorosaurs,
troodontids, and dromaeosaurs), especially in the
Chinese Early Cretaceous oviraptorosaur Caudipteryx,
which preserves modern avian pennaceous primary remiges
attached to the manus, as is the case in modern birds.
Was Caudipteryx derived from earth-bound theropod dinosaurs,
which is the predominant view among palaeontologists,
or was it secondarily flightless, with volant avians
or theropods as ancestors (the neoflightless hypothesis),
which is another popular, but minority view. The discovery
here of an aerodynamic propatagium in several specimens
provides new evidence that Caudipteryx (and hence oviraptorosaurs)
represent secondarily derived flightless
ground dwellers, whether of theropod or avian affinity
,
 and
that their presence and radiation during the Cretaceous may
have been a factor in the apparent scarcity of many other
large flightless birds during that period.



The even more likely possibility is that some of these groups had both flying AND later secondarily-flightless members. 


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. 


Another point to consider is the following:
If the common ancestor (the basalmost Euparaves) was ground dwelling, then there have never been any secondarily-flightless primitive birds ever found:

Alan Feduccia1• Stephen A. Czerkas2, (2015) 
Testing the neoflightless hypothesis: propatagium reveals flying ancestry of oviraptorosaurs 
The absence in the Cretaceous fossil record of numerous large secondarily flightless birds has been considered a complex unsolved mystery (Feduccia 2012).
The loss of flight is of such common occurrence within Aves that it should be expected to have occurred any time after flight was initially achieved.
http://www.bio.fsu.edu/James/Ornithological%20Monographs%202009.pdf
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).  

--------------------------------------------------------------------------------------

Appendix 6

Exaptations

In the dino to bird theory, there is a good deal of claimed exaptation. Those exaptations are required due to the misplacement of the oviraptors and alvarezsaurids.

Abducted wrists, feathers and enlarged brains are claimed to have evolved before they were used for flight. These are simply stories. These stories are made up in response to evidence that contradicts the placement of the oviraptors and alvarezsaurids.

http://en.wikipedia.org/wiki/Exaptation
Exaptation and the related term co-option describe a shift in the function of a trait during evolution. For example, a trait can evolve because it served one particular function, but subsequently it may come to serve another.

ABDUCTED WRISTS

http://rspb.royalsocietypublishing.org/content/early/2010/02/24/rspb.2009.2281.full.ht
Carpal asymmetry [abducted wrists] would have permitted avian-like folding of the forelimb in order to protect the plumage, an early advantage of the flexible, asymmetric wrist inherited by birds.
However, it is likely that mobility of the wrist was initially associated with other functions, such as predation (Padian 2001).
http://www.smithsonianmag.com/science-nature/bird-wrists-evolved-among-dinosaurs-65035237/?no-ist
It had originally been proposed that this flexibility could be attributed to hunting, but the same changes are seen in maniraptorans that were herbivores and omnivores so it is unlikely that hunting provides the answer. Instead, the authors of the new study propose, the ability to fold the hands backwards would have protected the feathers of the arms. This would have prevented the feathers from getting damaged or from being in the way as the dinosaurs moved about, although the authors recognize that this hypothesis requires further evidence.
Perhaps more significant, however, is how this wing-folding mechanism may have allowed birds to take to the air. Birds do flex their wrists while flapping their wings to fly, and so it appears that the wrist flexibility that first evolved in dinosaurs was later co-opted for flight in birds. This is what is known as "exaptation," or when a previous adaptation takes on a new function. Indeed, as more is discovered about the evolution of birds, the more traits paleontologists find that evolved for one function but have been co-opted for another at a later point (feathers themselves being the most prominent
example). There is relatively little separating birds from their feathered dinosaur ancestors.

FEATHERS

http://en.wikipedia.org/wiki/Exaptation
As Darwin elaborated in the last edition of The Origin of Species,[14] many complex traits evolved from earlier traits that had served different functions. By trapping air, primitive wings would have enabled birds to efficiently regulate their temperature, in part, by lifting up their feathers when too warm. Individual animals with more of this functionality would more successfully survive and reproduce, resulting in the proliferation and intensification of the trait.
Eventually, feathers became sufficiently large to enable some individuals to glide. These individuals would in turn more successfully survive and reproduce, resulting in the spread of this trait because it served a second and still more beneficial function: that of locomotion. Hence, the evolution of bird wings can be explained by a shifting in function from the regulation of temperature to flight.
http://www.livescience.com/39688-exaptation.html
Exaptation is a term used in evolutionary biology to describe a trait that has been co-opted for a use other than the one for which natural selection has built it.
It is a relatively new term, proposed by Stephen Jay Gould and Elisabeth Vrba in 1982 to make the point that a trait’s current use does not necessarily explain its historical origin. They proposed exaptation as a counterpart to the concept of adaptation.
For example, the earliest feathers belonged to dinosaurs not capable of flight. So, they must have first evolved for something else. Researchers have speculated early feathers may have been used for attracting mates or keeping warm. But later on, feathers became essential for modern birds’ flight.
http://en.wikipedia.org/wiki/Microraptor#Wings_and_flight
This further supports the hypothesis that "flight feathers" that first evolved in dinosaurs for non-aerodynamic functions were later adapted to form lifting surfaces.[15]

ENLARGED BRAINS

http://www.bbc.com/news/science-environment-23514985
Several ancient dinosaurs evolved the brainpower needed for flight long before they could take to the skies, scientists say.
Bird brains tend to be more enlarged compared to their body size than reptiles, vital for providing the vision and coordination needed for flight.
Scientists using high-resolution CT scans have now found that these "hyper-inflated" brains were present in many ancient dinosaurs, and had the neurological hardwiring needed to take to the skies. This included several bird-like oviraptorosaurs and the troodontids Zanabazar junior, which had larger brains relative to body size than that of Archaeopteryx.

OTHER

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028964
Placed in context of avian evolution, the grasping foot of Deinonychus and other terrestrial predatory paravians is hypothesized to have been an exaptation for the grasping foot of arboreal perching birds. Here we also describe “stability flapping”, a novel behaviour executed for positioning and stability during the initial stages of prey immobilisation, which may have been pivotal to the evolution of the flapping stroke. These findings overhaul our perception of predatory dinosaurs and highlight the role of exaptation in the evolution of novel structures and behaviours.

GENERAL
See page 261 of "Riddle of the Feathered Dragons"
http://books.google.ca/books?id=SihlpQTlVdAC&pg=PA154&lpg=PA154&dq=parasagittal+stance+for+Archaeopteryx.&source=bl&ots=jTl0YCn6be&sig=B9WKpEcJJ8Xr3U4_haeHeZFUToE&hl=en&sa=X&ei=xHMYVMWbAsGOyAT3loGQDg&ved=0CDwQ6AEwAw#v=snippet&q=exaptations&f=false

Also:
http://onlinelibrary.wiley.com/doi/10.1111/evo.12363/full
Did preadaptations for flight precede the origin of birds (Aves)? The origin of flight in birds is one of the great evolutionary transitions and has received considerable attention in recent years (Padian and Chiappe 1998; Clarke and Middleton 2008; Dececchi and Larrson 2009; Benson and Choiniere 2013; Dececchi and Larrson 2013). The evolution of birds is often considered coincident with the origins of flight, but many traits associated with flight evolved before the origin of Aves (Padian and Chiappe1998).

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2756958/

This suggests that the initial conquest of the air was achieved using lower metabolic rates than are characteristic of today's avian flyers. It appears that the closest non-avialan relatives of birds were physiologically preadapted for powered flight and only anatomical adaptations were involved when birds first ventured into the air. 

http://www.bio.fsu.edu/James/Ornithological%20Monographs%202009.pdf
Although some or all of the flight-related characters of birds, including those found in the maniraptorans, may have evolved for purposes other than flight, current exaptational explanations offered by BMT proponents are often not fully formulated and rarely offer a biologically plausible hypothesis to account for their origin (Feduccia 1985, 1993, 1995; Paul 2002; Feduccia et al. 2005, 2007). Under such conditions, exaptational explanations should not be regarded as having priority (Rose and Lauder 1996), and adaptational accounts should not be discarded. If the most birdlike maniraptoran clades belong within Aves, problematic exaptational explanations, including those for the origin of flight feathers, are unnecessary.
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).  

https://en.wikipedia.org/wiki/Effigia
Effigia is noted for its remarkable similarity to ornithomimid dinosaurs. Nesbitt, in 2007, showed that Effigiawas very similar to Shuvosaurus, and is definitely a member of the crurotarsan group Suchia (in the line leading towards modern crocodilians), and that its similarity to ornithomimids represents a case of "extreme" convergent evolution. Nesbitt also demonstrated that Shuvosaurus was the same animal as Chatterjeea, and that it belonged to an exclusive clade containing closely related suchians such as Shuvosaurus and Poposaurus (Poposauridae). Within this group, Effigia forms an even more exclusive clade with Shuvosaurus and the South American Sillosuchus (Shuvosaurinae).[1] In 2007, Lucas and others suggested "Effigia" was synonymous with "Shuvosaurus" and used the new combination "Shuvosaurus okeeffeae" for the animal.

--------------------------------------------------------------------------------------------

Appendix 7

Reversals 

The dino to bird theory requires "remarkable" reversals. Those reversals are required due to the misplacement of the oviraptors and alvarezsaurids.

ANKLE:
http://www.nature.com/ncomms/2015/151113/ncomms9902/full/ncomms9902.html (2015)
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.
Also see here:
More remarkably, however, this finding reveals an unexpected evolutionary transformation in birds. In embryos of the landegg-laying animals, the amniotes (which include crocodilians, lizards, turtles, and mammals, who secondarily evolved live birth) the intermedium fuses to the anklebone shortly after it forms, disappearing as a separate element. This does not occur in the bird ankle, which develops more like their very distant relatives that still lay their eggs in water, the amphibians. Since birds clearly belong within landegg-laying animals, their ankles have somehow resurrected a long-lost developmental pathway, still retained in the amphibians of today -- a surprising case of evolutionary reversal.
WRIST:
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001957
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.
FINGERS:
http://www.nature.com/articles/nature08124.epdf?referrer_access_token=1LIOYM249T2ALXmHhUVXQtRgN0jAjWel9jnR3ZoTv0NAxxXDTxDgb7tt7vNCs5i7CDx_p1E8pIL0dPMGIw0CIZ1LRnUZIDT1a3FIDY_UW4FRwpODRDVwWg-KbK448VK63yIXiGAa_H8fA42yVK8TsNhr_ASjWKKTbM-PJCMVzpKKElR4FEstewHl9DZGaHr9&tracking_referrer=www.nature.com
(Xu et al 2009)
Based on this study, the most parsimonious alignment is for the four digits of ceratosaurs to be I-II-III-IV and the three (and sometimes four) digits of all Tetanurae to be II-III-IV(V). Accepting such a topological shift at the base of Tetanura requires that the positional homology of the three digits of tetanurans is II-III-IV(-V), as suggested by Wagner and Gauthier34. Because the four digits of ceratosaurs are therefore most parsimoniously interpreted as I-II-III-IV, the small lateral metacarpal ossification of Guanlong35, Sinraptor36, and Coelurus represents the re-ossification of metacarpal V after it is lost at the base of Ceratosauria. The poor phylogenetic resolution for basal tetanurans in our study precludes us from hypothesizing whether this re-ossification event occurred once or more than once in the evolution of Theropoda. Likewise, the fourth metacarpal, which is reduced in primitive theropods and bears an unknown number of phalanges in Ceratosauria, re-acquires at least three phalanges in Tetanurans.

This implies the reduction of digit I before the divergence of the Ceratosauria and the
Tetanurae, the appearance of some polleciform features in digit II and the acquisition of a novel phalangeal formula (X-2-3-4-X) early in tetanuran evolution. Both modifications are partially indicated by the manual morphologies of ceratosaurs and more basal theropods. Also, they are indirectly supported by observations in living animals that a digit will display features normally associated with the neighbouring medial digit if the latter fails to chondrify in early development21, that phalangeal counts can vary even within species29, 42 and that secondarily cartilaginous elements can regain their ability to ossify43.

If BDR [Bilateral Digit Reduction] applies to the more inclusive Averostra, as the II-III-IV hypothesis suggests, early stages of tetanuran evolution must have involved loss of the already highly reduced metacarpal I, reduction in the length of metacarpal II, and the reappearance of additional phalanges on metacarpal IV. Both the I-II-III and II-III-IV hypotheses can claim a degree of support from morphological data, but the II-III-IV hypothesis is more parsimonious when developmental data from extant birds are considered.
There is no actual evidence for these reversals.

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Appendix 8

Stratigraphic Incongruence

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


Oviraptors   (Temporal range: Late Cretaceous, 75 Ma)
Alvarezsaurids (Temporal range: Late Cretaceous, 86–66 Ma)


------------------------------------------------------------------------------------------------

Appendix 9

Character Optimization 

http://www.gwu.edu/~clade/bisc%20207/Agnarsson_and_Miller_2008.pdf


De Pinna (1991, p. 386) argued that ‘‘… absences stand at a lower ontological level as observations, when compared to presences (Nelson and Platnick, 1981: 29; Patterson, 1982: 30).’’ In other words, there can be asymmetry in the information content of primary homology statements of character states. Complex features share detailed similarities strengthening the conjecture of homology between them, whereas absences are a weaker form of primary homology statements (see also Rieppel and Kearney, 2002). Therefore, a theoretical basis may exist for favouring some equally parsimonious optimizations over others. In the absence of compelling evidence to the contrary, ambiguous optimization is better resolved in favour of secondary losses (reversals) over parallel gains of complex structures. This is more consistent with the stronger conjecture of homology based on observable detailed similarity, rather than mere absence (De Pinna, 1991); complexity tests similarity (Agnarsson and Coddington, 2008; see also Richter, 2005; Scholtz, 2005; Agnarsson et al., 2007). When characters lack asymmetry in character state complexity (e.g. the states ‘‘red’’ and ‘‘blue’’), little, if any, grounds exist to favour one optimization over another (Richter, 2005).
https://books.google.ca/books?id=2MQeh1KCp7sC&pg=PA442&lpg=PA442&dq=cladistic+analysis+character+optimization&source=bl&ots=Ftbf4Ee7SX&sig=pS3M-6_KbgLXR8-suHW2vcN2T7w&hl=en&sa=X&ved=0ahUKEwiVi9yA9a7KAhWGeT4KHXYNAyQQ6AEIQTAG#v=onepage&q=cladistic%20analysis%20character%20optimization&f=false
See page 442.



http://www.sciencedirect.com/science/article/pii/S0960982214008434
Zhonghe Zhou (2014)
However, contrary to Foth and colleagues [11], it is probably premature to reject a four-winged stage during the origin of avian flight. The leg feathers of Archaeopteryx are relatively short, yet they are weakly curved like the flight feathers and are not so short that an aerodynamic function can be excluded. There is still no evidence showing unequivocally that leg feathers lacked aerodynamic function in the direct ancestor of birds. In fact, Microraptor probably represents only one of many extinct feathered dinosaurs that maintained an ancestral aerodynamic role in the leg feathers [2]. A recent study on the leg feathers of a primitive bird, Sapeornis, suggested a distal-to-proximal pattern of reduction during leg feather evolution [13]. It is possible that an aerodynamic function of pennaceous feathers could have evolved several times in various theropod lineages; however, it is also more likely that flight and aerodynamic functions of the pennaceous feathers could have been lost many times in theropod (including birds) evolution — during evolution, the loss of features is far more common than the evolution of novel features.


http://www.gwu.edu/~clade/faculty/lipscomb/Cladistics.pdf
The cladogram on the left represents the scenario of the basalmost Euparaves being a flying primitive bird (secondary loss). The cladogram on the right represents the basalmost Euparaves being a ground dwelling creature (homoplasy).


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Appendix 10

Implausible rates of evolution

Mark N Puttick,1,2 Gavin H Thomas,3 Michael J Benton,1 and P David Polly (2014)
Before the origin of Aves, on the branch leading to Paraves, high rates of evolution led to a smaller body size and a relatively larger forelimb in Paraves. These changes are on a single branch leading to Paraves, representing a shift to a new smaller size and larger forelimb at this point. Rapid miniaturization and relative forelimb elongation at the root of Paraves explain the similarities between early birds and other Paraves (Padian and Chiappe 1998; Turner et al. 2007; Clarke and Middleton 2008; Novas et al. 2012). As with previous studies, we find strong evidence for paravian miniaturization (Xu et al. 2003; Turner et al. 2007; Novas et al. 2012) and no trend for forelimb elongation (Dececchi and Larrson 2013), but the identification here of increased rates of evolution of size-dependent forelimb and body size at the origin of Paraves emerges from our novel analytical approach. As with a recent study (Deccechi and Larrson 2013), we find evidence for a different allometric relationship between forelimb size and body size in Aves, but this result is altered by different phylogenetic topologies, and we find little evidence for elevated rates leading to or within Aves.

Michael S. Y. Lee1,2,*, Andrea Cau3,4, Darren Naish5, Gareth J. Dyke5,6 (2014)
Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds
Abstract:
http://www.sciencemag.org/content/345/6196/562
Full study:
http://www.researchgate.net/publication/264386153_Sustained_miniaturization_and_anatomical_innovation_in_the_dinosaurian_ancestors_of_birds
Recent discoveries have highlighted the dramatic evolutionary transformation of massive, ground-dwelling theropod dinosaurs into light, volant birds. Here, we apply Bayesian approaches (originally developed for inferring geographic spread and rates of molecular evolution in viruses) in a different context: to infer size changes and rates of anatomical innovation (across up to 1549 skeletal characters) in fossils. These approaches identify two drivers underlying the dinosaur-bird transition. The theropod lineage directly ancestral to birds undergoes sustained miniaturization across 50 million years and at least 12 consecutive branches (internodes) and evolves skeletal adaptations four times faster than other dinosaurs. The distinct, prolonged phase of miniaturization along the bird stem would have facilitated the evolution of many novelties associated with small body size, such as reorientation of body mass, increased aerial ability, and paedomorphic skulls with reduced snouts but enlarged eyes and brains.

https://en.wikipedia.org/wiki/Paraves
The ancestors of Paraves first started to shrink in size in the early Jurassic 200 million years ago, and fossil evidence show that this theropod line evolved new adaptations four times faster than other groups of dinosaurs,[8] and was shrinking 160 times faster than other dinosaur lineages were growing.[9] 

Daniel T. Ksepka
Evolution: A Rapid Flight towards Birds http://www.sciencedirect.com/science/article/pii/S0960982214011385
Rates of morphological evolution can be quantified using time-calibrated phylogenetic trees. Brusatte et al. [1] employ the new phylogeny as the framework for conducting likelihood analyses of skeletal character evolution. These tests recover high rates of evolution both within the bird clade and also along a series of nodes on the theropod ‘backbone’ leading to birds. In agreement with these results, a recent Bayesian analysis using a different character dataset also found support for a sustained higher rate of skeletal evolution along this backbone [11], though the two studies disagree slightly on how deep in the tree the onset of higher rates occurs. A different set of tests in the Brusatte et al. [1] study compares rates between clades, revealing that birds as a clade exhibited a higher rate of skeletal evolution than other theropod clades. As a whole, these results suggest that birds are indeed a special case, leading to the hypothesis that the completion of the avian skeletal plan and development of powered flight opened the door to new ecological niches and triggered a burst of evolution [1].
Here again, the lineage leading to birds stands out as an exception, with maniraptoran theropods sustaining high rates of size evolution relative to other dinosaur lineages [12]. A third recent study [13] employing likelihood methods capable of detecting branch-specific rate shifts places the shift to higher rates of size evolution on the branch leading to Paraves (the clade uniting birds, dromaeosaurids, and troodontids).

The theropod tree.Evolutionary tree of theropod dinosaurs, simplified from ...

------------------------------------------------------------------------------------------------


Appendix 11


http://onlinelibrary.wiley.com/enhanced/doi/10.1111/evo.12363/
Before the origin of Aves, on the branch leading to Paraves, high rates of evolution led to a smaller body size and a relatively larger forelimb in Paraves. These changes are on a single branch leading to Paraves, representing a shift to a new smaller size and larger forelimb at this point.
Paraves, rather than Aves alone, shifted to a different evolutionary model relative to other coelurosaurian theropods (Table 2). On all trees and for both femur and forelimb size, the model with a regime shift at Paraves, rather than Aves, is favored (Table S10). We found strong support for a reduction in femur length within Paraves (57.5 mm for Paraves, 147.9 mm for other coelurosaurians) with weaker evidence for a concurrent reduction in evolutionary rates (Table 2). Importantly, the best-fitting paravian regime-shift model for femur length is substantially better than the best-fitting avian regime shift model (ΔAICc = 6.15; Table 1). The paravian forelimb reduced slightly in size (Paraves = 158.4 mm; other taxa = 234.4 mm; Table 2). In contrast, the equivalent model that incorporates a reduction in rate within Aves (Table 2) is an inferior fit (ΔAICc = 2.48).

http://www.sciencedirect.com/science/article/pii/S0960982214011385

Here again, the lineage leading to birds stands out as an exception, with maniraptoran theropods sustaining high rates of size evolution relative to other dinosaur lineages [12]. A third recent study [13] employing likelihood methods capable of detecting branch-specific rate shifts places the shift to higher rates of size evolution on the branch leading to Paraves (the clade uniting birds, dromaeosaurids, and troodontids).

http://science.sciencemag.org/content/317/5843/1378.full
Fossil evidence for changes in dinosaurs near the lineage leading to birds and the origin of flight has been sparse. A dinosaur from Mongolia represents the basal divergence within Dromaeosauridae. The taxon's small body size and phylogenetic position imply that extreme miniaturization was ancestral for Paraves (the clade including Avialae, Troodontidae, and Dromaeosauridae), phylogenetically earlier than where flight evolution is strongly inferred.

https://www.researchgate.net/publication/26861082_Hu_D_L_Hou_L_Zhang_and_X_Xu_A_pre-Archaeopteryx_troodontid_theropod_from_China_with_long_feathers_on_the_metatarsus_Nature
This distal-first development led to a four-winged condition at the base of the Paraves.

==========================================================


General Reference


Godefroit, Cau, Yu, Escuillie, Wenhao & Dyke. 2013a.
http://phenomena.nationalgeographic.com/2013/05/29/the-changing-science-of-just-about-birds-and-not-quite-birds/
A Jurassic avialan dinosaur from China resolves the early phylogenetic history of birds.




https://en.wikipedia.org/wiki/Paraves
.... the work of Xu et al. (2003), (2005) and Hu et al. (2009) provide examples of basal and early paravians with four wings,[11][12][13] 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.[14] 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.[15]
Let's analyze this:
"basal and early paravians with four wings,[11][12][13] 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".
In the early stage of flapping flight, the basal Euparaves did not yet have the derived supracoracoideus which would later provide much greater ability to lift the wings. They compensated for this by using their hindwings for additional lift. Thus they were capable of full flapping flight. When they developed a derived supracoracoideus (in Euavialae) they no longer needed hindwings for flight. 



Arboreal
Pascal Godefroit, Helena Demuynck, Gareth Dyke, Dongyu Hu, François Escuillié & Philippe Claeys (2013b)
Reduced plumage and flight ability of a new Jurassic paravian theropod from China Pascal Godefroit1,2, Helena Demuynck3, Gareth Dyke4, Dongyu Hu5,6, Franc¸ois Escuillie´7 & Philippe Claeys3
with large foot remiges cursorial locomotion was likely problematic for Anchiornis.
 https://en.wikipedia.org/wiki/Anchiornis
Anchiornis had very long legs, usually an indication that they were strong runners. However, the extensive leg feathers indicate that this may be a vestigial trait, as running animals tend to have reduced, not increased, hair or feathers on their legs.[2] The forelimbs of Anchiorniswere also very long, similar to archaeopterygids.


Here are the apomorphies (distinguishing characteristics) of Euparaves:
They possessed remiges and rectrices, that is, enlarged, stiff-shafted, closed-vaned (= barbules bearing hooked distal pennulae), pennaceous feathers arising from the distal forelimbs and tail
AND
they possessed feathered wings used in flapping flight.

https://en.wikipedia.org/wiki/Microraptor
Like Archaeopteryx, well-preserved fossils of Microraptor provide important evidence about the evolutionary relationship between birds and dinosaurs. Microraptor had long pennaceous feathers that formed aerodynamic surfaces on the arms and tail but also on the legs. This led paleontologist Xu Xing in 2003 to describe the first specimen to preserve this feature as a "four-winged dinosaur" and to speculate that it may have glided using all four limbs for lift. Subsequent studies have suggested that it is possible Microraptor were capable of powered flight as well.
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.[10][12]


To begin, we need to understand the categories of creatures involved.
There are dinosaurs (eg. coelurosaur dinosaurs), primitive birds and modern birds.

Dinosaurs
Tyrannosaurs and compsognathids are examples of coelurosaur dinosaurs. According to the dinosaur to bird theory, it is claimed that the primitive birds evolved from coelurosaur dinosaurs. In cladistic terms, it is claimed that birds are coelurosaur dinosaurs.

Primitive birds 
Primitive birds were pennaceous-feathered, flying, arboreal, long-bony-tailed, four-winged birds. They were capable of normal sustained flapping flight, They could take off from tree branches but their shoulder mechanism was such that they could not take off from level ground.
Examples include ScansoriopterygidaeTetrapterygidae (Anchiornis, Aurornis, Xiaotingia, Microraptor), Pedopenna, Zhongornis. 
Oviraptors, Alvarezsaurids and Eudromaeosaurs were secondarily-flightless primitive birds that descended from earlier flying primitive birds.

Modern birds
Modern birds do not have a long-bony-tail, they have a pygostyle. Most can take flight from the ground.


Important note:
The standard clade labelled "Paraves" is not directly comparable to Euparaves, since Paraves is a branch-based clade, based on the idea that Oviraptors were dinosaurs that existed before Paraves.
"Paraves is a branch-based clade defined to include all dinosaurs which are more closely related to birds than to oviraptorosaurs."
However the actual membership of basal Paraves is all the primitive birds, so in that sense, the Paraves primitive birds are synonymous with the Euparaves primitive birds.


https://en.wikipedia.org/wiki/Paraves
Paraves is a branch-based clade defined to include all dinosaurs which are more closely related to birds than to oviraptorosaurs.
The ancestral paravian is a hypothetical animal: the first common ancestor of birdsdromaeosaurids, and troodontids which was not also ancestral to oviraptorosaurs. Little can be said with certainty about this animal. But the work of Xu et al. (2003), (2005) and Hu et al. (2009) provide examples of basal and early paravians with four wings,[11][12][13] 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.[14] 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.[15]
The name Paraves was coined by Paul Sereno in 1997.[18] The clade was defined by Sereno in 1998 as a branch-based clade containing all Maniraptora closer to Neornithes (which includes all the birds living in the world today) than to Oviraptor.[19]Also in 1997, a node-based clade called Eumaniraptora ("true maniraptorans") was named by Padian, Hutchinson and Holtz. They defined their clade to include only avialans and deinonychosaurs. Paraves and Eumaniraptora are generally considered to be synonyms, though a few phylogenetic studies suggest that the two groups have a similar but not identical content; Agnolín and Novas (2011) recovered scansoriopterygids and alvarezsaurids as paravians that were not eumaniraptorans,[20] while Turner, Makovicky and Norell (2012) recovered Epidexipteryx as the only known non-eumaniraptoran paravian.[21] A nearly identical definition, "the theropod group that includes all taxa closer to Passer than to Dromaeosaurus", was used by Agnolín and Novas (2013) for their clade Averaptora.[22]


https://en.wikipedia.org/wiki/Oviraptorosauria
Oviraptorosaurs ("egg thief lizards") are a group of feathered maniraptoran dinosaurs from theCretaceous 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 tonGigantoraptor.[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] The most complete oviraptorosaur specimens have been found in Asia.[7] The North American oviraptorosaur record is sparse.[7]


Ostrich shown for comparison:

Struthio camelus - Etosha 2014 (3).jpg


http://en.wikipedia.org/wiki/Alvarezsauridae
Alvarezsauridae is a family of small, long-legged running dinosaurs. Although originally thought to represent the earliest known flightless birds, a consensus of recent work suggests that they are primitive members of the Maniraptora. Other work found them to be the sister group to the Ornithomimosauria. Alvarezsaurs are highly specialized. They bear tiny but stoutly proportioned forelimbs with compact birdlike hands and their skeleton suggests they had massive breast and arm muscles, possibly adapted for digging or tearing. They have tubular snouts, elongate jaws, and minute teeth. They may have been adapted to prey on colonial insects such as termites.
Assignments of alvarezsaurs to birds were caused primarily by:
features that are strikingly, or even uniquely, avian. The sternum, for example, is elongated and deeply keeled for an enlarged pectoralis muscle, as it is in neognathous birds and volant ratites. One bone in the skull of Shuvuuia appeared to be an ectethmoid fused to a prefrontal. The ectethmoid is an ossification known only in Neornithes. Other birdlike characters included the palatine, foramen magnum, cervical and caudal vertebrae, and many others.[9]
https://en.wikipedia.org/wiki/Haplocheirus 
Haplocheirus is a genus of alvarezsauroid theropod dinosaur. It is the most basal member of its clade.[1] It is the oldest known alvarezsauroid, predating all other members by about 63 million years.


http://prumlab.yale.edu/sites/default/files/prum_n_brush_2002.pdf
Feathers, however, are hierarchically
complex assemblages of numerous
evolutionary novelties—the feather follicle,
tubular feather germ, feather branched structure,
interacting differentiated barbules—that
have no homolog in any antecedent [dinosaur] structures

(Brush 1993, 1996, 2000; Prum 1999). Genuine
evolutionary novelties are distinct from
simple microevolutionary changes in that they
are qualitatively or categorically different from
any antecedent or homonomous structure.
"In conclusion, the morphological and
molecular developmental details shared by
avian feather and scales support homology
between these structures at the level of the
placode. The morphology and development
of all subsequent structures within the feather
are evolutionary novelties that have no homologs
in avian or reptilian scales.
 "Many features of feathers and feather development meet this definition and qualify as evolutionary novelties. The follicle, the differentiated sheath and feather germ, differentiated barb ridges, barb rami, barbules, differentiated pennulae of the proximal and distal bar bules, and the rachis are all evolutionary novelties, as are the derived mechanisms by which these novel structures develop. At a molecular level, the derived 10 kilodalton -keratins of feathers are also novel"


Fingers

Dinosaur fingers do not align with bird fingers. 

 https://en.wikipedia.org/wiki/Origin_of_birds#Digit_homology
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.

For years, people have been striving to reconcile the I-II-III digits of dinosaurs with the II-III-IV digits of birds. 
Why?
Because they believe that birds evolved from dinosaurs.
Why do they believe that?
Because the cladistic analyses seemed to support that idea. 
How so?
Because they showed oviraptors and alvarezsaurs as intermediates (outgroups) between dinosaurs and primitive birds (Euparaves). 
BUT recent studies show that oviraptors and alvarezsaurs are WITHIN Euparaves. 
So there is no cladistic analysis evidence to support the dino to bird theory. 
Therefore there is no reason to strive to reconcile the I-II-III digits of dinosaurs with the II-III-IV digits of birds. 
Which is good, because there is no credible way to reconcile them in the first place.

The pyramid reduction hypothesis is a credible explanation of the origin of bird fingers. It is "developmentally plausible, and is also consistent with the phalangeal reduction pattern seen in basal birds."
It is inconsistent with a dinosaur to bird theory.

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) [5,62–64].
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.

And concerning the alternative homeotic shift (frameshift):
Also, it is difficult to identify plausible selective pressures that would drive this type of homeotic shift, considering that the post-frameshift adult hand would be morphologically identical to the pre-frameshift condition [69].

http://precedings.nature.com/documents/6375/version/1/files/npre20116375-1.pdf
Reply to “Limusaurus and bird digit identity” Xing Xu1, James Clark2, Jonah Choiniere2, David Hone1 & Corwin Sullivan1
Morphological data from extinct theropods, even without considering Limusaurus and ceratosaurs, clearly contains two contradictory signals for the identification of tetanuran manual digits. Thus, neither our hypothesis [lateral shift] nor the frameshift hypothesis is able to avoid a substantial number of homoplasies.

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.

Note the following from Xu and Mackem 2013:
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) [5,62–64].

Xu and Mackem note that the Pyramid Reduction Hypothesis "is inconsistent with the digital reduction data from basal theropods".
But it is only inconsistent if birds evolved from dinosaurs. If birds did not evolve from dinosaurs, then there is no inconsistency.
In fact, as Xu and Mackem acknowledge, one possible implication of the Pyramid Reduction Hypothesis is that birds are not descended from theropod dinosaurs.





Types of clades
https://en.wikipedia.org/wiki/Phylogenetic_nomenclature






http://blogs.scientificamerican.com/observations/reanalysis-of-four-winged-dinosaur-may-illuminate-evolution-of-bird-flight/
Not everyone is convinced by the team’s arguments. Kevin Padian of the University of California at Berkeley, an expert on bird evolution, observed that the presentations focused on the effect of the hindlimb on a gliding animal instead of one that flapped its wings. Last year at the SVP meeting he presented evidence that gliders and flyers are completely unrelated to each other. He says that “there is not a shred of evidence that says gliding is involved in the evolution of flapping flight.” He questioned why the team's model would focus on gliding parameters when the forelimb shape was consistent with flapping, not gliding, and the hindlimb would have generated so much drag.



http://palaeos.com/systematics/cladistics/cladistics_and_paleontology.html





https://en.wikipedia.org/wiki/Flight_feather
Flight feathers (Pennae volatus[1] are the long, stiff, asymmetrically shaped, but symmetrically paired pennaceous feathers on the wings or tail of a bird; those on the wings are called remiges(singular remex) while those on the tail are called rectrices (singular rectrix). The primary function of the flight feathers is to aid in the generation of both thrust and lift, thereby enabling flight




Therizinosaurs and Ornithomimosaurs 
When oviraptors and alvarezsaurids are placed within Euparaves, then only Therizinosaurs and Ornithomimosaurs are left as claimed sister-groups, branching from the proposed line from dinosaurs to birds. 

https://en.wikipedia.org/wiki/Therizinosaur
Therizinosaurs had a very distinctive, often confusing set of characteristics. Their long necks, wide torsos, and hind feet with four toes used in walking resembled those of basal sauropodomorph dinosaurs. Their unique hip bones, which pointed backwards and were partially fused together, initially reminded paleontologists of the "bird-hipped"ornithischians. Among the most striking characteristics of therizinosaurs are the enormous claws on their hands, which reached lengths of around one meter in Therizinosaurus. The unusual range of motion in therizinosaur forelimbs, which allowed them to reach forward to a degree other theropods could not achieve, also supports the idea that they were mainly herbivorous. Therizinosaurs may have used their long reach and strongly curved claws to grasp and shear leafy branches, in a manner similar to the ground sloths.[1]
The therizinosaurs are so "confusing" that no conclusions can be drawn from them.


https://en.wikipedia.org/wiki/Ornithomimosauria
Ornithomimosauria has variously been used for the branch-based group of all dinosaurs closer to Ornithomimus than to birds, and in more restrictive senses. The more exclusive sense began to grow in popularity when the possibility arose that alvarezsaurids might fall under Ornithomimosauria if an inclusive definition were adopted. Another clade, Ornithomimiformes, was defined by Sereno (2005) as (Ornithomimus velox > Passer domesticus) and replaces the more inclusive use of Ornithomimosauria when alvarezsaurids or some other group are found to be closer relatives of ornithomimosaurs than maniraptorans, with Ornithomimosauria redefined to include dinosaurs closer to Ornithomimus than to alvarezsaurids. Gregory S. Paul has proposed that Ornithomimosauria might be a group of primitive, flightless birds, more advanced than Deinonychosauria and Oviraptorosauria.[11]
The fore limbs ("arms") were long and slender and bore powerful claws. The hind limbs were long and powerful, with a long foot and short, strong toes terminating in hooflike claws. Ornithomimosaurs were probably among the fastest of all dinosaurs. Like other coelurosaurs, the ornithomimosaurian hide was feathered rather than scaly. 


http://phenomena.nationalgeographic.com/2013/03/14/the-rise-and-fall-of-four-winged-birds/
Xu thinks that these feathers might have helped the owners to fly. They could have produced extra lift or maybe helped the birds to turn more easily. But other scientists who work on the evolution of flight are not convinced. “[Xu] has basically just taken a punt that because the feathers were stiff, they were probably aerodynamic in function,” says Michael Habib from the University of Southern California. “It is a bit of a weak argument.”
Habib thinks that the long asymmetric leg feathers of Microraptor probably did play some role in gliding or flying, but the smaller plumes of other baggy-legged species “might have merely been there because of a developmental quirk”. If some genes are producing large feathers on the front limbs, “it might not take much to tweak a set onto the hind limbs too,” he says.
Kevin Padian from the University of California, Berkeley agrees. He points out that no one has actually done any proper tests to show if the leg feathers were involved in flight. They would certainly have created drag, but they could only have provided lift if they sat in a flat sheet like the wings of modern birds. Xu claims that they were, but Padian says that the feathers could just have been flattened into a plane as they became fossilised. “It hasn’t been shown that this is really an aerodynamically competent wing,” he says.


http://www.nature.com/nature/journal/v387/n6635/full/387799a0.html

Wing upstroke and the evolution of flapping flight

Samuel O. Poore, A. Sánchez-Haiman1 & G. E. Goslow, Jr1



Movements of the wing during upstroke in birds capable of powered flight are more complex than those of downstroke1,2, 3. The m. supracoracoideus (SC) is a muscle with a highly derived morphology that is generally considered to be the primary elevator of the wing4, 5, 6.

Drawings:
http://phenomena.nationalgeographic.com/files/2012/12/amnh30.jpg


http://phenomena.nationalgeographic.com/2013/03/14/the-rise-and-fall-of-four-winged-birds/
Why did the leg feathers, having first become large, eventually disappear? Xu thinks that it was because the birds set their two pairs of limbs towards different ends—the front pair for flying and the hind pair for walking or running. At the same time, they might have moved from life in the trees to life on the ground, or near water. Under all these scenarios, long leg feathers would have just got in the way, and were soon lost.
Something similar may have happened in other flying animals. For example, the earliest flying insects tend to have four wings, while some of the most competent flyers like, well, flies, only have two. The second pair has evolved into a pair of gyroscopes called halteres. “In the early evolution of flight, different animal groups always try to use as much surface as possible,” says Xu. “Once the major flight organ is well developed, the animal just fires the other organs.”

The possibility that Sinornithosaurus was capable of gliding has been presented several times, due to its close relation to flying or gliding dromaeosaurs like Microraptor. Chatterjee and Templin 2004 found S. millenii as grouping within dinosaurs with aerodynamical potential for aerial locomotion,[14] an opinion latter also expressed by Darren Naish,[7] while Longrich & Currie 2009 have expressed that it was probably too heavy to fly,[15] though it is worth to note that this latter study was published before the formal description of Changyuraptor, a similar sized microraptorine with evident flight capacities.

The ability to fly or glide has been suggested for at least five dromaeosaurid species. The first, Rahonavis ostromi (originally classified as avian bird, but found to be a dromaeosaurid in later studies[8][42]) may have been capable of powered flight, as indicated by its long forelimbs with evidence of quill knob attachments for long sturdy flight feathers.[43] The forelimbs of Rahonavis were more powerfully built than Archaeopteryx, and show evidence that they bore strong ligament attachments necessary for flapping flight. Luis Chiappe concluded that, given these adaptations, Rahonavis could probably fly but would have been more clumsy in the air than modern birds.[44]

Anchiornis huxleyi (Xu et al. 2009, Late Jurassic, Oxfordian, 34 cm, IVPP V14378) was originally and correctly identified as a proto-bird. Derived from a sister to Jinfengopteryx Anchiornis is basal to Aurornis. It has large wing feathers, long leg feathers and short tail feathers, plus a crest of feathers over its head and plumage covering the body.
Distinct from sister taxa the rostrum bent down. The coracoid was disc-like, so it had not yet begun to flap with sufficient power to fly.

https://en.wikipedia.org/wiki/Paraves
Fossils shows that all the earliest members of Paraves found to date started out as small, while Troodontidae and Dromaeosauridae gradually increased in size during the Cretaceous period.[10]
The clade "Aviremigia" was conditionally proposed along with several other apomorphy-based clades relating tobirds by Jacques Gauthier and Kevin de Queiroz in a 2001 paper. Their proposed definition for the group was "the clade stemming from the first panavian with ... remiges and rectrices, that is, enlarged, stiff-shafted, closed-vaned (= barbules bearing hooked distal pennulae), pennaceous feathers arising from the distal forelimbs and tail".[2]

Godefroit et al
long rectrices are now known to occur in at least one basal member of each of the five major known lineages in this region of the theropod tree, including basal avialans, the basal deinonychosaurians Archaeopteryx and Wellnhoferia6 , the basal troodontid Anchiornis18, the scansoriopterygid Epidexipteryx19 and the basal dromaeosaurid Microraptor20. The secondary loss of rectrices is regarded here as an unambiguous autapomorphy for E. brevipenna (Fig. 4). Pennaceous rectrices attached to the tibia were also a relatively ubiquotous adaptation among maniraptorans, present in Eosinopteryx, Anchiornis2, Xiaotingia3, Microraptor15, Pedopenna21, Archaeopteryx and Wellnhoferia6 ; this character is regarded here as an unambiguous synapomorphy for Deinonychosauria (Fig. 4).


However, in 2012, an expanded and revised study incorporating the most recent Dromaeosaurid finds recovered the Archaeopteryx-like Xiaotingia as the most primitive member of the clade Dromaeosauridae, which appears to suggest the earliest members of the clade may have been capable of flight.[65]

Corwin Sullivan, David W. E. Hone, Xing Xu, Fucheng Zhang
The asymmetry of the carpal joint and the evolution of wing folding in maniraptoran theropod dinosaurs

http://www.nature.com/news/theory-suggests-iconic-early-bird-lost-its-flight-1.14142
“Just because Archaeopteryx was the first feathered dinosaur found, doesn’t mean it has to play a central role in the actual history of the origins of birds,” says palaeontologist Thomas Holtz of the University of Maryland in College Park. “We have to remember it appears 10 million years or so after the oldest known bird-like dinosaurs and so our famous 'first bird' may really be a secondarily flightless one.”

Accordingly, Caudipteryx probably used a running mechanism more similar to that of modern cursorial birds than to that of all other bipedal dinosaurs. These observations provide valuable clues about cursoriality in Caudipteryx , but may also have implications for interpreting the locomotory status of its ancestors.
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. 
Xing Xu & Diego Pol (2013)
Archaeopteryx, paravian phylogenetic analyses, and the use of probability-based methods for palaeontological datasets

Archaeopteryx, which has often been considered the earliest avialan, is an iconic species, central to our understanding of bird origins. However, a recent parsimony-based phylogenetic study shifted its position from within Avialae, the group that contains modern birds, to Deinonychosauria, the sister-taxon to Avialae. Subsequently, probability-based methods were applied to the same dataset, restoring Archaeopteryx to basal Avialae, suggesting these methods should be used more often in palaeontological studies. Here we review two key issues: arguments recently advocated for the usefulness of probability-based methodologies in the phylogenetic reconstruction of basal birds and their close relatives, and support for different phylogenetic hypotheses. Our analysis demonstrates that Archaeopteryx represents a challenging taxon to place in the phylogenetic tree, but recent discoveries of derived theropods including basal avialans provide increased support for the deinonychosaurian affinities of Archaeopteryx. Most importantly, we underscore that methodological choices should be based on the adequacy of the assumptions for particular kinds of data rather than on the recovery of preferred or generally accepted topologies, and that certain probability methods should be interpreted with caution as they can grossly overestimate character support.



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