Thursday, April 20, 2017

"An abnormally rapid period of morphological evolution"

"Relative to the femur, the humerus is significantly longer and thicker in basal paravians than in non-paravian theropods." (Xu et al)
"The significant lengthening and thickening of the forelimbs indicates a dramatic shift in forelimb function at the base of the Paraves." (Xu et al)
"We find an increase in rates of body size and body size dependent forelimb evolution leading to small body size relative to forelimb length in Paraves." (Puttick et al)

To try to rationalize the gap at basal Paraves, the researchers claim that the rate of evolution itself was "abnormally rapid".   

http://www.cell.com/current-biology/fulltext/S0960-9822(14)01047-1
Stephen Brusatte et al
Gradual Assembly of Avian Body Plan Culminated in Rapid Rates of Evolution across the Dinosaur-Bird Transition
There is growing evidence that changes in discrete character evolution, body size, and limb anatomy occurred quickly in the vicinity of the origin of birds, either at the node Avialae, in close avialan outgroups [basal paraves] or beginning with slightly more derived birds [3, 4, 5, 6, 19, 20, 21, 22]. It is likely that different types of data will pinpoint changes at slightly different positions on phylogeny, but in general, recent studies converge in identifying the dinosaur-bird transition as an abnormally rapid period of morphological evolution.
The initial results of the branch (Dryad Fig. S4-13) and clade (Fig. S3; Dryad Fig. S14-23) tests strongly support significantly high rates in Avialae, and to a lesser degree Tyrannosauroidea.
Other clades show significantly low or non-significant rates, with the exception of two smaller clades: Graciliraptor + Microraptor + Shanag + Sinornithosaurus + Tianyuraptor (within Dromaeosauridae), and Anchiornis + Aurornis + Eosinopteryx + Xiaotingia (within Troodontidae) [basal Paraves] which frequently show high rates. 
 Important note:
Anchiornis + Aurornis + Eosinopteryx + Xiaotingia (within Troodontidae) [basal Paraves] frequently show high rates. 
In other words, the authors recognize the gap at Paraves.

http://www.ivpp.cas.cn/qt/papers/201403/P020140314389417822583.pdf (2011)
An Archaeopteryx-like theropod from China and the origin of Avialae
Xing Xu1,2, Hailu You3 , Kai Du4 & Fenglu Han2
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.
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).

http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.915.8222&rep=rep1&type=pdf (2014)
http://science.sciencemag.org/content/sci/suppl/2014/07/30/345.6196.562.DC1/1252243.Lee.SM.revision1.pdf
Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds
Michael S. Y. Lee,1,2* Andrea Cau,3,4 Darren Naish,5 Gareth J. Dyke5,6
Although there is no overall theropod-wide trend (fig. S7 and SM, part D), there is an exceptional trend within the single lineage that comprises much of the avian stem.
Our study quantifies rates of evolutionary innovation in dinosaurs using 1549 (data set 1) and 421 (data set 2) skeletal and other anatomical traits distributed across the entire body. A clear pattern emerges: Branches along the bird stem undergo substantially faster morphological evolution than those of the rest of the tree. 
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.

These results reconcile contradictory studies identifying presence (4–8) or absence (9–11) of a trend toward size reduction in theropods. Although there is no overall theropod-wide trend (fig. S7 and SM, part D), there is an exceptional trend within the single lineage that comprises much of the avian stem.
http://science.sciencemag.org/content/sci/suppl/2014/07/30/345.6196.562.DC1/1252243.Lee.SM.revision1.pdf
Also see Figure S6.



Let's look at body size and forelimb length.
Notice that the changes appear for the first time at the origin of Paraves (not earlier).

https://www.scientificamerican.com/article/how-dinosaurs-shrank-and-became-birds/

That shrinkage sped up once bird ancestors grew wings and began experimenting with gliding flight. Last year, Benton’s [Puttick] team showed that this dinosaur lineage, known as paraves, was shrinking 160 times faster than other dinosaur lineages were growing. “Other dinosaurs were getting bigger and uglier while this line was quietly getting smaller and smaller,” Benton said. “We believe that marked an event of intense selection going on at that point.”
http://www.bris.ac.uk/news/2014/february/origin-of-birds.html
Mark Puttick and colleagues investigated the rates of evolution of the two key characteristics that preceded flight: body size and forelimb length.  In order to fly, hulking meat-eating dinosaurs had to shrink in size and grow much longer arms to support their feathered wings. 
"We were really surprised to discover that the key size shifts happened at the same time, at the origin of Paraves," said Mr Puttick of Bristol's School of Earth Sciences.  "This was at least 20 million years before the first bird, the famous Archaeopteryx, and it shows that flight in birds arose through several evolutionary steps."                                     
High rates of evolution preceded the origin of birds (2014)
Puttick, M.N., Thomas, G.H., and Benton, M.J. in Evolution: DOI: 10.1111/evo.12363 
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, but some may be unique to Aves, such as relative elongation of the forelimb. We study the evolution of body size and forelimb length across the phylogeny of coelurosaurian theropods and Mesozoic Aves. Using recently developed phylogenetic comparative methods, we find an increase in rates of body size and body size dependent forelimb evolution leading to small body size relative to forelimb length in Paraves, the wider clade comprising Aves and Deinonychosauria. The high evolutionary rates arose primarily from a reduction in body size, as there were no increased rates of forelimb evolution. In line with a recent study, we find evidence that Aves appear to have a unique relationship between body size and forelimb dimensions. 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.
Also see:
http://pterosaurnet.blogspot.ca/2014/03/body-size-and-forelimb-length.html

Friday, March 17, 2017

Support indices do not support the dino to bird theory

This is a summary and continuation of the material of the Jan 17 post.
It is widely believed that the dinosaur to bird theory is well supported. That is believed because cladistic analyses have been run and presented that appear to support that theory. However when we drill down into the analyses that have been done we see that the calculated statistical support values for all the core nodes are “poorly supported”.

The nodes on a cladogram are evaluated by calculating support indices (Bremer, bootstrap/jackknife, GC). 
The support indices for the core nodes in the dino to bird cladograms show that all the core nodes are poorly supportedFor example:
Maniraptoriformes is poorly supported
Maniraptora is poorly supported.
Oviraptorosauria + Paraves (Pennaraptora) is poorly supported.
Paraves is poorly supported.

1. Rationalizations of the poor support:

Homoplasies

http://www.ivpp.cas.cn/qt/papers/201403/P020140314389417822583.pdf (2011)
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 (see Supplementary Information). This low support is partly caused by various homoplasies, many of which are functionally significant, that are widely distributed across coelurosaurian phylogeny29.
But this does not explain why these particular nodes (which are the core nodes) are poorly supported when the other subgroups are supported.  


Lack of knowledge

http://evolution.berkeley.edu/evolibrary/article/phylogenetics_03
Lack of knowledge
Usually, a polytomy means that we don't have enough data to figure out how those lineages are related. By not resolving that node, the scientists who produced the phylogeny are telling you not to draw any conclusions — and also to stay tuned: often gathering more data can resolve a polytomy.
However note that there are enough characters in the study to make conclusions about all of the other major coelurosaurian subgroups so it is not a problem of not having enough data:

http://www.cell.com/current-biology/fulltext/S0960-9822(14)01047-1 (2014)
Gradual Assembly of Avian Body Plan Culminated in Rapid Rates of Evolution
across the Dinosaur-Bird Transition 

Stephen L. Brusatte, Graeme T. Lloyd, Steve C. Wang, and Mark A. Norell 

All of the major coelurosaurian subgroups that have long been considered monophyletic are also found to be monophyletic here. These include Tyrannosauroidea, Compsognathidae, Ornithomimosauria, Alvarezsauroidea, Therizinosauroidea, Oviraptorosauria, Dromaeosauridae, Troodontidae, and Avialae

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%.
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%.

2. Contradictions:

Not only are the support indices low but the analyses also underestimate the amount of contradiction.
The studies include a very large number of characteristics.
Let's look at the very first one:

1. Vaned feathers on forelimb symmetric (0) or asymmetric (1). The barbs on opposite sides of the rachis differ in length; in extant birds, the barbs on the leading edge of flight feathers are shorter than those on the trailing edge.

Note that there is no value for when the taxon does not have any form of feather. This means that the dinosaurs (without feathers) are scored as "?" (unknown).

This means that they are not scored as contrary to the feathered taxa.
This underestimates the contradiction between dinosaurs and primitive birds.




3. Basal Polytomies

http://www.cell.com/current-biology/fulltext/S0960-9822(14)01047-1 (2014)
Gradual Assembly of Avian Body Plan Culminated in Rapid Rates of Evolution
across the Dinosaur-Bird Transition 

Stephen L. Brusatte, Graeme T. Lloyd, Steve C. Wang, and Mark A. Norell 
There is a large polytomy at the base of the clade that includes all coelurosaurs more derived (closer to avialans) than tyrannosauroids.




http://www.ivpp.cas.cn/qt/papers/201403/P020140314389417822583.pdf (2011)
An Archaeopteryx-like theropod from China and the origin of Avialae
Xing Xu1,2, Hailu You3 , Kai Du4 & Fenglu Han2

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.






4. Few characters support each node

https://www.researchgate.net/publication/305748962_Binary_Particle_Swarm_Optimization_Versus_Hybrid_Genetic_Algorithm_for_Inferring_Well_Supported_Phylogenetic_Trees

Binary Particle Swarm Optimization versus Hybrid Genetic Algorithm for Inferring Well Supported Phylogenetic Trees


Bassam AlKindy, Bashar Al-Nuaimi, Christophe Guyeux, Jean-François Couchot, Michel Salomon, Reem Alsrraj, Laurent Philippe
If, for example, you recover the same node through 95 of 100 iterations of taking out one character and resampling your tree, then you have a good idea that the node is well supported (your bootstrap value in that case would be 0.95 or 95%).
If we get low support, that suggests that only a few characters support that node, as removing characters at random from your matrix leads to a different reconstruction of that node. 

https://projecteuclid.org/euclid.ss/1063994980
http://projecteuclid.org/download/pdf_1/euclid.ss/1063994980
Pamela Soltis
bootstrap values are low because of the small number of characters supporting each node
Could it be that those few characters are homoplasies or symplesiomorphies? Or autapomorphies acquired independently.

https://en.wikipedia.org/wiki/Symplesiomorphy
plesiomorphy refers to the ancestral trait state, usually in reference to a derived trait state. A symplesiomorphic trait is also shared with other taxa that have an earlier last common ancestor with the taxa under consideration.
https://en.wikipedia.org/wiki/Synapomorphy
The concept of synapomorphy is relative to a given clade in the tree of life. What counts as a synapomorphy for one clade may well be a primitive character or plesiomorphy at a less inclusive or nested clade. For example, the presence of mammary glands is a synapomorphy for mammals in relation to tetrapods but is a symplesiomorphy for mammals in relation to one another, rodents and primates, for example. 

http://digitallibrary.amnh.org/handle/2246/6352
Turner et al
Maniraptora is poorly supported in the analysis (GC = 5). Most other derived maniraptoran clades, however, show surprisingly high levels of jackknife support. Alvarezsauroidea
is moderate to weakly supported
(GC = 25), but the less inclusive Alvarezsauridae
and its constituent clades have high
jackknife support (ranging from 70 to 83).
The sister taxon relationship of Patagonykus
puertai with Shuvuuia deserti and Mononykus
olecranus is strongly supported (GC = 80).

Tuesday, February 7, 2017

Ontogeny and Phylogeny

Let's step back a bit and look at ontogeny (development) and phylogeny (evolution).
What are the different ways researchers have tried to relate ontogeny to phylogeny?
Some of the people involved: Meckel, Haeckel, von Baer, Gould.


 https://en.wikipedia.org/wiki/Von_Baer's_law_(biology)
The von Baer's law is a concept in biology introduced by Karl Ernst von Baer to explain the details of embryo development.[1] He specifically aimed at rebutting the recapitulation theory introduced by Johann Friedrich Meckel in 1808. According to Meckel's theory, embryos pass through successive stages that represent the adult forms of less complex organisms in the course of development, and that ultimately reflects scala naturae (the great chain of being).[2] von Baer believed that such linear development is impossible. He posited that instead of linear progression, embryos started from one, or a few, basic forms that are similar for different animals, and then developed in a branching pattern into increasingly different looking organisms. Defending his ideas, he was also opposed to the theory of common ancestry and descent with modification as proposed by Charles Darwin in 1859, and particularly the revised recapitulation theory ("ontogeny recapitulates phylogeny") of Ernst Haeckel, a supporter of Darwin's theory in Germany.[3][4]

https://en.wikipedia.org/wiki/Ontogeny_and_Phylogeny_(book)
Gould's hope was to show that the relationship between ontogeny and phylogeny is fundamental to evolution, and at its heart is a simple premise—that variations in the timing and rate of development provide the raw material upon which natural selection can operate."[2]

Summary:

Meckel
embryos pass through successive stages that represent the adult forms of less complex organisms in the course of development, and that ultimately reflects scala naturae (the great chain of being)

von Baer
embryos started from one, or a few, basic forms that are similar for different animals, and then developed in a branching pattern into increasingly different looking organisms.

Haeckel
ontogeny recapitulates phylogeny
https://embryo.asu.edu/pages/ontogeny-and-phylogeny-1977-stephen-jay-gould
Ernst Haeckel's theory of recapitulation, had an evolutionary perspective. Evolutionary recapitulation differed from other forms of recapitulation as it integrates the theory of common ancestry for all organisms. 

Gould
variations in the timing and rate of development provide the raw material upon which natural selection can operate


Background:

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

Ontogeny is the developmental history of an organism within its own lifetime, as distinct from phylogeny, which refers to the evolutionary history of a species. In practice, writers on evolution often speak of species as "developing" traits or characteristics. This can be misleading. While developmental (i.e., ontogenetic) processes can influence subsequent evolutionary (e.g., phylogenetic) processes[1] (see evolutionary developmental biology), individual organisms develop (ontogeny), while species evolve (phylogeny).


Relationship to feather development:

http://prumlab.yale.edu/sites/default/files/prum_1999_mde_development.pdf
In general, the polarities of developmental novelties in the model are congruent with von Baer’s rule—the hypothesis that stages that occur earlier in development are phylogenetically more broadly distributed and historically plesiomorphic (e.g., Gould, ’77). However, the model does not rely solely on relative timing of events in ontogeny to justify these polarities. The stages of the model are inferred from the hierarchical nature of the developmental mechanisms of the follicle rather than from an analysis of the ontogenetic progression of plumages grown within the follicles of birds. Thus, plumulaceous feathers (stage II) are not primitive to pennaceous feathers (stage IIIa and beyond) because the first plumage of extant birds is usually downy, but because the simplest differentiated follicle collar would have produced plumulaceous feathers.
One detail, however, of feather development appears to violate von Baer’s rule. During the development of the first feather papillae in the embryo (before day 12 in the chick, Gallus gallus), the barb ridge primordia appear as longitudinal condensations within the feather papillae before the follicle and collar are fully formed (Lucas and Stettenheim, ’72). However, this developmental event—the origin of the feather before the follicle and collar—is clearly derived because barb ridges would be unable to grow without the spatial organization provided by the collar.



https://en.wikipedia.org/wiki/Von_Baer's_law_(biology)
The most important supporter of von Baer's law was Charles Darwin, who wrote in his Origin of Species:
[The] adult [animal] differs from its embryo, owing to variations supervening at a not early age, and being inherited at a corresponding age. This process, whilst it leaves the embryo almost unaltered, continually adds, in the course of successive generations, more and more difference to the adult. Thus the embryo comes to be left as a sort of picture, preserved by nature, of the ancient and less modified condition of each animal. This view may be true, and yet it may never be capable of full proof.[9]
In terms of taxonomic hierarchy, characters in the embryo will be formed in the order, first from those of phylum, then class, order, family, genus, and finally species.[6] 

https://embryo.asu.edu/pages/karl-ernst-von-baers-laws-embryology
Von Baer's second law states that embryos develop from a uniform and noncomplex structure into an increasingly complicated and diverse organism. For example, a defining and general characteristic of vertebrates is the vertebral column. This feature appears early in the embryonic development of vertebrates. However, other features that are more specific to groups within vertebrates, such as fur on mammals or scales on reptiles, form in a later developmental stage. Von Baer argued that this evidence supporting epigenetic development rather than development from preformed structures. He concluded from the first two laws that development occurs through epigenesis, when the complex form of an animal arises gradually from unformed material during development. 

IMPORTANT

It is important to realize that the feather stages up to developmental Stage IIIa are ALREADY present in the actinofibrils of the pterosaur. In other words, there is no need to evolve those stages (in the transition to basal Paraves) because they are already present in the pterosaur ancestor.


Tuesday, January 17, 2017

Support Indices

The nodes on a cladogram are statistically evaluated by calculating support indices (bootstrap/jackknife, Bremer, GC). 
It is significant that all the core nodes in the hypothesized dinosaur to bird phylogeny are poorly supported. 
For example:
Maniraptoriformes is poorly supported 
Maniraptora is poorly supported.
Oviraptorosauria + Paraves (Pennaraptora) is poorly supported.
Paraves is poorly supported.

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.life.umd.edu/labs/delwiche/MSyst/lec/bootstrap.html
Low bootstrap values (below 50%) are essentially meaningless
Gradual Assembly of Avian Body Plan Culminated in Rapid Rates of Evolution
across the Dinosaur-Bird Transition 

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%.
Both Bremer supports and jackknife percentages (absolute values) were calculated in TNT using standard scripts. The jackknife was run using the default parameter of 36% character removal probability and 1000 replicates.
Note that there are enough characters in the study to make conclusions about all of the other major coelurosaurian subgroups so it is not a problem of not having enough data:
All of the major coelurosaurian subgroups that have long been considered monophyletic are also found to be monophyletic here. These include Tyrannosauroidea, Compsognathidae, Ornithomimosauria, Alvarezsauroidea, Therizinosauroidea, Oviraptorosauria, Dromaeosauridae, Troodontidae, and Avialae
And
Perhaps surprisingly, Ornithomimosauria is not found to be monophyletic and there is a large polytomy at the base of the clade that includes all coelurosaurs more derived (closer to avialans) than tyrannosauroids. This lack of resolution is due to the uncertain phylogenetic position of a small handful of taxa, including the fragmentary basal coelurosaur Kinnareemimus (a purported ornithomimosaur:
[S49]), the aberrant coelurosaur Epidendrosaurus (which is known only from two juvenile individuals: [S50]), the paravians Pyroraptor and Hesperonychus, and the avialan Limenavis. Pyroraptor and Limenavis were also found to be unstable in the analysis of Turner et al. (2012) [S9], whereas Epidendrosaurus was excluded from the primary version of that analysis
Note that the core nodes are poorly supported even after the removal of those 5 taxa! 
Ornithomimosaurs vs. tyrannosauroids: 29 axes, Mahalanobis distance=783720, p=0.00049975
The reduced strict consensus topology is shown in Figures S1-S2 (and Dryad Figs. S2-S3) and is used here as the preferred phylogeny and basis for character optimization and discussion of coelurosaurian phylogeny and evolution. This topology is considerably more resolved than the strict consensus, and recovers a monophyletic Ornithomimosauria and better resolution among basal coelurosaurs and paravians.
http://datadryad.org/resource/doi:10.5061/dryad.84t75
See Figure S1 for the large polytomy.

Reduced consensus tree:
  Opens large image


Numbers next to nodes denote Bremer support value/jackknife percentage. Those nodes without any numbers are characterized by Bremer values of 1 and a jackknife percentage of less than 60%




Xu et al

http://www.ivpp.cas.cn/qt/papers/201403/P020140314389417822583.pdf (2011)
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 (see Supplementary Information). This low support is partly caused by various homoplasies, many of which are functionally significant, that are widely distributed across coelurosaurian phylogeny29.
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 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?
We evaluated the relative length and robustness of the forelimbs of major theropod groups by comparing the length and diameter of the humerus to the corresponding measurements for the femur in selected theropod taxa that represent the major theropod clades (Table S1). The plotted graph (Figure S4) indicates that the humerus is proportionally longer and more robust in basal avialans, archaeopterygids, and basal dromaeosaurids than in non-paravian theropods, troodontids, and derived dromaeosaurids. The last two groups are interpreted as having secondarily shortened forelimbs.
Figure S4. 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).



http://evolution.berkeley.edu/evolibrary/article/phylogenetics_03
Lack of knowledge
Usually, a polytomy means that we don't have enough data to figure out how those lineages are related. By not resolving that node, the scientists who produced the phylogeny are telling you not to draw any conclusions — and also to stay tuned: often gathering more data can resolve a polytomy.
Rapid speciation
Sometimes a polytomy means that multiple speciation events happened at the same time. In this case, all the daughter lineages are equally closely related to one another. The researchers who have reconstructed the tree you are examining should tell you if they feel that the evidence indicates that this is the case.

http://peter.unmack.net/molecular/programs/tnt.bootstrapping.html
This provides minimal instructions for running a bootstrap analysis.
https://www.geol.umd.edu/~tholtz/G331/lectures/cladistics5.pdf
Figure 4 shows the relevant screen where you can set how many replications you would like (I would recommend no fewer than 1000), what kind of tree search you want (Heuristic and Branch & Bound are the only options) and what set level of the majority rule consensus tree you want (you would normally leave this at 50%).


http://www.sciencedirect.com/science/article/pii/S0960982214011385
...as the authors and others have noted, low support values indicate that many branches near the origin of birds remain unstable 1, 2, 4 and 5.
      • However, it was acknowledged that the new phylogeny required further investigation, owing to weak support (Bremer support of 2 and bootstrap less than 50%; []). Also, as with most morphological studies, only parsimony (cladistic) methods were employed. 

https://www.researchgate.net/publication/305748962_Binary_Particle_Swarm_Optimization_Versus_Hybrid_Genetic_Algorithm_for_Inferring_Well_Supported_Phylogenetic_Trees
If, for example, you recover the same node through 95 of 100 iterations of taking out one character and resampling your tree, then you have a good idea that the node is well supported (your bootstrap value in that case would be 0.95 or 95%).
If we get low support, that suggests that only a few characters support that node, as removing characters at random from your matrix leads to a different reconstruction of that node. 

https://en.wikipedia.org/wiki/Monophyly
Monophyletic groups are typically characterized by shared derived characteristics (synapomorphies).


Turner et al 

http://digitallibrary.amnh.org/handle/2246/6352 (2012)
A review of dromaeosaurid systematics and paravian phylogeny. (Bulletin of the American Museum of Natural History, no. 371)
Turner, Alan H. (Alan Hamilton); Makovicky, Peter J.; Norell, Mark.

See Figures 66, 67, 68 (GC) and 69, 70, 71 (Bremer)

The results from the entire dataset reflect a wide range of support for nodes across the entire tree (figs. 66–68). Unsurprisingly, coelurosaurian monophyly is extremely well supported (GC 95) with little contradictory evidence. The basal Tyrannosauroidea clade is also well supported as is the less inclusive Tyrannosauridae node (GC 79 and 73, respectively).
Most of the intervening nodes between Proceratosaurus bradleyi, Ornithomimosauria, and derived maniraptorans have extremely low support (GC values between 2 and 12). This is neither surprising nor very informative given that most of these nodes collapse in the strict consensus topology of the phylogenetic analysis due to the labile positions of Proceratosaurus bradleyi, Dilong paradoxus, and Coelurus fragilis. 
Maniraptora is poorly supported in the analysis (GC 5).
The monophyly of Paraves is poorly supported (GC 3) in part because of the placement of Epidexipteryx at the base of the clade. Analyses excluding Epidexipteryx find less contradictory data for the clade (GC 54).
On the other hand:
Within Avialae, basal nodes show extremely high support (GC values between 92 and 75) with little contradictory data present. 
Using raw frequencies is not recommended because there are cases in which groups lacking support have a frequency of 0.5 (Goloboff et al., 2003). GC frequencies are preferable because they reflect the balance between the amount of evidence that corroborates a given clade with the amount that falsifies that group.

Here are the GC values for the 4 groups we are looking at:
See Figures 66 and 67.

Maniraptoriformes 2
Maniraptora: 5
Oviraptorosauria and Paraves: 0? 
Paraves: 3

Analysis of the Turner et al study:
The exceptionally low values for Maniraptoriformes (2) and for Maniraptora (5) show that there is a break at that point. Anything beyond that is not attached to Coelurosauria.


For reference on GC:
http://www.ctoz.nl/cgi/t/text/text-idx?c=ctz;sid=f00ad86e4a09afab87790276f0f94154;idno=m7903a02;view=text;rgn=div2;cc=ctz;node=m7903a02%3A3.4
The difference in frequencies GC was chosen because it is calculated as the difference between the frequency in which a given group is retrieved in the jackknife replicates and the most frequent contradictory group (Goloboff et al., 2003). Absolute frequencies (the usual method of counting frequencies in jackknife or bootstrap analysis) do not distinguish between a group with a frequency of 0.6 that is never contradicted, and a group with a frequency of 0.6 that is contradicted with a frequency of 0.4. GC frequencies distinguish these two cases, giving lower support values to the second type of groups (Goloboff et al., 2003).
https://www.academia.edu/4605777/Behaviour_of_resampling_methods_under_different_weighting_schemes_measures_and_variable_resampling_strengths
Golobo et al. (2003a) proposed that what actually measures the support is not the absolute frequency (F), but the dierence in frequency between a group and its most frequent contradictory group (GC, for ‘‘group present   ⁄   contradicted’’). GC values of  -1, 0 and 1indicate maximum contradiction, indierence, and max-imum support, respectively. GC is useful to measure strength of contradiction and to obtain support values for groups with positive but low support, which are otherwise not reported by methods using absolute frequencies (real groups with frequencies below 50% that are not retained in the majority consensus tree).


Cau et al

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4476167/
The phylogenetic affinities of the bizarre Late Cretaceous Romanian theropod Balaur bondoc (Dinosauria, Maniraptora): dromaeosaurid or flightless bird? (2015)
Andrea Cau,1 Tom Brougham,#2 and Darren Naish#2
Note that Coelurosauria and the derived clades have exceptionally low values.

Figure 5: Updated dataset of Brusatte et al. (2014).

Updated dataset of Brusatte et al. (2014).



Figure 6: Updated dataset of Lee et al. (2014).


Updated dataset of Lee et al. (2014).




https://projecteuclid.org/euclid.ss/1063994980
http://projecteuclid.org/download/pdf_1/euclid.ss/1063994980
Pamela Soltis
bootstrap values are low because of the small number of characters supporting each node

Dinosaur to bird theorists claim that their purported dinosaur to bird lineage is the only solution available (given the data and the analytical method).
But that is not correct.
See:
http://www.bio.fsu.edu/James/Ornithological%20Monographs%202009.pdf

AND of course the other possibility is that birds evolved from pterosaurs which is the idea being presented in this site.

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

Abnormally rapid period of morphological evolution 

Not only do the support indices indicate a problem, the dino to bird theory also requires a completely implausible rate of evolution. This is because there is a significant gap between paravians and non-paravians.

http://www.cell.com/current-biology/abstract/S0960-9822(14)01047-1
http://www.cell.com/current-biology/fulltext/S0960-9822(14)01047-1
Stephen Brusatte et al
Gradual Assembly of Avian Body Plan Culminated in Rapid Rates of Evolution across the Dinosaur-Bird Transition

recent studies converge in identifying the dinosaur-bird transition as an abnormally rapid period of morphological evolution. 
Birds evolved significantly faster than other theropods, but they are indistinguishable from their closest relatives in morphospace.
The initial results of the branch (Dryad Fig. S4-13) and clade (Fig. S3; Dryad Fig. S14-23) tests strongly support significantly high rates in Avialae, and to a lesser degree Tyrannosauroidea.
Other clades show significantly low or non-significant rates, with the exception of two smaller clades: Graciliraptor + Microraptor + Shanag + Sinornithosaurus + Tianyuraptor (within Dromaeosauridae), and Anchiornis + Aurornis + Eosinopteryx + Xiaotingia (within Troodontidae), which frequently show high rates. 
This provides robust evidence that birds (and their stem lineage) evolved faster than other theropods and that their origin was associated with an “early burst” of rapid morphological evolution. Previous studies have found significant changes in body size and limb morphology either progressively prior to the origin of birds or within more derived birds [356192022], but our analysis of the overall phenotype puts the major rate shift at the origin of Avialae itself.

https://www.scientificamerican.com/article/how-dinosaurs-shrank-and-became-birds/
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] 
Xu, X.; Zhang, F. (2005). "A new maniraptoran dinosaur from China with long feathers on the metatarsus". Naturwissenschaften92 (4): 173–177. Bibcode:2005NW.....92..173Xdoi:10.1007/s00114-004-0604-yPMID 15685441.

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.

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


http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.915.8222&rep=rep1&type=pdf
http://science.sciencemag.org/content/sci/suppl/2014/07/30/345.6196.562.DC1/1252243.Lee.SM.revision1.pdf
Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds
Michael S. Y. Lee,1,2* Andrea Cau,3,4 Darren Naish,5 Gareth J. Dyke5,6
Although there is no overall theropod-wide trend (fig. S7 and SM, part D), there is an exceptional trend within the single lineage that comprises much of the avian stem.
Our study quantifies rates of evolutionary innovation in dinosaurs using 1549 (data set 1) and 421 (data set 2) skeletal and other anatomical traits distributed across the entire body. A clear pattern emerges: Branches along the bird stem undergo substantially faster morphological evolution than those of the rest of the tree. 
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.






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Ghost lineages

As if this is not bad enough this assumes millions of years of ghost lineages!
On the other hand:
https://en.wikipedia.org/wiki/Ornithomimosauria
Gregory S. Paul has proposed that Ornithomimosauria might be a group of primitive, flightless birds, more advanced than Deinonychosauria and Oviraptorosauria.[15]

(Source)



Notice the ghost lineages:
https://www.researchgate.net/publication/269715801_An_integrative_approach_to_understanding_bird_origins

Image result for coelurosaur maniraptoriformes maniraptora cladogram ghost lineage stratigraphic