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Some (finalish) results!

May 17, 2013 7 comments

Matt and I have been meeting weekly for the past three weeks to have ODP work days–just to crank through analyses, etc. Mostly, it’s a matter of sitting down and forcing each other to do stuff. Matt’s posting soon, but in the meantime I thought I’d throw out some “final” results. These are regressions on phylogenetically independent contrasts (PICs), with analyses considering the whole sample, unequivocal quadrupeds (following Maidment and Barrett’s assignments), and unequivocal bipeds (following Maidment and Barrett, again).

A few quick notes (all of which are going into the main article text at some point)…PICs were calculated in the PDAP package of Mesquite. Limb lengths were log-transformed prior to analyses (which helped to move things towards normality a little bit, but not entirely). Branch lengths were initially set to divergence times, but we found that these violated the assumptions of PICs, and thus some transforms were used (to be outlined in the manuscript as well as a future post, once we’ve pulled that text together).

Below, I’m including the preliminary results text for this part of the analysis, the associated table, and table caption. Enjoy! And feel free to throw in some comments if you have any.

RESULTS
Intra- and interlimb scaling
Analyses including all taxa as well as analyses considering only unequivocal quadrupeds showed similar scaling patterns. Forelimb length scaled with strong positive allometry relative to hind limb length, whereas the distal hind limb elements (tibia and metatarsal III) collectively scaled with strong negative allometry relative to femur length. The distal forelimb (radius and metacarpal III) scaled isometrically relative to the humerus; however, we note that the lower confidence interval for the entire sample only barely excludes positive allometry. We thus speculate that a larger sample may ultimately demonstrate positive allometry.
When considering only unequivocal bipeds, none of the slopes differed from isometry. However, we note that this subset of taxa also had some of the smallest sample sizes considered here, and a larger sample might uncover allometric scaling patterns.

Table. Results of RMA (reduced major axis) regressions of PICs (phylognetically-independent contrasts) for logged limb segment lengths in ornithischian dinosaurs. In the “Allometry” column, “0” indicates a slope indistinguishable from isometry, “+” indicates a slope consistent with positive allometry, and “-” indicates a slope consistent with negative allometry. The numbers in parentheses in the “Slope” indicate the 95 percent confidence interval for the slope.

Grouping

X

Y

Allometry

Slope

R2

N

All

Humerus

Distal Forelimb

0

1.139 (0.996–1.301)

0.78

50

All

Femur

Distal Hind Limb

-

0.812 (0.715–0.921)

0.77

59

All

Hindlimb

Forelimb

+

1.301 (1.198–1.413)

0.94

39

Quadruped Only

Humerus

Distal Forelimb

0

1.138 (0.929–1.393)

0.72

29

Quadruped Only

Femur

Distal Hind Limb

-

0.742 (0.581–0.949)

0.57

30

Quadruped Only

Hindlimb

Forelimb

+

1.237 (1.027–1.489)

0.84

21

Biped only

Humerus

Distal Forelimb

0

0.829 (0.588–1.17)

0.75

11

Biped only

Femur

Distal Hind Limb

0

0.903 (0.739–1.105)

0.80

22

Biped only

Hindlimb

Forelimb

0

1.009 (0.543–1.876)

0.23

10

Regressions for PICs including the entire sample. The blue line indicates isometry.

Regressions for PICs including the entire sample. The blue line indicates isometry.

 

 

 

Presentation Draft – Early Results

October 12, 2012 4 comments

On Saturday, I’ll be giving a short presentation about (very) preliminary results from the ODP, for the 1st Annual Southwest Regional Joint DVM&DCB (Division of Vertebrate Morphology and Division of Comparative Biology) meeting of SICB (Society of Integrative and Comparative Biology). This conference is a one-day event held on the campus of Cal State San Bernardino, and targets functional morphologists and their kin (including paleontologists).

The presentation is entitled “Morphological disparity, locomotion and limb proportions in ornithischian dinosaurs,” and it’s set up as a 5 minute talk. One of the cool things about DVM is the option of a 5 minute format – perfect for work that is in its nascent stages or “crazy” ideas that you just want to throw out there. Given the very preliminary nature of the analysis (and the fact that I’m co-author on three posters at the Society of Vertebrate Paleontology meetings next week), I jumped at the chance for this format. Plus, the talk was a good opportunity to kick my butt in gear and do some real analysis.

I don’t have a lot of time at this second to detail every aspect of the methods, but here is a sketch:

  • Data were trimmed down to one entry per taxon, choosing the largest and most complete specimen possible. In a handful of cases, missing data were interpolated via regression (to estimate tibia length from fibula length) or other specimens of the same taxon.
  • Taxa were binned into five time categories, each spanning roughly 34 million years. Any finer bins, and there just weren’t enough taxa.
  • I ran principal coordinates analyses on the data, for forelimb, hindlimb, and all limbs together. Within each temporal bin from the results, I calculated the sum of variance and nth root of variance. This gives a measure of morphological disparity in each bin – high variance, high disparity. The analyses were run with the raw data, as well as data that were standardized within each taxon by the geometric mean. This was to attempt to remove the effects of body size.
  • I plotted the data in each bin. In order to compare the raw results vs. geometric mean results, I normalized the data to the largest value in each category.
  • A few notes of caution – I did not perform any statistical tests on the data (bootstrapping, confidence intervals, etc.). So, the results should not be considered to have particular statistical significance at any level. Also, no attempt was made to accommodate for sampling effects or phylogeny. Caveat emptor.
  • In any case, there are some cool results. Looking at hind limbs, there is a big jump in disparity after the first 60 million years (or so) of evolution – not unexpected, given the explosion of forms in the mid-Jurassic. What was more interesting was the fact that the disparity stayed constant when looking at raw values, but when values were corrected for size using a geometric mean, there was a big drop in disparity during the last 60 million years or so. On first consideration, this suggests to me that body size is driving some of the disparity values. Body size stayed big after the Middle Jurassic, but overall morphological disparity (in what those large body forms looked like) decreased. I wonder if some of this is due to the extinction of stegosaurs (with their bizarro limbs) at the end of the Jurassic / early Cretaceous. Forelimb disparity (when correcting with a geometric mean) by contrast takes a big jump in the late Cretaceous – I wonder if this is due to hadrosaurs, with their conventional hind limbs but really, really weird forelimbs. Food for thought.

Tonight I put together a first draft of the slides for my presentation. Supporting data are here, and a PDF of the slides is here. I’m going to do some more editing tomorrow, so any suggestions are welcome. Keep in mind that the slides are pretty rough right now, so forgive any ugliness there. Also, remember that I’m dealing with a 5 minute format, so there’s only so much more I can add (and I think I’ll have to trim some stuff – we’ll see how much time is in the mix after I run through it once out loud).

The final version, after presentation on Saturday, will be archived at figshare.

Quick Update

October 8, 2012 1 comment

The best way to spur work on a project is to agree to present it at a professional conference. Thus, I submitted a title (no abstract necessary) for the upcoming Southwest Regional Meeting for the Division of Vertebrate Morphology / Division of Comparative Biomechanics within the Society of Integrative & Comparative Biology (short title, isn’t it?). The beauty of this conference is that they have “5 minute talks,” where you can give short and succinct presentations of in-progress research. The ODP definitely qualifies! I’ve got a few days break from teaching (and my most time-intensive classes are completely done after the SVP meeting), so this week has the promise of productivity. Look for news on preliminary analyses, etc., in this space. Presentation is Saturday.

Oh yeah. . .I almost forgot! The submitted title was “Morphological Disparity, Locomotion and Limb Proportions in Ornithischian Dinosaurs.”

Categories: Uncategorized

Is there a finish line? (and how to get there)

September 12, 2012 14 comments

Yes. . .I hope there is a finish line. As with many things started with the best of intentions, the ODP (and its heads – particularly me) has gotten waylaid. That said, it would be a shame to let the numerous contributions and hours of volunteer effort go to waste. So, Matt and Mike and I have been having some serious conversations about finishing this once and for all! So, here’s the deal.

  • I want to finish this. You want to finish this. It just needs to be finished.
  • Analysis and write-up are the main things that need to be done. It requires a bit of concentrated effort (primarily on my part).
  • The way I see it, the most productive product of the analysis would be to examine limb disparity in ornithischian dinosaurs through time. This would entail binning the dinos and running the analysis. Riffing off of recent work by numerous authors, this would involve running a PCO (principal coordinates analysis) on the measurements for each bin. This can then be converted to a metric that shows overall morphological disparity. The primary question this asks is, “How did ornithischians diversify in their limb bone proportions through time?” Was it something that happened right away? Or something that happened later? A related question concerns how to accommodate phylogeny. As with many recent papers, the main thing we’re interested in here are ghost lineages. Given the incomplete nature of the fossil record, ancestral state reconstruction of some sort is probably needed. The problem, however, is that these methods are often. . .vague. . .at best. Perhaps maximum likelihood reconstruction in the relevant R packages? (see this link for an example ) Or perhaps skip trying to reconstruct stuff altogether and take the results with appropriate caution?
  • I envision three analyses: all limbs together (for all animals that are appropriately complete), forelimbs, and hind limbs. This would help account for animals that preserve only forelimbs, or only hind limbs.

Tasks to do:

Timeline:

  • Realistically, upcoming major events in the real world mean that I (Andy) have to get this thing off my plate by December 1 at latest. This is also best for Matt and Mike, too (and everyone, right?). This means a finished, submitted manuscript.
  • If the December 1 thing doesn’t happen, realistically we need a way to “cut the data loose.” Although we’ve had a general statement on the blog that we would rather others hold off on using our data until the paper is published, it isn’t fair to sit on the data for years at a time. So, this means that we would step aside from right of first refusal for publication with the data. This means that others are welcome to use the data without explicit permission (although the ODP should still be cited as the data source). The data would be archived at figshare, which provides a stable link, long-term archiving, and DOI for future linking.

Mopping Up the Data

March 8, 2012 6 comments

Thanks to Alexandre Fabre, Falko Gauß, and others, we are starting to close out some of the nagging verification entries for the data set (all of which are now accordingly updated in the public files). David Dreisigmeyer has also noted a few formatting issues and other quirks in the dataset (which I will work to correct in the next few days).

In any case, we are very close to finalizing the database. For the sake of time, I want to call attention to just a few last bits of data entry. These represent taxa and clades that are otherwise poorly represented in the sample. Some entries (e.g., those concerning the outgroup or indeterminate, fragmentary taxa) are just going to have to go by the wayside, or else we’ll never finish!

References That Have Data That Need to be Entered a First Time

Prieto-Marquez A. Cranial and appendicular ontogeny of Bactrosaurus johnsoni, a hadrosauroid dinosaur from the Late Cretaceous of northern China. Palaeontology (in press). DOI: 10.1111/j.1475-4983.2011.01053.x [link] [if this contains only disarticulated and unassociated material, it is not usable for our dataset - can anyone confirm one way or another?] [contains only disarticulated and unassociated specimens - thanks to John Dziak for checking!]

References For Data In Need of Cross-Checking

Godefroit P, Pereda Suberbiola X, Li H, Dong Z-M (1999) A new species of the ankylosaurid dinosaur Pinacosaurus from the Late Cretaceous of Inner Mongolia (P.R. China). Bulletin de l’Institut Royal des Sciences Naturelles de Belgique 69-Supp. B: 17-36.

Wang X, Pan R, Butler RJ, Barrett PM. 2011 (for 2010). The postcranial skeleton of the iguanodontian ornithopod Jinzhousaurus yangi from the Lower Cretaceous Yixian Formation of western Liaoning, China. Earth and Environmental Science Transactions of the Royal Society of Edinburgh 101: 135-159.

Zhao X, Li D, Han G, Zhao H, Liu F, Li L, Fang X (2007) Zhuchengosaurus maximus from Shandong Province. Acta Geoscientica Sinica 28: 111-122

Categories: Uncategorized

On continua and categories in paleoecology. . .or, an example application of ODP data

July 14, 2011 9 comments

Today we’re delighted to have a guest post from Dr. Chris Noto, a new assistant professor at University of Wisconsin-Parkside, and an old friend of mine from our graduate school days together at Stony Brook University. Chris has had a long-running interest in dinosaur paleoecology, and thus it only seemed natural for him to apply these interests to the ODP data. Enjoy!

Chris Noto

Chris Noto, at home in the field

In describing the ecology of an organism our first inclination may be to simply go observe it in its day-to-day existence. Therefore, at its core, ecology is primarily a science of the living and this is reflected in the methods and theories one finds in the literature. Over the past couple decades there has been a growing interest in the relationship between organismal morphology and ecology, which is now often referred to as “ecomorphology”(Losos 1990; Ben-Moshe et al. 2001; Aguirre et al. 2002; Zeffer et al. 2003; Sacco and Van Valkenburgh 2004). This has opened entire new areas of research into the covariation between organisms and their environment, which is also the basic foundation for understanding evolutionary change over longer spans of time.

Some paleontologists have applied ecomorphological principles to reconstructing the paleoecology of certain extinct groups, including carnivorans (Palmqvist et al. 1999), birds (Hertel 1995), and especially ungulates (Solounias and Semprebon 2002; Meehan and Martin 2003; DeGusta and Vrba 2005; Klein et al. 2010). Changes in the types and/or proportions of ecomorphs in a fossil community have also been used as evidence of environmental and evolutionary responses to climate change(Van Valkenburgh 1995; Meehan and Martin 2003; Badgley et al. 2008; Noto and Grossman 2010). You will note though that a lot of this research relies on comparison to living analogs related to the fossil groups in question. How do we explore the paleoecology of groups that completely lack extant analogs?

If there’s one thing we’ve learned through all this research, it’s the fact that:

  1. Certain morphological adaptations occur regardless of species (convergence) because of specific habitat constraints, and
  2. Morphological differences between species will occur due to diverging ecologies, even if we don’t know exactly what ecological functions those morphological differences actually represent.

But, we won’t know those differences exist until we look for them. Paleoecology is first and foremost comparative: we take our fossils and compare them to other related taxa and living forms to better understand their place in the original community. Often we assign categories to taxa, such as “carnivore”, “biped”, etc.; however, differences between species are often better described by a continuum than a set of categories(Carrano 1999). The morphology of an organism reflects the amount of time it spends doing certain activities or performing certain functions. For example, a sloth can swim on occasion even if it is not particularly well adapted for it. Dinosaur paleoecology is finally moving in the direction of our mammalian colleagues by using quantitative measures of morphology (which allow for continua) instead of assigning discreet categories.

The ODP is one of the first large-scale projects to bring together the kind of dataset necessary to study dinosaur ecomorphology. In a recent paper I published looking at differences between dinosaur fossil communities (Noto and Grossman 2010), I was forced to use categories in assigning ecomorphs, which artificially restricted the analysis by forcing me to choose a category when uncertainty existed. In this case it was whether certain non-hadrosaur ornithopods were bipedal or quadrupedal. With ODP data, it is now possible to take a more quantitative (and nuanced) approach to this question.

To explore possible trends in ornithischians, I used humerus length and mediolateral width measurements to calculate Mike Taylor’s Gracility Index (GI; Taylor 2009) using only the largest individual from each species. These data were log transformed and plotted against the log of humerus length (to help minimize the effects of size and codependency). The resulting plot clearly separates the taxa, with more bipedal taxa having relatively gracile humeri and quadrupedal groups have more robust humeri. There are two ways to use this graph. First, we can look at the distribution of taxa from each group and see whether they fit more towards a bipedal or quadrupedal type; those intermediate to the extremes are referred to as facultative. These are my own divisions based on where I see breaks in the data. Basal ceratopsians, for example, occur mainly towards the bipedal or facultative ends of the spectrum, while derived Neoceratopsians are firmly on the quadrupedal end of things. Another way to look at the plot is how robust we may expect the humerus to be for a taxon of a given size. The dashed line is drawn across the middle of the plot. For a given humerus length we can compare GI between taxa. For example, Iguanodon has a more robust humerus (lower GI) than most ornithopods in the dataset. Furthermore, we can spot outliers, which may point to either extreme specialization or faulty data. The theropod Mononykus has an extremely robust humerus, approaching the level of Triceratops, which is related to its specialized digging forelimb. On the other hand, Cerasinops appears to have the most robust humerus of all, however as Mike pointed out to me, the original paper describes the humerus as extremely gracile and gives no width measurement. So where did the width measurement come from? This particular data point is worth another look.

Ecomorphology Plot

Humeral robustness as a function of humeral length. Select taxa labeled in gray. Cera.=Cerasinops, Gypo.=”Gyposaurus”, Herr.=Herrerasaurus, Igua.=Iguanodon, Mono.=Mononykus, Post.=Postosuchus, Psit.=Psittacosaurus, Scut.=Scutellosaurus, Stego.=Stegosaurus, Thec.=Thecodontosaurus, Tric.=Triceratops.

As you can see, the distribution of humeral morphologies indicates a gradual continuum of locomotor strategies from fully bipedal to full quadrupedal. Quantitative data such as this could then be fed into a paleoecological analysis instead of categories, allowing for more refined analysis of ecological differences and similarities among paleocommunities over space and time. While evolutionary trends are certainly important, we must not forget the ecological context of the morphological patterns we are studying.

References

Aguirre LF, Herrel A, van Damme R et al. (2002) Ecomorphological analysis of trophic niche partitioning in a tropical savannah bat community. Proceedings of the Royal Society of London Series B-Biological Sciences 269:1271-1278

Badgley C, Barry JC, Morgan ME et al. (2008) Ecological changes in Miocene mammalian record show impact of prolonged climatic forcing. Proc Natl Acad Sci U S A 105:12145-12149

Ben-Moshe A, Dayan T, Simberloff D (2001) Convergence in morphological patterns and community organization between Old and New World rodent guilds. Am Nat 158:484-495

Carrano MT (1999) What, if anything, is a cursor? Categories versus continua for determining locomotor habit in mammals and dinosaurs. J Zool 247:29-42

DeGusta D, Vrba E (2005) Methods for inferring paleohabitats from discrete traits of the bovid postcranial skeleton. J Archaeol Sci 32:1115-1123

Hertel F (1995) Ecomorphological indicators of feeding behavior in recent and fossil raptors. Auk 112:890-903

Klein RG, Franciscus RG, Steele TE (2010) Morphometric identification of bovid metapodials to genus and implications for taxon-free habitat reconstruction. J Archaeol Sci 37:389-401

Losos JB (1990) Ecomorphology, performance capability, and scaling of West Indian Anolis lizards: an evolutionary analysis. Ecol Monogr 60:369-388

Meehan TJ, Martin LD (2003) Extinction and re-evolution of similar adaptive types (ecomorphs) in Cenozoic North American ungulates and carnivores reflect van der Hammen’s cycles. Naturwissenschaften 90:131-135

Noto CR, Grossman A (2010) Broad-scale patterns of Late Jurassic dinosaur paleoecology. PLoS ONE 5:e12553

Palmqvist P, Arribas A, Martinez-Navarro B (1999) Ecomorphological study of large canids from the lower Pleistocene of southeastern Spain. Lethaia 32:75-88

Sacco T, Van Valkenburgh B (2004) Ecomorphological indicators of feeding behaviour in the bears (Carnivora : Ursidae). J Zool 263:41-54

Solounias N, Semprebon G (2002) Advances in the reconstruction of ungulate ecomorphology with application to early fossil equids. Am Mus Novit:1-49

Taylor M (2009) A re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria, Sauropoda) and its generic separation from Giraffatitan brancai (Janensch 1914). J Vert Paleontol 29:787-806

Van Valkenburgh B (1995) Tracking ecology over geological time – evolution within guilds of vertebrates. Trends Ecol Evol 10:71-76

Zeffer A, Johansson LC, Marmebro A (2003) Functional correlation between habitat use and leg morphology in birds (Aves). Biol J Linn Soc 79:461-484

A First Pass at Figures

July 5, 2011 13 comments

Even though our paper is intended for a technical audience, it is still important to ensure that a broad range of readers can access and understand the information contained within the text. For instance, not even a competent dinosaur paleontologist is necessarily familiar with all of the intricacies of ornithischian clade names like “Ankylopolexia” or “Neornithischia.” Thus, we want to provide a brief bit of background for readers of the paper.

One option, of course, is to write out brief definitions of various clades as they are introduced. This works okay in some cases – for instance, we definitely want to briefly explain what an ornithischian is – but to do this for every term can get a little unwieldy. An old adage states, “A picture is worth a thousand words,” and this is just as true in scientific writing as it is in popular writing.

So, I suggest that Figure 1 for the paper include a simplified cladogram of the major clades discussed in the paper. A first pass at this is given below (click on the image to see at full resolution):

Figure 1. Phylogeny

Figure 1. Phylogeny of Ornithischia (from multiple recent sources), showing major clades discussed in the text. Outlines show representative members of each clade; names in bold indicate clades with quadrupedal taxa.

There are a few things I should mention. First, the content of the figure is nowhere near finalized. However, there were a few principles I wanted to adhere to:

  • Keep it simple. Because this is only an overview figure, I did not deem it practical to include all of the taxa that we discuss. Instead, I just chose the “important” ones that will appear over and over again.
  • Terminology. In a few cases, such as Neornithischia, including only major named clades oversimplifies things just a little too much. For instance, there are a bunch of important neornithischians (e.g., Agilisaurus and Othnielosaurus) that don’t fit comfortably within ornithopods or marginocephalians, and I want to find ways to include such taxa. Thus, I’ve created terms like “Early neornithischians”. I realize that this may imply that they are a clade in their own right, where instead they form a comb or polytomy, but perhaps this is a simplification that just has to be made. If anyone has a suggestion for a better way to title the groups, please let me know. For now, I prefer “early neornithischians” over “basal neornithischians” and the like. “Basal” implies a ranking that just isn’t there for cladograms, but maybe other folks think this is less of a deal than I do.
  • Notation of quadrupedal taxa. Because quadrupedalism vs. bipedalism is so important for the paper, I bolded relevant taxa as outlined in the caption. The icons (discussed next) provide an additional clue. If I recall correctly (Andrew McDonald is probably most up to speed on this of anyone who follows this blog), there are probably a few non-hadrosaurid ornithopods that should be inferred to be quadrupedal, too.
  • Icons. I consider it very important to include at least a small figure for each taxon, so that readers who are not familiar with all of the terms can picture each clade in their mind. The icons that are shown here (from Mike Keesey’s Phylopic) are of generally high quality, but should be considered only temporary. Ideally, I would like to generate new images to go with our figure, if only because there has been such a hubbub over the running dinosaur pose recently.
  • Orientation. I opted for portrait rather than landscape orientation for the figure, primarily because I thought it was a more efficient and readable format. Any thoughts?
  • Time calibration. One option for the figure would be to time-calibrate it, and show the duration and estimated time of origin for each clade. I feel this might make things just a little too complex (and crowd other parts of the figure), but am open to alternative interpretations. Thoughts?

At any rate, that’s what we’ve got for now. Please chime in in the comments!

Image Sources: All images are from Phylopic, and are licensed accordingly under a Creative Commons License. Individual credits are as follows: Oscar Alcober & Ricardo Martinez (http://phylopic.org/image/246), Scott Hartman (http://phylopic.org/image/25; http://phylopic.org/image/48; http://phylopic.org/image/43; http://phylopic.org/image/33), Loewen et al. (http://phylopic.org/image/142), FunkMonk (http://phylopic.org/image/128), Lukas Panzarin (http://phylopic.org/image/140), Remes et al. (http://phylopic.org/image/146); Ville-Veikko Sinkkonen (http://phylopic.org/image/261)

Categories: Figures, Progress Reports
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