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


Tuesday, January 17, 2017

Support Indices

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

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

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

Stephen L. Brusatte, Graeme T. Lloyd, Steve C. Wang, and Mark A. Norell 
This clade—Maniraptoriformes—is only poorly supported (Bremer support of 1 and jackknife percentage of less than 50%), and relationships at its base are unresolved. There is a basal polytomy consisting of four clades: Ornitholestes, Compsognathidae, Ornithomimosauria, and Maniraptora (i.e., the clade of all taxa more closely related to birds than to Ornithomimus: [S52]). 
Maniraptora—the clade defined as all taxa closer to birds than to Ornithomimus—is comprised in the present study of Alvarezsauroidea, Therizinosauroidea, Oviraptorosauria, and Paraves. This clade is supported by a Bremer value of 2 but a jackknife percentage of less than 50%.
The clade consisting of Oviraptorosauria and Paraves is supported by a Bremer value of 1 and a jackknife percentage of less than 50%
Paraves—consisting of dromaeosaurids, troodontids, and avialans—is also poorly supported, as it also has a Bremer value of 1 and a jackknife of less than 50%.
The scansoriopterygid + oviraptorosaur clade is poorly supported (Bremer support of 1, jackknife percentage of less than 50%).  
Both Bremer supports and jackknife percentages (absolute values) were calculated in TNT using standard scripts. The jackknife was run using the default parameter of 36% character removal probability and 1000 replicates.

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



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

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

http://peter.unmack.net/molecular/programs/tnt.bootstrapping.html
This provides minimal instructions for running a bootstrap analysis.
https://www.geol.umd.edu/~tholtz/G331/lectures/cladistics5.pdf
Figure 4 shows the relevant screen where you can set how many replications you would like (I would recommend no fewer than 1000), what kind of tree search you want (Heuristic and Branch & Bound are the only options) and what set level of the majority rule consensus tree you want (you would normally leave this at 50%).
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4476167/
The phylogenetic affinities of the bizarre Late Cretaceous Romanian theropod Balaur bondoc (Dinosauria, Maniraptora): dromaeosaurid or flightless bird?
Andrea Cau,1 Tom Brougham,#2 and Darren Naish#2
The modified  analysis recovered 1,152 shortest trees of 6,350 steps each (CI = 0.2672, RI = 0.5993). The strict consensus of the shortest trees found is in general agreement with the Maximum Clade Credibility Tree recovered by , the most relevant difference being the unresolved polytomy among AurornisJinfengopteryx, Dromaeosauridae, Troodontidae and Avialae (Fig. 6). The a posteriori pruning of the above mentioned genera does not resolve the polytomy among the three suprageneric clades. It is noteworthy that an unresolved polytomy among the main paravian lineages was also obtained by , and by our updated version of the latter dataset.


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

https://www.researchgate.net/post/How_can_I_interpret_bootstrap_values_on_phylogenetic_trees_built_with_Maximum_Likelihood_method
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 you 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. 

http://digitallibrary.amnh.org/handle/2246/6352
See Figures 66, 67, 68 (Bootstrap) and 69, 70, 71 (Bremer)

Saturday, January 14, 2017

Studies

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

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

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

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


Friday, January 13, 2017

Humerus

Again we see that Paraves are not like dinosaurs.

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

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

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

Friday, January 6, 2017

Beak

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

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


http://theropods.wikia.com/wiki/Scansoriopterygidae
Scansoriopterygidae dinosaurs were very small, bipedal dinosaurs, the size of sparrows and pigeons. They had also a few quite amazing features, such as a unusually long third finger on the hand, beaks, and very short tails with very long feathers at the end of it.

Fibula

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

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

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




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

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

fig. 34.


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

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

The reason why this happens though remains a bit of a mystery. Modern birds of different sizes and ecologies all show evidence of this fibula reduction. This suggests that it is what is called a ‘non-adaptive’ process, as it is highly unlikely that such a feature would play a part in such different roles.
 http://teachmeanatomy.info/lower-limb/bones/the-fibula
The fibula, along with the tibia, makes up the bones of the leg. The fibula is found laterally to the tibia, and is much thinner. As it does not articulate with the femur at the knee joint, its main function is to act as an attachment for muscles, and not as a weight bearer.
So when the fibula is reduced it is no longer acts so much as an attachment for muscles.  

https://answersingenesis.org/dinosaurs/feathers/can-scientists-rewind-supposed-evolution-of-dinosaurs-to-birds/
Below your knee you don’t have a chicken-like drumstick. You have two leg bones: the thicker shinbone (the tibia) and the thinner fibula. The knobs on the sides of your ankle are the lower ends of these bones. These paired bones are a great design, and the hind legs of dinosaurs and of most other tetrapods are similarly equipped. Though the fibula is much thinner than the tibia and supports comparatively little weight even among those of us who walk on two legs, it serves an important role in stabilizing the ankle and providing leverage for the muscles attached below the knee.
But a bird’s lower limbs are designed differently. A bird’s knee and the thighbone above it are hidden up inside the bird’s body. This hidden part of the bird’s leg helps prevent abdominal air sacs from collapsing and helps it breathe. Because it walks with its hips and legs at different angles from biped humans and theropod dinosaurs, a bird doesn’t need the stability and leverage afforded by a full-length fibula and its attachments. The fibula on a chicken is very thin and so short it doesn’t even reach the ankle, leaving the bird to support its weight on its tibias.