Learning to Write My Science

It is no secret that the craft of writing, scientific or otherwise, takes practice. Some folks of course write better than others, but this skill is not usually without a hefty helping of rough drafts, frank feedback, and deft editing. As a young student, I thought “With just a little more practice and a Ph.D., I’m finally going to be a good writer.” How naive that was!

Upper Cretaceous rocks that are Late Cretaceous in age. Dinosaur Provincial Park, Alberta, Canada. Photo by A. Farke, CC-BY.

Upper Cretaceous rocks that are Late Cretaceous in age. Dinosaur Provincial Park, Alberta, Canada. Photo by A. Farke, CC-BY.

Speaking immodestly, I’m a decent scientific writer. My command of grammar is OK, I can spell most words correctly, and I’ve published enough to know how to string together a paper within the conventions of the field. My writing today is certainly better than it was 10 years ago. But, here’s the thing…just when I think I’ve got it together, I get a helpful reminder that I don’t know everything quite yet.

A week or two ago, some colleagues and I submitted a paper for review. The project had a lengthy gestation, and lots of back-and-forth as we crafted the manuscript. One of my co-authors is a fantastic writer with hefty editorial experience–although I did the bulk of writing as lead author, he did the bulk of the editing (along with some text, of course). Drafts came back with tighter prose, queries for clarification, and helpful stylistic reminders. Beyond some fun science, it was really satisfying to learn a little bit more about how to improve the style and clarity of my writing. I liked getting a reminder that I have more to learn.

As a bit of reinforcement, this morning paleontologist Tom Holtz tweeted a link to a paper from back in 2009 (PDF freely available here; more here too) on how to correctly use terminology for stratigraphy and geological time. For instance, consider the terms “Lower Jurassic” and “Early Jurassic”. The first refers to place–e.g., the position in the rock column. The latter refers to time–that time before the Late Jurassic. Although these terms are sometimes used interchangeably, this is really quite incorrect. You can’t say that rocks are “Lower Jurassic in age”! Although I knew a bit about this from my geology training (thanks to my undergrad professors for that one), I was pleased to learn some other specifics that I hadn’t really known–for instance, correct use of the abbreviation “Ma” (referring to millions of years before the present). You can say that the Cretaceous is the time between 145 and 66 Ma, but not that it lasted 79 Ma (it lasted 79 million years, or 79 Myr). If we want to write with maximum clarity, and not have our arguments dismissed for incorrect formulation, correct usage is important.

So, here’s a big thank you to all of my friends and colleagues who keep pushing me to improve. You know who you are. And to those who are earlier in your careers…don’t worry, you will always be learning how to write, too!

Below are a handful of my favorite writing/stylistic tips that I’ve learned over the years. None of these are my own–they were all acquired in class or in reviews of my own papers, some as recently as a few months ago. What would you add?

Andy’s Scientific Writing Tips

  • Avoid starting a sentence with “There is” or “There are”. It’s wordy and often less direct than desirable. E.g., change “There is a big foramen piercing the head of the femur,” to “A big foramen pierces the head of the femur.”
  • “is present” can often be replaced with the more succinct “occurs,” or other phrases. E.g., “A big ridge is present in the middle of the bone,” reads better as “A big ridge occurs in the middle of the bone.” Or even better, “A big ridge bisects the middle of the bone.”
  • Adverbs describing adjectives don’t need a hyphen. E.g., “poorly preserved,” not “poorly-preserved”. [I just learned this one a few months ago--thanks, Reviewer 1!]
  • “Triangular” and similar adjectives describing shape stand on their own. E.g., “triangular jugal,” not “triangular-shaped jugal.”
  • Words like “big” and “small” should be quantified or at least justified whenever possible.
  • Don’t mix directional terminology. E.g., using “posterior” in one part of the paper and “caudal” in another.
  • Learn the difference between hyphen, en-dash, and em-dash. [thanks to Louise in the comments! I'm still very much working on this one.]

Links
Owen, D. E. 2009. How to use stratigraphic terminology in papers, illustrations, and talks. Stratigraphy [a new journal for earth science] 6(2):106-116. [freely available pdf]

Category: Geology, Navel Gazing, Nuts and Bolts, Paleontology | Tagged , , | 9 Comments

Dinosaurs and Open Access: the State of the Field

Open access publication has, for the most part, long since ceased to be controversial. Although it certainly isn’t without its minor issues, open access is generally accepted to be a good thing by most scientists. So, how is that reflected in the scientific literature? As one barometer, I took a look at the new dinosaur species named in 2013.

The armored dinosaur Europelta, one of many open access dinosaurs named in 2013

The armored dinosaur Europelta, one of many open access dinosaurs named in 2013. Image  modified from Kirkland et al. 2013, CC-BY.

A total of 38 new species of non-avian dinosaur were coined in 2013 (including a handful that were new genus names for previously described species). Of these, 16 (~42%) were published as freely readable publications (note that this is a very broad definition of open access–12 of the 16 names were in CC-BY journals).

Seven different journals are represented in the mix for freely readable papers; of these, PLOS ONE is the most frequently utilized (7/16 names – that’s 44% of the open access dinosaur species). In fact, more new dinosaurs (seven) were named in PLOS ONE  in 2013 than in any other journal.

So, what does this mean for paleontology? A few random thoughts:

  • There doesn’t seem to be a major bias for which dinosaurs are named in the open access literature, either by clade or geographic location.
  • It would be really, really nice to see more non-dinosaurs named in open access publications. For whatever reason (probably related to a broader uptake of open access within the dinosaur researcher community), dinosaurs seem to predominate in the open access literature. We need more open access insects, trilobites, plants, and foraminifera!
  • New names are nice, but it is absolutely crucial that newly coined names hold up to scientific scrutiny. The last thing anyone wants to see are unneeded names cluttering up the literature. My glance through the list of 2013 dinosaurs shows that those published in open access journals are probably just as robust (or not robust) as those published in closed access journals.
  • There is room to diversify the open access ecosystem within dinosaur paleontology. I do love PLOS ONE [full disclosure - I am a volunteer editor, and have published there, in addition to my PLOS blogging activities], but it can only be a good thing if more open access venues are used and available. Competition encourages quality.
  • In 2008, only 7 of the 28 (25%) named new species of dinosaurs were in freely readable or open access publications.
  • 2014 is on track to meet or exceed the “openness” of 2014 – 7 of the 13 new dinosaur species named so far have been named in open access journals!

Why do I care so deeply about this issue? Beyond my general interest in open access and dinosaurs, I feel that we paleontologists have a unique opportunity in hand. Our field generates a disproportionate amount of media interest compared to many other fields. This in turn is shown by the number of individuals without easy journal access who want to read and engage with the scientific literature. There are numerous bulletin boards, art websites, and the like where amateurs discuss and build upon the scientific literature (and, let’s be frank, share non-open access papers without publisher authorization). Sure, most of these won’t lead to direct citations–but does that matter? This is public engagement with our work!!! How many botanists working on an obscure but threatened plant species would kill to get that kind of exposure?

Furthermore, there is a renewed interest within the professional community for engaging directly with amateur paleontologists (e.g., The FOSSIL Project) and other enthusiasts. Paleontologists are working hard to limit the black market for poached fossils and devise workable regulations for legally collecting fossils on public lands, in recognition that fossils are part of our shared planetary heritage. This is often up against claims of elitism and an “ivory tower” mentality leveled against some vertebrate paleontologists. I generally disagree with these accusations (when I was on the amateur side of things, I found the majority of paleontologists to be open, helpful, and accessible, and not at all opposed to most forms of legal amateur fossil collecting*), but I do think that the field of paleontology has a special obligation to be accessible, if only on grounds of public interest. Open access publications are one way to reach this goal.

Partial skull of the tyrannosaur Lythronax.

Partial skull of the tyrannosaur Lythronax. Modified from Loewen et al. 2013.

*to stem the inevitable quibble, amateur fossil collecting is NOT the same as commercial fossil collecting.

APPENDIX

Dinosaurs named in freely readable (“open access”) publications in 2013. Source: Wikipedia. Note: I counted only those names for which the papers were available from the journal website; a handful of other papers naming new dinosaurs can be found on the open web, but these are on author websites or other venues of dubious permanence.

Dinosaur   Journal
Canardia garonnensis ornithopod PLOS ONE
Dahalokely tokana theropod PLOS ONE
Dongyangopelta yangyanensis ankylosaur Acta Geologica Sinica
Europelta carbonensis ankylosaur PLOS ONE
Gannansaurus sinensis sauropod Acta Geologica Sinica
Jianchangosaurus yixianensis theropod PLOS ONE
Jiangxisaurus ganzhouensis theropod Acta Geological Sinica
Juratyrant langhami theropod Acta Palaeontologica Polonica
Lythronax argestes theropod PLOS ONE
Nankangia jiangxiensis theropod PLOS ONE
Nasutoceratops titusi ceratopsian Proceedings of the Royal Society B
Nyasasaurus parringtoni [named in 2012, not 2013] dinosaur(?) Biology Letters
Oohkotokia horneri ankylosaur Acta Palaeontologica Polonica
Saurolophus morrisi ornithopod Acta Palaeontologica Polonica
Wulatelong gobiensis theropod Vertebrata PalAsiatica
Xinjiangtitan shanshanesis sauropod Global Geology
Yunganglong datongensis ornithopod PLOS ONE

Update: Nyasaurus was first published in 2012, so I have adjusted the stats in this post accordingly.

Category: Dinosaurs, Navel Gazing, Open Access, PLOS ONE | 6 Comments

Thrills and Uncertainties: Discovering a New Dinosaur in Madagascar

“$%@# rain. It was sprinkling last night when I went to bed, and [it] was full-scale rain by 3 [a.m.] or so. Still raining at 7. Off and on rain, up to 9 a.m. as I write this. This is the most rain we’ve ever had in the history of the Mahajanga Basin Project.” – Field notes, 19 July 2005, Andrew A. Farke

Earlier this week, a mysterious dinosaur from the island of Madagascar finally received a name. Vahiny depereti – meaning “Depéret’s traveler” — designates a species of long-necked sauropod that roamed northwestern Madagascar around 70 million years ago. As a dinosaur fan, I of course love learning all about the latest discoveries. This one is particularly special for me, though. Way back in 2005, I found the piece of skull (a braincase, the part enclosing the brain) that allowed paleontologists Kristi Curry Rogers and Jeff Wilson to pin a name on the new species. When I learned about its publication, I pulled out my field notes to relive the story of that discovery.

Exposures of rocks from the Maevarano Formation pop up between dry grassy areas outside of Berivotra, Madagascar. The highly seasonal climate is not greatly different from how it was during the end of the Mesozoic. Photo by Andy Farke, CC BY 3.0.

The fossil of Vahiny was found in 70 million year old exposures of the Maevarano Formation, outside of Berivotra, Madagascar. I had the opportunity to conduct field here with the Mahajanga Basin Project, a joint effort between Stony Brook University (my Ph.D. alma mater), University of Antananarivo, and others. Photo by Andy Farke, CC BY 3.0.

“Into the field by 1:45…Robin [Whatley] & I went out to GPS–hit our first site around 2:15. We found that the ox cart road, just starting past the first bridge towards Mahajanga after camp, is an exceedingly efficient way to achieve insertion into the field area…We hit sites 99-43 & 99-43 near, amid some drizzle….After this, we ended up @ 96-07.”

The original specimen for a species, known scientifically as the “holotype,” is the standard upon which all comparisons are based. If the holotype later turns out to be insufficient to distinguish one species from another, the species name can be sunk. Even if a more complete specimen is found later, the holotype is still essential for defining the species. Not much more than 1,000 species of dinosaurs have been named, so the set of people who have found a holotype is pretty small. As a little kid nuts about dinosaurs, and even as a graduate student, I dreamed of joining that elite club. I of course have been lucky to be involved with naming several species, which was a tremendous privilege in its own right, and helped collect a holotype or two, but never before have I actually been the human who first laid eyes on the specimen.

“This site shows some real potential–maybe it’s the multi-taxon bonebed Dave [Krause] wanted? I found a braincase-looking thing which I soaked with consolidant. That, or it’s a vert [vertebra] chunk. It started to pour rain ~4:15, so we had to ‘abandon ship.’”

When a fossil is discovered in the field, it is usually covered in rock. As a result, a confident identification can be quite difficult. What is thought to be a flying reptile turns out to be a crocodile, or what is thought to be a fish jaw turns out to be a bird bone. In the rocks of the Maevarano Formation, where Vahiny (pronounced “va-heenh”) was discovered, sauropod bones are ridiculously common. This is great if you want to learn about sauropods (and who doesn’t?), but can be problematic when trying to make field identifications. The insides of many sauropod vertebrae are riddled with complex empty spaces, where air sacs once resided. When a vertebra weathers out, the interesting shapes on the fragments can fool even a trained eye into seeing a dinosaur skull piece, bird limb bone, or other find of great importance. During my years in Madagascar, I quickly learned to temper expectations for a freshly discovered bone.

“The braincase / sauropod vert frag is a braincase after all. Basioccipitals are distinct, & I found an occipital condyle which fits on nicely. The specimen is a little weathered, being on the flat, but should prep out nicely. The rostral end is heading down into the ground, but the dorsal bit seems a little gone. I would really like it to be sauropod. But maybe croc?”– Field notes, 21 July 2005, Andrew A. Farke

The braincase of Vahiny, as it looked upon discovery. The piece at the tip of my index finger is the occipital condyle, the ball where the skull attached to the neck. Photo by Andy Farke, CC-BY.

The braincase of Vahiny, as it looked upon discovery. The piece at the tip of my index finger is the occipital condyle, the ball where the skull attached to the neck. Photo by Andy Farke, CC-BY.

A rounded knob of loose bone that fit onto the mystery fossil confirmed its identity as a braincase–the part of the skull that encloses the brain and connects to the neck. Even once you figure out what bone is exposed, obscuring rock still makes it tough to determine the kind of animal that the bone came from. On top of that, paleontologists are always learning new anatomy. When I found the skull bone of Vahiny, I had some experience with crocodile braincases, and horned dinosaur braincases, and a few other types of braincases, but not much with sauropods. I also knew that sauropod skull bones are pretty rare. The tiny heads perched on the end of the long neck don’t fossilize well, compared to the robust limb bones or even the somewhat delicate vertebrae. I really, really wanted my discovery to be part of a sauropod skull–but, I knew based on what else we had been finding nearby that part of a crocodilian skull was far more likely.

“I collected loose frags of the braincase in a small bag. Jacketed it in a specialist; perhaps a good specimen to CT before prepping? Esp. if it is sauropod (I can always hope!)”

Once a fossil is exposed in the field, it has to be carefully packaged in order to survive the trip back to the lab. Durable jackets, made from cloth strips soaked in plaster of paris, cradle the fossil and its surrounding rock just like a broken arm in a cast.

After the end of the 2005 field season, the mysterious fossil was shipped back to the fossil preparation lab at Stony Brook University, where technicians Joe Groenke and Virginia Heisey began work. First, they ran the specimen through a CT scanner, to see what was inside–and it turned out to be a sauropod braincase! After weeks of cleaning and stabilization, the fossil was ready for scientific study. Kristi Curry Rogers (an expert on the sauropods of Madagascar) and Jeff Wilson (another expert on sauropod dinosaurs) collaborated to figure out just what kind of sauropod the braincase came from.

I had expected that the braincase came from Rapetosaurus [pronounced "ruh-PAY-too-SAWR-us"]. This animal is well known from several partial skulls, and another braincase would be nice to fill in some details on individual variation. Interesting, but not terribly exciting. So, my jaw dropped when Kristi told me that the bone I found wasn’t Rapetosaurus, but something totally different! Based on other odd bones found in that part of Madagascar, she had long suspected that there was another species of sauropod lurking in the area, but never had evidence good enough to confidently name an animal. Fortunately, sauropod species are readily distinguished by their braincases. The little fossil I found was the key to unlocking the puzzle.

Rapetosaurus, a sauropod dinosaur that lived alongside Vahiny. Although they were only distantly related, they superficially probably looked pretty similar. Image by Nobu Tamura, CC-BY.

Rapetosaurus, a sauropod dinosaur that lived alongside Vahiny. Although they were only distantly related, the two animals superficially probably looked pretty similar. Unfortunately, we just don’t have enough of Vahiny yet to know how its body proportions may have differed from RapetosaurusImage by Nobu Tamura, CC-BY.

The scientific paper naming Vahiny depereti clocks in at 12 printed pages (sadly, not open access), with a detailed description and copious figures of the fossil. A second specimen, a fragment from the braincase of a juvenile, has also turned up, adding a little more information. Kristi and Jeff showed that the braincase of Vahiny was quite different from that of Rapetosaurus, and in fact was most similar to the fossils of an animal from India called Jainosaurus. This is not terribly surprising, because Madagascar and India were connected until around 88 million years ago, so the dinosaurs from both land masses are fairly similarVahiny also showed some resemblances to sauropods from South America, again unsurprising given paleogeography.

For now, only the skull bones can definitively be called Vahiny. As mentioned above, other bones from the same part of Madagascar may also belong to the animal, but it will take an associated skull and skeleton to dispel any doubts. There is always more work to do!

Nearly 10 years after that discovery of an unremarkable looking bone, it has been fun to look over my field notes from those days. During our training as paleontologists, we learn all about the scientific importance of these notes, for recording information on geographic location, rock type, associated fossils, maps, and the like. However, our notes also preserve the highs and lows of a field season, and the thrills and uncertainties associated with any discovery. These emotions and memories are just as much a part of science as the fossils themselves.

“Awoke at 3 a.m. to a sound of guitar music — I guess it was probably a cattle man with the omby [cattle]. Some of the omby wandered through camp in the night…” – Field notes from fieldwork near Lac Kinkony, Madagascar, 5 August 2005, Andrew A. Farke

Citation
Kristina Curry Rogers & Jeffrey A. Wilson (2014) Vahiny depereti, gen. et sp. nov., a new titanosaur (Dinosauria, Sauropoda) from the Upper Cretaceous Maevarano Formation, Madagascar, Journal of Vertebrate Paleontology, 34:3, 606-617, DOI: 10.1080/02724634.2013.822874 [paywall]

The field note excerpts presented here have been edited for style, brevity, and profanity. Thank you to Dave Krause and the other leaders of the Mahajanga Basin Project, for the opportunity to participate in this fieldwork. The MBP is funded by National Science Foundation and National Geographic Society grants to Krause and others.

Category: Dinosaurs, Navel Gazing, Paleontology | Tagged , , , , , , , , , | 2 Comments

Bony body tube for a bizarre marine reptile

Prehistoric marine reptiles were a weird lot, especially in light of their lizard-like ancestors on land. You take something that roughly looks like an iguana, and evolve it into the shape of a dolphin (icthyosaurs), or evolve it into the shape of a turtle (turtles), or stretch out its neck and grow paddles on the limbs (plesiosaurs). That said, as a paleontologist I’ve grown fairly jaded when it comes to marine reptiles. Most of the major groups have been widely known since the dawn of paleontology, so I read all about them as a kid. I knew the story of Mary Anning and her 19th century quest for fossils, and how long-necked elasmosaurs used to swim over what are now the farms, ranches, and prairies of my home state of South Dakota. So, it’s nice to be surprised by a new marine reptile every once in awhile!

Hupehsuchus, in silhouette. Public domain image by Neil Kelley via PhyloPic.

Hupehsuchus in silhouette. Public domain image by Neil Kelley via PhyloPic.

Hupehsuchians were a group of marine reptiles that lived around 248 million years ago in Hubei Province, east-central China. It would be an understatement to say that they were bizarre (hence my surprise in learning more about them). Only three genera are known from this fairly tiny geographic region, and none of them exceeded a meter in total body length. They have a long and toothless snout, an elongated body, and flipper-like hands and feet, sometimes with six or seven fingers and toes (a post from microecos back in 2008 provides a helpful summary, as does the Wikipedia page). Addtionally, the first hupehsuchian–Nanchangosaurus–wasn’t named until 1959. Probably owing in part to various geopolitical factors, as well as the fact that they aren’t carnivorous dinosaurs, the group didn’t receive much attention until fairly recently. Their evolutionary relationships are also a little uncertain, with the only consensus being that they are diapsids (the group including lizards, dinosaurs, birds, and most other marine reptiles).

Skeleton of Hupehsuchus, modified from Chen et al. 2014. The head is to the left of the image. CC-BY.

Skeleton of Hupehsuchus, modified from Chen et al. 2014. The head is to the left of the image, and note the densely packed ribs in the torso. CC-BY.

Last week in PLOS ONE, a paper by Xiao-hong Chen, Ryosuke Motani, Long Cheng, Da-yong Jiang, and Olivier Rieppel announced a new and even more bizarre hupehsuchian–the one that takes it all to the next level. Known from a headless skeleton, Parahupehsuchus longus is notable for its truly odd rib cage, which is pretty remarkable given that some hupehsuchians have an odd rib cage from the start.

For most four-limbed animals with ribs, each rib is separated from the next by a little gap. You might be able to feel it on yourself, and you are certainly familiar with it from pictures of human skeletons. These gaps are nice in allowing the flexibility of the rib cage needed for locomotion and breathing. Animals that close these gaps–such as turtles–simultaneously develop new ways of breathing with special internal muscles and have to alter their locomotion, too. It turns out that Parahupehsuchus gets funky with its ribs also, by expanding the leading and trailing edges of each individual rib so that it runs into the adjacent ribs (see picture below).

Close-up of the rib cage in Parahupehsuchus; note how the ribs (in blue-ish gray, labeled "ri") run into each other.

Close-up of the rib cage in Parahupehsuchus; note how the ribs (in blue-ish gray, labeled “ri”) run into each other. From Chen et al. 2014, CC-BY.

The result is a “body tube” of bone surrounding all of the squishy, tasty viscera in the torso of Parahupehsuchus. What good is this kind of structure, especially if it makes it hard to breathe conventionally? The authors of the paper hypothesize that the odd rib arrangement was a defense against large predators that were evolving at just about that same time.

This seems intuitively appealing, but I do wonder if an alternative explanation is possible. It is fairly certain that the overlapping ribs of Parahupesuchus stiffened the trunk–but could this be related to locomotion rather than defense? Many aquatic organisms store and release elastic energy within the body for efficient swimming–effectively, treating the body as a spring that is tensed and un-tensed through the movement cycle. All else being equal, an animal with a stiff body stores more elastic energy than one with a “floppy” body during equivalent undulations. As small aquatic animals, perhaps the stiff torsos of Parahupehsuchus and relatives were selected for locomotor efficiency. This is certainly an idea worth investigating…and it doesn’t rule out other functions for the stiff body (including defense).

In any case, hupehsuchians are a fun group of organisms that display some pretty darned unique anatomy. Lots of food for thought, and that’s a good thing! It’s going to take quite a bit of brain power to figure out these odd-balls.

A headless wonder--the skeleton of Parahupehsuchus.

A headless wonder–the skeleton of Parahupehsuchus. The front of the body is to the left of the photo (sans skull), and the tail is to the right (with the end missing). Modified from Chen et al. 2014, CC-BY.

Citation
Chen X-h, Motani R, Cheng L, Jiang D-y, Rieppel O (2014) A carapace-like bony ‘body tube’ in an Early Triassic marine reptile and the onset of marine tetrapod predation. PLoS ONE 9(4): e94396. doi:10.1371/journal.pone.0094396

Category: Paleontology, PLOS ONE | Tagged , , , , | 1 Comment

Sharing Paleodata (Part 3): MorphoBank

Today I am making good on an old promise to highlight more repositories for paleontological raw data. Previous posts in this series can be found here and here.

MORPHOBANK (http://morphobank.org/)

Full Disclosure: The statements about MorphoBank in the “Nitty Gritty” section were checked for accuracy by Maureen O’Leary (MorphoBank Project Director) and Seth Kaufman (software developer). The impressions are my own: I have submitted, published, and downloaded MorphoBank data.

Impressions: MorphoBank is not just a data repository, but also a collaborative tool to produce, edit, illustrate, and annotate morphological character matrices for phylogenetic analysis. It’s not a tree-making, tree-visualizing, or tree-using site; it’s a tree data site, and it’s built to accommodate large groups who are working in the same project. In service of this goal, each character or character state can be linked to an image or video of that character state, which can then be edited or annotated. MorphoBank is cloud-based, meaning you don’t have to concatenate dozens of files from collaborators to build a final matrix; everyone can see what you coded immediate (and why, if you load images). You can use MorphoBank just to create matrices, just as a media repository, or a combination.

There are lots of cool toys that make collaboration easier – these include an image annotation menu, comment screens (facilitating discussions of identity and homology), the ability to restriction which taxa/rows each person can edit (preventing people from accidentally coding/editing the wrong thing), the ability to merge many source matrices into one combined matrix, and the ability to keep all the relevant documents in one place. You can batch upload taxa, specimens, and media, which is convenient. The how-to’s are thorough and easy to use, and so is the site itself.

The matrix editor is quite user-friendly. You can create one from scratch or import from a TNT or Nexus file (and even if you don’t generate your matrix in MorphoBank, you can still host the data files there). The comments and annotations feature make it easy to discuss morphology or calls on codings with colleagues, without having to get them on the phone or in person. You can also track changes if you think someone has messed up, and assign different levels of editing ability to prevent such things from happening in the first place. I like this feature a lot, because it enables students and volunteers (and colleagues) to participate in different roles. Another cool feature is that it records and displays how many cells each team member has scored, as well as the taxa, media and citations they added.  This provides greater demonstration of exactly who did what work in a collaboration.

MorphoBank is one of the best, if not the best, repositories for 2D images.  The allowed file and image sizes are generous, and the built-in viewer enables you to zoom in/out and label/annotate your images. As a bone histologist, this is my preferred way to share my raw data – my dissertation involved over 700 large format images, and this was how I presented them to my committee. As a supplement to papers, MorphoBank is top notch: you can present detailed images at their original resolution without worrying about page sizes or file sizes, and you can show way more images than you could get into even in the most generous of journals. Having a permalink (and coming soon: DOIs) for each image means those images can be cited later, getting credit for all your work. Those permalinks also can be given to media outlets as part of your outreach or research promotion (yay broader impacts).

Overall, I have no big issues with MorphoBank, and from personal experience I can report that all the minor speedbumps I’ve experiences were quickly resolved by their excellent support team. However, there is one feature I’d like to see added that would integrate MorphoBank with other sites better: it would be nice to be able to link specimens and publications externally. For example, links from the vouchered specimens to their museum database pages, or bibliography publications to their journal page (both are features GenBank offers).

Bottom line: Grant writers should feel comfortable listing MorphoBank in their Data Management Plan because it’s safe, easy to use, and your reviewers will (should) have heard of it; reviewers should feel comfortable asking authors post data to MorphoBank when appropriate, for the same reasons. 

Postcranial skeleton of Sebecus icaeorhinus, MPEF/PV 1776. (c) 2012 Diego Pol, licensed under CC-BY-NC-ND. MorphoBank accession M106695, accessed here.

Postcranial skeleton of Sebecus icaeorhinus, MPEF/PV 1776. Image © 2012 Diego Pol, licensed under CC-BY-NC-ND. MorphoBank accession number M106695, accessed here.

MORPHOBANK: THE NITTY GRITTY

What it is: Both a collaborative tool and repository for the scientific data associated with peer-reviewed scientific publications. The focus is on data related to phylogenetic tree-building and the evolution of morphological phenotypes in general. It allows research teams to work on a single shared copy of a character matrix in real time over the Web. These data matrices can be linked to images of different anatomical characters/character states, or the images can stand on their own. “Morphology” is intepreted broadly – really, any type of phenomic data is welcome.

What it is, in their words: “…a web application for conducting phylogenetics or cladistics research on morphology. It enables teams of scientists who use anatomy to study the Tree of Life (phylogeny) to work over the web – in real time – and to do research they could not easily do using desktop programs alone.”

Who runs it: The MorphoBank Project, which has an executive committee that consists of academic researchers (including one student representative). The Project Director is Maureen O’Leary (Stony Brook University), and the Executive Committee is chaired by Nancy Simmons (American Museum of Natural History).

Who funds it: Currently: NSF (direct), with in-kind support from the American Museum of Natural History and Stony Brook University (as server hosts). Previously: American Museum of Natural History, NESCENT, NOAA (NA04OAR4700191), NSF (DBI-0743309, DEB-9903964 and EAR-0622359), San Diego Supercomputer Center, Stony Brook University.

Who uses it: Researchers who use or submit data; journals allow you to cite MorphoBank data. Project/media links could be used for media promotion and outreach as well.

Nasutoceratops titusi

Nasutoceratops titusi UMNH VP 16800. Image © Mark Loewen, licensed under CC0. MorphoBank accession number M307812, accessed here.

Cost to submit: Free.

Cost to access: Free.

Data and file types supported: Data related to systematics or morphology, including text, audio, images, video, and more. 2D images: JPEG, GIF, PNG, TIFF and PSD are allowed, but a file in CMYK or with layers may not render properly. 3D images: Three dimensional surfaces in STL and PLY format will be supported soon. Video: MPEG-4 (preferred), QuickTime, and Windows Media. Audio: MP3, AAC, AIFF or WAV.  Phylogenetics: The matrix editor/viewer accepts data in Nexus or TNT format.  Other files not in this format are stored in the Documents folder. Other: No PPT or PPTX.

File sizes allowed: Doesn’t say. In the past, my files have been limited to 40MB, but by emailing tech support I was able to request an increase in maximum file size. The image viewer sometimes has difficulty processing gigapixel images, but this can be fixed by resizing or emailing tech support.

Copyright status: Settings are currently available for Media (images, video, and the like). Your choice: CC0, CC BY, CC BY-NC, CC BY-NC-SA, CC BY-SA, CC BY-ND, CC BY-NC-ND. You can also post copyrighted media released for one-time use. Cool feature: option to upload your copyright permissions document.

Data available during peer review? Yes, if you set it up. Password protected. This is not streamlined into the journal submission process, and from personal experience, journal editors don’t pass on this info if it’s in the cover letter only. I make sure to include the login information in the body of the manuscript, so the reviewers can see it.

Allowed to post data from previous pubs? Yes, even publications published before MorphoBank existed, and they invite and encourage this practice. Example: http://morphobank.org/permalink/?P694

Skeleton Vulpavus ovatus (AMNH 11498)

Skeleton of Vulpavus ovatus (AMNH 11498). Image © American Museum of Natural History, licensed under CC BY-NC-SA. MorphoBank accession number M150920, accessed here.

Accession numbers provided? Yes. Every project gets a unique project number and stable URL (permalink), and each image gets its own accession number (similar to GenBank), assigned as you upload them. You can also assign media to folios (subsets of media), and these also get unique stable URLs. DOIs for Projects, Media and Matrices will be available before the end of April 2014 and this will be retroactive (!!!).

Data goes live when: You choose to publish the project. Data can stay as an unpublished project forever, or you can publish it when the manuscript is accepted, when embargo is lifted, when the paper is published, or any time after. You can choose to publish all or some of your files when the project is published.

Data is backed up? Yes, to tape at Stony Brook University and off-site mirror servers at the American Museum of Natural History.

Stats provided? Project views, project downloads, media views, media downloads, document downloads, data on team member efforts.

How to cite your data in your manuscript? Varies by journal, but some thoughts:

  1. Definitely cite the MorphoBank publication software. Currently, this is: O’Leary MA and SG Kaufman. 2012. MorphoBank 3.0: Web application for morphological phylogenetics and taxonomy. http://www.morphobank.org.
  2. You should additionally cite the peer-reviewed publication: O’Leary MA and SG Kaufman. 2011. MorphoBank: Phylophenomics in the “cloud”. Cladistics 27: 1-9.
  3. You should also cite your data. I recommend citing within text, something like:
    Image data available on MorphoBank: http://morphobank.org/permalink/?P494 (but where ‘494’ is replaced with your own project number). I’ve also included lists of image accession numbers as tables (for larger projects, I think this is more appropriate for the SI).

How to cite data you download? Cite the permalink (the DOI once that feature goes live) and project number, and if you refer to a particular image, the accession number.

Can update after publication? No. Once the project is published, it cannot be modified.

Eryon arctiformis (Houston Museum of Natural Science). Image by Daderot, licensed under CC0 1.0. MorphoBank accession number M326412, accessed here.

Eryon (Houston Museum of Natural Science). Image by Daderot, licensed under CC0 1.0. MorphoBank accession number M326412, accessed here.

Exciting Future Developments: The MorphoBank group is about to release a version of the Matrix Viewer that will allow you view published matrices on iPad and Android tablets (the previous, Flash-based viewer is being replaced with a new, HTML 5-based viewer). In the future, they plan to do the same for the Matrix Editor, as well. MorphoBank also talks to a new NSF-supported site called the Evolution Project (now in beta testing).  The Evolution Project allows people who have matrices in MorphoBank to crowdsource their data collection. Interested people (e.g., students, volunteers) can score cells from images (!!!).  It is designed to speed up morphological data collection.  Also coming soon: the ability to viewing CT images within the MorphoBank environment, and support for continuous characters.

Benefits in a nutshell:

  • Secure cloud storage of image and character matrix data.
  • Real-time collaborative editing of phylogenetic matrices and their associated data in the cloud.
  • Images illustrate exactly what you mean by a given character or character state. As the MB site says, “Seeing the images that document the basis for homology – a character state or a cell score – is enormously helpful to researchers during their research project.”
  • Nigh-infinite choices for: number of images, copyright, image size and resolution.
  • Batch uploads and batch edits to metadata allowed.
  • The ability to label and otherwise annotate images (without altering the original image).
  • The ability to zoom in when viewing large or high-resolution images.

Three recent paleo papers using it:
Evans SE, JR Groenke, MEH Jones, AH Turner, DW Krause. 2014. New material of Beelzebufo, a hyperossified frog (Amphibia: Anura) from the Late Cretaceous of Madagascar. PLoS ONE 9(1): e87236. MorphoBank data here.

O’Leary MA, et al. 2013. The placental mammal ancestor and the post K-Pg radiation of placentals. Science 339:662-667. MorphoBank data here.

Nesbitt SJ, PM Barrett, S Werning, CA Sidor, AJ Charig. 2013. The oldest dinosaur? A Middle Triassic dinosauriform from Tanzania. Biology Letters 9:5pp. MorphoBank data here.

Category: Digitization, Open Access, Open Data, Paleontology, Technology | 1 Comment

Paleontology in a Sink Hole: Spring Break Edition

Last week, I spent time at the Bahamas Natural History Symposium in Nassau, Bahamas. Seeing policy makers, ecologists, educators, geologists, and anthropologists come together was awesomely inspiring for the future of The Bahamas, a wonderful place with a magnificent natural environment! If you are fossil hunting ,The Bahamas might not immediately come to mind as a paleontological destination, but you would be wrong! The Bahamas is a large carbonate platform that may have started forming as early as the Cretaceous. The carbonate rock was exposed to the air during the Pleistocene, and during this time sand dunes lithified and formed the islands. During the last glacial maximum, the Bahamas bank was exposed greatly increasing the landmass and connectivity of the Caribbean, fostering biotic interchange between the islands. Now this shelf is submerged again so the islands remain isolated. The limestone that the islands are based on is porous and can be dissolved, so during glacial maxima, weathering of this limestone lead to features that make these islands so special today—underground caves, sink holes, and pits.

The Bahamas. The light blue shallow water is the carbonate shelf that was once exposed during the Last Glacial Maximum. From NASA on Wikimedia Commons

When sink holes and caves fill with water, these underground networks become submerged ethereal mazes that preserve unique life forms. Besides looking beautiful, blue holes as they are called, become a quiet resting place for anything –animal or human—that might end up in there. The blue holes of Abaco in The Bahamas have preserved a rich paleontological and anthropological history spanning thousands of years. On Great Abaco Island, there are a few of these astonishing features, but especially notable is Sawmill Sink. Sawmill Sink, one of the most famous blue holes in The Bahamas, contains the bones of numerous vertebrates that no longer live on the islands or are completely extinct. It is a spectacularly preserved graveyard of tortoises, birds, and crocodiles. Even human bones have found in Sawmill Sink, a remnant of the original prehistoric inhabitants of The Bahamas, the Lucayan people. Since these underwater caves were not always filled with water—as I previously mentioned, sea level was lower—the Lucayans were able to bury individuals in these limestone caves. The bones in the cave are perfectly preserved and also contain organic collagen, so they can be dated using carbon-14. The human remains in Sawmill Sink date from 1050 to 920 calendar years before present, making this the earliest evidence of human inhabitance of the Bahamian Archipelago.

320px-Dean_Blue_Hole_Long_Island_Bahamas_20110210

Dean’s Blue Hole in Long Island, The Bahamas. By Ton Engwirda Wikimedia Commons

Up to 54 individual crocodile specimens have been found in Sawmill Sink that are dated to 2780 years before present, predating any human occupation of The Bahamas. The species of crocodile is Crocodylus rhombifer, the Cuban crocodile. There are currently no crocodiles in The Bahamas, and the Cuban crocodile is limited only to a very small region of Cuba. How the Cuban crocodiles found in Sawmill Sink are genetically related to the current Cuban population remains unknown, but it is quite possible ancient DNA can be obtained from the well preserved specimens. Additionally, why did they go extinct from most of the West Indies? It is supposed that the extinction was caused by human encroachment and hunting, which make sense, because C. rhombifer bones are found in archaeological middens, along with other extinct tortoises that would have been a tasty meal, throughout the islands of The Bahamas.

Cuban crocodile in a Miami zoo. By Alexf Wikimedia Commons

Cuban crocodile in a Miami zoo. By Alexf Wikimedia Commons

Birds, such as the now extinct Bahamas caracara, and the Bermuda petrel (now only in Bermuda) are found preserved in blue holes indicating the avifauna of the Caribbean was once very different and perhaps a lot more diverse. These fossil deposits preserve a unique time in geological history when both humans and large vertebrates were inhabiting space-limited environments. Detailed study of these fossils can potentially help us see at a fine-scale the impact human settlement can have on biodiversity. Since blue holes are so spectacular, there are a myriad of great photographs out there, specifically through National Geographic. I suggest you take a look because the images are just fantastic.

Now if you’ll excuse me I am off to spring break. Paleontologists need some beach time too!

Additional reading:

Morgan, G.S. and N. A. Albury. 2013. The Cuban crocodile (Crocodylus rhombifer) from the Late Quaternary fossil deposit in The Bahamas and Cayman Islands. Bulletin of the Florida Museum of Natural History 52(3): 161-236.

 

Category: Geology, Paleontology, Zoology | Tagged , , , , | Comments Off

Shake Your Tail Bone! (and shape your skeleton, if you’re a bird)

This is either a cheap tactic to increase blog traffic via cats, or an oddly relevant image. The Manx cat has a mutation that results in a shortened tail.

This is either a cheap tactic to increase blog traffic via the internet’s unhealthy obsession with cats, or an oddly relevant image. The Manx cat has a mutation that results in a shortened tail. Image by Karen Slemmer, CC-BY.

Those poor tail bones, always getting shortened and lost during the course of evolution. A long tail is the default condition for four-limbed vertebrates, but this tail disappears with shocking regularity. Frogs ditched theirs early in their evolutionary history. Humans and other apes did the same. And, of course, birds.

Well, perhaps disappear isn’t quite the right word for what happened in these groups. The tail is still there–just with many fewer vertebrae. Those of us who have carved up a turkey or chicken don’t pay much attention to their pitiful tails. It’s a fatty little nub, without much in the way of meat, bound for making soup stock. If you’re weird like me (when I was 12 or so, I cleaned and mounted the bones of our Thanksgiving turkey), you might have picked apart the tail and noticed a few things. First, the bones are pretty simple…most of the vertebrae behind the hip are short and squat. But most intriguingly, the last little chunk of tail is particularly weird: a flattened mass of bones, formed from several vertebrae fused together. The technical term for this structure is a pygostyle.

Peregrine Pygostyle.

Skeleton of a peregrine falcon–the bone highlighted in green is the pygostyle. Image from Eyton 1867, in the public domain.

Even though the pygostyle is a pitiful-looking bone, it (and its surrounding tissues) are important for anchoring the spectacular tail feathers of many birds. In turn, these tail feathers are shaped in part by how birds use these tails–whether in slow soaring flight, rapid plunges through the air, or long aquatic dives in pursuit of fish. A close relationship between the anatomy of the wing bones and locomotion style has been documented in many bird groups–after all, the wings are the obvious system to investigate for birds. But do the same relationships between locomotion and bony anatomy apply to the tail?

Ryan Felice, a Ph.D. student at Ohio University, and Pat O’Connor, Ryan’s graduate advisor, documented shapes and sizes for the loose tail vertebrae and pygostyles from 51 species representing a variety of waterbirds and shorebirds. The sample included everything from loons to penguins to storks to seagulls, spanning a variety of body sizes and locomotion styles. So, what did the researchers find?

It turns out that pygostyle shape is closely related to foraging style–birds that forage underwater, such as penguins, have a shape that is quite different from that seen in birds that forage from the air. And similar shapes appear convergently in evolutionarily distant lineages. Penguins, puffins, and boobies are separated by at least 60 million years of evolution, but all have a long and straight pygostyle. They also all chase after their prey underwater.

What a long and straight pygostyle you have there, Penguin. Then again, I say that to all of the underwater foragers. Image by LoKiLeCh, CC-BY.

What a long and straight pygostyle you have there, Penguin. Don’t feel special, though. I say that to all of the underwater foragers. Image by LoKiLeCh, CC-BY.

So why these convergences? Felice and O’Connor suggest that underwater locomotion has a unique set of demands on the skeleton from aerial locomotion, perhaps related to particular patterns of muscle development or to resist forces applied to the skeleton when using the tail as an underwater rudder. Or, it might have something to do with the orientation of the tail feathers in diving birds (more research is required on this latter point).

The new study, published last week in PLoS ONE, documents yet another way that bird skeletons reflect their lifestyles. From a paleontological perspective, the work will hopefully open another path to infer the behavior of fossil species. So the next time you see that pygostyle on a bird, make sure to say thank you for being such a nifty feature!

Want to learn more? Read the paper in PLoS ONE!
Felice RN, O’Connor PM (2014) Ecology and caudal skeletal morphology in birds: the convergent evolution of pygostyle shape in underwater foraging taxa. PLoS ONE 9(2): e89737. doi:10.1371/journal.pone.0089

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The asteroid started the fire (or did it?)

Poor guys didn’t know what hit em. Public Domain via Wikimedia Commons by Donald E. Davis

In December, I listened to the Radiolab “Apocolyptical” show which was all about the Cretaceous-Paleogene boundary event. Famously, in 1980, Walter Alvarez and colleagues described an iridium anomaly at the K/Pg (also known at K/T) boundary which was subsequently specifically tied to an extraterrestrial impact event. The crater from this impact is around 200-km wide off the coast of the Yucatán in Mexico, known at the Chicxulub Crater.

But what happens when a 10 km (6 mile) wide rock smashes into Earth’s surface? When this object made impact, hot, melted rock was ejected and these little rock balls (spherules) rained down and can be found in deposits of K/Pg age rocks worldwide. There is little debate that this enormous disruption to the entire Earth was responsible for the large-scale extinction we see at the K/Pg boundary. But what, more specifically, did the molten rock and rock vapor have to do with it?

Back to the Radiolab. I was surprised as I listened to it that the hosts were taking an angle of “everything you have learned about dinosaur extinctions is wrong!” From my own experience, it is taught that the final nail in the coffin for dinosaurs, plants, and other animals was a long-lasting “impact winter.” The amount of debris kicked up into the atmosphere would have been so extreme, it would have blocked out the sun, reduced photosynthesis, and caused a cooling period. This cooling period, although it probably only lasted about 2,000 years, would be devastating to ecosystems worldwide. I don’t think there is much doubt an impact winter actually happened, but the stance this radio show took was that this was absolutely not the cause of the massive vertebrate extinction.

Their source on this was work done last year, mainly through computer modeling, that calculated the infrared (IR) radiation heat pulse and subsequent probability of global wildfires caused by molten ejecta re-entering the atmosphere. Douglas Robertson published a comprehensive review of the heat-fire hypothesis, noting that by calculating the kinetic energy converted to IR radiation by ejecta re-entering the atmosphere, a temperature could be reached on the surface of the Earth that is sufficient to ignite plant matter and tinder, causing global wildfires.

Much of this review is dedicated to addressing the problems with this hypothesis raised by other researchers. This often comes down to the morphology and fine structure of the soot found in K/Pg age rocks. While proponents of the heat-fire hypothesis say that soot found is clearly from widespread forest fires, the research of scientists like Claire Belcher suggests otherwise. Her research indicates that these soot deposits are not soot from the burning of plant matter, but actually hydrocarbon combustion from the impact site. Additionally, she puts forth compelling evidence that while there would have been IR radiation coming from the spherules, it mainly would have been shielded from the Earth by the spherules actually settling and forming a cloud in the atmosphere. The spherules’ interaction with the atmosphere potentially prevented the surface of the Earth from being completely incinerated. Of course, the other camp argues the charcoal deposits have signs of coming from ignition of plants and not of hydrocarbons. The debate rages on.

So was every living thing not underground or in the water burned up almost immediately by an IR radiation pulse? Or was there not truly enough heat reaching the Earth’s surface to cause such widespread fire, and extinction was driven mainly by other factors such as acid rain or impact winter? It is hard to know if we will ever be 100% certain, but I find the debate fascinating. Do I think it is right to tell the public everything the know about the dinosaur extinction is wrong? Honestly, I don’t think it is the best way to go about things, because there is still so much debate on this topic and scientists have not reached a consensus, and may never have a unified theory. What do you think about this debate? Any strong opinions either way? If you are an educator, what do you teach your students?

Photo representation of what the non-avian dinosaur extinction may have looked like

Photo representation of what the non-avian dinosaur extinction may have looked like

Category: Climate Change, Dinosaurs, Paleontology | Tagged , , , | 5 Comments

Did Dinosaurs Enjoy Chocolate?

Dinosaurs dining on a chocolate kiss - image (c) Emily Willoughby, used with permission.

Dinosaurs dining on a chocolate kiss…did they ever encounter a cocoa bean? – image (c) Emily Willoughby, used with permission.

Every living thing has a remarkable evolutionary history, stretching back through the eons. Sometimes it’s fun to think about common plants and animals alongside the dinosaurs of the Mesozoic–particularly when there is a fossil record to match! For instance, ancient relatives of ginger are pretty common in the fossil record, so Triceratops might have enjoyed a good herbal tea, and giant Jurassic sauropods could have been serenaded by chirping katydids. But, it’s Valentine’s Day, so I want to know: Did Velociraptor (or its cousin Deinonychus, shown above) trade boxes of chocolates?

That’s obviously a frivolous question, so let’s rephrase it in paleontological terms…was chocolate (or at least its source plant) around with the dinosaurs? To investigate that, we need to delve into the fossil record.

Chocolate is made from the cocoa bean, which is the seed from the fleshy fruit of the cacao tree (Theobroma cacao). The cacao tree is part of a group of plants called the Byttnerioideae, which in term belong to a group called Malvaceae. We could go on and on from there, but suffice to say they are angiosperms, or flowering plants. So, do cacao trees or any of their relatives show up in the fossil record?

Cocoa pods on the tree. Image by medicaster (public domain).

Cocoa pods on the tree. Image by medicaster (public domain).

An alleged fossil cocoa pod–named Theobroma fossilium [PDF of the original description]–was found in rocks of uncertain age in Colombia (dated to sometime in the last 65 million years), but it later turned out to be part of a fossil jaw [paywalled article]! So, that’s a bit of a dead end.

Byttnerioideae, the group of plants most immediately including the cacao tree, has a pretty dismal (i.e., virtually nonexistent) fossil record. Estimates from molecular clocks (based on gene sequences of modern plants) suggest the group split from other plants between 36 and 20 million years ago–well after the non-avian dinosaurs went extinct! The fossil record for the Malvaceae (the group containing Byttnerioideae and their relatives) is a little better, with possible wood known from around 75 million year old sediments in Texas, and some leaves from around the same time. If you’re interested in a detailed account of fossil Malvaceae, there is a nice summary in a recent paper by Carvalho and colleagues.

The short version of all of this is that only the most distant relatives of cocoa beans grew alongside Velociraptor and friends. But, the news isn’t so bad for every prehistoric animal, especially those from the last million years. Some researchers speculate that giant ground sloths and gomphotheres (elephant relatives) feasted on big fruits like those from the cacao tree. So, even if our beloved dinosaurs never enjoyed chocolate, we can be comforted by the fact that cocoa beans may have passed through a ground sloth butt sometime in the Pleistocene.

Painting by Heinrich Harder, in the public domain.

Poor Megatherium, stuck eating raw cocoa pods. No chocolate kisses for this ground sloth. Painting by Heinrich Harder, in the public domain.

A big thank you to scientific illustrator Emily Willoughby, for letting use her artwork for this post. Be sure to check out her website for more gorgeous renderings!

Category: Dinosaurs, Paleontology | Tagged , , | Comments Off

Turtles Lost and Turtles Found

Science is built upon repeatability, but this means different things in different fields. For instance, a chemist in one lab should be able to follow the procedures of another lab and get the same results. In a historical science like paleontology, repeatability depends in part upon being able to restudy previously published fossils in order to verify and expand upon previous observations. Nowadays, museums are the custodians of these irreplaceable specimens. But what happens when a fossil goes missing?

Sinathropus_pekinensis

With the originals lost in the chaos of World War 2, replicas are all that remain of the Homo erectus fossils known as ”Peking Man.” Image by José-Manuel Benito Álvarez (public domain).

Sadly, the disappearance of fossils is not totally unheard of. This can happen in wartime (as in the case of the sail-backed dinosaur Spinosaurus or with the fossils of “Peking Man”), by outright theft, or if a privately owned fossil was published upon and then later lost after the death of the owner. The published descriptions remain, of course, but they cannot be verified (e.g., if there is a question on what is reconstructed versus what is real bone), nor can the fossil be reprepared or restudied using “modern” techniques (such as CT scans, geochemistry, or histology). Science always suffers as a result.

Sometimes, paleontologists get a second chance. Let’s follow the twisted tale of a Jurassic turtle for one such case.

Way back in 1857–two years before Charles Darwin published On the Origin of Species–Swiss paleontologists François Jules Pictet de la Rive and Aloïs Humbert named a new species of extinct turtleEmys etalloni. The fossil consisted of a shell (carapace and plastron, in the technical terminology) collected in the Jura Mountains of eastern France, from rocks now dated to around 150 million years old. That much is straightforward, but from here the story gets tangled up in church politics.

The shell of Emys etalloni in side view (from Pictet and Humbert 1857)

The shell of Emys etalloni in side view (from Pictet and Humbert 1857)

The fossil of Emys etalloni was collected by a French priest, who passed it along to another priest (in fact, the vicar general of the Saint-Claude diocese, Joseph Célestin Girod), who in turn let paleontologists Pictet and Humbert study the fossil. Girod’s superior, Bishop Mabile, helpfully offered to turn the fossil over to a local scientific society, and from there the specimen briefly ended up in the Natural History Museum of Besançon. This apparently didn’t please Vicar Girod, because he claimed that he never agreed to part ownership with the specimen. As a result, the fossil was returned to Girod, and then lost to the mists of history after he passed into the great beyond in 1863.

The original description remained in the scientific literature, and a few plaster replicas of variable quality were scattered across museums in France and Switzerland. Emys etalloni was later moved into the genus Plesiochelys, but any rigorous study of the original fossil was severely limited. This was particularly problematic, because the identity and relationships of Jurassic-aged turtles from Europe are on the messy side. Depending upon which article you read, Plesiochelys etalloni was the same as some other species or its own species. In fact, up to six other turtle species had been lumped in with P. etalloni. Some more recently discovered fossils were assigned to P. etalloni outright, too. But, were they all really the same thing as the lost French turtle? Subtle textures and markings on the shell that were necessary to resolve the issue couldn’t be confirmed from the published illustrations, and plaster replicas didn’t help either. In the end, the real fossil was needed to settle the score.

The problem has particular relevance to paleontologists because turtles like Plesiochelys branched off near the origin of modern cryptodire turtles (the most common group of turtles, including everything from your typical pond turtle to the giant Galapagos tortoises), and are thus important for tracing turtle evolution. Although more recently discovered fossils in some ways made up for the missing fossil, which name went to which fossil was pretty nebulous. There was no way to know for sure without the original fossil of Plesiochelys etalloni!

In the worst case, perhaps the fossil shell had been thrown away after Vicar Girod’s death (after all, a heavy rock isn’t the most logical thing to keep). Somewhat miraculously, this wasn’t the case. It turned out that Vicar Girod sold the fossil to a collector, and the fossil stayed in this collector’s family for over 100 years. Perhaps wanting to properly dispose of a weighty heirloom (we can speculate), the family donated their inheritance to Musée d’archéologie du Jura in Lons-le-Saunier, France, back in 1994. Twenty years later, paleontologists Jérémy Anquetin​, Sylvie Deschamps, and Julien Claude recognized the specimen in the museum collection. Finally, they were able to redescribe the fossil in a recently published article in the open access journal PeerJ [full disclosure: I was the editor who handled their paper].

Top (A) and bottom (B) views of the turtle shell.

Top (A) and bottom (B) views of the shell of Plesiochelys etalloni. From Anquetin et al. (2014), CC-BY.

With the fossil in hand, Anquetin and colleagues answered some long-standing questions about Plesiochelys etalloni–most importantly, confirming its distinct identity. Of course, a thorough redescription and refiguring of the specimen led the way. Scientists who can’t visit the specimen in person now benefit from clear color figures and measurements. On top of this, the research team verified that at least three other previously named species (P. langii, P. sanctaeverenae, and P. solodurensis) were the same thing as P. etalloni. This is a critical finding, because specimens of these other “species” had skulls with them, which the recently rediscovered turtle did not. Skulls are important for unraveling fossil turtle relationships and behavior, so being able to more confidently match skulls and shells across the board is really nice!

Skull of Plesiochelys etalloni, from a specimen discovered in 1950 in Switzerland. Modified from Carabajal et al. 2013, CC-BY.

Digital reconstruction of the skull of Plesiochelys etalloni, from a specimen discovered in 1950 in Switzerland. Modified from Carabajal et al. 2013, CC-BY.

From the seas of the Jurassic to the ecclesiastical politics of 19th century France to the digital pages of 21st century journals, Plesiochelys has quite a story to tell. With its original fossil safely (and hopefully permanently) in a museum, the next chapter finally can be written.

Citations
Anquetin J, Deschamps S, Claude J. 2014. The rediscovery and redescription of the holotype of the Late Jurassic turtle Plesiochelys etalloni. PeerJ 2:e258 http://dx.doi.org/10.7717/peerj.258

Carabajal AP, Sterli J, Müller J, Hilger A. 2013. Neuroanatomy of the Marine Jurassic Turtle Plesiochelys etalloni (Testudinata, Plesiochelyidae). PLoS ONE 8(7): e69264. doi:10.1371/journal.pone.0069264

Pictet F-J, Humbert A. 1857. Description d’une émyde nouvelle (Emys etalloni) du terrain jurassique supérieur des environs de St-Claude. In: Pictet F-J, ed. Matériaux pour la paléontologie suisse. Première série. Genève: J. Kessmann. 1-10 [freely available via Google Books]

Above: 3D scan of Plesiochelys etalloni, from Anquetin et al. 2014. CC-BY.

Category: Museums, Paleontology | Tagged , , , , | 2 Comments