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

Rodents of the Caribbean: The Curse of the Quaternary Extinction

The Caribbean is typically thought of as a lovely spring break destination. If you are an animal lover, the area is great for diving and birding, but there are not many land mammals to be found. Sure, you will find bats, some endemic rodents, and of course invasive cats and rats, but besides that you will not find anything larger, like, oh, a sloth.

Where's my piña colada? Public Domain- Wikimedia Commons

Where’s my piña colada?
Public Domain- Wikimedia Commons

That’s right, up until a few thousand years ago, sloths weren’t just a South American thing. There were also primates, specifically New World monkeys like the Jamaican monkey, on islands throughout the Greater Antilles. The Greater Antilles consist of Cuba, Hispaniola, Puerto Rico, Cayman Islands, and Jamaica.

Map of the Greater Antilles in green. Other Caribbean islands like the Bahamas and Turks and Caicos have had mammalian extinctions Wikimedia Commons

Map of the Greater Antilles highlighted in green. Other Caribbean islands like the Bahamas and Turks and Caicos have also had mammalian extinctions
Wikimedia Commons

This now extinct terrestrial fauna of the Greater Antilles still remains very mysterious for a variety of reasons. As previously mentioned, only a few species of endemic rodents remain on Caribbean islands. The two biggest questions in this evolutionary conundrum are how did the mammals arrive? And then, how did they go extinct? The arrival debate is probably the most contentious- if we know the ancestors of extinct Antillean sloths, primates, and rodents originated in South America, how did the end up on islands in the middle of the Caribbean Sea? Did they all come from South America? It is possible, but seemingly unlikely, these different groups of mammals came in a series of overwater dispersals. A sloth floating its way to Jamaica may seem unbelievable, but overwater dispersals can be viable migration methods.

There is another theory though—perhaps there was a late Eocene- early Oligocene land bridge that connected the Greater Antillean Ridge and South America via the Aves Ridge. Welcome to:

Gaarlandia

GAARlandia was proposed by Iturralde-Vincent and MacPhee in 1999 as a way to explain the dispersal of land mammals from South America to the Caribbean islands in one continuous event, rather than a series of random overwater dispersals. Phylogenetic evidence has both supported and refuted the potential for the existence of GAARlandia, so the debate can still continue.

This month, in the Journal of Vertebrate Paleotology, Vélez-Juarbe et al. describe rodent incisors from Puerto Rico that date to the Oligocene- making them the earliest rodent fossils in the Caribbean. They are just incisors, so we cannot learn too much about the actual animal they belonged to (besides the fact their enamel structure indicates they belonged to a caviomorph rodent), but the existence of this fossil pushes back the date of rodent arrival in the Greater Antilles by approximately 9 million years. This new date is consistent with other molecular divergence estimations of caviomorph rodent groups in South America. In addition, a dated molecular phylogeny indicates there was a split between a Greater Antillean toad and its sister taxon in South America during the late Eocene- early Oligocene.  The coincidence between molecular divergence dates, paleontological finds, and the hypothesized date of the land-bridge adds support to the idea there may have been a short lived sub-aerial land bridge bringing non-flying mammals to the Greater Antilles.  Of course, this new evidence still does not preclude the possibility of overwater dispersal! These biogeographic hypotheses are very difficult to disprove so the debate rages on.

So where have the Caribbean monkeys and sloths gone? The Caribbean mammalian fauna experienced extremely high rates of extinction during the Quaternary, and these extinctions seemed to occur both before and after humans were a factor in the environments. During the Holocene, climate change could have potentially altered the environments these mammals were living in and this caused their extinction. But with the arrival of humans, overhunting, habitat destruction, disease, and introduction of invasive predators could also have been extremely damaging to biodiversity. The zooarchaeological and paleontological records on these islands can be spotty, but much more remains to be done to figure out the complex history of the ancient life of the Caribbean. Ancient DNA, stable isotopes, and re-examination of the taxonomy of fossils and sub-fossils from the Caribbean will continue to inform biogeographic theory and help us understand what drove such a unique mammalian biota to extinction.

References:

Iturralde-Vincent, M. A., R. MacPhee. 1999. Paleogeography of the Caribbean region: implications for Cenozoic biogeography. Bulletin of the American Museum of Natural History 238:1-95.

Velez-Juarbe, J., T. Martin, R. D. E. MacPhee, D. Ortega-Ariza. 2014. The earliest Caribbean rodents: Oligocene caviomorphs from Puerto Rico. Journal of Vertebrate Paleontology 34:157-163.

Category: Geology, Paleontology | Tagged , , , , | 3 Comments

Paleo Podcasts

When I work out, I sometimes listen to a mix of aggressive electronica and high-energy dance music to get me moving. But usually, I use my gym time to catch up on podcasts. My new year’s fitness resolutions mean I’ve been updating my mp3 player with new podcasts, including some paleontology-themed ones. The problem is, when you go to iTunes and search “paleontology”, “palaeontology”, or even “dinosaurs”, you don’t get much. Here are a few for the paleo-minded.

http://www.pasttime.org/

I’ll begin with a plug for my peeps: Past Time is hosted by Stony Brook University grad students Adam Pritchard and Matt Borths. Every couple weeks they post a ~20-25 minute show on some topic relating to vertebrate paleontology, and despite the hominid focus at Stony Brook, it’s rarely about humans. In addition to their entertaining and informative banter (Adam is a perfect straight man to Matt’s charming goofiness), each episode includes an interview with a paleontologist who worked on the topic of discussion. For example, recently they chatted about all these new tyrannosaur species discovered by University of Utah scientists, with Utah professor Dr. Randy Irmis as a guest. The interviews are woven into the discussion on the topic rather than longform interviews. One really awesome feature of Past Time is that they create a “field guide” for each episode, an associated page with tons more information, photos, maps, and further reading, including links to the original scientific papers (here’s the tyrannosaur field guide). The most recent episode is “The Hobbit – An Unexpected Discovery“, which discusses the species of tiny hominids living in Indonesia just 17,000 years ago, Homo floresiensis. This show is definitely kid-friendly (no swearing, shorter), and it’s accessible to non-scientists in language/themes).

For more Past Time, head to their website, subscribe on iTunes, and follow them on Twitter and Facebook.

http://www.palaeocast.com/

You should also check out Palaeocast, a UK show hosted by Dave MarshallLaura Soul, Joe Keating, and Jon Tennant. This show is a bit longer, 30-60 minutes per episode, with a new ep every two weeks. It’s a different style than Past Time; the interviewees are the focus and they have a longer chance to explain their research. Some recent shows I liked are a general overview of marsupial evolution and a discussion of the Riversleigh fauna, both featuring Dr. Robin Beck from the University of New South Wales. Another rad aspect of Palaeocast is that they cover scientific meetings; for example, these recent eps on the Society of Vertebrate Paleontology and the Palaeontological Association annual meetings. The pages for each podcast are image-rich, with pictures from the meetings or from the scientific papers the interviewee discusses. You could play this podcast with your kids in the car (no swearing), but younger kids with short attention spans might not like the longform interviews. Adults, however, will appreciate the clarity and depth of the discussions.

For more Palaeocast, head to their website, subscribe on iTunes, and follow them on Twitter. You can also like them on Facebook.

paleo after dark

Palaeo After Dark features ”informal discussions about evolutionary biology and palaeontology… over beer”, and is hosted by four current or recent University of Kansas geology graduate students: Curtis Congreve, Amanda Falk, James Lamsdell, and Randol Wehrbein. This is also a biweekly podcast, and it’s easily the longest of the bunch (some episodes are close to two hours). This podcast is stylistically a lot different from the ones above; it’s four friends discussing topics relevant to their shared research interests or primary literature. It’s neat to get this perspective into how academics interact with each other; this is far closer to how most science conversations start than the stodgy, formal, or awkward stereotype you see in movies or Big Bang Theory. Palaeo After Dark assumes their listeners are already pretty familiar with paleontological and evolutionary terminology, so it might not be as accessible to nonscientists. It also usually takes a long time to get to the meat of the episode. For example, the gang has over 26 minutes of amusing banter before they begin this interesting discussion of dinosaur ontogeny, taxonomy, and geologic dating. Because this is an informal podcast and alcohol is involved, there is a lot of swearing, so it’s probably not kid-appropriate.

For more Palaeo After Dark, head to the website, subscribe on iTunes, and like them on Facebook.

Dragon Tongues paleontology podcast

Our final paleo-exclusive podcast is Dragon Tongues, a show so new its first episode just aired on January 7th. Hosted by Sean Willett (an undergrad! at University of Calgary who also writes a dino column for UBC Okanagan’s The Phoenix News), Dragon Tongues will air the first Wednesday every month. It’s pretty short if the first episode (15 minutes) is a good indication. The first show begins with a statement of purpose: Sean’s goal is to tell the stories of fossils and Earth history in an accessible format, with each episode focusing on a species, and each season focusing on a theme. Season 1 is about dynasties, and episode one focuses on Carcharodon megalodon. I’m excited about this podcast; Sean has a dynamite radio voice and stylistically it’s sort of a paleontology-version of This American Life. Rather than fanboy gushing over mega-sharks, he tells the story of the role C. megalodon played in understanding what fossils are, and how they shaped our understanding of past life being different. Dragon Tongues is kid-appropriate and non-scientist accessible.

For more Dragon Tongues,  follow it on Twitter and subscribe on iTunes.

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If your main source for podcasts is iTunes, that’s it. Those are the only four paleo-only podcasts they host. However, there are several other science-themed podcasts aimed for a general audience, that feature paleontological topics.

http://tetzoo.com/

Tetrapod Zoology is a relatively new podcast hosted by SciAm blogger Darren Naish and palaeoartist John Conway. As with the blog, its topics include vertebrate paleontology in addition to the biology of living tetrapods, science fiction movies, and cryptozoology. These topics are all mixed into each ~60-90 minute episode, so there are no pure-paleo shows (so far). Recent episodes include discussions of woolly rhinos, mesosaurs (fossil vertebrates somewhat closely related to reptiles), and the tail of Jeholornis (a fossil bird from the Cretaceous of China). The show jumps right into the topic, and usually begins with zoology or paleontology. It shares the tone that makes the original blog work so well; Darren and John are both genuinely interested and it shows. It would be cool if they added links to the papers/books being plugged/discussed to the website, but it’s still new, so maybe this will happen in the future. The shows are kid-friendly and generally accessible to non-scientists (they explain technical stuff), but as I said above, not paleo-exclusive.

Follow TetZoo on their website and subscribe on iTunes. Also, you really should read the blog itself.

radiolab logo

Nothing else sounds like Radiolab. You might have heard it on public radio; it’s nationally syndicated. Each week, a different topic (often scientific, sometimes news or philosophical) is explored, presented from the perspective of the hosts as if they are learning about it in real time. Clips from interviews are woven into the discussion, so listeners follow how the scientists made their discoveries and changed their thought processes. Check out this recent ep in which University of Chicago paleontologists discuss using fossil corals to track changes in the number of days per year through time. Definitely kid- and non-scientist friendly: anyone who is natively curious about the world should like it. It’s one of my favorites, even when the topic isn’t science.

Follow Radiolab on their website, Twitter, Facebook, or iTunes.

science friday

Science fans are probably already familiar with the weekly Science Friday podcast, which is also aired on public radio stations across the US. Each week, host Ira Flatow examines several topics from recently published research, including short interviews with the researchers themselves. Recent episodes include discussions with NSCU grad student Edwin Cadena about car-sized giant turtles from Colombia and a conversation about Utah’s fossil history with Utah professor Dr. Randy Irmis, science writer Brian Switek, and BYU professor Dr. Brooks Britt. And just last week, Dr. Ted Daeschler from the Academy of Natural Sciences, Philadelphia was on the show to chat about the hind limbs of Tiktaalik. Go! Subscribe! Now!

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Given that people find paleontology so fascinating, it’s really weird that there aren’t more dedicated paleo-podcasts. I would have assumed  that there would at least be one weekly or bi-weekly “dinosaur roundup” show…

Do you blast your quads to a different science podcast? Have I missed some in this list? Let me know in the comments section!

Category: Miscellaneous, Paleontology | Tagged , , | 5 Comments

Sharing Phylogenetic Data — Public Comment Invited

Data sharing is important–it helps scientists to reproduce others’ results, add data to previous analyses, and otherwise maximize the impact of an individual publication. This isn’t really news, of course. But, now that we are in a world where data sharing is increasingly the norm, how do we make sharing as easy as possible? It’s not enough to slap some tables up on a personal website or even on an official data repository; the data have to be easily readable by humans and machines, easily reusable, and easily accessible for the long term.

One major goal of biology is to understand the arrangement of the branches on the Tree of Life (phylogenetics). Beyond the general drive to understand what is most closely related to what, a solid tree can help answer all sorts of interesting questions about the patterns and process of evolution. How did gigantism evolve in some dinosaurs? How did bird brains evolve? How did bone-cracking dogs get their beefy skulls? Of course, published trees are “just” hypotheses. The arrangement changes slightly (or occasionally even radically) with the discovery of new species, sequencing of new genomes, development of new tree reconstruction methods, and reinterpretation of old anatomy. Thus, data sharing is crucial for phylogenetics–scientists need to be able to add data, reanalyze old data sets, and reevaluate previous work in order to have the best possible tree.

Evolutionary trees help scientists understand the evolution of bird brains. Image from Smith and Clarke 2012. CC-BY.

Evolutionary trees help scientists understand the evolution of bird brains in concert with the evolution of their lifestyles. Image from Smith and Clarke 2012. CC-BY.

Data tables form the core of phylogenetic analyses, whether the data are in the ACGT of a DNA sequence or the 1′s and 0′s that mark presence or absence for the anatomy of a fossil organism. Alongside the data table are lists of characters, lists of specimens, and all of the other important supporting information. This makes for a complex situation, and there is considerable variability in how different researchers, and even different publishers, present these critical data. Standardization is a must!

Karen Cranston, Luke Harmon and Maureen O’Leary, lead researchers on the NSF-funded “Assembling, Visualizing, and Analyzing the Tree of Life” (AVAToL) project, are drafting a document that lays out best practices for sharing phylogenetic data. This includes trees, aligned gene sequences, data matrices, character lists, and all of the other technical details that underpin an analysis. Maureen relayed to me that she is particularly interested in comments on how to deal with time and other metadata. Are you someone who works with or is interested in phylogenetic data? They’re looking for your input!

The draft “best practices” guidelines are available as a Google Document, freely editable by anyone. In particular, input is requested on guidelines for data storage and formatting. The coordinators for this effort request your comments soonJanuary 22 or 23 at the latest, so act now if you are interested! There are already some great comments on the document.

I applaud the steps that Cranston, Harmon, and O’Leary are taking to make this a true community effort. Too often these kinds of “best practices” documents are crafted in the proverbial “smoke-filled back room,” catering to a handful of insiders. The more open the process, the better the guidelines and the more likely people are to use them! May this serve as a model for future efforts.

Want to add your input? Check out the draft guidelines for more information! 

Category: Miscellaneous, Open Data, Paleontology, Zoology | Tagged , , , , , | 2 Comments