In mammals — certainly the most-studied vertebrates — regional differentiation of the vertebral column is distinct and easy to spot. But things aren’t so simple with sauropods. We all know that the neck of any tetrapod is made up of cervical vertebrae, and that the trunk is made up of dorsal vertebrae (subdivided into thoracic and lumbar vertebrae in the case of mammals). But how do we tell whether a given verebra is a posterior cervical or an anterior dorsal?

Here two vertabrae: a dorsal vertebra (D3) and a cervical vertebra (C13) from CM 84, the holotype of Diplodocus carnegii, modified from Hatcher (1901: plates III and VII):

It’s easy to tell these apart, even when as here we have only lateral-view images: the dorsal vertebra is tall, its centrum is short, its neural spine is anteroposteriorly compressed and its parapophysis is up on the dorsal half of the centrum; but the cervical vertebra is relatively low, its centrum is elongated, its neural spine is roughly triangular and its parapophysis hangs down well below the centrum (and has a cervical rib fused to it and the diapophysis).

But things get trickier in the shoulder region because, in sauropods at least, the transition through the last few cervicals to the first few dorsals is gradual — the vertebrae become shorter, taller and broader — and tends to have no very obvious break point. In this respect, they differ from mammals, in which the regional differentiation of the spinal column is more abrupt. (Although even here, things may not be as simple as generally assumed: for example, Gunji and Endo (2016) argued that the 1st thoracic vertebra of the giraffe behaves functionally like an 8th cervical.)

So here are those two vertebrae in context: the sequence D3 D2 D1 C15 C14 C13 in CM 84, the holotype of Diplodocus carnegii, modified from Hatcher (1901: plates III and VII):

Given that the leftmost is obviously a dorsal and the rightmost obviously a cervical, where would you place the break-point?

The most usual definition seems to be that the first dorsal vertebra is the first one that has a free rib, i.e. one not fused to the vertebra: in the illustration above, you can see that the three cervicals on the right all have their cervical ribs fused to their diapophyses and parapophyses, and the three dorsals on the left do not. This definition of the cervical/dorsal distinction seems to be widely assumed, but it is rarely explicitly asserted. (Does anyone know of a paper that lays it out for sauropods, or for dinosaurs more generally?)

But wait!

Hatcher (1903:8) — the same dude — in his Haplocanthosaurus monograph, writes:

The First Dorsal (Plate I., Fig. 1). […] That the vertebra now under consideration was a dorsal is conclusively shown not by the presence of tubercular and capitular rib facets showing that it supported on either side a free rib, for there are in our collections of sauropods, skeletons of other dinosaurs fully adult but, with the posterior cervical, bearing free cervical ribs articulating by both tubercular and capitular facets as do the ribs of the dorsal region. The character in this vertebra distinguishing it as a dorsal is the broadly expanded external border of the anterior branch of the horizontal lamina [i.e. what we would now call the centroprezygapophyseal lamina]. This element has been this modified in this and the succeeding dorsal, no doubt, as is known to be the case in Diplodocus to give greater surface for the attachment of the powerful muscles necessary for the support of the scapula.

Hatcher’s illustrations show this feature, though they don’t make it particularly obvious: here are the last two cervicals and the first dorsal, modified from Hatcher (1903:plate I), with the facet in question highlighted in pink: right lateral view at the top, then anterior, and finally posterior view at the bottom. (The facet is only visible in lateral and anterior views):

Taken at face value, Hatcher’s words here seem to imply that he considers the torso to begin where the scapula first lies alongside the vertebral column. Yet if you go back to the Diplodocus transition earlier in this post, a similar scapular facet is not apparent in the vertebra that he designated D1, and seems to be present only in D2.

Is this scapular-orientation based definition a widespread usage? Can anyone point me to other papers that use it?

Wilson (2002:226) mentions a genetic definition of the cervical/dorsal distinction

Vertebral segment identity may be controlled by a single Hox gene. The cervicodorsal transition in many tetrapods, for instance, appears to be defined by the expression boundary of the Hoxc-6 gene.

But this of course is no use in the case of extinct animals such as sauropods.

So what’s going on here? In 1964, United States Supreme Court Justice Potter Stewart, in describing his threshold test for obscenity, famously said “I shall not today attempt further to define the kinds of material I understand to be embraced within that shorthand description, and perhaps I could never succeed in intelligibly doing so. But I know it when I see it.” Is that all we have for the definition of what makes a vertebra cervicals as opposed to dorsal? We know it when we see it?

Help me out, folks! What should the test for cervical-vs-dorsal be?

References

  • Gunji, Mego, and Hideki Endo. 2016. Functional cervicothoracic boundary modified by anatomical shifts in the neck of giraffes. Royal Society Open Science 3:150604. doi:10.1098/rsos.150604
  • Hatcher, Jonathan B. 1901. Diplodocus (Marsh): its osteology, taxonomy and probable habits, with a restoration of the skeleton. Memoirs of the Carnegie Museum 1:1-63 and plates I-XIII.
  • Hatcher, J. B. 1903b. Osteology of Haplocanthosaurus with description of a new species, and remarks on the probable habits of the Sauropoda and the age and origin of the Atlantosaurus beds; additional remarks on Diplodocus. Memoirs of the Carnegie Museum 2:1-75 and plates I-VI.
  • Wilson, Jeffrey A. 2002. Sauropod dinosaur phylogeny: critique and cladistic analysis. Zoological Journal of the Linnean Society 136:217-276.

I have several small ordered sequences of data, each of about five to ten elements. For each of them, I want to calculate a metric which captures how much they vary along the sequence. I don’t want standard deviation, or anything like it, because that would consider the sequences 1 5 2 7 4 and 1 2 4 5 7 equally variable, whereas for my purposes the first of these is much more variable.

Here is a matric that I think does what I want, and will allow me to compare different sequences for variability-along-the-sequence.

For the n-1 pairs along the sequence of n elements, I take the difference (absolute value, so always positive) between elements i and i+1. Then I average all those differences. Then I divide the result by the average of the values themselves, to normalise for magnitude.

Some example calculations:

  • For the sequence 1 5 2 7 4, the differences are 4 3 5 3, for a total of 15 and an average of 3.75. The average of the values is 1+5+2+7+4 = 19/5 = 3.8, which gives me a metric of 3.75/3.8 = 0.987.
  • For the sequence 1 2 4 5 7, the differences are 1 2 1 2, for a total of 6 and an average of 1.5. The average of the values is again 3.8, which gives me a metric of 1.5/3.8 = 0.395.
  • So the first sequence is 0.987/0.395 = 2.5 times as sequentially variable as the second sequence.
  • And for the sequence 10 20 40 50 70 (which is the same as the previous one, but all values ten times greater), the differences are 10 20 10 20, for a total of 60 and an average of 15. The average of the values is 38, which gives me a metric of 15/38 = 0.395, the same as before — which is as it should be.

And now, my question! Does this metric, or something similar, already exist? If so, what is it called? Or if I should be using something else instead, what is it?

(It happens that my sequences are the aspect ratios of the cotyles of consecutive vertebrae, but that’s not important: whatever metric we land on should work for any sequences.)

Taylor 2015: Figure 8. Cervical vertebrae 4 (left) and 6 (right) of Giraffatitan brancai lectotype MB.R.2180 (previously HMN SI), in posterior view. Note the dramatically different aspect ratios of their cotyles, indicating that extensive and unpredictable crushing has taken place. Photographs by author.

A couple of months ago, I asked for your help in compiling a list of all known complete sauropods necks. This has gone really well, and I want to thank everyone who chipped in, and all the various authors I have contacted for details as a result.

My next step is to take the raw data in the Google spreadsheet that I have been maintaining, and write it up as prose for the paper that I am shortly going to resubmit, having first done so back in 2015. And I thought it would make sense to draft that section here on SV-POW!, so I can get any further feedback before I finalize it for the manuscript.

Young and Zhao (1972:figure 3). Mamenchisaurus hochuanensis holotype CCG V 20401 as is occurred in the field.

So here goes: any additional comments at this stage will be welcome!


Unambiguously complete necks are known from published accounts of only a few sauropod specimens. In chronological order of description, the following specimens were found with their necks complete and articulated, and have been adequately described:

  • CM 11338, a referred specimen of Camarasaurus lentus described by Gilmore (1925). This is a juvenile specimen, and thus does not fully represent the adult morphology. (McIntosh et al. 1996:76 claim that this specimen is the holotype, but this is not correct: YPM 1910 is the holotype — see below.)
  • CM 3018, the holotype of Apatosaurus louisae, described by Gilmore (1936). The neck was separated from the torso but articulated from C1–C15, though the last three cervicals were badly crushed: see below for details.
  • CCG V 20401, the Mamenchisaurus hochuanensis holotype, described by Young and Zhao (1972). Each vertebra is broken in half at mid-length, with the posterior part of each adhering to the anterior part of the its successor; and all the vertebrae are badly crushed in an oblique plane.
  • ZDM T5402, a Shunosaurus lii referred specimen, described in Chinese by Zhang (1988), with English figure captions. Figure 22 depicts the atlas. Unlike the holotype T5401, this specimen is mature.
  • BYU 9047, the Cathetosaurus lewisi holotype, described by Jensen (1988). (Jensen incorrectly gives the specimen number as BYU 974.) This specimen was redescribed, and the species referred to Camarasaurus, by McIntosh et al. (1996). Although all 12 cervicals are present, “10–12, particularly 12, have suffered such severe damage that it is impossible to restore them” (McIntosh et al. 1996:76).
  • MACN-N 15, the holotype of Amargasaurus cazaui MACN-N 15, described by Salgado and Bonaparte (1991) who desribed “22 presacral vertebrae articulated with each other and attached to the skull and sacrum, relatively complete” (Salgado & Bonaparte 1991:335, translated.
  • ZDM 0083, the holotype of Mamenchisaurus youngi, described in Chinese by Ouyang and Ye (2002) with English figure captions. Figure 14 depicts the atlas and axis.
  • MUCPv-323, the holotype of Futalognkosaurus dukei, initially described by Calvo et al. 2007a and redescribed by Calvo et al. 2007b. The neck was found in two articulated sections which fit together without needing additional vertebrae in between (Jorge O. Calvo, pers. comm., 2021).
  • SSV12001, the holotype of Xinjiangtitan shanshanesis, described by Zhang et al. (2018). The original description of this specimen by Wu et al. 2013 included only the last two cervicals, which were the only ones that had been excavated at that time.

A few additional specimens are known to have complete and articulated necks, but have not yet been described:

  • USNM 13786, a referred subadult specimen of Camarasaurus lentus recently mounted at the Smithsonian. The specimen “was almost completely buried before the sinews had allowed the bones to separate” (letter from Earl Douglass to William J. Holland, 22 August 1918), and photographs kindly supplied by Andrew Moore show that the atlas was preserved.
  • MNBH TIG3, the holotype of Jobaria tiguidensis. Sereno et al. (1999:1343) assert that this species has 12 cervicals in all and say “One articulated neck was preserved in a fully dorsiflexed, C-shaped posture”. Sereno (pers. comm., 2021) confirms that the articulated neck is MNBH TIG3
  • SMA 002, referred to Camarasaurus sp. Tschopp et al. (2016), in a description of its feet, say that this specimen “lacks only the vomers, the splenial bones, the distal end of the tail, and one terminal phalanx of the right pes. The bones are preserved in three dimensions and in almost perfect articulation”.
  • MAU-Pv-LI-595, the “La Invernada” Titanosaur. Filippi et al. (2016) give a very brief account in an abstract. Filippi, pers. comm, 2021) says that the entire preserved specimen was articulated.
  • MAU-Pv-AC-01, an unnamed titanosaur mentioned in abstracts by Calvo et al. (1997) and Coria and Salgado (1999). The specimen was found in perfect articulation from skull down to the last caudal vertebrae (Rodolfo Coria, pers. comm., 2021).

The first cervical (the atlas) in sauropods is very different in form from the other vertebrae, and small and fragile. Consequently it is easily lost. Some further specimens have necks that are complete and articulated from C2 (the axis) backwards:

  • MB.R.4886, the holotype of Dicraeosaurus hansemanni, described by Janensch (1929), has a neck that complete and well preserved from C2 to C12 (the last cervical). Janensch referred to this as “specimen m” and writes “It was found articulated from the 19th caudal vertebra to the 9th cervical vertebra inclusive. The proximal part of the neck from the 8th cervical vertebra up to the axis was bent ventrally and lay at right angles to the distal part of the neck.” (Janensch 1929:41).
  • PMU 233, the holotype of Euhelopus zdanskyi, described by Wiman (1929) as “exemplar a” and redescribed by Wilson and Upchurch (2009).
  • ZDM T5401, the subadult holoype of Shunosaurus lii, described in Chinese by Zhang et al 1984. The quarry map (Zhang et al. 1984:figure 1) suggests that the atlas is missing.
  • MCT 1487-R, informally known as “DGM Series A”, described by Powell (2003). Gomani (2005:9) summarises as “12 cervical vertebrae, except the atlas, preserved in articulation with three proximal dorsal vertebrae”.
  • GCP-CV-4229, the holotype of Spinophorosaurus nigerensis, described by Remes et al. (2009). The specimen was found in very good condition and well articulated from C2 to C13, the last cervical. The atlas seems to be missing (Remes, pers. comm., 2021.

One other sauropod is complete from the first cervical, but probably not to the last:

  • MOZ-Pv1232, the holotype of Lavocatisaurus agrioensis, described by Canudo et al. (2018). This is complete from C1-C11. Canudo’s guess is that this is complete neck (Canudo, pers. comm, 2021), but the specimen doesn’t demand that conclusion and no known eusauropod has fewer than 12 cervicals.

Other sauropod specimens have necks that are complete and articulated from further back in the cervical sequence:

  • YPM 1910, Camarasaurus lentus, a mounted specimen described by Lull (1930). The neck is complete from C2 or C3, Lull was uncertain which.
  • SMA 0004, Kaatedocus siberi, described by Tschopp and Mateus (2012). Cervicals 3-14 are preserved.
  • AODF 888 (informally “Judy”), probably referrable to Diamantinasaurus, briefly described by Poropat et al. (2019). Preserved from C3 or maybe C4. “One posterior cervical (XIII or XIV) found several metres from articulated series, but appears to slot nicely into the gap between the articulated cervical series and the unprepared thoracic section, which might include at least one additional cervical (XIV or XV)” (Poropat, pers. comm. 2021).

Several necks are probably nearly complete, but it is not possible to knew due to their not being found in articulation:

  • CM 84, the holotype of Diplodocus carnegii, described by Hatcher (1901). C2–C15 are preserved, though not all in articulation; C11 may be an intrusion: see below for details.
  • ZDM T5701, the holotype of Omeisaurus tianfuensis, described by He et al. (1988). The neck was not articulated (He et al. 1988:figure 1), and was missing “two elements or so” (He et al. 1988:120).
  • QJGPM 1001, the holotype of Qijianglong guokr, described by Xing et al. (2015). On page 8, the authors say “The axis to the 11th cervical vertebra were fully articulated in the quarry. The atlas intercentrum and the 12th–17th cervical vertebrae were closely associated with the series.”
  • MNBH TIG9, a referred specimen of Jobaria tiguidensis. Wilson (2012:103) writes that this specimen “includes a partially articulated series of 19 vertebrae starting from the axis and extending through the mid-dorsal vertebrae.”
  • MNBH TIG6, another referred specimen of Jobaria tiguidensus, which has not been mentioned in the literature. Sereno (pers. comm., 2021) says that it is “a subadult partial skeleton with excellent neck” and that “the sequence was articulated from C2–11. Most of the ribs were attached as well.”

At the time of writing, the Paleobiology Database (https://paleobiodb.org/) lists more than 270 sauropod species. The nine unambigously complete and articulated necks therefore represent only one in 30 known sauropod species.

Note. The Jobaria tiguidensis individuals previously had specimen numbers beginning MNN, but the Musee National du Niger changed its name to Musée National Boubou Hama and the specimen numbers have changed with it.

Today marks the one-month anniversary of my and Matt’s paper in Qeios about why vertebral pneumaticity in sauropods is so variable. (Taylor and Wedel 2021). We were intrigued to publish on this new platform that supports post-publication peer-review, partly just to see what happened.

Taylor and Wedel (2021: figure 3). Brontosaurus excelsus holotype YPM 1980, caudal vertebrae 7 and 8 in right lateral view. Caudal 7, like most of the sequence, has a single vascular foramen on the right side of its centrum, but caudal 8 has two; others, including caudal 1, have none.

So what has happened? Well, as I write this, the paper has been viewed 842 times, downloaded a healthy 739 times, and acquired an altmetric score 21, based rather incestuously on two SV-POW! blog-posts, 14 tweets and a single Mendeley reader.

What hasn’t happened is even a single comment on the paper. Nothing that could be remotely construed as a post-publication peer-review. And therefore no progress towards our being able to count this as a peer-reviewed publication rather than a preprint — which is how I am currently classifying it in my publications list.

This, despite our having actively solicited reviews both here on SV-POW!, in the original blog-post, and in a Facebook post by Matt. (Ironically, the former got seven comments and the latter got 20, but the actual paper none.)

I’m not here to complain; I’m here to try to understand.

On one level, of course, this is easy to understand: writing a more-than-trivial comment on a scholarly article is work, and it garners very little of the kind of credit academics care about. Reputation on the Qeios site is nice, in a that-and-two-bucks-will-buy-me-a-coffee kind of way, but it’s not going to make a difference to people’s CVs when they apply for jobs and grants — not even in the way that “Reviewed for JVP” might. I completely understand why already overworked researchers don’t elect to invest a significant chunk of time in voluntarily writing a reasoned critique of someone else’s work when they could be putting that time into their own projects. It’s why so very few PLOS articles have comments.

On the other hand, isn’t this what we always do when we write a solicited peer-review for a regular journal?

So as I grope my way through this half-understood brave new world that we’re creating together, I am starting to come to the conclusion that — with some delightful exceptions — peer-review is generally only going to happen when it’s explicitly solicited by a handling editor, or someone with an analogous role. No-one’s to blame for this: it’s just reality that people need a degree of moral coercion to devote that kind of effort to other people’s project. (I’m the same; I’ve left almost no comments on PLOS articles.)

Am I right? Am I unduly pessimistic? Is there some other reason why this paper is not attracting comments when the Barosaurus preprint did? Teach me.

References

 

Early in my 2015 preprint on the incompleteness of sauropod necks, I wrote “Unambiguously complete necks are known from published account of only six species of sauropod, two of which are species of the same genus”, and listed them.

Taylor 2015: Figure 3. W. H. Reed’s diagram of Quarry C near Camp Carnegie on Sheep Creek, in Albany County, Wyoming. The coloured bones belong to CM 84, the holotype of Diplodocus carnegii; other bones belong to other individuals, chiefly of Brontosaurus, Camarasaurus and Stegosaurus. Modified (cropped and coloured) from Hatcher (1901: plate I). Cervical vertebrae are purple (and greatly simplified in outline), dorsals are red, the sacrum is orange, caudals are yellow, limb girdle elements are blue, and limb bones are green.

Haha, stupid me! I had hugely under-counted. With thanks to the three peer-reviewers of the submitted manuscript and to SV-POW! commenters, I have revised this list, in preparation for forthcoming resubmission. The table as it stands currently consists of 24 candidates, not all of them very solid. Of these, 15 were found in articulation, the others mostly not — though we don’t know for sure in all cases. Not all of the necks have been properly described, and not all of the ones that have been described have been named. And other questions hang over some of them, very briefly summarised in notes.

Here is the list, sorted by date of description. If I got the Google-docs permissions right, you should be able to see it but not edit it. (If you can edit, please don’t! And let me know.)

Please let me know if you find any mistakes, or if you think I have missed anything. Everyone who contributes will get a mention in the acknowledgements.

 

We’ve noted many times over the years how inconsistent pneumatic features are in sauropod vertebra. Fossae and formamina vary between individuals of the same species, and along the spinal column, and even between the sides of individual vertebrae. Here’s an example that we touched on in Wedel and Taylor (2013), but which is seen in all its glory here:

Taylor and Wedel (2021: Figure 5). Giraffatitan brancai tail MB.R.5000, part of the mounted skeleton at the Museum für Naturkunde Berlin. Caudal vertebrae 24–26 in left lateral view. While caudal 26 has no pneumatic features, caudal 25 has two distinct pneumatic fossae, likely excavated around two distinct vascular foramina carrying an artery and a vein. Caudal 24 is more shallowly excavated than 25, but may also exhibit two separate fossae.

But bone is usually the least variable material in the vertebrate body. Muscles vary more, nerves more again, and blood vessels most of all. So why are the vertebrae of sauropods so much more variable than other bones?

Our new paper, published today (Taylor and Wedel 2021) proposes an answer! Please read it for the details, but here’s the summary:

  • Early in ontogenly, the blood supply to vertebrae comes from arteries that initially served the spinal cord, penetrating the bone of the neural canal.
  • Later in ontegeny, additional arteries penetrate the centra, leaving vascular foramina (small holes carrying blood vessels).
  • This hand-off does not always run to completion, due to the variability of blood vessels.
  • In extant birds, when pneumatic diverticula enter the bone they do so via vascular foramina, alongside blood vessels.
  • The same was probaby true in sauropods.
  • So in vertebrae that got all their blood supply from vascular foramina in the neural canal, diverticula were unable to enter the centra from the outside.
  • So those centra were never pneumatized from the outside, and no externally visible pneumatic cavities were formed.

Somehow that pretty straightforward argument ended up running to eleven pages. I guess that’s what you get when you reference your thoughts thoroughly, illustrate them in detail, and discuss the implications. But the heart of the paper is that little bullet-list.

Taylor and Wedel (2021: Figure 6). Domestic duck Anas platyrhynchos, dorsal vertebrae 2–7 in left lateral view. Note that the two anteriormost vertebrae (D2 and D3) each have a shallow pneumatic fossa penetrated by numerous small foramina.

(What is the relevance of these duck dorsals? You will need to read the discussion in the paper to find out!)

Our choice of publication venue

The world moves fast. It’s strange to think that only eleven years ago my Brachiosaurus revision (Taylor 2009) was in the Journal of Vertebrate Palaeontology, a journal that now feels very retro. Since then, Matt and I have both published several times in PeerJ, which we love. More recently, we’ve been posting preprints of our papers — and indeed I have three papers stalled in peer-review revisions that are all available as preprints (two Taylor and Wedels and a single sole-authored one). But this time we’re pushing on even further into the Shiny Digital Future.

We’ve published at Qeios. (It’s pronounced “chaos”, but the site doesn’t tell you that; I discovered it on Twitter.) If you’ve not heard of it — I was only very vaguely aware of it myself until this evening — it runs on the same model as the better known F1000 Research, with this very important difference: it’s free. Also, it looks rather slicker.

That model is: publish first, then filter. This is the opposite of the traditional scholarly publishing flow where you filter first — by peer reviewers erecting a series of obstacles to getting your work out — and only after negotiating that course to do get to see your work published. At Qeios, you go right ahead and publish: it’s available right off the bat, but clearly marked as awaiting peer-review:

And then it undergoes review. Who reviews it? Anyone! Ideally, of course, people with some expertise in the relevant fields. We can then post any number of revised versions in response to the reviews — each revision having its own DOI and being fixed and permanent.

How will this work out? We don’t know. It is, in part, an experiment. What will make it work — what will impute credibility to our paper — is good, solid reviews. So if you have any relevant expertise, we do invite you to get over there and write a review.

And finally …

Matt noted that I first sent him the link to the Qeios site at 7:44 pm my time. I think that was the first time he’d heard of it. He and I had plenty of back and forth on where to publish this paper before I pushed on and did it at Qeios. And I tweeted that our paper was available for review at 8:44 — one hour exactly after Matt learned that the venue existed. Now here we are at 12:04 my time, three hours and 20 minutes later, and it’s already been viewed 126 times and downloaded 60 times. I think that’s pretty awesome.

References

  • Taylor, Michael P. 2009. A re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria, Sauropoda) and its generic separation from Giraffatitan brancai (Janensch 1914). Journal of Vertebrate Paleontology 29(3):787-806. [PDF]
  • Taylor, Michael P., and Mathew J. Wedel. 2021. Why is vertebral pneumaticity in sauropod dinosaurs so variable? Qeios 1G6J3Q. doi: 10.32388/1G6J3Q [PDF]
  • Wedel, Mathew J., and Michael P. Taylor 2013b. 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]

I’ve got a problem. For a paper I’m working on, I need to run a phylogenetic analysis based on that of Mannion et al. (2013) — the Lusotitan paper. The most recent version of that matrix, greatly expanded from the original version, is that of Mannion et al. (2019) — the Jiangshanosaurus paper — so I am working from that matrix.

But what exactly do I do with that Matrix? The analysis protocol is described on pages 12-13 of the PDF:

Several unstable and fragmentary taxa were excluded from the analyses (Astrophocaudia, Australodocus, Brontomerus, Fukuititan, Fusuisaurus, Liubangosaurus, Malarguesaurus, Mongolosaurus). Using equal weighting of characters, this pruned data matrix was analysed using the ‘Stabilize Consensus’ option in the ‘New Technology Search’ in TNT v. 1.5. Searches employed sectorial searches, drift and tree fusing, with the consensus stabilized five times, prior to using the resultant trees as the starting topologies for a ‘Traditional Search’, using Tree Bisection-Reconstruction. We then re-ran the analysis, using the same pruned matrix and protocol, but also applying extended implied weighting in TNT.

There is no problem downloading TNT: it’s freely available thanks to subsidy by the Willi Hennig Society. But the program is tricky to use, and documentation is rather cryptic. You drive TNT with scripts that look like this (short excerpt):

ttags =;
<tag generating commands>
ttags );
tsave *tags.tre;
save * <tree number>;
tsave /;

It seems, for example that = and ) are values that the ttags command accepts. But I’ve not been able to find documentation that spells out such things. (There is a help command, but its output too is cryptic.)

So here is my problem: how do I translate the Mannion et al. (2019) protocol into a TNT script? If anyone can help me with this, I will acknowledge the heck out of them the paper that eventually emerges from this rubble.

(Why not just ask Phil Mannion, you ask? I’ve been talking with Phil and he has been super-helpful: but he’s been using a Windows-only version of TNT in which you don’t write scripts, but invoke various menu options, so he’s not able to help with this directly.)

Thank you!

References

 

I was lucky enough to have Phil Mannion as one of the peer-reviewers for my recent paper (Taylor 2018) showing that Xenoposeidon is a rebbachisaurid. During that process, we got into a collegial disagreement about one of the autapomorphies that I proposed in the revised diagnosis: “Neural arch slopes anteriorly 30°–35° relative to the vertical”. (This same character was also in the original Xenoposeidon paper (Taylor and Naish 2007), in the slightly more assertive form “neural arch slopes anteriorly 35 degrees relative to the vertical”: the softening to “30°–35°” in the newer paper was one of the outcomes of the peer-review.)

The reason this is interesting is because the slope of the neural arch is measured relative to the vertical, which of course is 90˚ from the horizontal — but Phil’s comments (Mannion 2018) pushed me to ask myself for the first time: what actually is “horizontal”? We all assume we know horizontality when we see it, but what precisely do we mean by it?

Three notions of “horizontal”

The idiosyncratic best-preserved caudal vertebra of the Snowmass Haplocanthosaurus MWC 8028, illustrating three different versions of “horizontal”. A. horizontality defined by vertical orientation of the posterior articular surface. B. horizontality defined by horizontal orientation of the roof of the neural canal (in this case, rotated 24˚ clockwise relative to A). C. horizontality defined by optimal articulation of two instances of the vertebra, oriented such the a line joining the same point of both instances is horizontal (in this case, rotated 17˚ clockwise relative to A). Red lines indicate exact orthogonality according to the specified criteria. Green line indicate similar but diverging orientations: that of the not-quite-vertical anterior articular surface (A) and of the not-quite-horizontal base of the neural canal (B).

There are at least three candidate definitions, which we can see yield noticeably different orientations in the case of the Snowmass Haplocanthosaurus vertebra that Matt’s been playing with so much recently.

Definition A: articular surfaces vertical

In part A, I show maybe the simplest — or, at least, the one that is easiest to establish for most vertebrae. So long as you have a reasonably intact articular surface, just rotate the vertebra until that surface is vertical. If, as is often the case, the surface is not flat but concave or convex, then ensure the top and bottom of the surface are vertically aligned. This has the advantage of being easy to do — it’s what I did with Xenoposeidon — but it conceals complexities. Most obviously, what to do when the anterior and posterior articular surfaces are not parallel, in the 7th cervical vertebra of a giraffe?

Cervical vertebra 7 of Giraffa camelopardalis FMNH 34426, in left lateral view. Note that the centrum is heavily “keystoned” so that the anterior and posterior articular surfaces are 15-20˚ away from being parallel.

Another difficulty with this interpretation of horizontality is that it can make the neural canal jagged. Consider a sequence of vertebrae oriented as in part A, all at the same height: the neural canal would rise upwards along the length of each vertebra, before plunging down again on transitioning from the front of one to the back of the next. This is not something we would expect to see in a living animal: see for example the straight line of the neural canal in our hemisected horse head(*).

Definition B: neural canal horizontal

Which leads us to the second part of the illustration above. This time, the vertebra is oriented so that the roof of the neural canal is horizontal, which gives us a straight neural canal. Nice and simple, except …

Well, how do we define what’s horizontal for the neural canal? As the Haplocanthosaurus vertebra shows nicely, the canal is not always a nice, neat tube. In this vertebra, the floor is nowhere near straight, but dishes down deeply — which is why I used to the roof, rather than the floor of the canal. Rather arbitrary, I admit — especially as it’s often easier to locate the floor of the canal, as the dorsal margin is often confluent with fossae anteriorly, posteriorly or both.

And as we can see, it makes a difference which we choose. The green line in Part B of the illustration above shows the closest thing to “horizontal” as it would be defined by the ventral margin of the neural canal — a straight line ignoring the depression and joining the anteriormost and posteriormost parts of the base of the canal. As you can see, it’s at a significantly different angle from the red line — about 6.5˚ out.

And then you have human vertebrae, where the dorsal margin of the neural canal is so convex in lateral view that you really can’t say where the anteriormost or posteriormost point is.

Left sides of hemisected human thoracic vertebrae, medial view. Note how ill-defined the dorsal margin of the neural canal is.

So can we do better? Can we find a definition of “horizontal” that’s not dependent of over-interpreting a single part of the vertebra?

Definition C: same points at same height in consecutive vertebrae

I’ve come to prefer a definition of horizontal that uses the whole vertebra — partly in the hope that it’s less vulnerable to yielding a distorted result when the vertebra is damaged. With this approach, shown in part C of the illustration above, we use two identical instances of the vertebrae, articulate them together as well as we can, then so orient them that the two vertebrae are level — that a line drawn between any point on one vertebra and its corresponding point on the other is horizontal. We can define that attitude of the vertebra as being horizontal.

Note that, while we use two “copies” of the vertebra in this method, we are nevertheless determining the horizontality of a single vertebra in isolation: we don’t need a sequence of consecutive vertebrae to have been preserved, in fact it doesn’t help if we do have them.

One practical advantage of this definition is that its unambiguous as regards what part of the vertebra is used: all of it; or any point on it, at the measurement stage. By contrast, method A requires us to choose whether to use the anterior or posterior articular surface, and method B requires a choice of the roof or floor of the neural canal.

Discussion

I have three questions, and would welcome any thoughts:

  1. Which of these definitions do you prefer, and why?
  2. Can you think of any other definitions that I missed?
  3. Does anyone know of any previous attempts to formalise this? Is it a solved problem, and Matt and I somehow missed it?

Answers in the comments, please!

References

(*) Yes, of course we have a hemisected horse head. What do you think we are, savages?

I got an email a couple of days ago from Maija Karala, asking me a question I’d not come across before (among several other questions): how much poop did Argentinosaurus produce in a day?

I don’t recall this question having been addressed in the literature, though if anyone knows different please shout. Having thought about it a little, I sent the following really really vague and hand-wavy response.

Suppose Argentinosaurus massed 73 tonnes (Mazzetta et al. 2004). In cattle, food intake varies roughly with body mass to the power 0.7 (Taylor et al. 1986), so let’s assume that the same is true of sauropods.

Let’s also assume that sauropods are like scaled-up elephants, in that both would have subsisted on low-quality forage. Wikipedia says elephants “can consume as much as 150 kg (330 lb) of food and 40 L (11 US gal) of water in a day.” Let’s assume that the “as much as” suggests we’re talking about a big elephant here, maybe 6 tonnes. So Argentinosaurus is 73/6 = 12 times as heavy, which means its food intake would be 12 ^ 0.7 = 5.7 times as much. That’s 850 kg per day.

Hummel et al. (2008, table 1) show that for a range of foods, the indigestible “neutral detergent fibre” makes up something around half of the mass, so let’s assume that’s the bulk of what gets pooped out, and halve the input to get about 400 kg of poop per day.

References

  • Hummel, Jürgen, Carole T. Gee, Karl-Heinz Südekum, P. Martin Sander, Gunther Nogge and Marcus Clauss. 2008. In vitro digestibility of fern and gymnosperm foliage: implications for sauropod feeding ecology and diet selection. Proceedings of the Royal Society B, 275:1015-1021. doi:10.1098/rspb.2007.1728
  • Mazzetta, Gerardo V., Per Christiansen and Richard A. Farina. 2004. Giants and Bizarres: Body Size of Some Southern South American Cretaceous Dinosaurs. Historical Biology 2004:1-13.
  • Taylor, C. S., A. J. Moore and R. B. Thiessen. 1986. Voluntary food intake in relation to body weight among British breeds of cattle. Animal Science 42(1):11-18.

You could drive several trucks through the holes in that reasoning, but it’s a start. Can anyone help to refine the reasoning, improve the references, and get a better estimate?

I have before me the reviews for a submission of mine, and the handling editor has provided an additional stipulation:

Authority and date should be provided for each species-level taxon at first mention. Please ensure that the nominal authority is also included in the reference list.

In other words, the first time I mention Diplodocus, I should say “Diplodocus Marsh 1878″; and I should add the corresponding reference to my bibliography.

Marsh (1878: plate VIII in part). The only illustration of Diplodocus material in the paper that named the genus.

Marsh (1878: plate VIII in part). The only illustration of Diplodocus material in the paper that named the genus.

What do we think about this?

I used to do this religiously in my early papers, just because it was the done thing. But then I started to think about it. To my mind, it used to make a certain amount of sense 30 years ago. But surely in 2016, if anyone wants to know about the taxonomic history of Diplodocus, they’re going to go straight to Wikipedia?

I’m also not sure what the value is in providing the minimal taxonomic-authority information rather then, say, morphological information. Anyone who wants to know what Diplodocus is would be much better to go to Hatcher 1901, so wouldn’t we serve readers better if we referred to “Diplodocus (Hatcher 1901)”

Now that I come to think of it, I included “Giving the taxonomic authority after first use of each formal name” in my list of
Idiot things that we we do in our papers out of sheer habit three and a half years ago.

Should I just shrug and do this pointless busywork to satisfy the handling editor? Or should I simply refuse to waste my time adding information that will be of no use to anyone?

References

  • Hatcher, Jonathan B. 1901. Diplodocus (Marsh): its osteology, taxonomy and probable habits, with a restoration of the skeleton. Memoirs of the Carnegie Museum 1:1-63 and plates I-XIII.
  • Marsh, O. C. 1878. Principal characters of American Jurassic dinosaurs, Part I. American Journal of Science, series 3 16:411-416.