Tutorial 38: little projects as footsteps toward understanding
January 11, 2021
This is a very belated follow-up to “Tutorial 12: How to find problems to work on“, and it’s about how to turn Step 2, “Learn lots of stuff”, into concrete progress. I’m putting it here, now, because I frequently get asked by students about how to get started in research, and I’ve been sending them the same advice for a while. As with Tutorial 25, from now on I can direct the curious to this post, and spend more time talking with them about what they’re interested in, and less time yakking about nuts and bolts. But I hope the rest of you find this useful, too.
Assuming, per Tutorial 12, that you’ve picked something to investigate–or maybe you’re trying to pick among things to investigate–what next? You need a tractable way to get started, to organize the things you’re learning, and to create a little structure for yourself. My recommendation: do a little project, with the emphasis on little. Anyone can do this, in any area of human activity. Maybe your project will be creating a sculpture, shooting and editing a video, learning–or creating–a piece of music, or fixing a lawn mower engine. My central interest is how much we still have to discover about the natural world, so from here on I’m going to be writing as a researcher addressing other researchers, or aspiring researchers.

Arteries of the anterior leg, from Gray’s Anatomy (1918: fig. 553). Freely available courtesy of Bartleby.com.
I’ll start with a couple of examples, both from my own not-too-distant history. A few years ago I got to help some of my colleagues from the College of Podiatric Medicine with a research project on the perforating branch of the peroneal artery (Penera et al. 2014). I knew that vessel from textbooks and atlases and from having dissected a few out, but I had never read any of the primary (journal) literature on it. As the designated anatomist on the project, I needed to write up the anatomical background. So I hit the journals, tracked down what looked like the most useful papers, and wrote a little 2-page summary. We didn’t use all of it in the paper, and we didn’t use it all in one piece. Some sentences went into the Introduction, others into the Discussion, and still others got dropped entirely or cut way down. But it was still a tremendously useful exercise, and in cases like this, it’s really nice to have more written down than you actually need. Here’s that little writeup, in case you want to see what it looks like:
Wedel 2013 anatomy of the perforating branch of the peroneal artery
More recently, when I started working with Jessie Atterholt on weird neural canal stuff in dinosaurs, I realized that I needed to know more about glycogen bodies in birds, and about bird spinal cords generally. I expected that to be quick and easy: read a couple of papers, jot down the important bits, boom, done. Then I learned about lumbosacral canals, lobes of Lachi, the ‘ventral eminences’ of the spinal cord in ostriches, and more, a whole gnarly mess of complex anatomy that was completely new to me. I spent about a week just grokking all the weird crap that birds have going on in their neural canals, and realized that I needed to crystallize my understanding while I had the whole structure in my head. Otherwise I’d come back in a few months and have to learn it all over again. Because it was inherently visual material, this time I made a slide deck rather than a block of text, something I could use to get my coauthors up to speed on all this weirdness, as well as a reminder for my future self. Here’s that original slide deck:
Wedel 2018 Avian lumbosacral spinal cord specializations
If you’re already active in research, you may be thinking, “Yeah, duh, of course you write stuff down as you get a handle on it. That’s just learning.” And I agree. But although this may seem basic, it isn’t necessarily obvious to people who are just starting out. And even to the established, it may not be obvious that doing little projects like this is a good model for making progress generally. Each one is a piton driven into the mountainside that I’m trying to climb: useful for me, and assuming I get them out into the world, useful for anyone I’d like to come with me (which, for an educator and a scientist, means everyone).

A view down the top of the vertebral column in the mounted skeleton of Apatosaurus louisae, CM 3018, showing the trough between the bifurcated neural spines.
If you’re not active in research, the idea of writing little term papers may sound like purgatory. But writing about something that you love, that fascinates you, is a very different proposition from writing about dead royalty or symbolism because you have to for a class.* I do these little projects for myself, to satisfy my curiosity, and it doesn’t feel like work. More like advanced play. When I’m really in the thick of learning a new thing–and not, say, hesitating on the edge before I plunge in–I am so happy that I tend to literally bounce around like a little kid, and the only thing that keeps me sitting still is the lure of learning the next thing. That I earn career beans for doing this still seems somewhat miraculous, like getting paid to eat ice cream.
* YMMV, history buffs and humanities folks. If dead royalty and symbolism rock your world but arteries and vertebrae leave you cold, follow your star, and may a thousand gardens grow.
Doing little projects is such a convenient and powerful way to make concrete progress that it has become my dominant mode. As with the piece that I wrote about the perforating branch of the peroneal artery, the products rarely get used wholesale in whatever conference presentation or research paper I end up putting together, but they’re never completely useless. First, there is the benefit to my understanding that I get from assembling them. Second, they’re useful for introducing other people to the sometimes-obscure stuff I work on, and nothing makes you really grapple with a problem like having to explain it to others. And third, these little writeups and slideshows become the Lego bricks from which I assemble future talks and papers. The bird neural canal slide deck became a decent chunk of our presentation on the Snowmass Haplocanthosaurus at the 1st Palaeontological Virtual Congress (Wedel et al. 2018)–and it’s about to become something even better. (Four months later: it did!)
The operative word at the start of the last paragraph is ‘concrete’. I don’t think this was always the case, but now that I’m in my mid-40s ‘what I know’ is basically equivalent to ‘what I remember’, which is basically equivalent to ‘what I’ve written down’. (And sometimes not even then–Mike and I both run across old posts here on SV-POW! that we’ve forgotten all about, which is a bit scary, given how often we put novel observations and ideas into blog posts.) Anyway, this is why I like the expression ‘crystallize my understanding’: the towers of comprehension that I build in my head are sand castles, and if I don’t find a way to freeze them in place, they will be washed away by time and my increasingly unreliable cerebral machinery.
Also, if I divide my life into the things I could do and the things I have done, only the things in the latter category are useful. So if you are wondering if it’s worthwhile to write a page to your future self about valves in the cerebral arteries of rats, or all of the dinosaurs from islands smaller than Great Britain, or whatever strange thing has captured your attention, I say yes, go for it. Don’t worry about finding something novel to say; at the early stages you’re just trying to educate yourself (also, talks and papers need intro and background material, so you can still get credit for your efforts). I’ll bet that if you set yourself the goal of creating a few of these–say, one per year, or one per semester–you’ll find ways to leverage them once you’ve created them. If all else fails, start a blog. That might sound flip, but I don’t mean for it to. I got my gig writing for Sky & Telescope because I’d been posting little observing projects for the readers of my stargazing blog.
A final benefit of doing these little projects: they’re fast and cheap, like NASA’s Discovery missions. So they’re a good way to dip your toes into a new area before you commit to something more involved. The more things you try, the more chances you have to discover whatever it is that’s going to make you feel buoyantly happy.
You may have noticed that all of my examples in this post involved library research. That’s because I’m particularly interested in using little projects to get started in new lines of inquiry, and whenever you are starting out in a new area, you have to learn where the cutting edge is before you can move it forward (Tutorial 12 again). Also, as a practical consideration, most of us are stuck with library research right now because of the pandemic. Obviously this library research is no substitute for time in the lab or the field, but even cutters and diggers need to do their homework, and these little projects are the best way that I’ve found of doing that.
P.S. If you are a student, read this and do likewise. And, heck, everyone else who writes should do that, too. It is by far the advice I give most often as a journal editor and student advisor.
P.P.S. As long as you’re reading Paul Graham, read this piece, too–this whole post was inspired by the bit near the end about doing projects.
References
- Gray, Henry. 1918. Anatomy of the Human Body. Lea & Febiger, Philadelphia. Bartleby.com, 2000. www.bartleby.com/107/.
- Penera, K., Manji, K., Wedel, M., Shofler, D., and Labovitz, J. 2014. Ankle syndesmotic fixation using two screws: Risk of injury to the Perforating Branch of the Peroneal Artery. The Journal of Foot and Ankle Surgery 53(5):534-8. DOI: 10.1053/j.jfas.2014.04.006
- Wedel, M.J., Atterholt, J., Macalino, J., Nalley, T., Wisser, G., and Yasmer, J. 2018. Reconstructing an unusual specimen of Haplocanthosaurus using a blend of physical and digital techniques. 1st Palaeontological Virtual Congress / PeerJ Preprints 6:e27431v1
What if Amphicoelias fragillimus was a rebbachisaurid?
October 21, 2018
An important paper is out today: Carpenter (2018) names Maraapunisaurus, a new genus to contain the species “Amphicoelias“ fragillimus, on the basis that it’s actually a rebbachisaurid rather than being closely related to the type species Amphicoelias altus.
And it’s a compelling idea, as the illustration above shows. The specimen (AMNH FR 5777) has the distinctive dorsolaterally inclined lateral processes of a rebbachisaur, as implied by the inclined laminae meeting at the base of the SPOLs, and famously has the very excavated and highly laminar structure found in rebbachisaurs — hence the species name fragillimus.
Ken’s paper gives us more historical detail than we’ve ever had before on this enigmatic and controversial specimen, including extensive background to the excavations. The basics of that history will be familiar to long-time readers, but in a nutshell, E. D. Cope excavated the partial neural arch of single stupendous dorsal vertebra, very briefly described it and illustrated it (Cope 1878), and then … somehow lost it. No-one knows how or where it went missing, though Carpenter offers some informed speculation. Most likely, given the primitive stabilisation methods of the day, it simply crumbled to dust on the journey east.

Carpenter 2018: Frontispiece. E. D. Cope, the discoverer of AMNH FR 5777, drawn to scale with the specimen itself.
Cope himself referred the vertebra to his own existing sauropod genus Amphicoelias — basically because that was the only diplodocoid he’d named — and there it has stayed, more or less unchallenged ever since. Because everyone knows Amphicoelias (based on the type species A. altus) is sort of like Diplodocus(*), everyone who’s tried to reconstruct the size of the AMNH FR 5777 animal has done so by analogy with Diplodocus — including Carpenter himself in 2006, Woodruff and Foster (2014) and of course my own blog-post (Taylor 2010).
(*) Actually, it’s not; but that’s been conventional wisdom.
Ken argues, convincingly to my mind, that Woodruff and Foster (2014) were mistaken in attributing the great size of the specimen to a typo in Cope’s description, and that it really was as big as described. And he argues for a rebbachisaurid identity based on the fragility of the construction, the lamination of the neural spine, the extensive pneumaticity, the sheetlike SDL, the height of the postzygapophyses above the centrum, the dorsolateral orientation of the transverse processes, and other features of the laminae. Again, I find this persuasive (and said so in my peer-review of the manuscript).

Carpenter 2018: Figure 3. Drawing made by E.D. Cope of the holotype of Maraapunisaurus fragillimus (Cope, 1878f) with parts labeled. “Pneumatic chambers*” indicate the pneumatic cavities dorsolateral of the neural canal, a feature also seen in several rebbachisaurids. Terminology from Wilson (1999, 2011) and Wilson and others (2011).
If AMNH FR 5777 is indeed a rebbachisaur, then it can’t be a species of Amphicoelias, whose type species is not part of that clade. Accordingly, Ken gives it a new generic name in this paper, Maraapunisaurus, meaning “huge reptile” based on Maraapuni, the Southern Ute for “huge” — a name arrived at in consultation with the Southern Ute Cultural Department, Ignacio, Colorado.
How surprising is this?
On one level, not very: Amphicoelias is generally thought to be a basal diplodocoid, and Rebbachisauridae was the first major clade to diverge within Diplodocoidae. In fact, if Maraapunisaurus is basal within Rebbachisauridae, it may be only a few nodes away from where everyone previously assumed it sat.
On the other hand, a Morrison Formation rebbachisaurid would be a big deal for two reasons. First, because it would be the only known North American rebbachisaur — all the others we know are from South America, Africa and Europe. And second, because it would be, by some ten million years, the oldest known rebbachisaur — irritatingly, knocking out my own baby Xenoposeidon (Taylor 2018), but that can’t be helped.
Finally, what would this new identity mean for AMNH FR 5777’s size?

Carpenter 2018: Figure 7. Body comparisons of Maraapunisaurus as a 30.3-m-long rebbachisaurid (green) compared with previous version as a 58-m-long diplodocid (black). Lines within the silhouettes approximate the distal end of the diapophyses (i.e., top of the ribcage). Rebbachisaurid version based on Limaysaurus by Paul (2016), with outline of dorsal based on Rebbachisaurus; diplodocid version modified from Carpenter (2006).
Because dorsal vertebrae in rebbachisaurids are proportionally taller than in diplodocids, the length reconstructed from a given dorsal height is much less for rebbachisaurs: so much so that Ken brings in the new version, based on the well-represented rebbachisaur Limaysaurus tessonei, at a mere 30.3 m, only a little over half of the 58 m he previously calculated for a diplodocine version. That’s disappointing for those of us who like our sauropods stupidly huge. But the good news is, it makes virtually no difference to the height of the animal, which remains prodigious — 8 m at the hips, twice the height of a giraffe’s raised head. So not wholly contemptible.
Exciting times!
References
- Carpenter, Kenneth. 2006. Biggest of the big: a critical re-evaluation of the mega-sauropod Amphicoelias fragillimus Cope, 1878. pp. 131-137 in J. Foster and S. G. Lucas (eds.), Paleontology and Geology of the Upper Jurassic Morrison Formation. New Mexico Museum of Natural History and Science Bulletin 36.
- Carpenter, Kenneth. 2018. Maraapunisaurus fragillimus, n.g. (formerly Amphicoelias fragillimus), a basal rebbachisaurid from the Morrison Formation (Upper Jurassic) of Colorado. Geology of the Intermountain West 5:227–244.
- Cope, Edward D. 1878. A new species of Amphicoelias. American Naturalist 12:563–565.
- Paul, Gregory S. 2016. The Princeton field guide to dinosaurs. Princeton, Princeton University Press. 360 pages.
- Taylor, Michael P. 2010. How big was Amphicoelias fragillimus? I mean, really? Sauropod Vertebra Picture of the Week, 19 February, 2010. https://svpow.com/2010/02/19/how-big-was-amphicoelias-fragillimus-i-mean-really/
- Taylor, Michael P. 2018. Xenoposeidon is the earliest known rebbachisaurid sauropod dinosaur. PeerJ 6:e5212. doi: 10.7717/peerj.5212
- Woodruff, D. Carey, and John R. Foster. 2014. The fragile legacy of Amphicoelias fragillimus (Dinosauria: Sauropoda; Morrison Formation — latest Jurassic). Volumina Jurassica 12(2):211-220. doi:10.5604/17313708.1130144
How crazy are the cervicals of Mendozasaurus?
February 1, 2018
There’s a new paper out, describing the Argentinian titanosaur Mendozasaurus in detail (Gonzalez Riga et al. 2018): 46 pages of multi-view photos, tables of measurement, and careful, detailed description and discussion. But here’s what leapt out at me when I skimmed the paper:

Gonzalez Riga et al. (2018: figure 6). Mendozasaurus neguyelap cervical vertebra (IANIGLA-PV 076/1) in (A) anterior, (B) left lateral, (C) posterior, (D) right lateral, (E) ventral and (F) dorsal views. Scale bar = 150 mm. Sorry it’s monochrome, but that’s how it appears in the paper.
Just look at that thing. It’s ridiculous. In our 2013 PeerJ paper “Why Giraffes have Short Necks” (Taylor and Wedel 2013), we included a “freak gallery” as figure 7: five very different sauropod cervicals:

Taylor and Wedel (2013: figure 7). Disparity of sauropod cervical vertebrae. 1, Apatosaurus “laticollis” Marsh, 1879b holotype YPM 1861, cervical ?13, now referred to Apatosaurus ajax (see McIntosh, 1995), in posterior and left lateral views, after Ostrom & McIntosh (1966, plate 15); the portion reconstructed in plaster (Barbour, 1890, figure 1) is grayed out in posterior view; lateral view reconstructed after Apatosaurus louisae (Gilmore, 1936, plate XXIV). 2, “Brontosaurus excelsus” Marsh, 1879a holotype YPM 1980, cervical 8, now referred to Apatosaurus excelsus (see Riggs, 1903), in anterior and left lateral views, after Ostrom & McIntosh (1966, plate 12); lateral view reconstructed after Apatosaurus louisae (Gilmore, 1936, plate XXIV). 3, “Titanosaurus” colberti Jain & Bandyopadhyay, 1997 holotype ISIR 335/2, mid-cervical vertebra, now referred to Isisaurus (See Wilson & Upchurch, 2003), in posterior and left lateral views, after Jain & Bandyopadhyay (1997, figure 4). 4, “Brachiosaurus” brancai paralectotype MB.R.2181, cervical 8, now referred to Giraffatitan (see Taylor, 2009), in posterior and left lateral views, modified from Janensch (1950, figures 43–46). 5, Erketu ellisoni holotype IGM 100/1803, cervical 4 in anterior and left lateral views, modified from Ksepka & Norell (2006, figures 5a–d).
But this Mendozasaurus vertebra is crazier than any of them, with its tiny centrum, its huge, broad but anteroposteriorly flattened neural spine, and its pronounced lSPRLs.
I just don’t know what to make of this, and neither does Matt. And part of the reason for this may be that neither of us has had that much to do with titanosaurs. As Matt said in email, “Those weird ballooned-up neural spines in titanosaurs kind of freak me out.” And I could not agree more.
And of course as sauropodologists, we really should familiarise ourselves with titanosaurs. There are a lot of them, and they account for a lot of sauropod evolution. Someone recently made the point, either in an SV-POW! comment or on Facebook, that titanosaurs may be to sauropods what monkeys and apes are to primates: a subclade that is way more diverse than the rest of the clade put together.
It’s starting to look like an extreme historical accident that Camarasaurus, diplodocines and brachiosaurids — all temporally and/or geographically restricted groups — were the first well-known sauropods, and for decades defined our notion of what sauropods were like. Meanwhile, the much more widespread and long-surviving rebbachisaurs and titanosaurs were poorly understood until really the last 25 years or so. For the first century of sauropodology, our ideas about sauropods were driven by weird, comparatively short-lived outliers.
That our appreciation of titanosaur diversity has come so late says something about how our discovery of the natural world is more to do with geopolitics and the quirks of exploration than what’s actually out there. Sauropods were defined by diplodocids for so long because that’s what happened to be in the ground in the exposed rocks of North America, and that’s where the well-funded museums and expeditions were.
We at SV-POW! towers have often wondered how different our idea of what dinosaurs even were would be if the Liaoning deposits had been available to Buckland, Mantell, and Owen. It seems like that unavoidable that, if they’d first become familiar with feathered but osteologically aberrant (by modern standards) birds, one of two things would have happened. Either they would either have never coined the term “Dinosauria” at all, recognizing that Megalosaurus (and later Allosaurus and Tyrannosaurus) were just big versions of their little feathered ur-birds. Or they would have included Dinosauria as a primitive subclass of Aves.
References
- González Riga, Bernardo J., Philip D. Mannion, Stephen F. Poropat, Leonardo D. Ortiz David and Juan Pedro Coria. 2018. Osteology of the Late Cretaceous Argentinean sauropod dinosaur Mendozasaurus neguyelap: implications for basal titanosaur relationships. Zoological Journal of the Linnean Society, 46 pages, 28 figures. doi:10.1093/zoolinnean/zlx103
- Taylor, Michael P., and Mathew J. Wedel. 2013. Why sauropods had long necks; and why giraffes have short necks. PeerJ 1:e36. 41 pages, 11 figures, 3 tables. doi:10.7717/peerj.36
Note. This post contains material from all three of us (Darren included), harvested from an email conversation.
The bizarre caudal neural spines of Tambatitanis amicitiae
August 13, 2014
Today for the first time I saw Saegusa and Ikeda’s (2014) new monograph describing the Japanese titanosauriform Tambatitanis amicitiae. I’ve not yet had a chance to read the paper — well, it’s 65 pages long — but it certainly looks like they’ve done a nice, comprehensive job on a convincing new taxon represented by good material: teeth, braincase, dentary, atlas, and as-yet unprepared fragmentary cervical, fragmentary dorsals, sacral spines, some nice caudals, some ribs and chevrons, and pubis and ilium.
What catches the eye immediately is the bizarre forward-curved neural spines of the anterior caudals:

Saegusa and Ikeda (2104: fig. 8): Tambatitanis amicitiae gen. et sp. nov., holotype (MNHAH D-1029280). A, Cd2–Cd11 in right lateral view. B, Cdx1–Cdx2 in right lateral view.
Here’s the third caudal in detail. (The first is fragmentary, and the second has some minor reconstruction near the tip of the spine which sceptical readers might think is covering up a misconstruction):

Saegusa and Ikeda (2014: fig. 11): Tambatitanis amicitiae gen. et sp. nov., holotype (MNHAH D-1029280). A–F, stereopairs of Cd3. A, right lateral view. B, left lateral view of the neural spine. C, anterior view. D, posterior view. E, dorsal view. F, ventral view. G, CT slices through the neural spine of Cd3, part corresponding to the matrix that filling the internal chamber is removed from the image. Greek letters in B and D indicate the position of CT slices shown in G. Scale bar = 10cm.
And here is the right-lateral view in close-up:

Saegusa and Ikeda (2014: fig. 11): Tambatitanis amicitiae gen. et sp. nov., holotype (MNHAH D-1029280) in right lateral view.
A phylogenetic analysis based on that of D’Emic (2012) recovers the new taxon in a polytomy with the Euhelopus clade that’s going to need a new name pretty soon, since it keeps growing and can’t be called Euhelopodidae for historical reasons: [that should probably be called Euhelopodidae: see discussion in comments]:

Saegusa and Ikeda (2014: fig. 23): Phylogenetic relationships of the titanosauriform sauropod Tambatitanis amicitiae gen. et sp. nov. from the Lower Cretaceous Sasayama Group of Tamba, Hyogo, Japan produced using the matrix of D’Emic (2012) with the addition of Tambatitanis. The final matrix, including 29 taxa and 119 characters, was analyzed in PAUP* 4.0b10. Left side, strict consensus of 81 most parsimonious trees (length = 207; CI = 0.609; RI = 0.8010; RC = 0.489), figures below nodes are decay indices. Right side, 50% majority rule consensus, figures above and below nodes represents the percentage of MPTs in which the node was recovered (only those relationships recovered in over 50% of the MPTs are shown).
Nice to see that new sauropods just keep on rolling out of the ground faster than we can blog about them!
References
- D’Emic, Michael D. 2012. The early evolution of titanosauriform sauropod dinosaurs. Zoological Journal of the Linnean Society 166:624-671.
- Saegusa, Haruo, and Tadahiro Ikeda. 2014. A new titanosauriform sauropod (Dinosauria: Saurischia) from the Lower Cretaceous of Hyogo, Japan. Zootaxa 3848(1):1-66. doi:10.11646/zootaxa.3848.1.1
Mounted skeleton of Emeus crassus
June 16, 2014
In a back room at the Field Museum, from my visit in 2012.
I took a lot of photos of the neck, which nicely records the transition in neural spine shape from simple to bifurcated–a topic of interest to sauropodophiles.
I think it’s fair to say that this “bifurcation heat-map”, from Wedel and Taylor (2013a: figure 9), has been one of the best-received illustrations that we’ve prepared:
(See comments from Jaime and from Mark Robinson.)
Back when the paper came out, Matt rashly said “Stand by for a post by Mike explaining how it came it be” — a post which has not materialised. Until now!
This illustration was (apart from some minor tweaking) produced by a program that I wrote for that purpose, snappily named “vcd2svg“. That name is because it converts a vertebral column description (VCD) into a scalable vector graphics (SVG) file, which you can look at with a web-browser or load into an image editor for further processing.
The vertebral column description is in a format designed for this purpose, and I think it’s fairly intuitive. Here, for example, is the fragment describing the first three lines of the figure above:
Taxon: Apatosaurus louisae
Specimen: CM 3018
Data: —–YVVVVVVVVV|VVVuuunnn-
Taxon: Apatosaurus parvus
Specimen: UWGM 155556/CM 563
Data: –nnn-VVV—V-V|VVVu——
Taxon: Apatosaurus ajax
Specimen: NMST-PV 20375
Data: –n–VVVVVVVVVV|VVVVYunnnn
Basically, you draw little ASCII pictures of the vertebral column. Other directives in the file explain how to draw the various glyphs represented by (in this case) “Y”, “V”, “u”, and “n”.
It’s pretty flexible. We used the same program to generate the right-hand side (though not the phylogenetic tree) of Wedel and Taylor (2013b: figure 2):
The reason I mention this is because I released the software today under the GNU General Public Licence v3.0, which is kind of like CC By-SA. It’s free for anyone to download, use, modify and redistribute either verbatim or in modified form, subject only to attribution and the requirement that the same licence be used for modified versions.
vcd2svg is written in Perl, and implemented in part by the SVG::VCD module, which is included in the package. It’s available as a CPAN module and on GitHub. There’s documentation of the command-line vcd2svg program, and of the VCD file format. Also included in the distribution are two documented examples: the bifurcation heat-map and the caudal pneumaticity diagram.
Folks, please use it! And feel free to contribute, too: as the change-log notes, there’s work still to be done, and I’ll be happy to take pull requests from those of you who are programmers. And whether you’re a programmer or not, if you find a bug, or want a new feature, feel free to file an issue.
A final thought: in academia, you don’t really get credit for writing software. So to convert the work that went into this release into some kind of coin, I’ll probably have to write a short paper describing it, and let that stand as a proxy for the actual program. Hopefully people will cite that paper when they generate a figure using the software, the way we all reflexively cite Swofford every time we use PAUP*.
Update (12 April 2014)
On Vertebrat’s suggestion, I have renamed the program VertFigure.
References
- Swofford, D. L. 2002. PAUP*: phylogenetic analysis using parsimony (* and other methods). Sinauer Associates, Sunderland, MA.
- Wedel, M.J., and Taylor, M.P. 2013. Neural spine bifurcation in sauropod dinosaurs of the Morrison Formation: ontogenetic and phylogenetic implications. Palarch’s Journal of Vertebrate Palaeontology 10(1): 1-34. ISSN 1567-2158.
- Wedel, Mathew J., and Michael P. Taylor. 2013. Caudal pneumaticity and pneumatic hiatuses in the sauropod dinosaurs Giraffatitan and Apatosaurus.PLOS ONE 8(10):e78213. 14 pages. doi:10.1371/journal.pone.0078213 [PDF]
Why giraffes have short necks
September 26, 2012
Today sees the publication, on arXiv (more on that choice in a separate post), of Mike and Matt’s new paper on sauropod neck anatomy. In this paper, we try to figure out why it is that sauropods evolved necks six times longer than that of the world-record giraffe — as shown in Figure 3 from the paper (with a small version of Figure 1 included as a cameo to the same scale):

Figure 3. Necks of long-necked sauropods, to the same scale. Diplodocus, modified from elements in Hatcher (1901, plate 3), represents a “typical” long-necked sauropod, familiar from many mounted skeletons in museums. Puertasaurus modified from Wedel (2007a, figure 4-1). Sauroposeidon scaled from Brachiosaurus artwork by Dmitry Bogdanov, via commons.wikimedia.org (CC-BY-SA). Mamenchisaurus modified from Young and Zhao (1972, figure 4). Supersaurus scaled from Diplodocus, as above. Alternating pink and blue bars are one meter in width. Inset shows Figure 1 to the same scale.
This paper started life as a late-night discussion over a couple of beers, while Matt was over in England for SVPCA back in (I think) 2008. It was originally going to be a short note in PaleoBios, just noting some of the oddities of sauropod cervical architecture — such as the way that cervical ribs, ventral to the centra, elongate posteriorly but their dorsal counterparts the epipophyses do not.
As so often, the tale grew in the telling, so that a paper we’d initially imagined as a two-or-three-page note became Chapter 5 of my dissertation under the sober title of “Vertebral morphology and the evolution of long necks in sauropod dinosaurs”, weighing in at 41 1.5-spaced pages. By now the manuscript had metastatised into a comparison between the necks of sauropods and other animals and an analysis of the factors that enabled sauropods to achieve so much more than mammals, birds, other theropods and pterosaurs.
(At this point we had one of our less satisfactory reviewing experiences. We sent the manuscript to a respected journal, where it wasn’t even sent out to reviewers until more than a month had passed. We then had to repeatedly prod the editor before anything else happened. Eventually, two reviews came back: one of them careful and detailed; but the other, which we’d waited five months for, dismissed our 53-page manuscript in 108 words. So two words per page, or about 2/3 of a word per day of review time. But let’s not dwell on that.)

Figure 6. Basic cervical vertebral architecture in archosaurs, in posterior and lateral views. 1, seventh cervical vertebra of a turkey, Meleagris gallopavo Linnaeus, 1758, traced from photographs by MPT. 2, fifth cervical vertebra of the abelisaurid theropod Majungasaurus crenatissimus Depéret, 1896,UA 8678, traced from O’Connor (2007, figures 8 and 20). In these taxa, the epipophyses and cervical ribs are aligned with the expected vectors of muscular forces. The epipophyses are both larger and taller than the neural spine, as expected based on their mechanical importance. The posterior surface of the neurapophysis is covered by a large rugosity, which is interpreted as an interspinous ligament scar like that of birds (O’Connor, 2007). Because this scar covers the entire posterior surface of the neurapophysis, it leaves little room for muscle attachments to the spine. 3, fifth cervical vertebra of Alligator mississippiensis Daudin, 1801, MCZ 81457, traced from 3D scans by Leon Claessens, courtesy of MCZ. Epipophyses are absent. 4, eighth cervical vertebra of Giraffatitan brancai (Janensch, 1914) paralectotype HMN SII, traced from Janensch (1950, figures 43 and 46). Abbreviations: cr, cervical rib; e, epipophysis; ns, neural spine; poz, postzygapophysis.
This work made its next appearance as my talk at SVPCA 2010 in Cambridge, under the title Why giraffes have such short necks. For the talk, I radically restructured the material into a form that had a stronger narrative — a process that involved a lot of back and forth with Matt, dry-running the talk, and workshopping the order in which ideas were presented. The talk seemed to go down well, and we liked the new structure so much more than the old that we reworked the manuscript into a form that more closely resembled the talk.
That’s the version of the manuscript that we perfected in New York when we should have been at all-you-can-eat sushi places. It’s the version that we submitted on the train from New York to New Haven as we went to visit the collections of the Yale Peabody Museum. And it’s the version that was cursorily rejected from mid-to-low ranked palaeo journal because a reviewer said “The manuscript reads as a long “story” instead of a scientific manuscript” — which was of course precisely what we’d intended.
Needless to say, it was deeply disheartening to have had what we were convinced was a good paper rejected twice from journals, at a cost of three years’ delay, on the basis of these reviews. One option would have been to put the manuscript back into the conventional “scientific paper” straitjacket for the second journal’s benefit. But no. We were not going to invest more work to make the paper less good. We decided to keep it in its current, more readable, form and to find a journal that likes it on that basis.
At the moment, the plan is to send it to PeerJ when that opens to submissions. (Both Matt and I are already members.) But that three-years-and-rolling delay really rankles, and we both felt that it wasn’t serving science to keep the paper locked up until it finally makes it into a journal — hence the deposition in arXiv which we plan to talk about more next time.
In the paper, we review seven characteristics of sauropod anatomy that facilitated the evolution of long necks: absolutely large body size; quadrupedal stance; proportionally small, light head; large number of cervical vertebrae; elongation of cervical vertebrae; air-sac system; and vertebral pneumaticity. And we show that giraffes have only two of these seven features. (Ostriches do the next best, with five, but they are defeated by their feeble absolute size.)
The paper incorporates some material from SV-POW! posts, including Sauropods were corn-on-the-cob, not shish kebabs. In fact, come to think of it, we should have cited that post as a source. Oh well. We do cite one SV-POW! post: Darren’s Invading the postzyg, which at the time of writing is the only published-in-any-sense source for pneumaticity invading cervical postzygapogyses from the medial surface.
As for the non-extended epipophyses that kicked the whole project off: we did illustrate how they could look, and discussed why they would seem to make mechanical sense:

Figure 10. Real and speculative muscle attachments in sauropod cervical vertebrae. 1, the second through seventeenth cervical vertebrae of Euhelopus zdanskyi Wiman, 1929 cotype specimen PMU R233a-δ(“Exemplar a”). 2, cervical 14 as it actually exists, with prominent but very short epipophyses and long cervical ribs. 3, cervical 14 as it would appear with short cervical ribs. The long ventral neck muscles would have to attach close to the centrum. 4, speculative version of cervical 14 with the epipophyses extended posteriorly as long bony processes. Such processes would allow the bulk of both the dorsal and ventral neck muscles to be located more posteriorly in the neck, but they are not present in any known sauropod or other non-avian dinosaur. Modified from Wiman (1929, plate 3).
But we found and explained some good reasons why this apparently appealing arrangement would not work. You’ll need to read the paper for details.
Sadly, we were not able to include this slide from the talk illustrating the consequences:
Anyway, go and read the paper! It’s freely available, of course, like all arXiv depositions, and in particular uses the permissive Creative Commons Attribution (CC BY) licence. We have assembled related information over on this page, including full-resolution versions of all the figures.
In the fields of maths, physics and computer science, where deposition in arXiv is ubiquitous, standard practice is to go right ahead and cite works in arXiv as soon as they’re available, rather than waiting for them to appear in journals. We will be happy for the same to happen with our paper: if it contains information that’s of value to you, then feel free to cite the arXiv version.
Reference
- Taylor, Michael P., and Mathew J. Wedel. 2012. Why sauropods had long necks; and why giraffes have short necks. arXiv:1209.5439. 39 pages, 11 figures, 3 tables. [Full-resolution figures]
Neural spine bifurcation in sauropods, Part 4: is Suuwassea a juvenile of a known diplodocid?
April 12, 2012
I don’t intend to write a comprehensive treatise on the morphology and phylogeny of Suuwassea. Jerry Harris has already done that, several times over (Harris 2006a, b, c, 2007, Whitlock and Harris 2010). Rather, I want to address the contention of Woodruff and Fowler (2012) that Suuwassea is a juvenile of a known diplodocid, building on the information presented in the first three posts in this series (Part 1, Part 2, Part 3).
In the abstract, Woodruff and Fowler (2012:1) wrote:
On the basis of shallow bifurcation of its cervical and dorsal neural spines, the small diplodocid Suuwassea is more parsimoniously interpreted as an immature specimen of an already recognized diplodocid taxon.
First of all, that’s not what ‘parsimoniously’ means. It’s just not. In a phylogenetic analysis using unweighted characters, there is no such thing as a ‘key’ character — which by the way means that the subtitle of the paper, “a critical phylogenetic character”, is wrong. All characters are equal. Even if the characters were weighted, neural spine bifurcation would have to be weighted pretty darned heavily for it to outweigh all the other characters combined, which is what the sentence quoted above suggests.
Comparisons with known diplodocids
Next problem: if Suuwassea is a juvenile of an already recognized diplodocid, it shouldn’t take long to figure out which one. There aren’t all that many candidates, and we can consider them in turn. There are loads of characters, especially cranial and appendicular, separating Suuwassea from Apatosaurus, Diplodocus and the rest, and anyone who wants to keep track of all of them is welcome to do so. I care about vertebrae, and I’m prepared to argue that Suuwassea is a distinct taxon based on cervical morphology alone.
Diplodocus
Here are the sixth cervical vertebrae of Suuwassea emiliae ANS 21122 (Harris 2006c:Text-fig. 7B) and Diplodocus carnegii CM 84/94 (Hatcher 1901:pl. 3, flipped left-to-right for ease of comparison). They are not to scale–I made the images the same cotyle diameter for ease of comparison.
Elongation first. C6 of S. emilieae has a centrum length of 257 mm, a cotyle diameter of 75 mm, and so an EI of 3.4. C6 of D. carnegii has a centrum length of 442 mm, a cotyle diameter of 99 mm, and an EI of 4.5. So Diplodocus is one third more elongate than Suuwassea. It is true that sauropod cervicals elongate through ontogeny, but the Suuwassea holotype is a decent-sized animal, and would be expected to have attained adult proportions even if it was not fully adult (also, ANS 21122 has more cervical ribs fused than CM 84/94). We know from the juvenile ?Sauroposeidon vertebra YPM 5294 (Wedel et al. 2000:372) that subadult sauropod cervicals attained great elongation: that element is from an animal young enough to have had an unfused neural arch but it has an EI exceeding 5.0.
Then there’s neural spine shape. Yes, it is variable in sauropods, but this is ridiculous. I strongly doubt that any non-pathological Diplodocus cervical anywhere ever has had a neural spine shaped like that of the Suuwassea vertebra.
Also note that the prezygapophyses of the D. carnegii C6 strongly overhang the condyle but are only slightly elevated, whereas those of S. emilieae are right above the condyle but strongly elevated, so that the prezygapophyseal rami might fairly be called pedestals. Such pedestaling of the prezygapophyses is present in some cervicals of Apatosaurus, although perhaps not to the same extreme. Some Apatosaurus cervicals have pretty funky, smokestack-looking neural spines, although–again–not to the same extreme as in Suuwassea. Still, from the mid-centrum on up, S. emiliae looks a bit apatosaur-ish. So let’s try that next.
Apatosaurus
Here we have C6 of Suuwassea as before, this time with Apatosaurus louisae CM 3018 (Gilmore 1936:pl. 24), again scaled to the same cotyle diameter.
C6 of A. louisae has a centrum length of 440 mm, a cotyle diameter of 150 mm, and an EI of 2.9 (I know it doesn’t look that short, but I’m going off Gilmore’s data, and I trust the measuring tape more than the drafting pen, no matter how skillfully the latter is wielded.) So this is not a bad match with the value of 3.4 for Suuwassea.
Of course, the glaring problem with suggesting that Suuwassea is a juvenile Apatosaurus is that it has normal-sized cervical ribs, not the insane scythes of doom that hang below the centrum of every post-axial Apatosaurus cervical (see these posts [#1, #2, #3] for some crazy examples, and this post for more pictures and discussion). The giant cervical ribs are present even in very juvenile Apatosaurus cervicals, such as the large collection of juvenile apatosaurs in the BYU collection from Cactus Park (albeit unfused; the immense parapophyses still point the way even if the ribs themselves are missing).
I know, I know, I just said that there is no such thing as a key character. But all of the known species of Apatosaurus have giant cervical ribs, and indeed are often identified in the field as Apatosaurus on that basis alone. I suppose it’s not impossible that Suuwassea is nested within the other Apatosaurus species, based on some bizarre combination of as-yet undiscovered characters and intermediate specimens, and lost the giant cervical ribs along the way, but now we’re into angels dancing on the heads of non-existent pins. If Suuwassea is an apatosaurine but outside the clade of giant-cervical-rib-bearing Apatosaurus, then whether we call it a species of Apatosaurus or a separate genus–say, Suuwassea–is more a matter of taste than anything else. Note that Lovelace et al. (2008) recovered Suuwassea as an apatosaurine, but not as Apatosaurus.
Lest anyone without access to the paper think I’m cheating by hiding serial variation, here are the other well-preserved cervicals of Suuwassea, to scale:

Suuwassea emilieae cervicals 3, 5, and 6 in left lateral view, from Harris (2006c:Text-figs. 5, 6, and 7)
So, if Suuwassea is a juvenile of a known diplodocid but it’s not Diplodocus or Apatosaurus, what’s left?
Barosaurus
Probably not.
Supersaurus
Unconvincing.
“Amphicoelias brontodiplodocus”

“Amphicoelias brontodiplodocus” cervicals 7-10 in left lateral view, from Galiano and Albersdorfer (2010:fig 10a)
Okay, now I’m just messing with you.
Is Suuwassea even a juvenile?
By now it is probably obvious, even from cervical morphology alone, that if ANS 21122 is a juvenile of anything, it’s a juvenile Suuwassea. But is it in fact a juvenile?
We-ell. The cervical neural arches are all fused, but not all of the cervical ribs are. Jerry did a fine job of describing exactly what was going on at each serial position (Harris 2006c). In C3, the left cervical rib is not attached, and the right one is attached at the parapophysis but not fused. In C5, the ribs are attached, not fused at the parapophyses, and fused at the diapophyses*. In C6, the ribs are fused at both attachment points. C7 lacks the ribs, but their absence appears to be caused by breakage rather than lack of fusion. One fragmentary posterior cervical of uncertain position is missing the diapophyses but has one rib fused at the parapophysis.
* This is cool because it is the first time that I know of that anyone has documented which of the two attachment points fused first within a single cervical rib. I wonder if other sauropods did it the same way?
So based on cervicals alone, we would infer that Suuwassea was not fully mature. However–and this is absolutely crucial for the synonymization hypothesis–the Suuwassea holotype ANS 21122 already has a greater degree of cervical element fusion than Diplodocus carnegii holotype CM 84/94 (which has unfused ribs back to C5) and Apatosaurus CM 555 (which has unfused arches back to C8 and unfused ribs throughout), both of which have attained essentially ‘adult’ morphology. So if Woodruff and Fowler (2012) are correct, the ontogenetic clock has to run forward from CM 555 and CM 84/94, through a Suuwassea-like stage, and then back to normal Apatosaurus or Diplodocus morphology.
But we don’t have to rely on cervicals alone, because ANS 21122 also includes some dorsals and caudals. And the caudals are very interesting in that the neural arches are not fused through most of the series. Harris (2006c:1107):
Of all the caudal vertebrae preserved in ANS 21122, only the distal, ‘whiplash’ caudals are complete. All the remaining vertebrae consist only of vertebral bodies that lack all phylogenetically informative portions of their respective arches. On the proximal and middle caudals, this absence is due to lack of fusion as evidenced by the deeply fluted articular surfaces for the arches on the bodies. In contrast, the arches on the most distal vertebrae that retain them are seamlessly fused, but everything dorsal to the bases of the corporozygapophyseal laminae are broken.
Now this is pretty darned interesting, because it shows that neural arch fusion in Suuwassea was not a simple zipper that ran from back to front (as in crocs [Brochu 1996] and phytosaurs [Irmis 2007*]) or front to back. We can’t really say, based on this one specimen, what the sequence was, but we can say for certain that the anterior and middle caudals came last. Oh, and for what it’s worth, the scap-coracoid joint is also unfused (Harris 2007), but we know that that’s often the case for substantially “adult” sauropods such as the mounted Berlin Giraffatitan.
* Relevant to this entire post series are the wise words of my homeboy and former Padian labmate Randy Irmis, who wrote in the abstract of his 2007 neurocentral fusion paper:
A preliminary survey indicates that there is considerable variation of both the sequence and timing of neurocentral suture closure in other archosaur clades. Therefore, it is unwise to apply a priori the crocodylian pattern to other archosaur groups to determine ontogenetic stage. Currently, apart from histological data, there are few if any reliable independent criteria for determining ontogenetic stage. I propose that histology be integrated with independent ontogenetic criteria (such as neurocentral suture closure) and morphometric data to provide a better understanding of archosaur ontogeny.
The unfused arches in the Suuwassea caudals are especially interesting because, for the first time that I know of, we have a sauropod with cervical neural arches and at least some cervical ribs fused, but with unfused neural arches elsewhere in the body. This is in contrast to D. carnegii CM 84/94, in which all the neural arches are fused but the anterior cervical ribs are not. So the developmental timing in Suuwassea is dramatically different than in D. carnegii, at least, which is one more problem for the synonymization hypothesis. Two more problems, actually, in that (1) Suuwassea probably isn’t Diplodocus, and (2) it doesn’t belong in the same ontogenetic series as Diplodocus, contra Woodruff and Fowler (2012:Figs. 3 and 9)–if the timing of the various fusions differs between the taxa, there is no basis for assuming that the hypothetical ontogenetic bifurcation would follow the same rules.
And speaking of ontogenetic bifurcation, a final point about the ‘bifurcations’ in Suuwassea.
The first line of the caption is misleading. Two of these vertebrae have weakly bifurcated neural spines because they are sixth cervicals (Suuwassea in B, Apatosaurus in D), and that’s what you expect in C6 in adult diplodocids. One of them, the C5 of Suuwassea in C, isn’t bifurcated at all: it’s broken. Harris (2006c:1099):
The spinous process expands mediolaterally toward its apex, attaining maximal width just proximal to its terminus. A long, narrow crack at the distal end gives the appearance of bifurcation, but the collinear dorsal margin indicates that no true split was present.
As for the final vertebra, MOR 592 in A, who knows? Woodruff and Fowler (2012) do not say what serial position it is from. Based on the shallow notch in the spine, I’ll bet it’s either a C6 or very close to it–and if so, no deeper split is expected.
So the entire rationale for the taxonomic side of Woodruff and Fowler (2012)–that Suuwassea has incompletely bifurcated neural spines because it is a juvenile –turns out be an illusion caused by not taking serial variation into account. Suuwassea ANS 21122 probably is a subadult, based on the unfused caudal neural arches, but its cervical vertebrae already show the expected adult morphology in neural arch fusion, cervical rib fusion, and–most importantly–neural spine bifurcation.
Envoi
The evidence that Suuwassea is not a juvenile of a known diplodocid is not in this post. It’s in the hard work, comprehensive descriptions, and detailed, thoughtful comparisons by Harris and Dodson (2004), Harris (2006a, b, c, 2007), Lovelace et al. (2008), Whitlock and Harris (2010), and Whitlock (2011). This post is just an arrow scratched in the dirt. Please, go read those papers. And then read all the monographs I cited in the first post in this series (and am too lazy to cite again here). Give those people their due by taking their work seriously and learning from it.
The rest of the series
Links to all of the posts in this series:
- Part 1: what we knew a month ago
- Part 2: why serial position matters
- Part 3: the evidence from ontogenetic series
- Part 4: is Suuwassea a juvenile of a known diplodocid?
- Part 5: is Haplocanthosaurus a juvenile of a known diplodocid?
- Part 6: more reasons why Haplocanthosaurus is not a juvenile of a known diplodocid
and the post that started it all:
References
- Brochu, C.A. 1996. Closure of neurocentral sutures during crocodilian ontogeny: implications for maturity assessment in fossil archosaurs. Journal of Vertebrate Paleontology 16:49-62.
- Galiano, H., and Albersdörfer, R. 2010. A new basal diplodocid species, Amphicoelias brontodiplodocus from the Morrison Formation, Big Horn Basin, Wyoming, with taxonomic reevaluation of Diplodocus, Apatosaurus and other genera. Dinosauria International, LLC, Wyoming. 50 pages.
- Gilmore, C.W. 1936. Osteology of Apatosaurus with special reference to specimens in the Carnegie Museum. Memoirs of the Carnegie Museum 11:175-300.
- Harris, J.D. 2006a. Cranial osteology of Suuwassea emilieae (Sauropoda: Flagellicaudata) from the Upper Jurassic Morrison Formation of Montana, U.S.A. Journal of Vertebrate Paleontology 26:88–102.
- Harris, Jerald D. 2006b. The significance of Suuwassea emiliae (Dinosauria: Sauropoda) for flagellicaudatan intrarelationships and evolution. Journal of Systematic Palaeontology 4: 185-198.
- Harris, J.D. 2006c. The axial skeleton of the dinosaur Suuwassea emilieae (Sauropoda: Flagellicaudata) from the Upper Jurassic Morrison Formation of Montana, USA. Palaeontology 49:1091-1121.
- Harris, Jerald D. 2007. The appendicular skeleton of Suuwassea emilieae (Sauropoda: Flagellicaudata) from the Upper Jurassic Morrison Formation of Montana (USA). Geobios 40:501-522. doi:10.1016/j.geobios.2006.02.002
- Harris, J.D., and Dodson, P. 2004. A new diplodocoid sauropod dinosaur from the Upper Jurassic Morrison Formation of Montana, USA. Acta Palaeontologica Polonica 49:197–210.
- Hatcher, J.B. 1901. Diplodocus (Marsh): its osteology, taxonomy, and probable habits, with a restoration of the skeleton. Memoirs of the Carnegie Museum 1:1-63.
- Irmis, R.B. 2007. Axial skeleton ontogeny in the Parasuchia (Archosauria: Pseudosuchia) and its implications for ontogenetic determination in archosaurs. Journal of Vertebrate Paleontology 27:350-361.
- Lovelace, D.M., Hartman, S.A., and Wahl, W.R. 2008. Morphology of a specimen of Supersaurus (Dinosauria, Sauropoda) from the Morrison Formation of Wyoming, and a re-evaluation of diplodocid phylogeny. Arquivos do Museu Nacional, Rio de Janeiro, 65 (4): 527-544.
- Wedel, M.J., Cifelli, R.L., and Sanders, R.K. 2000. Osteology, paleobiology, and relationships of the sauropod dinosaur Sauroposeidon. Acta Palaeontologica Polonica 45(4):343-388.
- Whitlock, J.A. 2011. A phylogenetic analysis of Diplodocoidea (Saurischia: Sauropoda). Zoological Journal of the Linnean Society 161:872-915.
- Whitlock, J.A., and Harris, J.D. 2010. The dentary of Suuwassea emilieae (Sauropoda: Diplodocoidea). Journal of Vertebrate Paleontology 30(5):1637-1641.
- Woodruff, D.C, and Fowler, D.W. 2012. Ontogenetic influence on neural spine bifurcation in Diplodocoidea (Dinosauria: Sauropoda): a critical phylogenetic character. Journal of Morphology, online ahead of print.