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Paring Down the Data

March 19, 2010 15 comments

Awhile back, I brought up the issue of how to handle specimens with multiple individuals, as well as juvenile individuals, and a lively discussion ensued. The general conclusions were:

  1. Any ratios must be calculated for individual specimens, not from Frankensteinian averages of elements from different specimens. It is OK to average ratios across specimens, just not the raw measurements.
  2. Extremely young juveniles should be excluded, as they may differ in body proportions from adults of the same or closely related species.

With this in mind, I’ve started to go through the data set to flag obviously small juveniles. I would propose that we use body size rather than sexual maturity or LAGs as an indicator. Recent studies (e.g., this one on pachycephalosaurs by Horner and Goodwin) have shown that some near-adult size dinosaurs are probably not fully mature. I suggest that we assume that the limb proportions approximate those of adults sufficiently in these individuals (even if the skull morphology doesn’t). This will allow us to keep a few interesting taxa in. For instance, Fruitadens is not fully adult, but probably pretty close to it (according to histology; see the original paper). It’d be a shame to ignore the world’s smallest known ornithischian!

This is pretty straightforward for taxa known from only single specimens of obviously young juveniles (e.g., Avaceratops, Nipponosaurus, etc.). These taxa can be pretty safely removed.

What about animals like Stegosaurus armatus, where we have many specimens of various sizes, from tiny to gigantic? Here, I suggest cutting the specimens that are smaller than 2/3 the size of the largest specimen in one or more measurements (modifying a suggestion from William Miller). This 2/3 is a completely arbitrary cut-off, but I feel that it removes the smallest individuals while recognizing that indeterminate growth means adults can have a range of sizes.

As an example, the longest Stegosaurus femur, from YPM 1853, is 1,334 mm in length. Two-thirds of this is 889 mm, so any specimen with a femur smaller than this would be cut. This includes YPM 1856 (883 mm), DNM 2438 (308 mm), and many more. Of course, we can use our judgment for specimens close to the line. Because some specimens lack a femur, we would look at other elements (e.g., the humerus) to narrow the sample down more.

This elimination method will give us a rarefied data set, with the most egregious juveniles out of the picture. I suggest that we then use the average of the ratios from the trimmed sample for further analysis. In cases where we need actual bone lengths, I suggest using the largest specimen with sufficiently complete data necessary for the analysis.

For Everyone to Check
Following these criteria, I have posted a new Google spreadsheet here. It has two worksheets. The first, titled “To Analyze” (you can find the tabs along the bottom of the screen), has specimens that should be considered for removal marked with a greenish color. Do you agree? Disagree? See another specimen that should be removed? Let me know in the comments.

The second worksheet, titled “Deletion Candidates,” has specimens and taxa that I think should be excluded from the final analysis. The reasoning is given in the final column. Examples include, “can’t match with actual specimen” (for cases where it looks like derivative data given without citation that couldn’t be tied to a particular specimen), “non-diagnostic taxon of uncertain affinity” (should be obvious), etc. Once again, please check it over. Do you agree? Disagree? Say something in the comments here.

Categories: Uncategorized

Sauropelta Solved!

March 19, 2010 2 comments
Sauropelta

The ever-problematic Sauropelta, as restored by John Conway.

A nagging problem in our dataset has been the issue of the Sauropelta edwardsi specimen AMNH 3032. Its tibia seems way, way too short (even for ankylosaurs), and it’s thus a bizarro outlier.

So, I finally got my behind into gear to check out the problem. Was the measurement a typo? Was the tibia incompletely preserved? Was it from a smaller individual? On p. 115, I found the answer. The tibia for AMNH 3032 is here listed as 57.5 cm (575 mm) in length. This makes much, much more sense, so we’ll go with that number. Apparently, the value given in the table was simply an error. On further looking, I was able to confirm that the table heading for Sauropelta measurements on p. 120 was actually transposed with a Tenontosaurus table (as Rob Taylor had ably picked up on some time ago)! It looks like the measurements here are all from AMNH 3032, not YPM 5456 and 5459. Mystery (finally) totally solved, and the database is fixed!

It also turns out that the tabular error has been perpetuated across a few more publications. The Tenontosaurus-turned-Sauropelta YPM 5456 makes an appearance in Ford and Kirkland 2001 as well as Maidment et al. 2008. It in no way harms the conclusions of these papers (after all, the error is in the specimen number, not the measurements). But, I have removed all references for a YPM 5456 Sauropelta from our data tables.

References
Ford TL, Kirkland JI (2001) Carlsbad ankylosaur (Ornithischia, Ankylosauria): an ankylosaurid and not a nodosaurid. In: Carpenter K, editor. The Armored Dinosaurs. Bloomington: Indiana University Press. pp. 239–260.
Maidment SCR, Norman DB, Barrett PM, Upchurch P (2008) Systematics and phylogeny of Stegosauria (Dinosauria: Ornithischia). Journal of Systematic Palaeontology 6: 367-407.
Ostrom JH (1970) Stratigraphy and paleontology of the Cloverly Formation (Lower Cretaceous) of the Bighorn Basin area, Wyoming and Montana. Bulletin of the Peabody Museum of Natural History 35: 1–234.

Image Credit: Restoration by John Conway, from Wikimedia Commons. This file is licensed under the Creative Commons Attribution ShareAlike 3.0 License. In short: you are free to share and make derivative works of the file under the conditions that you appropriately attribute it, and that you distribute it only under a license identical to this one. Official license

Categories: Miscellaneous

Analytical Software

March 10, 2010 10 comments

As the past two posts have attested, we are on the cusp of doing some actual, real-life analysis. If at all possible, I want to run the analyses using freely available, open source software. Fortunately, all of the major software packages for phylogenetically-informed, quantitative analaysis are free! Here are the ones I’m looking at:

  • For constructing trees and some simple analyses: Mesquite. (all of the tree plots you’ve seen have been done in this program)
  • For general statistical analysis: R, along with the smatr, ape and ggplot2 packages. I will make a serious effort to post all scripts that are used to generate graphics and analyses; I would encourage all of you to do the same.
  • For additional analysis of quantitative data in a phylogenetic context: COMPARE.
Categories: Basics, Miscellaneous

By Popular Demand. . .

March 10, 2010 11 comments
Ceratopsia

Femur:Tibia Ratio in Marginocephalians, and Relevant Outgroups

As a follow-up to our last post on thyreophorans, here are marginocephalians (ceratopsians and pachycephalosaurs) with some of their outgroups. Moving or removing the uncertainly-placed Stenopelix has little effect on character reconstruction.

Categories: Data Exploration

Data Are Pretty

March 9, 2010 18 comments

Now that we’ve gotten a reasonable phylogeny hammered out, it’s time to start putting it to use! Just for fun, I used the (open source and free to download) program Mesquite to plot the femur:tibia ratio (as John Dziak had talked about not so long ago) as it changed from basal ornithischians up through Thyreophora, the clade including ankylosaurs and stegosaurs. The cladogram shown here only illustrates taxa for which we know the ratio, and species with multiple individuals had their data averaged.

Femur:Tibia Ratio

Femur:Tibia Ratio, With a Focus on Thyreophora. Larger values equal relatively long femora.

Note that everything up through and including Scutellosaurus is presumed to be bipedal; after that, they’re quadrupedal. There’s a rather major change! Rather than the tibia being longer than or approximately equal in length to the femur, the femur ends up much longer than the tibia (and Stegosaurus is just insane in this respect)! Now the interpretation of this isn’t as easy as you might think. Is it due to being quadrupedal? Or is it due to being a big animal? The bipedal guys are all small, and the quadrupedal guys are all relatively large, so it’s tough to separate these two factors. Either way, we can say something interesting about locomotor evolution! And, note that the branches between nodes are reconstructed, with a reasonably wide error bar. So, please don’t consider them absolute truth.

And while I’m thinking of it. . .why didn’t theropods ever go quadrupedal? Some of them are as big as the largest quadrupedal ornithischians! Quadrupedal vs. bipedal locomotion can’t strictly be a size thing, then. Is there something about being a carnivorous dinosaur that discourages quadrupedalism? Perhaps the use of the forearms for prey acquisition? This is something we’ll want to touch on in the paper.

P.S.: The latest version of the combined spreadsheet is available here (Excel spreadsheet).

Categories: Data Exploration

Cladogram(s), Part III

March 8, 2010 6 comments

I think we’re now converging on a cladogram that reasonably captures the current state-of-the-art. Thank you to everyone who has contributed so far. The topology has incorporated most of the suggestions, and I think the nomenclature is finally up-to-date. As always, post something in the comments if you see anything that needs work.

A Disclaimer

The phylogeny, in general, is intended to be used for numerical analyses (e.g., phylogenetically independent contrasts) that incorporate information on the evolutionary relationships of organisms (that topic is crying out for a post, had I the time). Studies have shown that these methods are generally pretty robust, even if the phylogeny is incorrect in some details. So. . .it means that we shouldn’t sweat too much about uncertainties or the inevitable error/new data. In a handful of cases (hadrosaurs, perhaps?), we may want to run analyses with alternative trees, but we’ll worry about that when we get there. The position of some annoyingly fickle taxa (like Micropachycephalosaurus) will end up being a moot point, because we don’t have decent postcrania for them.

That said, this tree is a mutt (but a loveable one). We’ve done the best we can with the published analyses and our personal opinions. It’s pretty darned good for the most part (in my opinion), but it will never be perfect. Anyone is welcome to use it, but caveat emptor. If using the tree for other purposes, please refer to the notes given in previous posts so you have an understanding of the how’s and why’s of the tree. I am happy to send the NEXUS file to anyone who requests it (and we’ll want to include it as supplemental information when we publish).

The Current Version

The version below shows all of the taxa, with most corrections incorporated as suggested.

Cladogram, Version 3

Cladogram, Version 3 (click to enlarge)

I’ve also generated a version where taxa that aren’t in our database are trimmed out. This is what we’ll use for most of our analyses. See below:

ODP_7Mar2010trimmed

Trimmed Cladogram, Version 3. I accidentally took Eoraptor out.

Notes:

Notes from the previous version still apply.

Psittacosaurus xinjiangensis given as sister taxon to P. sinensis, following Sereno 1987, p. 267. This taxon, the measurements for which are based on a juvenile (Sereno 1988, original description), has not been included in any published phylogenetic analysis.

The species of Camptosaurus and Dryosaurus are placed so as to preserve monophyly for each genus.

Animantarx is given as sister to Edmontonia, following Hill et al. 2003, Figure 9

Both species of Postosuchus need to be shown

Edmontosaurus saskatchewanensis needs to be dealt with

Eoraptor needs to be added into the trimmed cladogram.

Categories: Progress Reports

Meet the Project Participants: David Dreisigmeyer

March 7, 2010 Leave a comment

It’s been a long time since we’ve featured one of our project participants. . .so, here’s a chat with a relative newcomer to the ODP, David Dreisigmeyer.

Tell us a little bit about yourself. Where are you from? What do you do (professionally)? Any other interesting facts?
I’m originally from Pennsylvania, where I attended Juniata College for my undergraduate degree in Pre-law.  After taking a year off, I relocated to Boulder, CO and then started grad school at Colorado State University (in Fort Collins, CO).  After a year in the Economics Department I switched over to the Mathematics Department.  I was first introduced to data/pattern analysis here while working with Michael Kirby.  After my M.S., I moved over to the Electrical Engineering Department for my Ph.D., specializing in signal processing and mathematical physics.

The Dreisigmeyer Family (David, Lisa and Dyson at Pueblo Bonito (Chaco Canyon, NM)

The Dreisigmeyer Family (David, Lisa and Dyson) at Pueblo Bonito (Chaco Canyon, NM)

After grad school, I moved back to the Math Department at CSU for a postdoc in image processing and dimensionality reduction.  After this, we (myself, my wife Lisa and our son Dyson) moved to Los Alamos for a second postdoc.  During this time I did signal and image processing and some protein modeling.  Now we’re in Pennsylvania while I’m at Pitt on a visiting position in the Medical School and the Math Department.  Currently, in addition to the ODP, I’m doing some modeling of the influenza virus (epidemiology and evolution), ecology and some fault detection methods.  I’m also just starting to help out on a developmental aid database.

My wife and I are really into climbing.  We loved New Mexico, especially the trail running (and seeing those bears nice and close up like).  Ghost Ranch was absolutely amazing (the hiking, not those other things you may be thinking of).  And if you have the chance to visit Chaco Canyon you should definitely do so.  My other interest are the American Revolution and history (a la Susan Wise Bauer).

Why did you decide to participate in the ODP?
First of all I always wanted to be a paleontologist until I was about twelve.  A couple months ago I decided to look back into it (after spending some time reading about the field again).  But, how could someone like me actually do research in this field?  A google search on ‘data analysis dinosaur’ led me to the ODP.  This what I had been looking for.  And it was open source — double bonus!

So far, what has been the best part of the ODP for you, and why?
Being able to deal with the data, both the analysis and the ‘cleaning’.  Since I’m a data analyst I love… data.  And, I can’t imagine neater data than dino data.

What have you learned from your participation in the ODP?
Working with paleontologists is a great experience.  It’s awesome to learn about the questions the field is interested in examining.

What advice would you give those who might be interested in helping out with the ODP?
Check everything.  In a database this large, put together ‘by hand’, there’s bound to be some errors, it’s unavoidable.  By having everyone help everyone else out the final product is only improved.

Categories: Uncategorized

The Cladogram, Version 2

March 7, 2010 11 comments

Thank you to everyone who commented on the first draft of the phylogeny. Based on all of this, I’ve updated the tree, incorporating most of what was recommended. As before, the rationale behind the topology is included at the end of the post. Note that I have also proposed a few taxa to cut from the end analysis. If you have any comments or suggestions, please feel free to post it in the comments!

Phylogeny, Version 2

Phylogeny, Version 2

Overall topology of Ornithischia:
From Butler et al. 2008, Figures 2, 3, and 4, with additional modifications from Butler et al. 2009, Figure S4
Contents of Thyreophora (Scutellosaurus, Emausaurus, Scelidosaurus, Stegosauria, Ankylosauria; with exception of Lesothosaurus) based on this phylogeny
Placement of Stenopelix within Pachycephalosauria based on this phylogeny (2009).
Position of Heterodontosauridae follows this reference (2008), as do positions of Stormbergia, Agilisaurus, and Hexinlusaurus.
The position of Othnielia (Othnielosaurus) follows Figures 2 (50% majority rule part), 3, and 4. (2008)
The position of Orodromeus follows Figures 3 and 4. (2008)
The position of Hypsilophodon relative to Jeholosaurus, Yandusaurus, Orodromeus, and Zephyrosaurus follows Figure 2 (50% majority rule part). (2008)
Jeholosaurus and Yandusaurus are arbitrarily placed as sister taxa. Their position basal to Hypsilophodon follows Fig. 2 (50% majority rule part), and Jeholosaurus‘s position more derived than Orodromeus follows Figure 4. (2008)
Bugenasaura is excluded from the tree following its synonymization with Thescelosaurus by Boyd et al. 2009.
The positioning of Thescelosaurus, Parksosaurus, and Gasparinisaura as more derived than Hypsilophodon and outside of the remaining ornithopods follows Figure 2 (50% majority rule part), Figure, and Figure 4. Thescelosaurus is arbitrarily placed as more derived than Parksosaurus+Gasparinisaura. (2008)
The positioning of Talenkauen follows that of Figure 2 (50% majority rule part). (2008)
The remainder of Ornithopoda is consistent across all versions of the cladogram, and this phylogeny is followed for the positions of Rhabdodontidae, Tenontosaurus, Dryosauridae, and Ankylopollexia.
The problematic taxa Zephyrosaurus, Echinodon, Lycorhinus, were excluded (and do not have postcrania, anyhow).
The placement of Lesothosaurus follows Butler et al. 2009, Figure S4.
The synonymy of Lesothosaurus and Stormbergia follows Knoll et al. 2010
The placement of Oryctodromeus and Orodromeus as sister taxa follows Varrichio et al. 2007, Figure 5

Topology of Rhabdodontidae:
Follows Weishampel et al. 2003

Topology of Stegosauridae:
From 50% Majority-Rule Consensus Tree of Mateus et al. 2009 (Miragaia paper, supplementary information, Figure S7B)

Topology of Ankylosauria:
From Vickaryous 2004, Figure 17.20 (strict consensus tree)
Pawpawsaurus, Sauropelta, and Silvisaurus were in a polytomy; their positions were assigned arbitrarily. This will not matter ultimately, because Pawpawsaurus and Silvisaurus do not have multiple postcranial elements known, and are thus excluded from the quantitative analysis. Saichania and Talarurus had polytomy arbitrarily resolved, too.
The placement of Cedarpelta as an ankylosaurid follows Lü et al. 2007 and an unpublished analysis by Nick Gardner (http://whyihatetheropods.blogspot.com/2008/12/cedarpelta-as-ankylosaurid.html). Ultimately, no postcrania for this taxon are included, so its placement is not terribly critical.
The topology of nodosaurids (including the placement of Hungarosaurus and Struthiosaurus) follows Ösi 2005, Figure 15. The monophyly of Edmontonia follows Vickaryous 2004, Figure 17.20
Dyoplosaurus is recognized as an ankylosaurid (Arbour 2009), and is arbitrarily placed as sister to Euoplocephalus.
Aletopelta is tentatively given as an ankylosaurid, based on text in Ford and Kirkland 2001.
Niobrarasaurus and Nodosaurus are arbitrarily given as sister taxa, because of their general similarity. Furthermore, Coombs (1990), in The Dinosauria, suggested that Nodosaurus is close to Sauropelta and Silvisaurus (p. 478, caption for Figure 22.14, “Nodosaurus probably fits just above or just below node 8.” [i.e., either between Sauropelta and Silvisaurus, or Silvisaurus and Panoplosaurus], so this opinion is followed here. Based on geography alone, they are given as sister to Sauropelta.
Polacanthus foxii is arbitrarily given the basal position within Nodosauridae occupied by Hylaeosaurus, for Coombs 1990, Fig. 22.14.
Zhejiangosaurus is completely arbitrarily placed as more derived than Polacanthus.
Because of great uncertainty in phylogenetic position, and because no phylogenetic analysis has adequately addressed the taxa, I recommend removing Aletopelta, Niobrarasaurus, Nodosaurus, Polacanthus, and Zhejiangosaurus from the analysis.

Topology of basal Iguanodontia:
Follows Norman 2004, figures 19.21 (strict consensus) and 19.22 (single most parsimonious tree following taxon deletion).
The position of Rhabdodontidae (Rhabdodon + Zalmoxes) does not follow this analysis, but instead follows Butler 2009
Tenontosaurus is treated as monophyletic, following Figure 19.22.
Jinzhousaurus and Nanyangosaurus are arbitrarily placed as sister taxa, more basal than Probactrosaurus+Ouranosaurus.
Eolambia+Altirhinus are placed between Ouranosaurus and Protohadros, following Figure 19.21 in Norman 2004.

Topology of hadrosaurids, hadrosauroids, and other derived iguanodontians:
Placement of Tethyshadros follows Dalla Vecchia 2009, Figure 8B (50% Majority Rule Tree). Mantellisaurus and Dollodon are given as sister taxa, following this analysis. Note that Claosaurus and Lophorothon are not included in this analysis, so the position of Tethyshadros relative to them has not been tested.
Rest of tree primarily follows Prieto-Marquez and Wagner 2009 (Figure 3).
Altirhinus is placed in clade with Eolambia and Protohadros after Fig. 19.21 of Norman 2004
Additional resolution within the Saurolophinae and Lambeosaurinae of Prieto-Marquez and Wagner was determined by re-running their tree using parsimony analysis, and then using the strict consensus tree. From this run, the placements of the clades Sahaliyania+Amurosaurus, Olorotitan+Parasaurolophus+Charonosaurus, and Corythosaurus+Lambeosaurus (all recovered in the published analysis) were determined. The placements of the remaining taxa were then placed from this, also. Koutalisaurus was not shown on their Figure 3, but was coded in the appendix, so its placement was derived from my run of the data.
Nipponosaurus is placed basal to Lambeosaurus+Corythosaurus+Hypacrosaurus+Olorotitan, after Evans and Reisz, 2007, Figure 9
Prosaurolophus is split into its species, assuming monophyly.
Gryposaurus resolved arbitrarily

Topology of Pachycephalosauridae:

Follows Schott et al. 2009 (Colepiocephale description in JVP 29(3)), Figure 8B. Stygimoloch is removed, following synonymization with Pachycephalosaurus by Horner et al. 2009. Colepiocephale is arbitrarily resolved as sister taxon to Stegoceras.

Topology of Ceratopsia:
For non-ceratopsids, follows Makovicky and Norell 2006, Figure 20A (strict consensus tree). Note that Xuanhuaceratops is equivalent to IVPP V12722
Placement of Cerasinops, and its relationships with Udanoceratops, Leptoceratops, Montanaceratops, and Prenoceratops, based on Figure 6 of Chinnery and Horner 2007
Graciliceratops placed as closer to Bagaceratops+Protoceratops than the least inclusive clade containing Leptoceratops and Asiaceratops. Graciliceratops‘ position relative to Microceratus is arbitrary (and ultimately doesn’t matter, because Microceratus has no limb material)
Placement of Yinlong and Micropachycephalosaurus after Figure S4 of Butler et al. supplementary information

Topology of Psittacosaurus:
Follows Figure 6 of You et al. 2008

Topology of Ceratopsidae:
Chasmosaurinae after Figure 23.8 of Sampson et al. 2004
Centrosaurinae after Figure 12 of Ryan 2007
Placement of Avaceratops based on unpublished analysis
Placement of Turanoceratops after Farke et al. 2009

Topology of Heterodontosauridae:
Follows Figure S4 of Butler et al. 2009 supplementary information.
Abrictosaurus and Tianyulong are placed arbitrarily.

Topology of basal dinosaurs, dinosauriforms, and dinosauromorphs
After Nesbitt et al. 2010, Figure S1

Topology of saurischians
After Nesbitt et al. 2009, Figure S7

Placement of Guaibasaurus:
Follows Irmis, personal communication

Placement of Panphagia:

Follows the original description

Placement of remainder of Sauropodomorpha:

Follows Yates et al. 2010, Figure S4 and S5. The position of Gyposaurus, which is not in S4 and S5, is based upon Figures S2 and S3.

Placement of Saurosuchus and Gracilisuchus
Follows Nesbitt 2009

Placement of Scleromochlus and Smilosuchus (as a member of “Phytosauridae”)
Ffollows Benton 1999

Placement of Hallopus victor and Protosuchus richardsoni:
As sister taxa based on personal communication from Randy Irmis. Placement of these taxa as sister to Dromicosuchus (on our restricted tree) from Sues et al. 2003 (description of Dromicosuchus), Figure 11.

Recommendations for Handling Data:

  • Removed all specimens represented only by a single skeletal element
  • Remove Barsboldia, because it is only represented by two metatarsals and a phalanx
  • Synonymize Anatotitan copei with Edmontosaurus annectens, because the former is supposed to be just a crushed E. annectens, following Dinosauria II.
  • Shantungosaurus giganteus is represented just by bonebed material, so it is removed from the analysis
  • Mandschurosaurus amurensis large mount and small mount from Yang et al. 1986 are removed, because they are composite skeletons
  • Altirhinus kurzanovi removed, because it includes only a humerus and one manual phalanx
  • Remove Podekosaurus, due to phylogenetic uncertainty and missing data
  • Remove Draconyx, because it is only MT I-III
  • Remove Dracopelta, because it is only known from manual phalanges
  • Sellosaurus gracilis is renamed to Plateosaurus gracilis, following Yates 2003
  • Remove Lexovisaurus durobrovensis and Chialingosaurus kuani, following their recognition as nomina dubia by Maidment et al. 2008
  • Remove Geranosaurus atavus, based on incompleteness of material (tibia and metatarsal II and pedal phalanx) and uncertainty of phylogenetic position
  • Gongbusauruswucaiwanensis and Xiaosaurus dashanpensis are excluded, following the lead of Butler et al. 2008, because the known material is not diagnostic or sufficient to allow phylogenetic placement
  • following Nesbitt et al. 2010 (supplemental information), Pseudolagosuchus major and Lewisuchus are synonymized
  • Machaeroprosopus gregorii is called Smilosuchus gregorii
  • Although the pterosaurs Dimorphodon and Eudimorphodon are on the tree, they are so derived relative to the rest (for flight) that I recommend leaving them out.
  • Aletopelta is an immature individual, based on generic description
Categories: Progress Reports

Behold, The Mighty Cladogram

March 5, 2010 23 comments

It’s taken awhile, but I finally put together a basic phylogeny to provide the evolutionary backbone for our phylogenetically-informed analyses. References (in very abbreviated format – we’ll have to flesh it out more for the paper) are given at the end of this post.

I created a “pseudo-supertree”, based on a number of what I (in my opinion) consider to be some of the better and more up-to-date published cladistic analyses. The vast majority of our species of interest are included here, and a draft is shown later in the post. But, we need your help in order to get to the final product.

Here’s What You Can Do
Below is a list of taxa that are not yet placed on the cladogram. In all cases, they were not featured in any of the cladistic analyses I looked at for my first pass. In order to incorporate them into the analysis effectively, though, we need to figure out where they belong. So. . .I’m looking for anything – a reference, personal opinion, cladogram I missed – to place them on the tree. Please mention it in the comments, and we’ll be able to get the tree updated! At the minimum, a reference would be helpful, so that we can be as explicit as possible in our reasoning for the paper. I focused my efforts so far on just ornithischians, so many of the problematic taxa are recently-published animals that are outside Ornithischia.

Also, if you see anything in the tree that you consider to be in gross error, please put a note in the comments section, and we can talk about it. We want the best phylogeny possible. But at the same time, studies have shown that some phylogeny – any phylogeny – is better than no phylogeny at all, so we don’t have to sweat things too much if new data later force us to revise.

Taxa to Place
Ankylosauria:
Aletopelta coombsi, Dracopelta zbyszewskii, Dyoplosaurus acutosquameus, Hungarosaurus tormai, Niobrarasaurus coleii, Nodosaurus textilis, Polacanthus foxii, Zhejiangosaurus lishuiensis
Ceratopsia: Graciliceratops mongoliensis, Psittacosaurus major, Psittacosaurus mongoliensis, Psittacosaurus neimongoliensis, Psittacosaurus ordosensis, Psittacosaurus sibiricus, Psittacosaurus sinensis, Psittacosaurus xinjiangensis, Xuanhuaceratops niei
Crurotarsi: Gracilisuchus stipanicicorum, Hallopus victor, Protosuchus richardsoni, Saurosuchus galilei, Pseudolagosuchus major, Scleromochlus taylori
Hadrosauroidea: Anatotitan copei (is there a consensus that this is just Edmontosaurus?), Barsboldia sicinskii, Claosaurus affinis, Edmontosaurus saskatchewanensis (how does it relate to other Edmontosaurus species?), Hadrosaurus foulkii, Mandschurosaurus amurensis, Shantungosaurus giganteus
Basal ornithischians: Eocursor parvus, Geranosaurus atavus
Ornithopods: Draconyx loureiroi, Gongbusaurus wucaiwanensis, Oryctodromeus cubicularis, Xiaosaurus dashanpensis
Parasuchia: Machaeroprosopus gregorii
Sauropodomorpha: Aardonyx celestae, Gyposaurus sinensis, Panphagia protos, Pantydraco caducus, Sellosaurus gracilis
Stegosauria: Chialingosaurus kuani, Lexovisaurus durobrivensis
Theropoda: Guaibasaurus candelariensis, Podokesaurus holyokensis

The Phylogeny

The Phylogeny, as of 4 March 2010. Click to see it in all of its glory.

Logic Behind the Tree
In the interest of Open Notebook Science, I have provided full references and justifications (if any) for the topology of the illustrated tree. All of this should go into the final paper, so that others can reproduce our work.

Overall topology of Ornithischia:
From Butler et al. 2008, Figures 2, 3, and 4, with additional modifications from Butler et al. 2009, Figure S4
Contents of Thyreophora (Lesothosaurus, Scutellosaurus, Emausaurus, Scelidosaurus, Stegosauria, Ankylosauria) based on this phylogeny
Placement of Stenopelix within Pachycephalosauria based on this phylogeny (2009).
Position of Heterodontosauridae follows this reference (2008), as do positions of Stormbergia, Agilisaurus, and Hexinlusaurus.
The position of Othnielia (Othnielosaurus) follows Figures 2 (50% majority rule part), 3, and 4. (2008)
The position of Orodromeus follows Figures 3 and 4. (2008)
The position of Hypsilophodon relative to Jeholosaurus, Yandusaurus, Orodromeus, and Zephyrosaurus follows Figure 2 (50% majority rule part). (2008)
Jeholosaurus and Yandusaurus are arbitrarily placed as sister taxa. Their position basal to Hypsilophodon follows Fig. 2 (50% majority rule part), and Jeholosaurus‘s position more derived than Orodromeus follows Figure 4. (2008)
Bugenasaura is excluded from the tree following its synonymization with Thescelosaurus by Boyd et al. 2009.
The positioning of Thescelosaurus, Parksosaurus, and Gasparinisaura as more derived than Hypsilophodon and outside of the remaining ornithopods follows Figure 2 (50% majority rule part), Figure, and Figure 4. Thescelosaurus is arbitrarily placed as more derived than Parksosaurus+Gasparinisaura. (2008)
The positioning of Talenkauen follows that of Figure 2 (50% majority rule part). (2008)
The remainder of Ornithopoda is consistent across all versions of the cladogram, and this phylogeny is followed for the positions of Rhabdodontidae, Tenontosaurus, Dryosauridae, and Ankylopollexia.
The problematic taxa Zephyrosaurus, Echinodon, Lycorhinus, were excluded (and do not have postcrania, anyhow).

Topology of Stegosauridae:
From 50% Majority-Rule Consensus Tree of Mateus et al. 2009 (Miragaia paper, supplementary information, Figure S7B)

Topology of Ankylosauria:
From Vickaryous 2004, Figure 17.20 (strict consensus tree)
Pawpawsaurus, Sauropelta, and Silvisaurus were in a polytomy; their positions were assigned arbitrarily. This will not matter ultimately, because Pawpawsaurus and Silvisaurus do not have multiple postcranial elements known, and are thus excluded from the quantitative analysis. Saichania and Talarurus had polytomy arbitrarily resolved, too.

Topology of basal Iguanodontia:
Follows Norman 2004, figures 19.21 (strict consensus) and 19.22 (single most parsimonious tree following taxon deletion).
Tenontosaurus is treated as monophyletic, following Figure 19.22.
Euijuubus is arbitrarily treated as more basal than Lurdusaurus.
Jinzhousaurus and Nanyangosaurus are arbitrarily placed as sister taxa, more basal than Probactrosaurus+Ouranosaurus.
Eolambia+Altirhinus are placed between Ouranosaurus and Protohadros, following Figure 19.21 in Norman 2004.

Topology of basal hadrosaurids, hadrosauroids, and other derived iguanodontians:
Follows Dalla Vecchia 2009, Figure 8B (50% Majority Rule Tree). Bactrosaurus and Gilmoreosaurus are arbitrarily resolved from their polytomy with more derived hadrosauroids. Mantellisaurus and Dollodon are given as sister taxa, following this analysis.

Topology of lambeosaurines:
Follows Evans and Reisz 2007, Figure 9
Corythosaurus arbitrarily resolved as closer to Hypacrosaurus than Olorotitan
Pararhabdodon as a basal lambeosaurine after Dalla Vecchia 2009

Topology of hadrosaurines:
Follows Fig. 16 of Gates and Sampson 2007
Edmontosaurus, Prosaurolophus, and Saurolophus are split into their species, assuming that each genus is monophyletic

Topology of Pachycephalosauridae:
Follows Schott et al. 2009 (Colepiocephale description in JVP 29(3)), Figure 8B. Stygimoloch is removed, following synonymization with Pachycephalosaurus by Horner et al. 2009. Colepiocephale is arbitrarily resolved as sister taxon to Stegoceras.

Topology of Ceratopsia:
For non-ceratopsids, follows Makovicky and Norell 2006, Figure 20A (strict consensus tree)
Placement of Cerasinops, and its relationships with Udanoceratops, Leptoceratops, Montanaceratops, and Prenoceratops, based on Figure 6 of Chinnery and Horner 2007
Placement of Yinlong and Micropachycephalosaurus after Figure S4 of Butler et al. supplementary information

Topology of Ceratopsidae:
Chasmosaurinae after Figure 23.8 of Sampson et al. 2004
Centrosaurinae after Figure 12 of Ryan 2007
Placement of Avaceratops based on unpublished analysis
Placement of Turanoceratops after Farke et al. 2009

Topology of Heterodontosauridae:
Follows Figure S4 of Butler et al. 2009 supplementary information.
Abrictosaurus and Tianyulong are placed arbitrarily.

Topology of basal dinosaurs, dinosauriforms, and dinosauromorphs
After Nesbitt et al. 2010, Figure S1

Topology of saurischians
After Nesbitt et al. 2009, Figure S7

Almost Done Aging Our Dinosaurs!

March 5, 2010 2 comments

Thank you to Rob Taylor, David Button, Christian Foth, ReBecca Hunt, Chris Noto, and Jordan Mallon for their work filling in the ages/dates for our dinosaur spreadsheet, as well as helping to update some of the taxonomy. We have just a handful of taxa to deal with now. These include:

  • Finding the ages of: Dyoplosaurus, Zhejiangosaurus, Pseudolagosuchus, Mandschurosaurus, Camptosaurus aphanoectes, Machaeroprosopus, Pantydraco, Loricatosaurus, and Stegosaurus mjosi.
  • How should we treat Iguanodon hollingtonensis? It’s synonymized with I. fittoni, but is that even a valid species anymore?

If you know of any references that can help answer these questions, please feel free to enter the data on the Google Spreadsheet. Thank you!

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