Wednesday, April 26, 2017

Secondarily flightless paravians

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4476167/#supplemental-informationtitle (2015)
Cau et al
Furthermore, phylogenetic analyses that incorporate sufficient character data are able to differentiate the members of such paravian lineages as Dromaeosauridae, Troodontidae and Avialae, as demonstrated by our present study. Nevertheless, reinterpretation of Balaur as a flightless avialan reinforces the point that at least some Mesozoic paravian taxa, highly similar in general form and appearance to dromaeosaurids, may indeed be the enlarged, terrestrialised descendants of smaller, flighted ancestors, and that the evolutionary transition involved may have required relatively little in the way of morphological or trophic transformation.

http://science.sciencemag.org/content/317/5843/1378.full (2007)
A Basal Dromaeosaurid and Size Evolution Preceding Avian Flight
Alan H. Turner
1,*, Diego Pol2, Julia A. Clarke3,4,1, Gregory M. Erickson5, Mark A. Norell1
Fossil evidence for changes in dinosaurs near the lineage leading to birds and the origin of flight has been sparse. A dinosaur from Mongolia [Mahakala] represents the basal divergence within Dromaeosauridae. The taxon's small body size and phylogenetic position imply that extreme miniaturization was ancestral for Paraves (the clade including Avialae, Troodontidae, and Dromaeosauridae), phylogenetically earlier than where flight evolution is strongly inferred. In contrast to the sustained small body sizes among avialans throughout the Cretaceous Period, the two dinosaurian lineages most closely related to birds, dromaeosaurids and troodontids, underwent four independent events of gigantism, and in some lineages size increased by nearly three orders of magnitude.  
So there is evidence of secondarily flightless paravians.
Let us now tie this with the issue of the statistically poorly supported core nodes. (See earlier posts).
Let's look at Pennaraptora. Pennaraptora is particularly poorly supported. Consequently Oviraptors may not be related to Paraves as sister taxa as commonly presented. Instead, Oviraptorids (that are dated 10's of millions of years later than basal Paraves) may well be secondarily flightless members of Paraves. And in fact that idea has been proposed over the years.

https://en.wikipedia.org/wiki/Caudipteryx#Implications
Halszka Osmólska et al. (2004) ran a cladistic analysis that came to a different conclusion. They found that the most birdlike features of oviraptorids actually place the whole clade within Aves itself, meaning that Caudipteryx is both an oviraptorid and a bird. In their analysis, birds evolved from more primitive theropods, and one lineage of birds became flightless, re-evolved some primitive features, and gave rise to the oviraptorids. This analysis was persuasive enough to be included in paleontological textbooks like Benton's Vertebrate Paleontology (2005).[11] The view that Caudipteryx was secondarily flightless is also preferred by Gregory S. Paul,[12]  et al.,[13] and Maryańska et al.[14]


There is a huge gap between Oviraptorids and basal Paraves. The jacknife/bootstrap for Pennaraptora confirms this.
But how can oviraptorids be secondarily flightless members of Paraves when they are so different than Paraves? One answer is that oviraptorids may be quite different than BASAL Paraves but not so different than very derived Paraves (eg Avialans/Avians).
The evidence all points to Oviraptorids being secondarily flightless members of derived Paraves. And of course, a few established researchers had already come to that conclusion.
The same logic applies to Ornithomimosaurs (as being secondarily flightless members of derived Paraves) which is confirmed by the fact that Maniraptoriformes is poorly supported.

http://www.bio.fsu.edu/James/Ornithological%20Monographs%202009.pdf
Paul (2002) has argued that the reason some maniraptoran taxa possess so many derived avian apomorphies is that they are, in fact, secondarily flightless birds that are more derived than basal avian taxa like Archaeopteryx. Although Paul (2002) retained a theropod ancestry for birds, support for his hypothesis would clearly complicate the consensus BMT view. A few cladistic analyses have retrieved Alvarezsauridae (e.g., Perle et al. 1993, 1994; Chiappe et al. 1998) and Oviraptorosauria (Lü et al. 2002, Marya´nska et al. 2002) as birds more derived than Archaeopteryx, and other noncladistic studies have proposed avian status for various oviraptorosaur (Elzanowski 1999, Lü et al. 2005) and dromaeosaur taxa (Czerkas et al. 2002, Burnham 2007). These studies have provided support for elements of Paul’s (2002) hypothesis.
https://en.wikipedia.org/wiki/Oviraptorosauria#Relationship_to_birds
Oviraptorosaurs, like deinonychosaurs, are so bird-like that several scientists consider them to be true birds, more advanced than ArchaeopteryxGregory S. Paul has written extensively on this possibility, and Teresa Maryańska and colleagues published a technical paper detailing this idea in 2002.[5][16][17]Michael Benton, in his widely respected text Vertebrate Paleontology, also included oviraptorosaurs as an order within the class Aves.[18] However, a number of researchers have disagreed with this classification, retaining oviraptorosaurs as non-avialan maniraptorans slightly more primitive than the deinonychosaurs.[19]

http://www.app.pan.pl/archive/published/app47/app47-097.pdf
Avialan status for Oviraptorosauria
TERESA MARYAŃSKA, HALSZKA OSMÓLSKA, and MIECZYSŁAW WOLSAN
This analysis places Oviraptorosauria within Avialae, in a sister−group relationship with Confuciusornis. Oviraptorosaurs are hypothesized to be secondarily flightless. 
The status of oviraptorosaurs as secondarily flightless birds, more advanced than is Archaeopteryx, has already been suggested (Paul 1988; Olshevsky 1991; Elżanowski 1999; Lü 2000)

http://theropoddatabase.blogspot.ca/2016/04/database-update-plus-predatory.html
Paul's phylogeny from his influential book.
You can see the saltation from Tyrannoraptora to Paraves.


https://www.researchgate.net/profile/Peter_Makovicky/publication/274270291_A_Review_of_Dromaeosaurid_Systematics_and_Paravian_Phylogeny/links/576d7b6708ae621947424576.pdf
A REVIEW OF DROMAEOSAURID SYSTEMATICS AND PARAVIAN PHYLOGENY ALAN H. TURNER et al
Constraining Epidexipteryx as a basal oviraptorosaur requires only one additional step in our dataset (fig. 75)
https://bio.unc.edu/files/2011/04/FeducciaCzerkas2015.pdf  (2015)
Testing the neoflightless hypothesis: propatagium reveals flying ancestry of oviraptorosaurs 
Alan Feduccia1 • Stephen A. Czerkas2
The presence of numerous flight features reveal that Caudipteryx, like the extant flightless ratites, originated from volant ancestors (de Beer 1956; Feduccia 2012, 2013), most likely via the evolutionary process of heterochrony, specifically paedomorphosis (arrested development), by which the adult retains the morphology of a younger stage of development (Livesey 1995).

(O'Connor and Sullivan 2014)
Reinterpretation of the Early Cretaceous maniraptoran (Dinosauria: Theropoda) Zhongornis haoae as a scansoriopterygid-like non-avian, and morphological resemblances between scansoriopterygids and basal oviraptorosaurs 

https://www.google.ca/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwjU_ujD5crTAhWa3oMKHUKrD4AQFggpMAA&url=http%3A%2F%2Fagro.icm.edu.pl%2Fagro%2Felement%2Fbwmeta1.element.agro-article-f0207f80-7285-42b0-a431-2ef5fa0d0c1b%2Fc%2Fapp50-101.pdf&usg=AFQjCNFNsUhAlBSjTbQ56gadn7tXHtdmuw&sig2=3boXRPl-fvXrXf6GDDZX6w
Dyke G J, Norell M A, 2005. Caudipteryx as a non-avialan theropod rather than a flightless bird. Acta Palaeont Pol, 50(1): 101–116
There is no reason—phylogenetic, morphometric or otherwise—to conclude that Caudipteryx is anything other than a small non−avialan theropod dinosaur.
NOTE:
"Non-avian theropod" could still be a member of Paraves.
Oviraptors were either secondarily flightless avialae or secondarily flightless non-avialae paraves.
They descended from flying ancestors. They are not transitional between dinosaurs and paraves.

Thursday, April 20, 2017

"An abnormally rapid period of morphological evolution"

We have seen that the statistical support values do not support the dinosaur to bird hypothesis. See earlier posts.
Consequently we are justified in looking at the dinosaur to bird hypothesis much more critically and to re-assess the explanations that have been given. For example, the "explanation" that the evolution rate was abnormally rapid.

http://www.cell.com/current-biology/fulltext/S0960-9822(14)01047-1
Stephen Brusatte et al
[R]ecent studies converge in identifying the dinosaur-bird transition as 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)

http://www.bris.ac.uk/news/2014/february/origin-of-birds.html
"We were really surprised to discover that the key size shifts [body size and forelimb length] 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."                     
As the quotes above show, basal paravians are very different than non-paravian theropods. The researchers who believe they are related, explain this as an "abnormally rapid period of morphological evolution". Of course that is not an explanation. It is an acknowledgement that they have no explanation.


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
Our results demonstrate that the rise of birds was a complex process: birds are a continuum of millions of years of theropod evolution, and there was no great jump between nonbirds and birds in morphospace, but once the avian body plan was gradually assembled, birds experienced an early burst of rapid anatomical evolution. 
Although birds are clearly distinct compared to all other living vertebrates, the avian bauplan isn’t especially distinct relative to other coelurosaurs, particularly their closest relatives.
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.

http://science.sciencemag.org/content/317/5843/1378.full
The taxon's small body size and phylogenetic position imply that extreme miniaturization was ancestral for Paraves (the clade including Avialae, Troodontidae, and Dromaeosauridae), phylogenetically earlier than where flight evolution is strongly inferred. In contrast to the sustained small body sizes among avialans throughout the Cretaceous Period, the two dinosaurian lineages most closely related to birds, dromaeosaurids and troodontids, underwent four independent events of gigantism, and in some lineages size increased by nearly three orders of magnitude.

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.