The Figure Makes the Fossil

As I wrap up revisions on a manuscript, as well as continuing the day to day work in “my” museum collection, I’ve been thinking a lot about what makes a good figure of a fossil. The thought is driven in part by wanting to illustrate the specimens we’re describing in detail, but it’s also driven by the need for my co-workers and me to be able to identify specimens as they come in from the field.

Illustrations, ideally, are used by more than just the few specialists on a group. Life at a museum makes me realize just how much collections staff* need good illustrations, too! It also makes me experience the complete inadequacy of the figures in the great majority of papers. Much of this inadequacy, I suspect, stems from historical space limitations in print journals…now that that is changing (for at least some journals), it’s a good time to talk about what makes a well-illustrated fossil.

*edit: and amateur collectors! I realized I had left this out in my initial post.

Multiple views of the skull of Nyanzachoerus khinzir, a fossil pig from Chad. CC-BY, from Boisserie et al., 2014.

Multiple views of a partial skull of Nyanzachoerus khinzir, a fossil pig from Chad. CC-BY, from Boisserie et al., 2014.

Lots of views
Most fossils are highly three-dimensional objects, so multiple views are essential to capture the anatomy. Unless we’re dealing with a heavily flattened fish or leaf imprint, multiple views are essential. An oblique view is nice too–sometimes that’s what it takes to better highlight a particular feature. Even better? 3D models. In ascending order of usefulness, this includes movies, 3D PDFs, and printable, freestanding 3D files (e.g., STL or PLY format).

Skeleton of the ankylosaur dinosaur Chuanqilong chaoyangensis, with photo and line drawing. CC-BY, from Han et al., 2014.

Skeleton of the ankylosaur dinosaur Chuanqilong chaoyangensis, with photo and interpretive line drawing. CC-BY, from Han et al., 2014.

Every fossil needs some interpretation, particularly in the case of skulls and other complex fossils. A good drawing will indicate sutures, important holes, and other features that may not be easily visible on a photograph. [Note: this includes not just line drawings, but also other renderings--a skilled artist can work wonders with a fossil!]

Detail of a Cretaceous crocodilian tooth at maximum published resolution. CC-BY, modified from Pol et al. 2014.

Detail of a Cretaceous crocodilian tooth at maximum published resolution. “de” indicates a denticle. CC-BY, modified from Pol et al. 2014.

High resolution
This should be a no-brainer, but it is amazing how many journals require high-resolution figures at submission and then publish heavily down-sampled images. This is a waste of the authors’ time, and it reduces the utility of the image for the reader. That extra bit of zoom can be really valuable sometimes, particularly for multi-part figures!

This is what a sample size should look like! One block from the new pterosaur discovery site--scale bar equals 200 mm. From Manzig et al., 2014, CC-BY.

A fantastic color image of a pterosaur (flying reptile) mass accumulation. CC-BY, from Manzig et al., 2014.

It is incredible what things pop out in a color versus a grayscale image. Areas of reconstruction, crushing, and changing bone type are often far more easily seen when all of the color data are left intact. Thankfully, many journals now encourage color images, even if the printed copy remains in grayscale.

Scales of an ancient acanthodian fish, Nerepisacanthus, showing the fossil in full-color and the counterpart coated to enhance detail. CC-BY, from Burrow and Rudkin, 2014.

Scales of an ancient acanthodian fish, Nerepisacanthus, showing the fossil in full-color and the counterpart coated to enhance detail. CC-BY, modified from Burrow and Rudkin, 2014.

Grayscale / Color-Free
Yes, this goes against everything I just said above. Some specimens, depending upon preservation, are mottled to a point where it is difficult to pick out morphology. In this case, a color-free representation can be invaluable. This is best achieved by either coating specimens with an appropriate substance (as in the above image), or digital scans reconstructed without the obstructing colors.

Hand bones of Nimbadon, an extinct, arboreal wombat-like marsupial. CC-BY, from Black et al. 2012.

Hand bones of Nimbadon, an extinct, arboreal wombat-like marsupial. CC-BY, from Black et al. 2012.

Illustrate everything
Fossils rarely manifest as complete skulls or highly diagnostic elements. Sure, teeth are the most diagnostic part for many mammals, but what about the rest of the skeleton? Many collection drawers are filled with isolated and unidentified wrist and ankle bones, the durable blocky elements that fossilize so nicely. Unfortunately, they’re often very poorly illustrated in the literature! Good luck trying to “figure out” an entocuneiform or a navicular (pun only somewhat intended). Collections staff and researchers can spend a lot of time trying to identify common, complete, and clearly diagnostic elements that just don’t have comparable material widely figured in the literature (particularly in the absence of a good, identified comparative collection). This even applies to some quite common fossils. For instance, horse teeth are quite well illustrated, but it’s surprisingly difficult to find figures of individual vertebrae or some of the more obscure ankle bones.

Parting Thoughts
As scientists, we should strive to make our work as accessible, reproducible, and useful as possible. Comprehensive and clearly rendered figures are essential for achieving this goal.

Category: Navel Gazing, Nuts and Bolts, Open Access, Paleontology, Technology | Tagged , , , | 3 Comments

Planting a Cretaceous Pond, South American Edition

If you close your eyes and visualize Mesozoic foliage, a few particular types of plants might spring to mind. There are probably some palm trees, a few ferns, a cycad (“sago palm”) or two, and if you are particularly in-the-know, a handful of monkey puzzles in the background.

Monkey puzzle tree

Just add dinosaur? Today’s monkey puzzle trees are a common (and not entirely unreasonable) trope in Mesozoic reconstructions. Photo by Scott Zona, CC-BY.

Of course, this only represents the shadow of an ecosystem. Today’s plant communities are ridiculously diverse affairs, with distinct species found from habitat to habitat. The same presumably holds for the Mesozoic, and this is confirmed by the fossils that are known. Due to the vagaries of preservation, however, some environments are better represented than others. Nice deciduous leaves from big oak-like trees? There are plenty to go around! Aquatic plants? Much harder to come by (in part because some of their parts are more delicate and less likely to preserve). Historical research biases also can play a role–for various reasons, the Mesozoic plants of North America are pretty well-known, but many aspects of those from the southern hemisphere are less studied. Paleontologists sometimes also pay more attention to collecting “showy” palm fronds and other tree leaves, at the expense of the equally important but less photogenic plant fossils.

One Mesozoic plant community that is particularly poorly known is that of freshwater aquatic plants from South America. This is particularly vexing, because a number of nice fossil localities are known from the northern hemisphere, combined with the fact that a lot was happening with plants during the Cretaceous (145 to 66 million years ago). During this interval, angiosperms (flowering plants) exploded onto the scene. Although aquatic plants are often stereotyped as primitive moss, flowering plants are a pretty important and visible part of freshwater ecosystems (think water lilies, lotuses, and duckweed, to name a few). Thus, it would be really nice to know what was going on “down south”. Were the same kinds of plants dominant as on northern continents? Or was it a unique ecosystem, as seen for the dinosaurs of the time?

Several fossil plant localities from Patagonia, Argentina, hold a trove of new information on ancient aquatic plants. Rocks of the La Colonia Formation represent a coastal ecosystem from the very end of the age of dinosaurs, during the Late Cretaceous. Although many of the sediments show marine or brackish water conditions (as indicated by the vertebrate fossils and rock types), some beds clearly preserve environments with more drinkable(?) water. Among these rocks, beautifully preserved plants–including everything from pollen to algae to leaves, roots and rhizomes–document a mostly previously unknown world. Although there are leaves and pollen of obviously “land-dwelling” species (e.g., tree ferns, shrubs, and palm trees), most intriguing are the remains of definitively water-bound plants.

Fossil lotus pollen with modern lotus leaves

Fossil pollen from Patagonia (inset), quite similar to that from modern lotus plants (background). CC-BY; pollen image from Cúneo et al., 2014; lotus leaves photographed by J.M. Garg.

A paper authored by N. Rubén Cúneo and colleagues, published last week in PLOS ONE, describes, identifies, and interprets these fossil plants in some detail. Previous contributions have focused on specific elements of the plant community, but this is the first major attempt to reconstruct the aquatic ecosystem as a whole. And what cool plants have been uncovered! To name a few:

So, what does this show? First, some of the plants (e.g., water ferns) are indicative of fresh water. Given the coastal nature of the rock deposits, this shows that the communities developed at times when saltwater was absent (even if relatively briefly). Furthermore, the types of plants are broadly similar to those found from the northern hemisphere at the same time. Many of today’s aquatic plant groups also show broad distributions, so not much has changed from the Mesozoic. Finally, the plants studied here are similar to plants that lived shortly after the big dinosaur extinction 66 million years ago. This suggests that the major global events and ecosystem changes didn’t make a permanent dent in the realm of aquatic botany.

Although the most cynical paleontologist might say the significance of this discovery is that we finally know what South American dinosaurs would have munched on if they waded into the water, the broader contribution of this study is even more exciting. Specimen by specimen, locality by locality, fossil assemblages such as the aquatic plants of Cretaceous Patagonia help us to better understand a fairly poorly known chapter of our planet’s life. There is a whole world to explore in those ancient ponds, wetlands, and marshes!


Schematic of a Cretaceous plant community, Argentina, with photographs of modern relatives. CC-BY, Figure 9 from Cúneo et al., 2014.

Cúneo NR, Gandolfo MA, Zamaloa MC, Hermsen E (2014) Late Cretaceous aquatic plant world in Patagonia, Argentina. PLoS ONE 9(8): e104749. doi:10.1371/journal.pone.0104749

Category: Paleobotany, Paleontology, PLOS ONE | Tagged , , , | Comments Off

Things That Make a Vertebrate Paleontologist Weep with Joy

Pity the poor invertebrate paleontologist, stuck with the dilemma of not knowing which fossil to measure first.

Pity the poor invertebrate paleontologist, stuck with the dilemma of not knowing which fossil to measure first. Image by Mark Wilson, in the public domain.

There are times when I really wish I were born an invertebrate paleontologist. For many of them*, a few kilograms of rock can contain dozens or even hundreds of specimens of a single species. This is awesome, because some of the best science happens with large sample sizes. The more fossils you have, the easier it is to study variation within a single species, or track evolutionary change, or study the response of a species to changes in local environment and global climate. A single spectacular fossil offers a wealth of information, but a thousand spectacular fossils opens up the firehose of knowledge.

Why are so many invertebrate fossils so common, and thus so easily studied? For one, many invertebrates are fairly small. The smaller the organism, the less likely it is to get broken up by the various forces of nature, and the more likely you are to get a completely intact fossil. Additionally, some invertebrates include quite durable hard parts; thus, the fossil records of snails and clams and corals are pretty awesome. Vertebrate animals include hard parts too–but the complex, multi-jointed skeletons tend to get disassembled pretty quickly. If the skeletons are fragile, such as the hollow bones of flying reptiles (pterosaurs), the situation is even more dismal.

Thus, it is pretty special for paleontologists to find a new, large sample of a single species of extinct vertebrate. Last week, just this sort of announcement from Manzig and colleagues, published in PLOS ONE, caught the interest of the pterosaur community [full disclosure: I was the volunteer academic editor who handled this paper].

This is what a sample size should look like! One block from the new pterosaur discovery site--scale bar equals 200 mm. From Manzig et al., 2014, CC-BY.

This is what a sample size should look like! One block from the new pterosaur discovery site–every one of the “white” elements that you see is a single bone. Parts of at least 14 different individuals are represented in this image. Scale bar equals 200 mm. From Manzig et al., 2014, CC-BY. Click to enlarge.

A locality in southern Brazil preserved the remains of at least 47 different individuals, all interpreted as belonging to a single species. They were found in at least four different (but closely spaced) layers of rock, with the bulk from two of the four layers. The researchers named the new animal Caiuajara dobruskii, reflecting both its geologic origins (within the Caiuá Group) and its discoverers (Alexandre Dobruski and his son João Dobruski). Caiuajara is distinguished from other pterosaurs by the unique shape of the bones forming its toothless beak, among other characteristics. If you were to see one alive, the most striking feature (after its giant leathery wings) would probably be a massive bony crest atop the skull.

Beyond the fact that pterosaurs are a pretty cool group of animals, and that Caiuajara represented an awesome-looking beastie, the sheer sample size takes one’s breath away. There are large and small individuals, presumably representing young and old alike. Although “only” 47 individuals have been unearthed so far, it is quite likely that hundreds more remain unexcavated at the same site. You don’t often get this kind of sample for any vertebrate animal, let alone one with such a delicate and easily broken skeleton. Indeed, the known bones of Caiuajara are quite three-dimensionally preserved. This is especially rare for pterosaurs, because their thin-walled bones tend to get smashed to roadkill-like oblivion.

Last week’s publication was only a preliminary report, primarily covering the basic description and naming of Caiuajara. Now, the hard work begins–excavating, cleaning, studying, and interpreting the entire sample in detail. We may have to wait awhile, but in the end I suspect this animal will be known better than just about any other pterosaur.

Silhouette of Tapejara, a close relative of Caiuajara. Image by Jaime Headden, via CC-BY.

Silhouette of Tapejara, a close relative of Caiuajara. Image by Jaime Headden, via CC-BY.

*It is a bit of a misconception that all invertebrate fossils are common, and that all vertebrate fossils are rare. However, the number of common invertebrate species far exceeds the number of common vertebrate species.

Manzig PC, Kellner AWA, Weinschütz LC, Fragoso CE, Vega CS, et al. (2014) Discovery of a rare pterosaur bone bed in a Cretaceous desert with insights on ontogeny and behavior of flying reptiles. PLoS ONE 9(8): e100005. doi:10.1371/journal.pone.0100005

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

Let’s Get Creative With Our Peer Review!

I’ve been around the editorial block a few times now, as a volunteer editor, peer reviewer, and author/co-author. One of the most dreaded steps of the whole process concerns author-recommended peer reviewers. It can be agonizing as an author to make the selections and hard work for an editor to figure out which suggestions have a likelihood of panning out as meaningful reviews. In the various papers I’ve authored, co-authored, and edited, a few problems appear with some frequency:

  1. Adding Dr. McFamous to the list of reviewers. Odds are non-negligible that this person is already overtaxed with review requests and will say no. If they do accept, odds are also non-negligible that their review will be about three sentences of fairly uninformative commentary, submitted 2-3 weeks after the deadline. Unless this person is a legitimate expert who has recently published on the specific topic of the paper, find someone else who is more qualified and more likely to have the time to review the paper in the detail it deserves. I am somewhat surprised by the frequency with which authors will suggest someone simply because they are well-known, without regard for whether the person is the best expert for the job.
  2. Submitting a “no fly” list of reviewers that is a mile long. There are legitimate reasons to request certain researchers to not review a paper (conflict of interest, real or perceived unprofessionalism, whatever), but anytime more than two or three people are listed, that raises all sorts of red flags for an editor. Possible explanations? 1) One of the authors has ticked off 90% of their colleagues. 2) The paper is so flimsy that anyone with real expertise is going to shoot it down. 3) The authors won’t accept even constructive criticism and are going to be a pain to both reviewers and editors. Note how none of this reflects well on the authors. As an editor, I do my very best to respect authors’ wishes, but there are times where some requests really stretch credulity.
  3. Suggesting reviewers from the same institution or research group as one of the authors. This happens with surprising frequency; even if you are at a quite large institution or within a fairly large research group, and even if the suggested reviewer is only a vague acquaintance, it has the appearance of a fairly major conflict of interest. If at all possible (yes, it can be difficult in small subfields or for certain taxa), suggest someone else.
  4. Same. Old. Reviewers. This syndrome regularly affects authors and editors alike. The result is a list of overwhelmingly male suggested reviewers, overwhelmingly from a handful of large Western European and North American research institutions. It is sometimes correlated with #1 (Dr. McFamous), because said expert once published a paper on the subject in Nature back in 1998, even if their research for the past 15 years has taken an entirely different direction. In all honesty, these scientists are not the only people qualified to review their papers, or often even the best people. Some really exciting science is happening at small research institutions, community colleges, and places outside the USA, by people from exceptionally varied backgrounds. If we say we want to diversify science (and we all hear this rhetoric frequently), let’s get serious about it when it comes to suggesting and inviting reviewers!
Your manuscript isn't as arcane as you think it is. The number of qualified peer reviewers may surprise you! Image of Codex Leicester, public domain, via Wikimedia Commons.

Your manuscript isn’t as arcane as you think it is. The number of qualified peer reviewers may surprise you! Image of Codex Leicester, by Leonardo da Vinci, public domain, via Wikimedia Commons.

If I had to guess, #4 (“Same. Old. Reviewers”) is the most prevalent, and I am undoubtedly guilty of it too, from both sides. That said, I’ve been making some serious efforts both as an editor and as an author to recognize and address the problem. Google Scholar is a major asset in this regard–a quick search on a topic, narrowed to the last two or three years of publications, will often bring up at least two or three reviewers with appropriate expertise. I tried the strategy with a paper I submitted recently and identified a couple of surprisingly logical and undoubtedly qualified researchers whom I had embarrassingly overlooked. The result was a deeper, more balanced suggested reviewer list and presumably a better review of my paper.

So, here’s my challenge to authors: be more creative on your list of suggested reviewers. And for editors: be more creative in whom you ask to review papers. Let’s build a better world of peer review!

[Just to reiterate, all opinions stated here are solely mine, and do not represent an official (or even unofficial) stance by any organization with which I am associated. Furthermore, the issues discussed here happen frequently enough over the years (seriously!) that it should be apparent I'm not talking about any paper in particular.]

Category: Miscellaneous, Navel Gazing, Open Access | Tagged , | 9 Comments

Pseudo-poo! All that glitters isn’t fecal gold

Coprolite? Or copro-might-be-just-a-rock? Image by Mark A. Wilson, in the public domain.

Coprolite? Or copro-might-be-just-a-rock? A problematic specimen from ancient Washington state. Image by Mark A. Wilson, in the public domain.

Fossil feces are the stuff of legend. Not only do they have the “gee-whiz-gross” factor, but they also preserve evidence of diet, parasites, and paleoecology in long-dead animals. An paleontological urban legend holds that the technical term–”coprolite”–was coined by an academic rival of the 19th century paleontologist Edward Drinker Cope. Sadly, this is just a fabrication, but the story illustrates our fascination with one of the more scatological ends of science.

This fascination extends into the world of fossil collecting as well as the commercial fossil trade–after all, what collector wouldn’t want a piece of dino dung? Purported coprolites are a fixture at rock shops and even some museum gift stores. Perhaps the most commonly available “coprolites” are from the Miocene (~6 million year old) aged Wilkes Formation of Washington State, USA. These specimens (such as the one at the head of this post) certainly look the part–squiggly, lumpy, and generally fecal in form. The Wilkes Formation preserves ancient wetlands, swamps, and plains, with abundant fossil plants but no vertebrate bones to speak of. Thus, the “coprolites” are blamed on ancient mammals, crocodilians, turtles, or even (erroneously, given the geological age) dinosaurs.

But, these alleged coprolites are probably too good to be true. Their mineral composition (mostly siderite, an iron-rich carbonate) as well as a complete lack of digested food remnants (such as bone bits, fish scales, or plant pieces) suggests to most geologists and paleontologists that something else is going on here. Essentially, it is now thought that the “coprolites” from the Wilkes Formation are simply mud squirted out under the pressure of burial or perhaps as decaying organic matter produced methane (Spencer 1993; Mustoe 2001). An alternative viewpoint is that the specimens are cololites–natural casts of the inside of an animal’s colon, with the skeleton itself dissolved away by soil chemistry (Seilacher et al. 2001). Although this explanation is intriguing, I find it unlikely given the very un-intestinal anatomy of many examples, including one recently publicized example of exceptional length (it’s on the auction block, so I won’t link to it directly). The same rocks produce many random “blobs” of similar composition, too; these just aren’t picked up and sold as coprolites! Finally, at least some of the specimens are found in nearly vertical orientations relative to the surrounding rock (Mustoe 2001), which would be highly unusual relative to typical preservation of vertebrate fossils.

So, how do you know if a poo-shaped rock is a genuine fossil or just pseudo-poo? The discovery of digested bits seems to be the best guide.

A copro-collage, organically and locally sourced from extinct moa. From Wood et al. 2012, CC-BY.

An authentic copro-collage, organically and locally sourced from extinct moa. From Wood et al. 2012, CC-BY.


Mustoe, G. E. 2001. Enigmatic origin of ferruginous “coprolites”: Evidence from the Miocene Wilkes Formation, southwestern Washington. Geological Society of America Bulletin 113:673–681. [paywall]

Seilacher, A., C. Marshall, H. C. W. Skinner, and T. Tsuihiji. 2001. A fresh look at sideritic “coprolites.” Paleobiology 27:7–13. [paywall]

Spencer, P. K. 1993. The “coprolites” that aren’t: The straight poop on specimens from the Miocene of southwestern Washington State. Ichnos 2:231–236. [paywall]

Yancey, T. E., G. E. Mustoe, E. B. Leopold, and M. T. Heizler. 2013. Mudflow disturbance in latest Miocene forests in Lewis County, Washington. PALAIOS 28:343–358. [paywall]

[Note to people working on "coprolites" of the Wilkes Formation in the future: make some of your stuff open access!]

Category: Geology, Paleontology | Tagged , | 5 Comments

Hupehwhat? Finding a home for some unusually odd marine reptiles

A more edible version of a hupehsuchian. Photo by TheBusyBrain, CC-BY

A more edible modern version of a hupehsuchian. Photo by TheBusyBrain, CC-BY 2.0

“Swimming sausage topped with armored mustard” is probably the best way to describe a hupehsuchian. These marine reptiles, known only from 248 million year old rocks in east-central China, were odd-balls at a time when a lot of odd-balls (by modern standards) roamed our planet. Hupehsuchians had tiny toothless heads, flippers with one or two extra embedded digits, and an elongated body swathed in close-knit ribs and armor plates. This heavily modified body makes hupehsuchians interesting as well as frustrating, because it has been tough for paleontologists to reach a consensus on how the group is related to other organisms.

Skeleton of Nanchangosaurus

Skeleton of the hupehsuchian Nanchangosaurus (click for a closer look). The head (incomplete in this fossil) is to the left. Modified from Chen et al., 2014, CC-BY 4.0.

Over the years, researchers have proposed any number of relationships for hupehsuchians, with the group being posited as closely allied with eosuchians (historically a junk bin for “primitive” lizard-like animals), archosaurs (the group including birds, crocodiles, and T. rex), or icthyosaurs (“fish lizards”). The superficially dolphin-like icthyosaurs have achieved broadest recognition in recent years as the sister group to hupehsuchians, but was this just the result of common adaptations for an aquatic lifestyle? Study of hupehsuchians has been hampered by poor access to specimens, minimal description in the literature, obscured anatomy for important features, and an overall scarcity of fossils.

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

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

In a paper published a few days ago in PLOS ONE, Xiao-hong Chen and colleagues use previously unpublished as well as reexamined hupehsuchian fossils to test the group’s relationships. The researchers focused in particular on Nanchangosaurus suni, which was the first hupehsuchian known to science when it was named over 50 years ago. For decades, only the original (holotype) specimen was around, and it was minimally studied. Fieldwork finally turned up another really nice skeleton in 2011, which forms the core of the new paper.

With two specimens in hand, Chen and co-authors assembled a ton of new data on Nanchangosaurus. Many previously unrecognized sutures between skull bones could be mapped (important for understanding evolutionary relationships), along with the forms of vertebrae and limb bones. Despite its historic importance, Nanchangosaurus had never been analyzed in a rigorous phylogenetic analysis. Thus, this animal could provide some critical evolutionary information.

Skull of Nanchangosaurus

Nanchangosaurus partial skull; the snout points to the left. Note in particular the lack of teeth in the impressions of the jaws. Modified from Chen et al., 2014. CC-BY 4.0.

The researchers ran numerous iterations of a phylogenetic analysis to reconstruct the evolutionary relationships of hupehsuchians and other extinct groups, utilizing 213 different anatomical features in 41 species. To explore the influence of convergent adaptations for the water, they ran one set of analyses with purported aquatic adaptations removed. In all cases, icthyosaurs were solidly identified as the closest relatives of hupehsuchians.

Of course, this doesn’t mean that hupehsuchians were ancestral to icthyosaurs–both are uniquely specialized in their own ways, and the oldest members of each group lived at approximately the same time. Either way, they aren’t far separated in time from their closest common ancestor. The analysis will probably get some criticism for its relatively small scale within the standards of contemporary phylogenetic analysis, as well as for the strategy of excluding perceived functional characters, but it certainly represents a unique contribution. Additionally, the greatly bolstered comparative data for Nanchangosaurus will pay big dividends for researchers in the future. Most interestingly, the relationships between all of the various marine and non-marine reptiles are still fairly poorly understood; more fossils and more detailed analyses are our best bet for sorting things out.


Cousin? The early icthyosaur Grippia. Image by Dmitry Bogdanov, CC-BY 3.0.

Chen X-h, Motani R, Cheng L, Jiang D-y, Rieppel O (2014) The enigmatic marine reptile Nanchangosaurus from the Lower Triassic of Hubei, China and the phylogenetic affinities of Hupehsuchia. PLoS ONE 9(7): e102361. doi:10.1371/journal.pone.0102361

Want to read more about hupehsuchians? Check out this old post on their bony body tubes.

Updated to correct typo in number of characters & taxa in the phylogenetic analysis (thanks, Nick Gardner!).

Category: Paleontology, PLOS ONE | Tagged , , , , , | 2 Comments

Baby moa bones: more than meets the eye

Best buddies Richard Owen and the giant moa, D. novaezealandiae. Image from Owen 1879, via Wikimedia Commons. Public domain.

Best buddies Richard Owen and the giant moa. Owen 1879, via Wikimedia Commons, public domain.

The name “moa” inevitably conjures up pictures of giant, lumbering bird-beasts, destined for extinction at the hands of humans. For fans of paleontological history, we usually recollect the grumpy looking Victorian era paleontologist Richard Owen, dwarfed by a mounted moa skeleton. Yet, this rather monotone popular conception itself is dwarfed by the true diversity of the fossil record.

Moas–members of the family Dinornithidae–were a group of flightless birds native to New Zealand. Although the number of recognized species has fluctuated as information on genetic, age-related, and sex-related differences trickle in, they were clearly a pretty diverse lot. The smallest were around 20 kg in adult body mass, roughly the same size as a modern rhea, and the biggest topped an estimated 200 kg, nearly twice the size of an adult ostrich. Most of the species have an excellent fossil record, including isolated bones, associated skeletons, naturally mummified body parts, and dried-out dung. Along with these remains are many bones of small, presumably young, moas. But what species are they?

A moa grab-bag, to scale next to a human female. Image by Conty, CC-BY.

A moa grab-bag, to scale next to a human female. Species depicted include (1) Dinornis novaezelandia; (2) Emeus crassus; (3) Anomalopteryx didiformis; and (4) Dinornis robustus. Image by Conty, CC-BY.

By being able to match young moas (“mini-moas”, if you will) to their corresponding adults, scientists can learn a whole bunch about the diversification and ecology of the group. Did moa species achieve different sizes by extending their growth phase, or growing more quickly over the same amount of time, or starting out at different sizes, or some combination? Did moa habits change over their lifetime?

Adult moas are fairly easy to tell apart, but moa chicks are another story altogether. The bones of young moas were not yet completely developed, so many characteristics used to distinguish species were absent. This is a pretty common problem across extinct animals and can be solved in a few different ways. If you only have one species of an animal in a rock of a given age, it’s probably a safe bet that any baby animals you find go with the adults. Things are complicated when you have multiple closely related species living in roughly the same place, as happens with moas in New Zealand. For extinct dinosaurs such as Centrosaurus, this can be solved by looking for localized fossil beds where only one species predominates, often representing a group killed in a single event. We don’t have such a luxury with moas, as far as I know, so it’s necessary to get a little creative.

Because moas went extinct relatively recently, extraction of their ancient DNA is quite feasible with modern technology. If you have DNA from samples for which the species is known, you can then use that DNA sequence to identify unknown samples. Leon Huynen and colleagues recovered DNA from 29 different baby moa bones–nearly all of which had never been identified to species before. Unique sequences for each species allowed a confident match between young and old.

DNA sequences from confidently identified coastal moa (Euryapteryx curtus; big skeleton here) allowed researchers to identify bones of babies, including the femur at top left. DNA sequence and baby femur photo (CC-BY) from Huynen et al. 2014; adult skeleton from Goupil & Cie 1879 (public domain).

DNA sequences from confidently identified coastal moa (Euryapteryx curtus; big skeleton here) allowed researchers to identify bones of babies, including the femur at top left. Not to scale. DNA sequence and baby femur photo (CC-BY) from Huynen et al. 2014; adult skeleton from Goupil & Cie 1879 (public domain).

The DNA work is cool enough in its own right, but it was only the beginning for the research team. Three-quarters of the identified specimens belonged to the coastal moa, Euryapteryx curtus. Some discussion has focused on how many subspecies the known fossils represent, based on evidence from DNA, bone anatomy, and growth rates. The DNA suggested that two forms are within the sample (represented by slightly different sequences), consistent with previous DNA work as well as their geographic separation.

Intriguingly, the shapes of the thigh bones measured for this study were fairly consistent across individuals of the same size for most of the species sampled. This indicates that any major changes in proportions didn’t show up until later in growth; a bigger sample will certainly help sort out these sorts of developmental and evolutionary questions.

The research, published last week in PLOS ONE, provides some important results–verifying the first bones from moa chicks of particular species, supporting additional hypothesized moa subspecies, and providing information on bone development in an extinct animal. With bigger samples from a broader range of specimens, there will be much to learn about how this surprisingly diverse group of birds grew. Some previous workers have speculated that the apparently slow growth and reproduction rates of moas doomed them to extinction at the hands of humans. Future studies on moa chicks, adolescents, and adults, will undoubtedly refine this picture.

Huynen L, Gill BJ, Doyle A, Millar CD, Lambert DM (2014) Identification, classification, and growth of moa chicks (Aves: Dinornithiformes) from the genus Euryapteryx. PLoS ONE 9(6): e99929. doi:10.1371/journal.pone.0099929. [open access]

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

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.]

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.


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

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