Time and Cladograms (1)

Because we are so used to the convention of time running from left to right on diagrams, we assume that a cladogram (like the one below) indicates that the creatures on the left of the diagram came before the creatures on the right. But this is not what a cladogram based on cladistic analysis shows. It only shows relationships of characteristics between creatures.



Here are some references to time and cladograms:

http://en.wikipedia.org/wiki/Coelurosauria
"The following phylogenetic results are taken from Senter (2007) "A new look at the Phylogeny of Coelurosauria (Dinosauria: Theropoda)."^[3] This cladogram does not represent time, but a crude estimate of the time can be inferred from morphological changes [differences]. The first coelurosaurs were similar to the coelurids Tanycolagreus and Coelurus, and differed only sightly from other early tyrannosauroids Dilong and Eotyrannus. The two most significant separations between subgroups are those between the Paraves [Eumaniraptors] and other coelurosaurs and between the paravian clades Avialae and Deinonychosauria." [Avialae and Deinonychosauria are the two major subgroups within Eumaniraptora].

https://kb.osu.edu/dspace/bitstream/1811/23829/1/V099N4_095.pdf

"Cladistic analysis is a powerful method of determining evolutionary relationships between organisms, but one weakness is its inability to consider time as part of the equation."

http://scienceblogs.com/tetrapodzoology/2009/06/birds_come_first_no_they_dont.php
"Firstly, we construct phylogenetic hypotheses by looking at the distribution of characters: the distribution of taxa within time is effectively irrelevant. It doesn't matter that some maniraptorans are geologically younger than the oldest known birds: phylogenetic analyses that have good sampling across taxa and morphology still show that those maniraptorans are more basal than birds." (Darren Naish)

I will expand on this topic in the next post.

Building upon the ideas of others

I have built upon the ideas of such people as Gregory Paul and Stephen Czerkas. For example, Paul, over 20 years ago, proposed some of the ideas I have been expressing:
From Gregory Paul:
http://en.wikipedia.org/wiki/Gregory_S._Paul
"Paul proposed that some of the bird-like feathered theropods were winged fliers, and that others were secondarily flightless, an idea supported by some fossils from China."

I am hypothesizing that the bird-like feathered creatures are the winged fliers that Paul hypothesized.

I am also saying that pterosaurs were the ancestors of the primitive winged fliers (Dromaeosauridae and Enantiornithes etc). Paul did not go that far, but the following is VERY interesting:

http://dml.cmnh.org/2002Sep/msg00255.html
"I've noted that the pterosaur-like tails of dromaeosaurs are probably pterosaur-like (with hyperelongated distal prezygapophyses and chevrons) because the tails evolved in fliers. The tail form is, after all, not present in any unambiguous nonfliers. A prediction of this hypothesis is that there should be avepods more derived than Archaeopteryx with long, dromaeosaur-like tails. Cryptovolans [a Dromaeosauridae] fits this bill to a tee. In Nature the description of the new basal bird Jeholornis states that its tail has "unexpected elongated prezygopophyses and chevrons, resembling that of dromaeosaurids." Unexpected only if one is locked into the conventional hypothesis. Yet again a prediction of the neoflightless hypothesis is fulfilled. Birds did experience a flight stage in which the tail functioned in the same manner as long tailed pterosaurs." (G. Paul)

From Stephen Czerkas:
http://en.wikipedia.org/wiki/Cryptovolans
-->"Czerkas also believed that Cryptovolans [a Dromaeosauridae] may have been able to fly better than Archaeopteryx, the animal usually referred to as the earliest known bird. He cited the fused sternum and asymmetrical feathers, and argued that Cryptovolans has modern bird features that make it more derived than 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 [another Dromaeosauridae] were secondarily flightless (Czerkas, 2002)."

http://en.wikipedia.org/wiki/Caudipteryx
"Others, such as Stephen Czerkas and Larry Martin have concluded that Caudipteryx [an Oviraptor] is not a theropod dinosaur at all.^[16] They believe that Caudipteryx, like all maniraptorans, is a flightless bird, and that birds evolved from non-dinosaurian archosaurs [eg. pterosaurs].<sup>[17]"

And of course the work of Larry Martin, John Ruben and Alan Feduccia has been immensely helpful.</sup>

The Tail End

We should consider the tails of the various creatures.
Let's start here:

RHAMPHORHYNCHOIDEA

http://en.wikipedia.org/wiki/Anurognathus
"Anurognathus had a short head with pin-like teeth for catching insects and although it traditionally is ascribed to the long-tailed pterosaur group "Rhamphorhynchoidea", its tail was comparatively short, allowing it more maneuverability for hunting.^[3] According to Döderlein the reduced tail of Anurognathus was similar to the pygostyle of modern birds.^[2] Its more typical "rhamphorhynchoid" characters include its elongated fifth toe and short metacarpals and neck.^[2]".

So we see that even some of the primitive pterosaurs were already developing shorter tails, "similar to the pygostyle of modern birds".

PTERODACTYLOIDEA

Of course we know that the more advanced pterosaurs, the pterodactyls, were even more bird-like:

http://en.wikipedia.org/wiki/Pterodactyloidea

"Pterodactyloidea (meaning "winged finger", "wing-finger" or "finger-wing") forms one of the two suborders of pterosaurs ("wing lizards"), and contains the most derived members of this group of flying reptiles. They appeared during the middle Jurassic Period, and differ from the basal rhamphorhynchoidea by their short tails and long wing metacarpals (hand bones). The most advanced forms also lack teeth.

http://dipbsf.uninsubria.it/paleo/kellner.htm

Among other features that diagnose the Perodactyloidea is the short tail with less than 15 caudal vertebrae. Although this number could be higher (complete tails are know for only a few specimens), this condition differs from all non-pterodactyloid that have a long tail. The sole exception is found in the anurognathid Anurognathus (and perhaps other members of the Anurognathidae) and, according to the present analysis, a short tail was achieved independently by those taxa.

http://pterodata.blogspot.ca/

http://en.wikipedia.org/wiki/Pygostylia

The group Pyostylia was intended to encompass all avialans with a short, stubby tail

  Here is some info on the tails of some of the primitive flying birds:

ENANTIORNITHES
http://en.wikipedia.org/wiki/Shanweiniao
"Shanweiniao is an extinct genus of long-beaked enantiornithine bird from Early Cretaceous China.
"The genus name Shanweiniao means "fan-tailed bird" in Chinese. The authors report that Shanweiniao is [so far] the only known enantiornithine bird with a tail surface capable of generating lift, as in modern birds.They also report that only one other Mesozoic bird, Yixianornis grabaui, which is a basal ornithurine, has been reported with this fan - shaped tail feather morphology.".


Here is some info on the tails of some of the secondarily flightless primitive birds:

OVIRAPTOROSAURIA
http://en.wikipedia.org/wiki/Oviraptorosauria
"Oviraptorosaurs, like dromaeosaurs, 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.^[8][9][10] Michael Benton, in his widely-respected text Vertebrate Paleontology, also included oviraptorosaurs as an order within the class Aves.^[11]
Their tails are very short compared to other maniraptorans. In Nomingia and Similicaudipteryx, the tail ends in four fused vertebrae which Osmólska, He, and others have referred to as a "pygostyle", but which Witmer found was anatomically different and evolved separately from the pygostyle of birds (a bone which serves as the attachment point for a fan of tail feathers).^[3][4]
Similarly, quill knobs (anchor points for wing feathers on the ulna) have been reported in the oviraptorosaurian species Avimimus portentosus.^[5]"


http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3655181/

The tails of theropods (bipedal carnivorous dinosaurs) underwent dramatic anatomical changes along the line of descent to modern birds [1], [2], [3], [4], [5]. Ancestrally,Carnotaurus and more basal forms had long, massive tails that were more similar to the tail of a crocodile than to the tail of a bird [6]. Theropod tails generally have two regions. Before the ‘transition point’ the caudal vertebrae have neural spines that are dorsoventrally tall and chevrons that are dorsoventrally deep, as well as wide spans between the tips of each vertebra’s transverse processes. After the transition point these features are greatly reduced or become absent. This transition is not actually a ‘point’ per se because the changes in the tail features are variable, unsynchronised and occur over several caudal vertebrae [3], [7]. In contrast, extant birds have short, light tails with caudal vertebrae that do not cross a transition point, but the tip of their tails are co-ossified (pygostyle) and support a tail fan [2], [3], [8].

Summary

This thinking has been revised.

Here is a summary of the major points:

1. Birds developed in a lineage which extends from the Pterosauria, through primitive flying birds (eg. Enantiornithes, Dromaeosaurids etc) to modern flying birds and modern flightless birds.

2. The first active fliers were the primitive pterosaurs, called the Rhamphorhynchoidea. They existed from the late Triassic to the late Jurassic.

http://en.wikipedia.org/wiki/Rhamphorhynchus_%28animal%29
"Rhamphorhynchus "beak snout", is a genus of long-tailed pterosaurs in the Jurassic period. Less specialized than contemporary, short-tailed pterodactyloid pterosaurs such as Pterodactylus, it had a long tail, stiffened with ligaments, which ended in a characteristic diamond-shaped vane."

http://en.wikipedia.org/wiki/Rhamphorhynchoidea
"This suborder is paraphyletic in relation to the Pterodactyloidea, which arose from within the Rhamphorhynchoidea, not from a more distant common ancestor."

3. Some Rhamphorhynchoidea developed into the Pterodactyloidea. They existed from the middle Jurassic to the late Cretaceous.

http://en.wikipedia.org/wiki/Pterodactyloidea
"Pterodactyloidea (meaning "winged finger", "wing-finger" or "finger-wing") forms one of the two suborders of pterosaurs ("wing lizards"), and contains the most derived members of this group of flying reptiles. They appeared during the middle Jurassic Period, and differ from the basal rhamphorhynchoidea by their short tails and long wing metacarpals (hand bones). The most advanced forms also lack teeth."

4. Some Pterodactyloidea developed into primitive, flying birds (eg. Dromaeosauridae, Enantiornithes etc) beginning in the middle to late Jurassic.

5a. Some primitive flying birds developed into modern flying birds (eg. Neognathae) by the late Cretaceous.

5b. But some primitive flying birds settled on the land and became primitive, secondarily flightless birds (eg. Ornithomimosauria, etc) in the early Cretaceous
AND
then those primitive, flightless birds developed into modern Ratites (ostrich, emu etc) in the late Cretaceous.

6. Dinosaurs developed in their own separate line from the late Triassic to the late Cretaceous. The dinosaur line went extinct at the end of the Cretaceous.

NOTE:
Also it is possible that within a particular bird group, there could be both original flying birds and secondarily flightless birds. For example there may have been flying Dromaeosauridae AND flightless Dromaeosauridae.

Early Flying Birds

I have mentioned that flying birds were around at the time of the earliest dinosaurs. Here is support for that:

http://en.wikipedia.org/wiki/Dromaeosauridae
"Dromaeosaurid fossils have been found in North America, Europe, North Africa, Japan, China, Mongolia, Madagascar, Argentina, and Antarctica.^[2] They first appeared in the mid-Jurassic Period (Bathonian stage, 167 million years ago) and survived until the end of the Cretaceous (Maastrichtian stage, 65.5 ma), existing for over 100 million years, up until the Cretaceous-Paleogene extinction event. The presence of dromaeosaurs as early as the Middle Jurassic has been confirmed by the discovery of isolated fossil teeth, though no dromaeosaurid body fossils have been found from this epoch.^[3]"

The Source of Confusion

The major source of confusion stems from the following:
There is a group of Cretaceous feathered, flightless birds such as the Ornithomimosauria, and Oviraptorosauria.
These are secondarily flightless birds. They are "secondary" because they developed from flying birds.
In the idea I am presenting, they fit in as follows:
Pterosaurs ---> Primitive flying birds (eg. Dromaeosauridae, Enantiornithes, Troodontidae etc)
---> Primitive flightless birds (Ornithomimosauria, Oviraptorosauria, ) ----> Modern Ratites (ostrich, emu etc)

However in the dino-to-bird idea they are misconceived as having evolved from dinosaurs and they are thought of as the forerunners to flying birds. So the dino-to-bird thinking has it exactly backward.
And the proof of this, is that flying birds were already around at the same time as the very earliest dinosaurs. (They may even pre-date the dinosaurs). The feathered, flightless birds (eg. Ornithomimosauria etc) developed from primitive flying birds.
The feathered, flightless creatures are not a transition from dinosaurs to flying birds.

Confirmation of the Discontinuity

Here is confirmation of the discontinuity between the bird line and the dinosaur line.
http://en.wikipedia.org/wiki/Coelurosauria
"The two most significant separations between subgroups are those between the Paraves and other coelurosaurs [dinosaurs] and between the paravian clades Avialae and Deinonychosauria."

Semilunate Carpal

In the standard cladograms presented by the dino-to-bird enthusiasts, the Tyrannosaurs are placed just before the Maniraptors. And the most primitive "maniraptora" creatures are the Therizinosauria. Let's look at how similar/different these creatures actually are.


https://royalsocietypublishing.org/doi/full/10.1098/rspb.2009.2281

Here is a table, showing the degree of wrist flexibility of various creatures.
Guanlong wucaii (8°) is a Tyrannosauroidea

Alxasaurus elesitaiensis	(39°) is a Therizinosauria
Falcarius utahensis	(26°) is a Therizinosauria.

Table 1.

Radiale angles in various theropods. (Bold indicates specimens that we examined directly.)

taxon	angle	specimen/source
Allosaurus fragilis	2°	Chure (2001, fig. 2c)
Huaxiagnathus orientalis	18°	Hwang et al. (2004, fig. 8a)
Sinosauropteryx prima	6°	Currie & Chen (2001, fig. 8a)
Guanlong wucaii	8°	IVPP V14531
Alxasaurus elesitaiensis	39°	IVPP RV93001
Falcarius utahensis	26°	Utah Museum of Natural History, Salt Lake City, USA (UMNH) VP 12294
Caudipteryx sp.	76°	IVPP V12430
Haplocheirus	15°	IVPP V15988
Sinovenator changii	35°	IVPP V14009
Deinonychus antirrhopus	31°	YPM 5208
Eoconfuciusornis zhengi	55°	IVPP V11977
Meleagris gallopavo	59°	IVPP 1222

Notice the low numbers up to Tyrannosauroidea (Guanlong wucaii) and the much higher numbers beginning with the Therizinosauroids (Alxasaurus elesitaiensis).
These two groups are not related. The creatures labeled "maniraptora" have just been artificially tacked onto the dinosaur group.

Here is what the authors said about the discontinuity between Tyrannosauroidea and Therizinosauroids:

"Therizinosauroids are probably the most basal [primitive] maniraptoran theropods (Zanno et al. 2009). In a well-preserved left carpus of Alxasaurus (IVPP, RV93001), the SLC is strongly convex and distinctly trochlear, despite being made up of two separate ossifications (figure 2). The radiale, in contrast to that of Guanlong, [Tyrannosauroidea] is distinctly wedge-shaped."

Also see here:
http://pterosaurnet.blogspot.ca/2014/10/wrists.html

Also see Appendix 3 here:
https://www.bio.fsu.edu/James/Ornithological%20Monographs%202009.pdf

Evolution of Birds

Here is a preliminary flow of the evolution of flying birds:
Pterosaurs ---> Primitive flying birds (eg. Dromaeosauridae, Enantiornithes, Troodontidae etc)
---> Modern flying birds (Neognathae).

Here is a preliminary flow of the evolution of flightless birds:
Pterosaurs ---> Primitive flying birds (eg. Dromaeosauridae, Enantiornithes, Troodontidae etc)
---> Primitive flightless birds (Ornithomimosauria, flightless Dromaeosauridae etc) ----> Modern Ratites (ostrich, emu etc)

A Fundamental Error

A fundamental error of the dino-to-bird idea, is thinking that the feathered creatures of the Late Jurassic and the Cretaceous had evolved from dinosaurs. They had not. They were primitive birds that had developed from the pterosaurs.
Flying (and secondarily flightless) birds already existed at the time of the very first dinosaurs. In fact, primitive birds may have even pre-dated the appearance of the dinosaurs.

* The Dino to Bird Cladogram

Here is the standard dino-to-bird diagram.
Notice the distinct difference between the maniraptors (on the right) and the dinosaurs (on the left). The maniraptors are primitive birds and do not belong with the dinosaurs.

Click to enlarge.

* Maniraptors are not dinosaurs

More evidence that maniraptorans are not dinosaurs.
"Maniraptorans are the most diverse clade of dinosaurs [birds]. None retain [have] a basal theropod form: indeed, very few retain [have] the ancestral [claimed ancestral] carnivorous condition."

http://www.geol.umd.edu/~tholtz/G104/lectures/104coelur.html

MANIRAPTORA"Maniraptorans show numerous specializations:

• Elongated forelimb

• Large bony sternum for attachment of the muscles that pull the arms inwards

• Semilunate carpal: a pully-shaped block of wrist bone that allowed greater folding motion while sacrificing motion in any other plane

One possible problematic shared derived feature of Maniraptora is a backwards-pointing pubis. Most coelurosaurs (and saurischians in generally) have a vertically-oriented or anteriorly-oriented pubis. In therizinosauroids, alvarezsaurids, the basal troodontid Sinovenator, dromaeosaurids, Archaeopteryx, and avialians the pubis points backwards; in the basal therizinosaur Falcarius, oviraptorosaurs, and troodontids other than Sinovenator it points vertically or anteriorly. So it is difficult to say which condition is found in the concestor of Maniraptora.
Changes in the muscle attachments in the hindlimbs of maniraptorans show a switch from the femur-and-tail power stroke found in other dinosaurs (inherited from the early diapsids) to one where the flexion of the knee is more important.
Maniraptorans are the most diverse clade of dinosaurs. None retain [have] a basal theropod form: indeed, very few retain [have] the ancestral carnivorous condition. Major groups include Oviraptorosauria, and Eumaniraptora [Paraves]"

BOTTOM LINE
The bottom line is that pterosaurs are very similar to birds while as we see from the quote above, dinosaurs are not similar at all.

Fingers and Wrists

More evidence that the maniraptors such as the dromaeosaurs and the ornithomimosaurs etc. are not dinosaurs. They are on a completely separate bird-related line stemming back to the pterosaurs.

http://en.wikipedia.org/wiki/Theropoda
"However, in coelurosaurs [maniraptors] such as ornithomimosaurs and especially dromaeosaurs, the hand itself had lost most flexibility, with highly inflexible fingers. Dromaeosaurs and other maniraptorans also showed increased mobility at the wrist not seen in other [actual dinosaurs] theropods, thanks to the presence of a specialized half-moon shaped wrist bone (the semi-lunate carpal) that allowed the whole hand to fold backward towards the forearm in the manner of modern birds.^[16]"

Pterosaur is a "suitable candidate" (2)

More on the question of suitability:
http://en.wikipedia.org/wiki/Temporal_paradox_%28paleontology%29
"Third, if the temporal paradox would indicate that birds should not have evolved from dinosaurs, then what animals are more likely ancestors considering their age? Brochu and Norell (2001) analyzed this question using several of the other archosaurs that have been proposed as bird ancestors, and found that all of them create temporal paradoxes — long stretches between the ancestor and Archaeopteryx where there are no intermediate fossils — that are actually worse. Thus, even if one used the logic of the temporal paradox, one should still prefer dinosaurs as the ancestors to birds.<sup>[8]"

Pterosaurs are more likely ancestors.</sup>

Pterosaur is a "suitable candidate" (1)

Those who promote the dino-to-bird idea, claim that "there are no other suitable candidates for avian ancestors."
They overlook the obvious candidates - PTEROSAURS.

http://www.ucmp.berkeley.edu/diapsids/avians.html
"Other arguments, such as the putative differences between theropod and bird finger development, or lung morphology, or ankle bone morphology, all stumble on the lack of relevant data on extinct theropods, misinterpretations of anatomy, simplifying assumptions about developmental flexibility, and/or speculations about convergence, biomechanics, or selective pressures. The opponents of the theropod hypothesis refuse to propose an alternative hypothesis that is falsifiable. This is probably because there are no other suitable candidates for avian ancestors.".

Early Birds

There are a number of flying creatures of the early Cretaceous that are recognized as birds:

http://en.wikipedia.org/wiki/Sapeornis
"Sapeornis^[1] is a genus of primitive bird which lived during the Early Cretaceous (late Aptian to early Albian, roughly 120-110 mya). The genus contains only the species Sapeornis chaoyangensis which is known from fossils found in Jiufotang Formation rocks near Chaoyang, PRC. Several nearly complete skeletons have been found (Zhou & Zhang 2003)."

http://en.wikipedia.org/wiki/Omnivoropteryx
"Omnivoropteryx (meaning "omnivorous wing") is a genus of primitive flying bird from the early Cretaceous Upper Jiufotang Formation of China. The authors who described Omnivoropteryx, Stephen Czerkas and Qiang Ji, stated that their specimen closely resembles Sapeornis, but the pubis was longer and, since no skull was known for Sapeornis, they did not consider the two names synonyms.^[1] The later discovery of Sapeornis skulls shows that they were indeed similar to Omnivoropteryx. This may make Omnivoropteryx a junior synonym of Sapeornis, and the name may be abandoned.<sup>[2]"

http://www.dinosaur-museum.org/featheredinosaurs/chapters.htm#Omnivoropteryx
"</sup>A preliminary report on a new bird, Omnivoropteryx sinousaorum, gen.et.sp.nov. from the Upper Jiufutang Formation (Early Cretaceous) of Liaoning, China. This new bird has a skull which most closely resembles that of Caudipteryx, but its body has proportionately long forelimbs indicating a strong ability to fly and comparatively short hindlimbs with feet that were strongly adapted for perching. The highly derived avian characteristics of the wings and hindlimbs, together with the unique morphology of the skull reveal that Omnivoropteryx had adapted to a different dietary ecological niche from that of predaceous birds. This demonstrates that a far greater diversity of birds co-existed during the Late Jurassic/Early Cretaceous than has been previously known. In addition to variations in behavior, the anatomical differences also present a broader understanding which has significant implications towards the phylogenetic relationships during the early stages of avian evolution."

http://www.dinosaur-museum.org/featheredinosaurs/flying_dromaeosaurs.pdf
"Described below are two such dromaeosaurs [Scansoriopteryx and Cryptovolans], but preserved with impressions of primary flight feathers extending from the manus which demonstrate an undeniable correlation towards the ability to fly. This compelling evidence refutes the popular interpretation of birds evolving from dinosaurs by revealing that dromaeosaurs were already birds and not the non-avian theropod dinosaurs as previously believed"

^{http://en.wikipedia.org/wiki/Confuciusornis}
"Confuciusornis is a genus of primitive crow-sized birds from the Early Cretaceous Yixian and Jiufotang Formations of China, dating from 125 to 120 million years ago. Like modern birds, Confuciusornis had a toothless beak, but close relatives of modern birds such as Hesperornis and Ichthyornis were toothed, indicating that the loss of teeth occurred convergently in Confuciusornis and living birds. It is the oldest known bird to have a beak.^[1]"
Note that the dino-to-bird explanation falls back on the idea of "convergence" to fill in the holes of the theory.

Pterosaur "Feathers"

Here is some very interesting information. Take note of the evidence that Pterorhynchus (a basal pterosaur) MAY have had plumaceous  feathers.
(Keep in mind that these quotes are not talking about actinofibrils).

^{http://encyclopedia2.thefreedictionary.com/plumaceous
Plumaceous:}"Referring to the portion of a feather vane near the base that lacks hooklets and is loosely bound."

http://en.wikipedia.org/wiki/Pterorhynchus
"The hairs were described as stranded or plumaceous and seen as corresponding to Stage II in the evolution of feathers and as indicative that pterosaur hair and dinosaur feathers were homologous.<sup>[2]"

http://wiki.cotch.net/index.php/Evolution_of_feathers
"</sup>The first stage is hypothesized to have originated with the first feather follicle. As above, the dermis would have pushed the epidermis into a collar, with the epidermis sinking around its base. This would have yielded a hollow, tubular structure much like the calamus of modern feathers. Stage II involves the origin of barbs. Derived from the collar, these would have opened up into a simple “tuft” extending from a calamus. Stage III has two stages which the theory cannot distinguish between in terms of temporal origination; either could have occurred first. What Prum labels IIIa involves the helical displacement of the stage II barbs and their fusion to form the rachis on the midline. The fully developed feather would have been pinnate, and superficially quite similar to modern feathers. With the evolution of stage IIIb, stage II barbs would have evolved barbules and ramus. Together, both stages would yield an open pennaceous feather complete with a rachis, ramus, barbs, and barbules. The following stage, stage IV, sees the evolution of distal and proximal barbules, built off IIIb, which would have hooked together and closed the vane. Fully developed, these are essentially modern, but symmetrical, feathers. All subsequent morphologic variety is subsumed under stage V, including asymmetrical flight feathers, and down."


http://en.wikipedia.org/wiki/Avifilopluma
"Some scientists have gone even further and suggested that the downy filaments present in some species of pterosaur are also feathers, and if this is the case, it would place the origin of feathers at or before the primitive split between dinosaurs and pterosaurs (Ornithodira).<sup>[3]"



http://www.dinosaur-museum.org/featheredinosaurs/rhamphorhynchoid.pdf
"Proto-feathers have been attributed to two
pterosaurs which are of similar animals (Ji and Yuan,
2002; Wang, et al., 2002). Even more so, the
morphology details seen in Pterorhynchus
demonstrate that the integumentary structures of
pterosaurs are not like hair, but are analogous to
being proto-feathers. Specifically, they resemble
natal down feathers where individual filaments are
seen to spread from a single follicle."</sup>

Caudipteryx (2)

Caudipteryx is a secondarily flightless bird of the early Cretaceous.
The appearance (shape, morphology) of Caudipteryx clearly shows it to be a flightless bird.
Also, let's consider the feathers. They are symmetrical and do not have barbules. This is exactly like modern flightless birds. See here (chapter 15).

In that light, let's look at the quote from Lawrence Witmer:
" The presence of unambiguous feathers in an unambiguously nonavian theropod has the rhetorical impact of an atomic bomb, rendering any doubt about the theropod relationships of birds ludicrous.”[3] (Witmer 2005)".
This is obviously a dino-to-bird point of view. It overlooks the more persuasive case that the "non-avian dinosaurs" were secondarily flightless birds.

Caudipteryx (1)

Here is some basic info on Caudipteryx (a member of Oviraptorosauria). I will analyze it in the next post.

http://en.wikipedia.org/wiki/Caudipteryx
"Caudipteryx (which means "tail feather") is a genus of peacock-sized theropod dinosaurs that lived in the Aptian age of the early Cretaceous Period (about 124.6 million years ago). They were feathered and remarkably  birdlike in their overall appearance.^[1]
Caudipteryx had uncinate processes on the ribs, birdlike teeth, a first toe which may or may not be partially reversed and overall body proportions that are comparable to those of modern flightless birds.
The hands of Caudipteryx supported symmetrical, pennaceous feathers that had vanes and barbs, and that measured between 15–20 centimeters long (6–8 inches). These primary feathers were arranged in a wing-like fan along the second finger, just like primary feathers of birds and other maniraptorans.
"Because Caudipteryx has clear and unambiguously pennaceous feathers, like modern birds, and because several cladistic analyses have consistently recovered it as a nonavian, oviraptorid, dinosaur, it provided, at the time of its description, the clearest and most succinct evidence that birds evolved from dinosaurs. Lawrence Witmer stated: “The presence of unambiguous feathers in an unambiguously nonavian theropod has the rhetorical impact of an atomic bomb, rendering any doubt about the theropod relationships of birds ludicrous.”^{[3] (Witmer 2005)}

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

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

Hesperornithiformes

http://en.wikipedia.org/wiki/Hesperornis
"Hesperornis is an extinct genus of flightless aquatic birds that lived during the Santonian to Campanian sub-epochs of the Late Cretaceous (89–65 mya).
Although some of the smaller species might have been able to fly, Hesperornis and Baptornis had only vestigial wings. Like living foot-propelled diving birds, the femur and metatarsus were short, whereas the tibia was long. The legs were also set far back on the body, as in loons, grebes or penguins."

http://en.wikipedia.org/wiki/Grebe
"The cladistics vs. phenetics debate of the mid-20th century revived scientific interest in generalizing comparisons. As a consequence, the discredited grebe-loon link was discussed again. This even went as far as proposing monophyly for grebes, loons, and the toothed Hesperornithiformes "

http://www.jstor.org/pss/2413412
"A cladistic analysis of the skeletons of loons (Gaviidae), grebes (Podicipedidae), and the Cretaceous diving birds, Hesperornis and Baptornis, supports the hypothesis that they form a monophyletic group (here called the Gaviomorphae) within the class Aves. Two lineages within the gaviomorphs can be delineated: (1) loons + grebes, and (2) Hesperornis + Baptornis. The Early Cretaceous Enaliornis and the Late Cretaceous Neogaeornis are related to the second lineage; the Late Cretaceous Lonchodytes, often placed near loons, is apparently not a gaviomorph but perhaps a charadriiform. Skeletal evidence also suggests that penguins (Spheniscidae) are the sister-group of the Gaviomorphae. Arguments that similarities of gaviomorph taxa represent convergence are not well founded. First, morphological differences among taxa do not constitute valid evidence against their monophyly, as many previous workers have argued. Second, in no case has anyone supporting convergence presented a corroborated alternative phylogenetic hypothesis. A close relationship among gaviomorphs, penguins, and apparently also the Procellariiformes and Pelecaniformes implies that a lineage of aquatic birds was established very early in avian history, presumably in the Early Cretaceous or Late Jurassic." (Joel Cracraft 1982)

Looks like Joel Cracraft was on the right track!
(Note the issue here is not whether grebes and loons go together but that hesperornithiformes is linked to modern birds such as grebes and/or loons.)