Tuesday, January 17, 2017

Support Indices

The support indices (Bremer, bootstrap/jackknife) do NOT support the dino to bird cladograms that are routinely published.

http://ib.berkeley.edu/courses/ib200a/labs/ib200a_lab10_bootstrap_jackknife_bremer.pdf
As a rule of thumb, a Bremer score of 3 is good and a score of 5 is “highly supported.”
Bootstrapping calculates a support value for each node based on the fraction of samples that support that node. The highest support value is 100, while values below 70 are usually considered weak. Values below 50 aren’t shown; in fact, branches below 50 are collapsed and shown as a polytomy. 

http://www.sciencedirect.com/science/article/pii/S0960982214010471
http://www.cell.com/cms/attachment/2019474733/2039573094/mmc1.pdf
Gradual Assembly of Avian Body Plan Culminated in Rapid Rates of Evolution
across the Dinosaur-Bird Transition (Supplemental Information)

Stephen L. Brusatte, Graeme T. Lloyd, Steve C. Wang, and Mark A. Norell 
This clade—Maniraptoriformes—is only poorly supported (Bremer support of 1 and jackknife percentage of less than 50%), and relationships at its base are unresolved. There is a basal polytomy consisting of four clades: Ornitholestes, Compsognathidae, Ornithomimosauria, and Maniraptora (i.e., the clade of all taxa more closely related to birds than to Ornithomimus: [S52]). Maniraptora—the clade defined as all taxa closer to birds than to Ornithomimus—is comprised in the present study of Alvarezsauroidea, Therizinosauroidea, Oviraptorosauria, and Paraves. This clade is supported by a Bremer value of 2 but a jackknife percentage of less than 50%. The clade consisting of Oviraptorosauria and Paraves is supported by a Bremer value of 1 and a jackknife percentage of less than 50%Paraves—consisting of dromaeosaurids, troodontids, and avialans—is also poorly supported, as it also has a Bremer value of 1 and a jackknife of less than 50%.
It must be stated, however, that the scansoriopterygid + oviraptorosaur clade is poorly supported (Bremer support of 1, jackknife percentage of less than 50%).  

http://www.ivpp.cas.cn/qt/papers/201403/P020140314389417822583.pdf
An Archaeopteryx-like theropod from China and the origin of Avialae
Xing Xu1,2, Hailu You3 , Kai Du4 & Fenglu Han2
It should be noted that our phylogenetic hypothesis is only weakly supported by the available data. Bremer support and bootstrap values for the recovered coelurosaurian subclades are, in general, low, and a bootstrap value less than 50% and a Bremer support value of 2 are obtained for a monophyletic Deinonychosauria including the Archaeopterygidae
We ran Bremer support and bootstrap analyses on the data matrix, using TNT with all default settings except that 1000 replications were used. Bremer support values for the recovered clades are indicated on Figure S8, and only clades with bootstrap values greater than 50% are shown in Figure S9It is notable that only a few clades meet this criterion in the present analysis.
Figure S9:



The published literature is filled with cladograms like those in S4 to S7. They are all misleading/invalid since they are unsupported by the support indices (Bremer, bootstrap/jackknife). What is the point of computing the support values and then ignoring them and presenting misleading/invalid cladograms?

http://www.sciencedirect.com/science/article/pii/S0960982214011385
the authors and others have noted, low support values indicate that many branches near the origin of birds remain unstable 124 and 5.


Saturday, January 14, 2017

Studies

The following study shows that there were 51 synapomorphies (unique defining characteristics) for Paraves (long-bony-tailed primitive birds). This means that of the 374 characteristics that were evaluated, 51 of them were different than the claimed dinosaur ancestor. This is a more than 1 in 8 saltation. This means that Paraves are NOT similar to dinosaurs, which is a point that I have being making for a very long time. It is good to see a cladistic analysis confirm this point. 
Note that this number would be very much larger if the oviraptors were taken as secondarily flightless.

2011 study (Xu et al):
http://www.nature.com/nature/journal/v475/n7357/full/nature10288.html
http://www.ivpp.cas.cn/qt/papers/201403/P020140314389417822583.pdf
An Archaeopteryx-like theropod from China and the origin of Avialae
Archaeopteryx is widely accepted as being the most basal bird, and accordingly it is regarded as central to understanding avialan origins; however, recent discoveries of derived maniraptorans have weakened the avialan status of Archaeopteryx. Here we report a new Archaeopteryx-like theropod from China. This find further demonstrates that many features formerly regarded as being diagnostic of Avialae, including long and robust forelimbs, actually characterize the more inclusive group Paraves (composed of the avialans and the deinonychosaurs). Notably, adding the new taxon into a comprehensive phylogenetic analysis shifts Archaeopteryx to the Deinonychosauria. Despite only tentative statistical support, this result challenges the centrality ofArchaeopteryx in the transition to birds. If this new phylogenetic hypothesis can be confirmed by further investigation, current assumptions regarding the avialan ancestral condition will need to be re-evaluated. (Characters 1-363 are from Hu et al. (2009), whereas 364-374 are newly added). 
Deinonychosauria: 29.1, 72.1, 75.1, 82.0, 111.1, 134.1, 171.2, 183.1, 189.0, 199.1, 233.1, 238.0, 255.0, 294.1, 297.1, 302.1, 323.1, 334.1, 335.2, 359.0, 364.0, 365.0, 366.1, 367.0, 368.0, 371.0, and 372.1 
Paraves (51):
1.1, 10.1, 13.0, 14.0, 15.1, 20.1, 21.1, 28.1, 39.0, 61.1, 65.0, 66.0, 69.0, 79.0, 91.0,
95.0, 96.1, 97.1, 106.0, 109.1, 119.1, 125.0, 127.1, 129.1, 137.1, 138.1, 139.1, 154.0, 155.1, 156.1, 160.1, 166.0, 176.1, 179.1, 180.1, 184.1, 202.1, 221.1, 232.0, 237.1, 262.1, 267.1, 277.2, 292.0, 304.2, 306.1, 319.1, 320.2, 336.1, 354.0, and 362.1
Paraves-Oviraptorosauria-Therizinosauroidea clade: 13.1, 14.1, 28.0, 29.0, 39.1, 41.2, 54.0, 66.2, 79.1, 91.2, 106.1, 116.1, 117.1, 119.0, 121.1, 125.1, 126.1, 127.0, 130.1, 131.1, 136.1, 144.1, 157.2, 166.2, 167.2, 200.1, 238.1, 255.1, 276.1, 284.1, 300.1, 329.1, 351.1, 354.1, 359.1, 363.1, 364.1, 365.1, 367.1, 368.1, and 371.1.
AND: Some other suggested synapomorphies are present in recently described basal deinonychosaurs, and are thus likely to represent paravian rather than avialan synapomorphies23,37. These features include an antorbital fossa that is dorsally bordered by the nasal and lacrimal, a relatively small number of caudal vertebrae, a relatively large proximodorsal process of the ischium, a relatively long pre-acetabular process of the ilium, and fusion of the proximal part of the metatarsus11,37,41
2009 study (Hu, D.Y. et al)
https://www.ncbi.nlm.nih.gov/pubmed/19794491
http://www.nature.com/nature/journal/v461/n7264/extref/nature08322-s1.pdf
A pre-Archaeopteryx troodontid from China with long feathers on the metatarsus. Nature 461, 640-643

2008 study (Zhang)
www.ivpp.ac.cn/qt/papers/201206/P020120601535055482173.pdf
http://www.nature.com/nature/journal/v455/n7216/suppinfo/nature07447.html
A bizarre Jurassic maniraptoran from China with elongate ribbon-like feathersCharacters 361-363 are newly added. Characters 4, 25, 33, 40-42, 65, 67, 69, 82, 85, 91,
99, 106, 110, 115, 116, 121, 122, 136, 138, 142, 146, 148, 151, 153, 163, 165-167,
169, 171, 178, 181, 200-203, 212, 230-360 are from Senter (2007); others are from
Kirkland et al. (2005).
http://www.nature.com/nature/journal/v435/n7038/abs/nature03468.html
Kirkland, J. I., Zanno, L. E., Sampson, S. D., Clark, J.M. & DeBlieux, D. D. 2005.
A primitive therizinosauroid dinosaur from the Early Cretaceous of Utah. Nature 435: 84–87.
Characters 1-222 based on Norell et al. (2001, with references) from Hwang et al. (2004).

http://peabody.yale.edu/scientific-publications/new-perspectives-origin-and-early-evolution-birds
http://peabody.yale.edu/sites/default/files/documents/scientific-publications/Norell.pdf
Norell, M.A., Clark, J.M., & Makovicky, P.J. 
Phylogenetic relationships among the coelurosaurian theropods, in New Perspectives on the Origin and Early Evolution of Birds (eds. Gauthier, J. & Gall, L.F.) 49-67 (Peabody Museum of Natural History, New Haven, 2001)


Friday, January 13, 2017

Humerus

Again we see that Paraves are not like dinosaurs.

http://www.ivpp.cas.cn/qt/papers/201403/P020140314389417822583.pdf

The relative length and diameter of the humerus in several theropod taxa. We use
the ratios of humeral length to femoral length, and humeral diameter to femoral diameter, as
indicators of forelimb length and robustness. Relative to the femur, the humerus is
significantly longer and thicker in basal paravians than in non-paravian theropods, derived
dromaeosaurids and troodontids (the relatively short and slender forelimbs in the last two
groups are secondarily evolved according to the current phylogenetic analysis).

The discovery of Xiaotingia further demonstrates that many features
previously regarded as distinctively avialan actually characterize the
more inclusive Paraves. For example, proportionally long and robust
forelimbs are optimized in our analysis as a primitive character state
for the Paraves (see Supplementary Information). The significant
lengthening and thickening of the forelimbs indicates a dramatic shift
in forelimb function at the base of the Paraves, which might be related
to the appearance of a degree of aerodynamic capability. This hypothesis
is consistent with the presence of flight feathers with asymmetrical
vanes in both basal avialans and basal deinonychosaurs6,23

Friday, January 6, 2017

Beak

Once again we see that dinosaurs are NOT like birds and that pterosaurs ARE like birds.

https://en.wikipedia.org/wiki/Rhamphorhynchus
Rhamphorhynchus ( "beak snout") is a genus of long-tailed pterosaurs in the Jurassic period.
https://en.wikipedia.org/wiki/Pterosaur
Most pterosaur skulls had elongated jaws with a full complement of needle-like teeth.[32] In some cases, fossilized keratinous beak tissue has been preserved, though in toothed forms, the beak is small and restricted to the jaw tips and does not involve the teeth.[33] 
http://onlinelibrary.wiley.com/doi/10.1111/evo.12684/full
The avian beak is a key evolutionary innovation whose flexibility has permitted birds to diversify into a range of disparate ecological niches.
However, the abrupt geometric gap between nonbeaked archosaurs [eg. dinosaurs] and birds and stem birds with beaks may suggest a rapid, comparatively saltational transformation. The difference in ontogenetic trajectories of shape change between nonbeaked forms, in which the premaxilla becomes shorter and broader with time, and beaked forms, in which it becomes longer and narrower, also suggests a discontinuous distinctiveness to the beak.
Pterosaurs already had keratinous beak tissue.
On the other hand, a dino to bird beak evolution requires a saltational transformation.

Fibula

Once again we see that pterosaurs are like birds and dinosaurs are NOT like birds. 

http://onlinelibrary.wiley.com/doi/10.1111/evo.12882/full
In fact, besides birds, distal fibular reduction also occurred independently within at least three other lineages of Ornithodira: Alvarezsauridae (Chiappe et al. 2002), Oviraptorosauria (Vickers-Rich et al. 2002), and Pterosauria (Dalla Vecchia 2003; Bonaparte et al. 2010; Fig. 7).

http://books.google.ca/books?id=idta6AVV-tIC&printsec=frontcover&source=gbs_v2_summary_r&cad=0#v=onepage&q&f=false
In pterosaurs, the tibia is much longer and more slender than the femur, and the fibula is considerably reduced as in birds.




https://en.wikipedia.org/wiki/Bird_feet_and_legs
The fibula is reduced[2][3] and adheres extensively to the tibia,[7] usually reaching only 2/3 of its length. Only penguins have full length fibula.[5]

http://dragons-nest.ru/dragons/books-and-articles/soputstvuyushchee/dragons_of_the_air_by_seeley.php

fig. 34.


https://books.google.ca/books?id=3N8VKVFuRJ4C&pg=PA7&lpg=PA7&dq=penguin+fibula+ankle+turning&source=bl&ots=C8ZgEULm3I&sig=xHB1VEjDbISUBpKLgFEa5s3s1-s&hl=en&sa=X&ved=0ahUKEwiqoduSprDRAhXJx4MKHXC7D-0Q6AEIWTAJ#v=onepage&q=penguin%20fibula%20ankle%20turning&f=false
Terrestrial flightless birds show adaptations to weight-bearing by legs alone. 
http://www.sciencealert.com/scientists-have-grown-dinosaur-legs-on-a-chicken-for-the-first-time
To figure out how this evolution occurred, researchers in Chile have manipulated the genes of regular chickens so they develop tubular, dinosaur-like [tetrapod-like] fibulas on their lower legs - one of the two long, spine-like bones you’ll find in a drumstick.
While modern bird embryos still show signs of developing long, dinosaur-like [tetrapod-like] fibulae, as they grow, these bones become shorter, thinner, and also take on the splinter-like ends of the Pygostylian bones, and never make it far enough down to the leg to connect with the ankle.
molecular-exp 

 http://onlinelibrary.wiley.com/doi/10.1111/evo.12882/full
The shank (zeugopod) of most tetrapods has two equally long bones—the medial (inner) tibia and the lateral (outer) fibula. In early theropod dinosaurs, which are bird ancestors, both bones were equally long, although the fibula is more narrow and in close contact to the tibia. This condition was still present in the basal bird Archaeopteryx (Ostrom 1973; Mayr et al. 2005). Within the Pygostylia, closer to modern birds, the fibula became shorter than the tibia and splinter-like toward its distal end, no longer reaching the ankle (O'Connor et al. 2011a). In modern birds, the fibula is typically about two-thirds the length of the tibia, but fibulo–tibial proportions show considerable evolutionary variation, with proportionally shorter or longer fibulae in different species (Owen 1866; Streicher and Muller 1992).


Tuesday, January 3, 2017

Dinosaur incubation not like birds

Again we see that birds are not like dinosaurs. 

http://www.pnas.org/content/early/2017/01/01/1613716114.full.pdf
Little is known regarding nonavian dinosaur embryology. Embryological period relates to myriad aspects of development, life history, and evolution. In reptiles incubation is slow, whereas in birds it is remarkably rapid. Because birds are living dinosaurs, rapid incubation has been assumed for all dinosaurs. We discovered daily forming growth lines in teeth of embryonic nonavian dinosaurs revealing incubation times. These lines show slow reptilian-grade development spanning months. The rapid avian condition likely evolved within birds prior to the Cretaceous–Paleogene (K–Pg) mass extinction event. Prolonged incubation exposed nonavian dinosaur eggs and attending parents to destructive influences for long periods. Slow development may have affected their ability to compete with more rapidly generating populations of birds, reptiles, and mammals following the K–Pg cataclysm.

Sunday, December 11, 2016

Feathers in Amber

'Beautiful' dinosaur tail found preserved in amber
The tail of a feathered dinosaur has been found perfectly preserved in amber from Myanmar.
The one-of-a-kind discovery helps put flesh on the bones of these extinct creatures, opening a new window on the biology of a group that dominated Earth for more than 160 million years.
Let's look at the study:

http://www.cell.com/current-biology/fulltext/S0960-9822(16)31193-9
The branched feathers have a weak pennaceous arrangement of barbs consistent with non-avialan coelurosaurs, particularly paravians. Although the feathers are somewhat pennaceous, none of the observed osteological features preclude a compsognathid [28] affinity. The presence of pennaceous feathers in pairs down the length of the tail may point toward a source within Pennaraptora [9], placing a lower limit on the specimen’s phylogenetic position. However, the distribution and shape of the feathers only strongly supports placement crownward of basal coelurosaurs, such as tyrannosaurids and compsognathids. In terms of an upper limit, the specimen can be confidently excluded from Pygostylia; in addition, it can likely be excluded from the long-tailed birds, based on pronounced ventral grooves on the vertebral centra.
That is a very nice Pennaraptoran/Paravian. It is not a dinosaur. The problem for the dinosaur to bird theory is that there is no connection between Pennaraptoran/Paravians and coelurosaur dinosaurs.

Saturday, December 10, 2016

Evolution of Feathers

The plumulaceous (downy) and pennaceous feathers of Pennaraptora/Paraves evolved from Pterosaur pycnofibres and actinofibrils.
Pycnofibres covered the body, while the actinofibrils were covered by the wing membrane.
Pycnofibres are comparable to Stage II feathers that have unfurled out of their sheaths.
Actinofibrils are comparable to Stage IIIa feathers that are still within their sheaths.

Actinofibrils

http://en.wikipedia.org/wiki/Pterosaur
While historically thought of as simple, leathery structures composed of skin, research has since shown that the wing membranes of pterosaurs were highly complex and dynamic structures suited to an active style of flight. The outer wings (from the tip to the elbow) were strengthened by closely spaced fibers called actinofibrils.[17] The actinofibrils themselves consisted of three distinct layers in the wing, forming a crisscross pattern when superimposed on one another.
The variation of space between adjacent actinofibrils in Jeholopterus, also reported in Rhamphorhynchus (Padian & Rayner 1993), suggests that those fibres were connected by some elastic tissue that enabled them to spread apart or join whenever necessary, making the actinopatagium more flexible (perhaps somewhat elastic
https://archosaurmusings.wordpress.com/2009/08/05/what-on-earth-are-pycnofibers/
For the first time we observe actinofibrils (those fibers that support the wings) lying in multiple layers (not just a single one) and these tend to cross each other a little, though they are essentially subparallel. This tells us something about the structure and to a lesser extent function of the wing.

https://archive.org/stream/The_Pterosaurs_From_Deep_Time_by_David_M._Unwin/The_Pterosaurs_From_Deep_Time_by_David_M._Unwin_djvu.txt
In this [Sordes], as in other pterosaurs, the wing fibers were embedded within the patagia [wing membranes] and typically measured a little less than one-tenth of a millimetre in diameter- about twice the thickness of a human hair. In some spots unravelled fibers reveal that they were composite structures composed of at least 20 or 30 very fine strands, wound together in a helical fashion. Each strand was only a few hundredth of a millimeter across and probably made of collagen a material that is common in the skin of vertebrates". 
http://www.ucmp.berkeley.edu/vertebrates/flight/pter.html
Bird feathers are analogous to the wing fibers of pterosaurs
http://www.springerlink.com/content/v8434087565413kk/fulltext.pdf?page=1
Wellnhofer [4, 5] and Padian [6, 7], following von Zittel [8],described a system of fine structural fibers investing the wing membrane, in a pattern similar to the orientation of the feather shafts of birds and the wing fingers of bats, both principal structural elements supporting the patagium and responsible for the transmission of aerodynamic force

http://www.jstor.org/pss/2400656
The wing membrane was supported and controlled through a system of stiffened, intercalated fibers,which were oriented like the main structural elements in the wings of birds and bats.
https://archosaurmusings.wordpress.com/2008/06/16/pterosaur-wings-2-structure/
Actinofibrils are unusual structures and we are not sure exactly what they are composed of. The best guess is collagen, but it could also be cartilage or keratin. Determining this in fossils is obviously near impossible but all three are realistic possibilities, though of course collagen is the most likely given the position of the fibres inside the wing membrane (rather than on the surface) and they do not connect to the bones of the wing finger. They lie sub-parallel to the wing towards the wingtips and then sub-perpendicular as we move more proximally. There are no actinofibrils in the proximal wing close to the body, and they get more densely packed the further away you go.
https://www.google.ca/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&cad=rja&uact=8&ved=0ahUKEwjs7aOI4OzQAhUI42MKHd4DCfAQFgggMAE&url=https%3A%2F%2Fwww.fhsu.edu%2Facademic%2Fresearch%2Freports%2FBennettSabbaticalAbstractF12%2F&usg=AFQjCNH5up6EVndVPejQhmiCw_TJqRhuOQ&sig2=clu3jNdQyuxYHSZTPoXd9Q&bvm=bv.141320020,d.cGc
Actinofibrils were formed in place by incremental addition of layer upon layer of hard keratin.




http://prumlab.yale.edu/sites/default/files/prum_n_brush_2002.pdf
Stage II — Origin of a collar with differentiated barb ridges results in a mature feather with a tuft of unbranched barbs and a basal calamus emerging from a superficial sheath.
Stage IIIa — Origin of helical displacement of barb ridges and the new barb locus results in a pinnate feather with an indeterminate number of unbranched barbs fused to a central rachis. 

Image result for stages of feather development cylinder tube tubular helical growth


https://en.wikipedia.org/wiki/Scansoriopteryx#Feathers_and_scales
One distinctive feature of Scansoriopteryx is its elongated third finger, which is the longest on the hand, nearly twice as long as the second finger (in most theropod dinosaurs, the second finger is the longest). This is unlike the configuration seen in most other theropods, where the second finger is longest. The long wing feathers, or remiges, appear to attach to this long digit instead of the middle digit as in birds and other maniraptorans. Shorter feathers are preserved attached to the second finger.[6] A relative of Scansoriopteryx, Yi, suggests that this elongated third finger supported a membranous wing of some kind alongside feathers.[7] 

Pycnofibres

http://www.dinosaur-museum.org/featheredinosaurs/rhamphorhynchoid.pdf
A NEW RHAMPHORHYNCHOID WITH A HEADCREST AND COMPLEX INTEGUMENTARY STRUCTURES
STEPHEN A. CZERKAS and QIANG JI
The [rhamphorhynchoid] “hair-like” structures [pycnofibres]
are also unique in being preserved in fully three
dimensionally forms as compared to two
dimensional staining or impressions. The hairs 
[pycnofibres] are shown to be complex multi-strand structures instead of single strands or actual hairs. The complex nature
of these filaments most closely resembles natal
down feathers, but apparently without having
barbules
.
 As such, they may represent the earliest
known form of feathers. This implies that such
integumentary structures may have originated
independently among pterosaurs from that of birds,
or that birds and pterosaurs may share a common
ancestor which had evolved this kind of insulation
before fight had been achieved in either group.
Feathers differ significantly from hair in that their multiple strands, the barbs,emanate from a single hollow structure, called the calamus. The integumentary structures seen in Pterorhynchus [a rhamphorhynchid] bear a striking similarity to that of a natal down feather with only the notable absence of having the additional barbules branching from the barbs. This absence is significant all the more because without the barbules, the barbs emanating from a calamus represents the hypothetical “Stage II” structure speculated as being an incipient step in the evolution of feathers (Prum, 1999).
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.
Therefore, the individual filaments are not representative of hair,
but are analogous to being the barbs of a feather.
Barbules, if present, cannot be discerned which
suggests that they either did not exist, or that the
limits of preservation have obscured them.
Nonetheless, the morphology of having several
barbs stemming from a short calamus indicates that
the body covering of Pterorhynchus 
are feather homologues. Without barbules, these structures would represent the second stage of feather
development as speculated by Prum (1999). The
feather homologues of Pterorhynchus also
demonstrate that a primary function achieved by
these plumulaceous feathers was that of thermal
insulation, and that feathers with a true rachis and
barbs aligned into well developed vanes represent
a derived condition.
The wing membranes are thought to have been stiffened by internal fibers, called aktinofibrils (Martill and Unwin, 1989; Wellnhofer, 1987, 1991). The distal end of a wing membrane is preserved in Pterorhychus which shows clear aktinofibrils that are aligned in parallel rows. 
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842671/
Kellner et al
On the tenopatagium close to the body and on the tail, a third type of fibre [pycnofibre] with somewhat diffuse edges is observed (figures 3a and ​and44a). Type C fibres can be easily separated from other fibres by their dark-brown colour and their general lack of organization. They are distributed along the body, the tail and the tip of the actinopatagium close to the fourth wing finger phalanx (figures 1​,22 and ​and44c). Sometimes clustering together, they are not found covering the external portion of the plagiopatagium and are apparently rare on the actinopatagium.

As Wang et al. (2002) pointed out, these fibres are best interpreted as structures covering the body, commonly referred to as ‘hair’ or hair-like structures (e.g. Sharov 1971Bakhurina & Unwin 1995). This pterosaur hair, which is not homologous to the mammalian hair (a protein filament that originates deep in the dermis and grows through the epidermis), is here called pycnofibre (from the Greek word pyknos, meaning dense, bushy). The pycnofibres are further formed by smaller fibrils of unknown nature. They were possibly mostly composed of keratin-like scales, feathers and mammalian hair.

Two other Chinese specimens were reported with integumental covering, coming from the same stratum (the Daohugou Bed) as Jeholopterus. So far we have not had the opportunity to examine this material. The first one is a small unnamed anurognathid with extensive preservation of soft tissue, including fibres that have been interpreted as protofeathers (Ji & Yuan 2002). The published pictures show that the soft tissue interpreted as protofeathers is of the same nature as the pycnofibres of Jeholopterus. There is no indication of branching structures that are expected for feather precursors. 

http://pterosaurnet.blogspot.ca/2014/01/helpful-background.html
http://pterosaurnet.blogspot.ca/2011/10/bird-feathers-are-analogous-to-wing.html
The strings cross the fibres at angles between 30° and 90°
http://pterosaurnet.blogspot.ca/2010/05/pterosaur-wing-covering-2.html


https://pterosaurheresies.wordpress.com/2016/03/page/2/

Several views of the Pterorhynchus wingtip. The ungual (manual4.5) has been colored magenta. Manual 4.4 (green) is broken.Figure 1. Several views of the Pterorhynchus wingtip. The ungual (manual4.5) has been colored magenta. Manual 4.4 is broken.


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842671/
Although no distinctive trailing edge is discernible, the wing membrane extends along the body and is connected to the hind limbs, reaching the ankle (). While the distal portion of the plagiopatagium shows several layers of closely packed fibres (actinofibrils), the more proximal part lacks these structures. This confirms the observations of , who recognized two distinct portions of the plagiopatagium, the actinopatagium and the tenopatagium, distinguished by the presence and absence of actinofibrils, respectively.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4202321/
Compared with contour feathers, flight feathers have a larger pennaceous vane and a longer and thicker rachis. Wing flight feathers also have a longer calamus for insertion deeper into the follicle and anchor more securely to sustain its aerodynamic function

http://www.peteducation.com/article.cfm?c=15+1829&aid=2776
The bases of the flight feathers are covered with smaller contour feathers called coverts. There are several layers of coverts on the wing. 

Both pycnofibres and actinofibrils are the same basic form. But they differ in that the pycnofibres proceeded through the stages to where the sheaths had disintegrated and the internal strands are visible on the surface. The actinofibrils did not proceed to that point. In the actinofibril, the internal strands (barbs) are still within the sheaths. And the sheaths are covered by the wing membrane.

The pycnofibres are on the body of the pterosaur. When the sheath disintegrates they unfurled into a form comparable to natal down and kept the body of the pterosaur warm.
The actinofibrils perform a different function. They stiffen and strengthen the wing membrane.

It is helpful to keep in mind that the actinofibrils and the wing membrane grew in synch as the pterosaur grew. (It is an example of facilitated variation.)


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386666/
In a fractal-like fashion, other morphogenetic processes take place within the barb plate to form numerous barbules (Figure 2cTable 1).
http://rspb.royalsocietypublishing.org/content/277/1685/1161



A schematic view of the three major structural components of the feather rachis. (a) (i) superficial layers of *fibres, the ultimate size-class in the hierarchy of feather keratin filaments (approx. 6 ┬Ám diameter), wound circumferentially round the rachis. (ii) The majority of the fibres extending parallel to the rachidial axis and through the depth of the cortex. Part of the section is peeled back to show why the fibres and even megafibrils are not usually recognized in histological sectioning, but rather only fibrils lower down the hierarchy (based on the electronic supplementary material, figure S2c). Any longitudinal section along the line of the arrows or at any point along the height of the fibre other than at the fibre surface (arrowheads) will fail to show the fibre. (iii) It shows the medulloid pith comprising gas-filled polyhedral structures (based on SEM images, electronic supplementary material, figures S5 and S6). Inset, part of a steel rebar with nodes, used in engineering technology to reinforce high-rise structures, analogous to rachidial fibres. (b) Schematic cross section of fibres and biodegraded ‘matrix’: (i) fibres; (ii) residual cytosol of keratinocytes presumably housing effete organelles and perhaps cytoskeletal elements—all degraded along with corneous envelope; (iii) interdigitating plasma membrane of the original keratinocytes with associated corneous envelope proteins. (c) A schematic three-dimensional cross section of the rachis showing approximate thickness (based on SEMs) of the three keratin layers comprising, (i) circumferential and (ii) longitudinal fibres of the cortex and (iii) polyhedra of medulloid pith. Asterisk denotes homologous with syncitial barbules.



http://prumlab.yale.edu/sites/default/files/prum_n_brush_2002.pdf

Figure 2. Schematic Diagram of Helical Growth of Barb Ridges of a Pennaceous Feather The branched structure of the barbs and the rachis of a feather form by helical growth and fusion of barb ridges within the tubular feather germ. Feathers grow from the base. Barb ridges form at the new barb locus on the posterior midline of the collar and grow helically around the collar toward the anterior midline where they fuse to form the rachis ridge. Subsequent barb ridges fuse to the rachis ridge. In feathers with an afterfeather, the new barb locus divides into two laterally displaced new barb loci. Subsequently, new barb ridges grow helically both anteriorly to the main rachis and posteriorly to form the hyporachis and vane of the afterfeather. The main vane and the afterfeather form separate vanes united within a single feather by the calamus (Figure 1A). Pennaceous feathers obtain their planar form only after emerging from the cylindrical feather sheath when growth is complete. The obverse (upper) and reverse (lower) surfaces of the vane develop from the outer and inner surfaces of the cylindrical feather germ. Illustration based on Lucas and Stettenheim (1972).

https://www.youtube.com/watch?v=_8ykumFZXFQ
Down Feather Development: Gallus domestics



Dinosaur Museum

http://dinosaur-museum.org/featheredinosaurs/arboreal_maniraptoran.pdf
AN ARBOREAL MANIRAPTORAN FROM NORTHEAST CHINA STEPHEN A. CZERKAS and CHONGXI YUAN

http://www.dinosaur-museum.org/featheredinosaurs/rhamphorhynchoid.pdf
A NEW RHAMPHORHYNCHOID WITH A HEADCREST AND COMPLEX INTEGUMENTARY STRUCTURES
STEPHEN A. CZERKAS and QIANG JI

AND

http://www.springer.com/gp/about-springer/media/springer-select/dinosaurs-are-not-the-great-great-grandparents-of-birds-/29304

https://waxing-paleontological.blogspot.ca/2015/05/scansoriopterygid-faq.html?showComment=1482173666510#c1515808862453816302
See how it's covered in skin already? There's a tendon running between the shoulder and the wrist, just like in pterosaurs, that anchors a skin membrane called the propatagium. The ulna is covered in thick skin that anchors the flight feathers. In many birds, the bottom of the upper arm is loosely connected to the body by skin as well. So you can imagine these membranes becoming larger and more parachute-like.
Czerkas & Yuan also noticed tissue impressions coming off the ulna and third finger of Scansoriopteryx—those might be better interpreted (now) as a flight membrane.

https://bio.unc.edu/files/2011/04/Journal-of-Ornithology-20141.pdf
Scansoriopteryx Feduccia and Czerkas
There are indications from where the feathers emanate below the ulna which suggest that a short patagium may have been present. Unlike most of the wing feathers, there appears to be a series of feathers that do not reach the bone itself. 

http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-95022007000100010

In barb medullary cells feather keratin is accumulated in few peripheral bundles that merge with those of cortical cells to form the wall of the ramus. The latter is joined with branching barbules.

https://blogs.scientificamerican.com/tetrapod-zoology/yi-qi-is-neat-but-might-not-have-been-the-black-screaming-dino-dragon-of-death/
What’s been mostly overlooked in discussions of Yi qi is that pennaraptoran maniraptorans already have patagia.
Look at the (perhaps familiar) pictures of nightjar wings below and observe all the ‘webbing’ that surrounds the fingers and arm. A membrane called the propatagium spans the space between the wrist and shoulder, and membranes run along the trailing (or posterior, or postaxial) edges of the hand and ulna too.
Xu et al. (2015) also note that these [Yi qi] patches have an unusual wrinkled texture, not typical of skin that would have been covered in filaments or feathers. But maybe they’re naked and wrinkled for taphonomic reasons.
 
As a Tet Zoo regular, you'll recognise these images from p. 19 of Katrina van Grouw's The Unfeathered Bird. They show the left wing of a European nightjar (Caprimulgus europaeus) in (at top) dorsal and ventral views. Note all the skin membranes around the more muscular parts of the wing. Image by Katrina van Grouw, used with permission.


Related image

Image result for Katrina van Grouw's The Unfeathered Bird.
Ostrich  http://en.wikipedia.org/wiki/Ostrich

http://veteriankey.com/avian-deflighting-techniques/
The four patagia of the wing include the propatagium, where the wing and the neck join the thorax; the postpatagium, which is located at the caudal angle of the carpus; the metapatagium at the caudal junction of the thorax and the wing, and the alular patagium between the alula and the carpometacarpus.
Image result for bird wing postpatagium


https://books.google.ca/books?id=livLBAAAQBAJ&pg=PA18&lpg=PA18&dq=humeral+patagium&source=bl&ots=COa0_l7raO&sig=XSQ8a63WrZ1qHXhZg-g12C0rito&hl=en&sa=X&ved=0ahUKEwiY95S3mo3RAhUiwYMKHfZLAgoQ6AEIIzAC#v=onepage&q=humeral%20patagium&f=false
"humeral patagium"

https://books.google.ca/books?id=KG86AgWwFEUC&pg=PA128&lpg=PA128&dq=bird+propatagium+feathers+rooted+in+tendon&source=bl&ots=RuJ5ZnWI1K&sig=B_bTFKkAMp5pM73VxpgyWdEtncg&hl=en&sa=X&ved=0ahUKEwib6tfiu5LRAhUM7YMKHYsQAwEQ6AEIGzAA#v=onepage&q=bird%20propatagium%20feathers%20rooted%20in%20tendon&f=false (Page 128)
propatagium and postpatagium
https://en.wikipedia.org/wiki/Flight_feather
Remiges (from the Latin for "oarsman") are located on the posterior side of the wing. Ligaments attach the long calami (quills) firmly to the wing bones, and a thick, strong band of tendinous tissue known as the postpatagium helps to hold and support the remiges in place.[2]

An alternate way to understand the pterosaur wing:
The pterosaur postpatagium helps to hold and support the actinofibrils in place.


http://rspb.royalsocietypublishing.org/content/277/1679/321.full
On the tenopatagium close to the body and on the tail, a third type of fibre with somewhat diffuse edges is observed (figures 3a and 4a). Type C fibres can be easily separated from other fibres by their dark-brown colour and their general lack of organization. They are distributed along the body, the tail and the tip of the actinopatagium close to the fourth wing finger phalanx (figures 1, 2 and 4c). Sometimes clustering together, they are not found covering the external portion of the plagiopatagium and are apparently rare on the actinopatagium.
Generally thicker than the actinofibrils (figure 4a), type C fibres have an average thickness ranging between 0.2 and 0.5 mm. In several places, it is clear that they are formed by smaller fibrils, the nature of which is unknown. The sediment between type C fibres tends to be light brown in colour, making the distinction of individual fibres more difficult. Several cross each other but lack the reticular pattern formed by the multi-layered superposition of the actinofibrils. In several areas, type C fibres are preserved associated with an amorphous whitish matter that has been interpreted as patches of the epidermis (and dermis, described earlier). Although not parallel to each other and lacking the organization of the actinofibrils, fibres C in most parts are generally displaced away from the skeleton.
As Wang et al. (2002) pointed out, these fibres are best interpreted as structures covering the body, commonly referred to as ‘hair’ or hair-like structures (e.g. Sharov 1971; Bakhurina & Unwin 1995). This pterosaur hair, which is not homologous to the mammalian hair (a protein filament that originates deep in the dermis and grows through the epidermis), is here called pycnofibre (from the Greek word pyknos, meaning dense, bushy). The pycnofibres are further formed by smaller fibrils of unknown nature. They were possibly mostly composed of keratin, like scales, feathers and mammalian hair.