Thursday, August 17, 2017

Incubation Period

New research suggests that dinosaur eggs were more similar to reptiles rather than their descendants, birds.
Scientists have long believed that dinosaur egg incubation periods would be similar to that of birds, roughly between 11 to 85 days. This would be proportional to the size of the eggs (the larger an egg, the slower the incubation period). However, research from the University of Calgary, Florida State University and the American Museum of Natural History suggests that this wasn't the case at all. 

http://www.pnas.org/content/114/3/540.full

Dinosaur incubation periods directly determined from growth-line counts in embryonic teeth show reptilian-grade development
Little is known regarding nonavian dinosaur embryology. Embryological period relates to myriad aspects of development, life history, and evolution. In reptiles incubation is slow, whereas in birds it is remarkably rapid. Because birds are living dinosaurs, rapid incubation has been assumed for all dinosaurs. We discovered daily forming growth lines in teeth of embryonic nonavian dinosaurs revealing incubation times. These lines show slow reptilian-grade development spanning months. The rapid avian condition likely evolved within birds prior to the Cretaceous–Paleogene (K–Pg) mass extinction event. 

Sunday, July 23, 2017

The digits transition

I am working with the following hypothesis of the transition of fingers and phalanges:
     I   II   III   IV  V
P-2-3-4-5-x Pterosaur
x-2-3-4-x-x Basal Paraves 
x-1-2-1-x-x Modern bird

P = pteroid. Numbers represent the number of phalanges. For example, this shows 5 phalanges in the fourth finger (IV) of pterosaur. Roman numerals represent fingers (digits). 

Summary of Changes:
The first step occurred in pterosaur with the loss of the fifth finger (V).
Then in the transition to basal paraves:
The pteroid was lost. (It is a prepollex).
The fourth finger (IV) was progressively shortened and finally lost 

This transition (from pterosaur digits to the digits of a creature like Scansoriopteryx) is consistent with all the known evidence. It is not contrary to any known evidence.

The set of changes I am proposing is similar to that descibed in the hexadactyl origin hypothesis (HOH).

HOH

https://vargaslab.files.wordpress.com/2009/03/vargasfallon2005b3.pdf
The early pantetrapod Devonian ancestors of
birds were polydactylous, with up to eight fingers
on both forelimbs and hindlimbs (Clack, 2002). In
the embryos of several modern tetrapods, it is
possible to observe the presence of mesenchymal
condensations other than those of digits 1-5 that
may represent vestiges of the additional digits of
early pan-tetrapods. A mesenchymal condensation
in front of digit 1 is called a prepollex
, and a
mesenchymal condensation found posterior to
digit 5 is called a postminimus.
Although only three digits develop in the wing of
the chicken, recent work on the expression of the
Sox9 gene allowing the visualization of mesenchymal
condensations has revealed that six mesenchymal
condensations can be found in the
developing wing that can be compared to digital
condensations (Welten et al., 2005). Remarkably,
it is possible to interpret these condensations as
consistent with the proposal that the anteriormost
condensation may be a prepollex the following
three digital condensations are digits 1, 2 and 3,
the next condensation is a vestige of digit 4, and
the posteriormost condensation (named ''element
X'' by Welten et al., 2005) can be assumed to be a
vestige of digit 5
In fact, there is no evidence of phalangeal initiation of any kind in the
brief Sox9-expressing region anterior to the first digit in the wing. It remains plausible that this is a prepollex
The prepollex has no phalanges just like the pteroid which has no phalanges!

Good reference:
http://dml.cmnh.org/2005Dec/msg00213.html


With the influence of SOCS2 there can be a graduated reduction of digit IV in the transition to basal Paraves:

SOCS2
https://www.academia.edu/1486957/Transcriptomic_analysis_of_avian_digits_reveals_conserved_and_derived_digit_identities_in_birds
To discover genes that specifically contribute to the second and third wing digit identities, we performed differential expression analysis of the mRNA-seq data between samples LFb and LFc. We found two genes, Tbx3 and Socs2, with high expression in sample LFc (Supplementary Fig. 9 and Fig. 3a). To our knowledge no studies have been published indicating a role for Socs2 in limb development. ISH confirms its strong expression in the third forelimb digit to the exclusion of all other digits in forelimb and hindlimb(Fig.3b-g). Recently it has been shown that the third forelimb digit has a unique mode of development in birds8. This, combined with our gene expression survey,supports the idea that the third wing digit has a unique derived identity in birds.
https://www.ncbi.nlm.nih.gov/pubmed/16419040
Suppressor of cytokine signaling (SOCS)-2 regulates normal postnatal growth and its deficiency in mice causes gigantism with increased bone length and proportional enlargement in skeletal muscles.
http://www.jci.org/articles/view/22710
SOCS2 negatively regulates growth hormone action in vitro and in vivoMice deficient in SOCS2 display an excessive growth phenotype characterized by a 30-50% increase in mature body size. Here we show that the SOCS2-/- phenotype is dependent upon the presence of endogenous growth hormone (GH) and that treatment with exogenous GH induced excessive growth in mice lacking both endogenous GH and SOCS2. This was reflected in terms of overall body weight, body and bone lengths, and the weight of internal organs and tissues.
http://www.tmd.ac.jp/artsci/biol/textbiodiv/17EvoDev7-18.pdf
Welten et al
The bird wing is of special interest to students of homology and avian evolution. Fossil and developmental data give conflicting indications of digit homology if a pentadactyl "archetype" is assumed. Morphological signs of a vestigial digit I are seen in bird embryos, but no digit-like structure develops in wild-type embryos. To examine the developmental mechanisms of digit loss, we studied the expression of the high-mobility group box containing Sox9 gene, and bone morphogenetic protein receptor 1b (bmpR-1b)-markers for precondensation and prechondrogenic cells, respectively. We find an elongated domain of Sox9 expression, but no bmpR-1b expression, anterior to digit II. We interpret this as a digit I domain that reaches precondensation, but not condensation or precartilage stages. It develops late, when the tissue in which it is lodged is being remodeled. We consider these findings in the light of previous Hoxd-11 misexpression studies. Together, they suggest that there is a digit I vestige in the wing that can be rescued and undergo development if posterior patterning cues are enhanced

https://pterosaurheresies.wordpress.com/2013/12/11/is-the-prepollex-radial-sesamoid-analogous-to-the-pteroid/





ALTERNATIVES

PROGENESIS
https://www.researchgate.net/profile/Tony_Thulborn/publication/43456034_Theropod_dinosaurs_progenesis_and_birds_Homology_of_digits_in_the_manus/links/567631d208ae0ad265c0e321.pdf
For instance, it is predictable that the loss of digit I from the manus should be simultaneous with loss of a single phalanx from one or more of the three remaining digits: as those losses are attributed to a single cause, the depletion of mesenehyme in the limb bud, they should not occur sequentially.  

THUMBS DOWN
https://www.researchgate.net/publication/259253962_Thumbs_Down_A_MolecularMorphogenetic_Approach_to_Avian_Digit_Homology
We argue that limb bud cells that would normally form the digit II condensation proliferate toward a more anterior direction, into the space made physically available by the loss of digit I. This causes the presumptive digit II to leave the Shh activity zone. At the same time its cells do not express hoxD12 (and other posterior digit markers) any more, and therefore its transcriptome becomes characteristic of digit I.
Its phalangeal number is reduced--whether due to weaker anterior FGF8 signaling, caused by lower Shh levels that would otherwise stabilize the expression, or because of different hox and downstream gene expression.
Experiments with molecular signaling pathways in early limb development have shown that  modulating interdigital bmp signaling (Dahn and Fallon, 2000) or blocking bmp with a dominant negative receptor (Zou and Niswander, '96) is able to remove one phalanx from each digit
A comparison of digits within each limb shows that the posterior forelimb digits are more strongly differentiated than the posterior hindlimb digits, and forelimb digit III exhibits a unique expression of Socs2. 
References
https://frontiersinzoology.biomedcentral.com/articles/10.1186/1742-9994-11-33

https://www.researchgate.net/publication/259253962_Thumbs_Down_A_MolecularMorphogenetic_Approach_to_Avian_Digit_Homology

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986427/

https://www.researchgate.net/publication/301913740_FANTASY_REALITY_A_Critique_of_Smith_'s_Bird_Origins

https://www.academia.edu/11078361/Pentadactyl_pattern_of_the_avian_wing_autopodium_and_pyramid_reduction_hypothesis

https://www.academia.edu/1486957/Transcriptomic_analysis_of_avian_digits_reveals_conserved_and_derived_digit_identities_in_birds

http://dml.cmnh.org/2000Dec/msg00446.html
Larry Febo

https://vargaslab.files.wordpress.com/2009/03/vargasfallon2005b3.pdf

https://pdfs.semanticscholar.org/c41f/be4e5fdc9b95780eefb7c396351290e43b23.pdf

https://www.academia.edu/13081883/Pentadactyl_ground_state_of_the_avian_wing

http://www.ivpp.ac.cn/qt/papers/201403/P020140314320497349455.pdf
Xu and Mackem

http://people.eku.edu/ritchisong/554notes1.html




Also see:
https://pterosaurnet.blogspot.ca/2014/07/pterosaur-fingers.html

Wednesday, June 7, 2017

More evidence against the dinosaur to bird theory that needs to be explained away.

http://rsbl.royalsocietypublishing.org/content/13/6/20170092
Tyrannosauroid integument reveals conflicting patterns of gigantism and feather evolution
Phil R. Bell, Nicolás E. Campione, W. Scott Persons, Philip J. Currie, Peter L. Larson, Darren H. Tanke, Robert T. Bakker
.
Abstract
Recent evidence for feathers in theropods has led to speculations that the largest tyrannosaurids, including Tyrannosaurus rex, were extensively feathered. We describe fossil integument from Tyrannosaurus and other tyrannosaurids (Albertosaurus, Daspletosaurus, Gorgosaurus and Tarbosaurus), confirming that these large-bodied forms possessed scaly, reptilian-like skin. Body size evolution in tyrannosauroids reveals two independent occurrences of gigantism; specifically, the large sizes in Yutyrannus and tyrannosaurids were independently derived. These new findings demonstrate that extensive feather coverings observed in some early tyrannosauroids were lost by the Albian, basal to Tyrannosauridae. This loss is unrelated to palaeoclimate but possibly tied to the evolution of gigantism, although other mechanisms exist.
In fact, the early tyrannosauroids did not have feathers either.


http://www.dinosaur-museum.org/featheredinosaurs/Are_Birds_Really_Dinosaurs.pdf
 

With the benefit of hindsight it is easy to see that if fossils of the small flying dromaeosaurs from China had only been discovered before the larger flightless dromaeosaurs like Deinonychus or Velociraptor were found, the interpretations of the past three decades on how birds are related to dinosaurs would have been significantly different. If it had already been established that dromaeosaurs were birds that could fly, then the most logical interpretation of larger flightless dromaeosaurs found afterwards would have to be that they represented birds, basically like the prehistoric equivalent of an Ostrich, which had lost their ability to fly. 

Friday, May 26, 2017

Following the logic

Cladograms which are based on bootstrap/jackknife, show that there is a large polytomy at the base of the coelurosaur clade. This is because the hypothesized nodes (Maniraptoriformes, Maniraptora, Pennaraptora) are not supported and have been collapsed. The result is a much more correct picture of the taxa involved.

Xu et al
http://www.ivpp.cas.cn/qt/papers/201403/P020140314389417822583.pdf
See Figure S9


AND

Brusatte et al
http://www.cell.com/cms/attachment/2019474733/2039573094/mmc1.pdf


This means (to take one example) that we cannot tell what the relationship is between oviraptorids and Paraves from the cladistic analysis. The two possibilities are that creatures similar to oviraptorids were transitional between dinosaurs and Paraves OR that oviraptorids were secondarily flightless members of  Paraves. It is important to note that the cladistic analyses cannot tell us which one is more credible.
Consequently we have to look for other indicators as to which is more credible.

We can immediately see that the alternative that oviraptorids were secondarily flightless members of Paraves means that we do not need to postulate ghost lineages. Also we do not need to postulate the pre-adaptations that are required by the idea that creatures similar to oviraptorids were transitional between dinosaurs and basal Paraves.

The same applies to ornithomimosaurs and alvarezsaurids.

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

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://datadryad.org/resource/doi:10.5061/dryad.84t75
BrusatteetalRevisionDryadFile2.pdf (13.57 Mb)
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. The “wildcard” nature of these five taxa is largely due to enormous amounts of missing data—each taxon can only be scored for a small fraction of the 853 characters in the analysis 

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.





Also see Figure 7 in:
http://www.bio.fsu.edu/James/Ornithological%20Monographs%202009.pdf



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).
https://en.wikipedia.org/wiki/Computational_phylogenetics#Bootstrapping_and_Jackknifing
The statistical rigor of the bootstrap test has been empirically evaluated using viral populations with known evolutionary histories,[35] finding that 70% bootstrap support corresponds to a 95% probability that the clade exists. However, this was tested under ideal conditions (e.g. no change in evolutionary rates, symmetric phylogenies). In practice, values above 70% are generally supported and left to the researcher or reader to evaluate confidence. Nodes with support lower than 70% are typically considered unresolved.
https://academic.oup.com/sysbio/article-abstract/42/2/182/1730933/An-Empirical-Test-of-Bootstrapping-as-a-Method-for?redirectedFrom=fulltext

Specifically, under conditions of equal rates of change, symmetric phylogenies, and internodal change of ≤20% of the characters, bootstrap proportions of ≥70% usually correspond to a probability of ≥95% that the corresponding clade is real. However, under conditions of very high rates of internodal change (approaching randomization of the characters among taxa) or highly unequal rates of change among taxa, bootstrap proportions >50% are overestimates of accuracy.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1924872/
The results show that there are strong correlations between clade confidence and the probability that a clade is valid for Bayesian posterior probabilities and for Maximum Likelihood bootstrap percentages and weaker correlations for Maximum Likelihood aLRT values.

CONTRARY

http://www.sciencedirect.com/science/article/pii/S1532046405001322
Numerous metrics have been developed that attempt to assess the reliability of phylogenetic trees. Several of these commonly used measures of tree and tree branch support are described and discussed in the context of their relationship to Popperian corroboration. Claims that measures of support indicate the accuracy of phylogenetic trees or provide information for tree choice are rebutted. Measures of support are viewed as being of heuristic value within a given phylogenetic framework for describing the precision of the data based on perturbations to the data. However, no direct link is observed between the calculation of measures of support and corroboration. Direct measures of support, but not re-sampling or randomization methods, may play a more specific role in phylogenetic inference by providing the tools to search for falsifiers that could be the subject of future rounds of hypothesis testing.
In this contribution we use the terms‘‘real’’for those groups present in the strict consensus of the unaltered data set, and‘‘spurious’’ for the opposite situation.

Brusatte et al bootstrap (from TNT):