Home > Figures, Progress Reports > A First Pass at Figures

A First Pass at Figures

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)

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Categories: Figures, Progress Reports
  1. July 5, 2011 at 9:50 am

    Thanks for putting this first draft together, Andy. A few points.

    — To my eyes the cladogram is upside down. I am used to seeing them start with the most basal taxa at the top and work their way down to the most derived, so that the ladder runs from northwest down to southeast.

    — I am happy with the terms “Early thyreophorans” etc. They convey more information than “basal”, which only EVER means “not the branch that I am currently concentrating on”.

    — We need to be clearer about what we do and don’t think is quadrupedal. Bolding “Saurischia” right next to a bipedal theropod icon looks silly; I think in this case we really need to split Saurischia into Theropoda and Sauropodomorpha, with only the latter bolded. And of course even that is a great simplification, but I think a warranted one in this context.

    — Also on quadrupedality: look at the amazing Shantungosaurus photos on Dave Hone’s blog: http://archosaurmusings.wordpress.com/2011/07/04/zhucheng-week-starting-with-shantungosaurus/ — those forefeet do not look like those of an obligate quadruped, do they? I don’t know what to do with this observation, just thought I should toss it in.

    — On icons: I feel strongly that we, as an avowedly open project, should use the Phylopic icons and in doing so publicise that excellent project. “Hubbub over the running dinosaur pose?” Screw that. Sound and fury signifying nothing. Don’t lend it legitimacy.

    — I agree that portrait orientation is better for this than landscape.

    — I agree that for an introductory figure, time-calibration is too much complexity. Then again, since we’re aiming for PLoS ONE where there are no limits on figures, why not TWO phylogeny pictures? This one as a gentle introduction, and another more technical one that includes more terminal taxa, omits the space-consuming icons and calibrates by time?

    On this last point, I think what we’re seeing here is one way that our thinking is being hobbled by what scientific papers looked like in the past: very compact, terse to the point sometimes of incomprehensibility, all to save paper. We’re past that now, or should be. Let’s stretch out an enjoy the spacious new all-digital environment. If we can best make our point, and bring along a non-specialist audience with us, by including partially redundant figures, then heck, let’s do it. We’re living in the Shiny Digital Future, after all.

  2. July 5, 2011 at 6:16 pm

    Very nice figure. I like its simplicity, especially those icons. I agree with a lot of Mike’s points too (top-down orientation, etc). I recommend that regardless of how we present additional tree-related figures in the paper, we submit the Nexus-format phylogeny file as a supplemental file with the paper. The tree alone might be the most useful thing to some researchers (and might result in citations to our paper too). It’s a pain in the butt for researchers to re-invent the wheel by making trees when other published trees haven’t supplied electronic supplementary files.

    One possibility on how to present limb bone ratio results in the context of the phylogenetic tree (i.e., to illustrate the phylogenetic pattern of limb ratios) is to plot ratios beside species in the tree. I’ve made a figure that does this for my butterfly research at http://mysite.science.uottawa.ca/jfitz049//ButterflyShifts.pdf. It’s not necessarily something we should do with our project, but it’s a possibility.

  3. Christian Foth
    July 5, 2011 at 6:59 pm

    hi guys,

    I like the figure. As Mike said, I would split the saurischians, too.

    i just wanted to know if we plan do transform the data into phylogenetic independent contrast. As we planing to analize the limb data in a evolutionary context, based on phylogeny we should test, if the factors we used show a phylogenetic signal. If so we should perform such a PIC transformation. However, to do that we have to do a time calibration. This is also true for mapping values as continuous characters on the tree.

  4. July 6, 2011 at 12:12 pm

    Actually, “early” is by its very nature a time statement: that is, “early iguanodontians” have to occur earlier in time than hadrosaurids. While this is true for the first branches in each of these clusters, it is not universally true: Zalmoxes postdates many hadrosaurids, for instance.

    I’d be happier with “basal” or “primitive” for these, or even “early branching”.

    Even better: put all grade names in quotes, and show double thin branches coming to them, indicating you are a dealing with grades and not clades.

  5. July 6, 2011 at 1:36 pm

    Actually, “early” is by its very nature a time statement: that is, “early iguanodontians” have to occur earlier in time than hadrosaurids. While this is true for the first branches in each of these clusters, it is not universally true: Zalmoxes postdates many hadrosaurids, for instance.

    This is true; the problem is balancing the immediate comprehensibility of this introductory diagram against precision.

    The problem with “early branching” is that it’s more or less meaningless. By definition, Neornithischia and Thyreophora branched at the exact same same; but then so did Eusauropoda and Vulcanodon, so it’s useless to call Vulcanodon “early branching” unless you’re going to say the same of Eusauropoda. (Sorry to use a sauropod example — I don’t know the name of an analogous branch-based most-but-not-all-ornithischians clade.) For the same reason, I am not fond of “basal”.

    Actually, the best term for this may be the inexplicably discredited “primitive”. It means something specific: having morphologically diverged only a little from the common ancestor. When a lineage splits into two reflexive clades, it’s perfectly reasonable to designate one as advanced and the other as primitive.

    Even better: put all grade names in quotes [...]

    I hate this superstition.

    [...] and show double thin branches coming to them, indicating you are a dealing with grades and not clades.

    Yes, that would be helpful.

  6. Christian Foth
    July 6, 2011 at 7:22 pm

    but this is the same problem with primitive. your ‘primitive’ guys are only similar to the stem species if they existed short after the time of branching. In constrast, if the respective group exist over long persiods (e.g. heterodontosaurids) it has its one ‘independent’ evolution over several million years. Furthermore, primitive implies that ancestor is less good developed than the descendent.
    Thus, I thin the term ‘basal’ is the best one – this also the term they used in The Dinosauria.

  7. July 6, 2011 at 9:53 pm

    Lots of good points – I’m on vacation now (hmmm, so what am I doing checking the blog? don’t tell my spouse. . .), but will put together a revised version on my return.

    How to name basal/primitive/whatever taxa is a tough one. And re: the laddering of taxa, sauropods are right where they belong, at the primitive end of the tree. ;-) Of course, I should probably put ceratopsians up top!

  8. July 6, 2011 at 10:13 pm

    It’s funny how traditions grow up around these things. In sauropod cladograms, you almost always have the macronarians coming “after” the diplodocoids, working their way down to Saltasaurus, which comes last of all. I always get the sense that in ornithischian cladograms, it’s hadrosaurs that “win”, appearing in the “pinnacle of evolution” slot right at the end.

  9. July 7, 2011 at 1:42 am

    Mike: true! Or birds for Theropoda, rather than the obviously more pinnacle-ly Tyrannosaurinae.

  10. Henrique Niza
    July 10, 2011 at 5:17 pm

    Still on the “basal/primitive/whatever taxa” like Andy Farke put it maybe “original” might be a better term, in which it might be less confused. Even when we are referring to less basal/early taxa their basic body scheme is pretty much the same as those more basal/early.

    Each of them somewhat fit I guess, even when one could point out something that seems fishy.

  11. William Miller
    July 12, 2011 at 10:12 pm

    Splitting saurischians into Sauropodomorpha/Theropoda sounds good, as do Phylopic icons.

    I don’t know whether primitive, basal or early is best. Maybe Ankylosauria/Stegosauria/”other thyreophorans”?

  12. Chris Noto
    July 15, 2011 at 8:21 pm

    Mike Taylor :
    – Also on quadrupedality: look at the amazing Shantungosaurus photos on Dave Hone’s blog: http://archosaurmusings.wordpress.com/2011/07/04/zhucheng-week-starting-with-shantungosaurus/ — those forefeet do not look like those of an obligate quadruped, do they? I don’t know what to do with this observation, just thought I should toss it in.

    Despite the fact that several partial skeletons have been discovered, it isn’t clear to me looking at the literature on hand what, if any, of the manus material is preserved. Looking at Dave Hone’s pictures the forelimbs appear very gracile with massively built hindlimbs. Reminds me a lot of Muttaburrasaurus actually. Perhaps using the gracility index or other measures, it will come out more on the bipedal (or at least facultative) side of things. However, it could be the the long tail is providing counterbalance to the massive body weight, allowing less to be carried by the forelimbs, or there were accessory soft tissues that provided added stability to the manus during weight bearing. Very interesting point. The forelimbs certainly do look different from that of most hadrosaurs I have seen.

  13. July 16, 2011 at 5:09 pm

    Dave’s posts say that pretty much all bones of Shantungosaurus have been recovered, but that’s the extent of my knowledge. Anyone out there know what the story is?

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