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.
https://www.nature.com/articles/ncomms14972 (2017)
Most significantly, the taxon has the earliest known asymmetrical troodontid feathers, suggesting that feather asymmetry was ancestral to Paraves.

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]

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).

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)
The great similarity that exists among basal paravians, basal oviraptorosaurs, and Epidexipteryx 

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 The condition present in Zhongornis resembles that seen in scansoriopterygids (Epidendrosaurus, Epidexipteryx) and basal oviraptorosaurs (Caudipteryx), which also have proportionately short tails compared to basal paravians

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.


Gregory Paul
https://books.google.ca/books?id=OUwXzD3iihAC&pg=PA252&lpg=PA252&dq=Oviraptorosauria+exaptation&source=bl&ots=H2Af0-ZfpR&sig=Z4NANr-dJbukOeiT_jnTL9Jya3g&hl=en&sa=X&ved=0ahUKEwj9-oGNwNbTAhUL2IMKHed9BngQ6AEIKTAB#v=onepage&q=Oviraptorosauria%20exaptation&f=false


http://evolutionwiki.org/wiki/Velociraptor_a_Mesozoic_kiwi%3F_A_look_at_the_neoflightless_hypothesis
The past two decades have witnessed the collapse of every single classical autapomorphy (or “holodiagnostic” to use Charig’s term) of Aves, from furculae, to feathers. Accordingly, distinguishing a par-avian theropod from a bona fide bird, is increasingly a matter of subjectivity. Add into this mess the argument that taxa traditionally classified as lying outside Aves are in fact neoflightless forms closer to Neornithes than is Archaeopteryx, and you have enough to drive the prospective student of avian phylogenetics to despair.

http://www.ivpp.cas.cn/qt/papers/201403/P020140314389417822583.pdf
In order to test previous suggestions that oviraptorosaurs might be basal avialans, we ran two additional analyses. The first of these analyses was constrained to produce a monophyletic group comprising all oviraptorosaurian and non-archaeopterygid avialan species, whereas the second was constrained to produce a monophyletic group comprising all oviraptorosaurian and avialan including archaeopterygid species. The first analysis resulted in 1096 most parsimonious trees, each having a length of 1410 steps. Figure S10 shows the strict consensus of the 1096 trees. The second analysis resulted in 216 most parsimonious trees, each having a length of 1413 steps. Figure S11 shows the strict consensus of the 216 trees. These analyses indicate that the hypotheses that recover an Oviraptorosauria-Avialae clade are considerably less parsimonious than the hypothesis shown in Figure 6. However, one reason that the Oviraptorosauria-Avialae hypotheses are worse supported by our dataset might be the large amount of missing data from the palates and braincases of the basal oviraptorosaurs and basal avialans, regions that represent important sources for oviraptorosaurian synapomorphies. 
In oviraptorosaurs and basal avialans the supraacetabular crest is absent.

https://www.geol.umd.edu/~tholtz/G104/lectures/104coelur.html
The remaining maniraptorans form the clade Pennaraptora ("feathered raptors"). These comprise the oviraptorosaurs, the scansoriopterygids, and the eumaniraptorans. These groups are united by several important characteristics:
  • Another increase of brain size
  • Laterally directed shoulder joint
  • Honest-to-goodness pennaceous feathers on at least the arms and tail (their presence on arms at least are documented further down the tree, at least shared with ornithomimosaurs)
  • Brooding on nests of eggs (may have been present in more basal coelurosaurs)

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