The Curse of the Horned Dinosaur Egg

Horned dinosaurs (ceratopsians) just can’t catch a break when it comes to their fossilized eggs. The first purported examples turned up in Mongolia during the 1920s, attributed to Protoceratops. A few unlucky “Protoceratops” eggs were fossilized next to the jaws of another dinosaur (Oviraptor, which means “egg thief”), presumably in the act of raiding the nest. Decades later, it turned out that the nest raider was probably the parent Oviraptor safeguarding its own eggs. Study of other eggs associated with embryos showed that everything we thought were Protoceratops eggs were actually from Oviraptor and related animals!

A nest of Oviraptor (formerly Protoceratops) eggs on display at the American Museum of Natural History. Image by Steve Starer, CC-BY.

A nest of Oviraptor (formerly Protoceratops) eggs on display at the American Museum of Natural History. Image by Steve Starer, CC-BY.

So, as a horned dinosaur fancier, I was pretty excited when an authentic ceratopsian egg and embryo were announced in 2008. Amy Balanoff and colleagues described an egg from Late Cretaceous-aged rocks (~90 to 70 million years old; the exact date is uncertain), which had a few tiny bones poking out of the end. Dinosaur embryo! Computed tomography (CT, a technique using x-rays to peek inside objects) revealed more of the bones, including two skull bones that appeared especially ceratopsian. One bone was identified as a predentary, the scoop-shaped bone at the front of the lower jaw used to lop off plants. The other skull bone appeared to be a quadrate, one of the bones of jaw joint. The predentary in particular narrowed identification to a plant-eating dinosaur (the bone doesn’t occur in theropods such as Oviraptor), and the shape of the quadrate further suggested a horned dinosaur. Yamaceratops (closely related to Protoceratops) is a ceratopsian found in the same rock layers and was thought to be the likely source.

One puzzle, though, was the eggshell itself. Eggshell appears simple to the naked eye, but the microscopic details can be pretty distinctive to the egg producer. The number of layers within the eggshell, for instance, and the arrangements of the minerals that make up the layers, vary from group to group. Some eggshells, such as those of turtles, have but a single layer. The Mongolian ceratopsian eggshell had three layers–a characteristic usually associated with theropod dinosaurs (Oviraptor and early birds, for instance). But, given the presence of ceratopsian bones in the egg and the fact that nobody knew what ceratopsian eggshell should look like, this suggested that horned dinosaurs had eggshell that converged on that of theropods. So, the three-layered eggshell evolved multiple times across dinosaurs.

"Protoceratops BW" by Nobu Tamura (http://spinops.blogspot.com) - Own work. Licensed under CC BY 2.5 via Wikimedia Commons - http://commons.wikimedia.org/wiki/File:Protoceratops_BW.jpg#/media/File:Protoceratops_BW.jpg

Protoceratops, by Nobu Tamura. CC-BY 2.5.

But…things are never that simple. A new paper in PLOS ONE, including the two senior authors from the original work, proposes a new identification. Ceratopsian no more…now it’s a bird!

Incredulity might be the first reaction of many people. How could you mix up a wingy, feathered bipedal thing with a big plant-munching quadruped? It should be obvious to even a casual observer, right?

Actually, no. Embryonic bones (those inside of an egg) can look vastly different from those of their adult counterparts, because many characteristic features don’t appear until the animal is out of the egg. As a result, it can be tough to orient and identify bones correctly. Additionally, even high-tech imaging (such as CT scanning) has a certain degree of interpretation to it. The researcher who digitally separates bone from rock has to make judgement calls all of the time. Is this bone or rock that looks like bone? Are these two bones stuck together, or one bone with a crack down the middle? Even under the best of circumstances, there is room for ambiguity.

Given what everyone knew at the time, and in light of the possible predentary and other bones, “ceratopsian” was a reasonable hypothesis as presented in the initial publication. But a second look at the data never hurts. Movies of the CT scans were posted online, allowing other researchers to take a peek. Undoubtedly following some pretty interesting discussions, two of the original authors (Amy Balanoff and Mark Norell) joined dino-bird expert Dave Varricchio (lead author on the new paper) to present a re-interpretation of all of the data.

Bird bones, with silhouette of an enantiornithine.

Bird bone pick-up sticks! At left, the digitally isolated bones from within the Mongolian bird egg. At lower right, the left hind limb bones within the egg (ghosted outline). In the original paper, the femur (yellow) was interpreted as a humerus. The silhouette in the upper right shows the appearance of a closely related Cretaceous bird, Protopteryx (image by Matt Martyniuk via PhyloPic.org, CC-BY). Fossil imagery modified from Varricchio et al. 2015. Scale bars equal 5 mm (left) and 10 mm (right).

It turns out that the egg was turned around in the original interpretation; the front of the animal could be identified instead as the back. Thus, many of the bones were mis-oriented in the original paper. What was thought to be a ceratopsian humerus turned out to be a bird femur, a tibia turned into an ulna, and so on. As described above, this is a pretty easy “mistake” to make, given how nondescript many embryonic bones are. The quadrate and predentary are more mysterious–the former may be a pelvic bone, but the true identification of the “predentary” is highly debatable. Perhaps it’s part of a vertebra, or a wishbone, or something else. In any case, when reoriented, most of the bones are a better match for bird than ceratopsian.

If the Gobi egg is from a bird, that also solves solves the problem of the three-layered eggshell. No longer distributed across dinosaurs, this type of eggshell is now firmly restricted to theropods (including many birds). Additionally, this embyro provides another rare data point for studying the embryology of ancient birds. Previous discoveries have shown some key developmental differences between non-avian dinosaurs, early birds, and modern birds, so the newly identified Gobi bird egg has an important story to tell on how these differences evolved over time.

One mystery remains–what do horned dinosaur eggs and embryos look like? There are undoubtedly unidentified examples in a museum drawer or outcrop. A nest of little Triceratops sure would help right about now.

Citation
Varricchio DJ, Balanoff AM, Norell MA (2015) Reidentification of avian embryonic remains from the Cretaceous of Mongolia. PLoS ONE 10(6): e0128458. doi:10.1371/journal.pone.0128458

Paleontology confession: I was an anonymous reviewer for the 2008 paper, and the predentary identification in particular was compelling support for calling it ceratopsian. Based on what the authors presented in 2008, and based upon the figures and interpretations available at the time, I thought there was a slim possibility the egg could be another kind of plant-eating dinosaur, but the thought of “bird” never crossed my mind. Seeing the new paper, “bird” is pretty blindingly obvious in the end, but that is only with the benefit of 20/20 hindsight, re-orientation of the specimen, and a whole bunch of additional information. I suppose this case is a good anecdata point showing how peer reviewers can be wrong sometimes.

Category: Birds, Digitization, Dinosaurs, Paleontology, PLOS ONE, Technology, Zoology | Tagged , , , , , , , , , , , , | 3 Comments

Guest Post: Can We Easily Distinguish Male and Female Protoceratops?

This guest post is from Leonardo Maiorino, a vertebrate paleontologist with a particular interest in understanding the evolution of the skull in horned dinosaurs. Leo was at the helm of a recent paper in PLOS ONE (I was a co-author), so I invited him to write up a post for the blog. — A. Farke

Anatomical and behavioral differences distinguish males and females in many extant and extinct animals. For instance, male peacocks have a large and flashy tail, whereas females are smaller and less brightly colored. Male lions have a mane and are larger than females. Red deer male sport antlers, lacking in females. This phenomenon is called sexual dimorphism and represents a product of sexual selection. It represents a key factor in the success of breeding within many species, as originally stated by Darwin, and mate choice.

Peacock (back) and peahen (front), in a classic example of sexual dimorphism. Image by Darkros, in public domain.

Peacock (back) and peahen (front), in a classic example of sexual dimorphism. Image by Darkros, in public domain.

Despite obvious sexual dimorphism in some modern animals, sexual dimorphism is hard to identify in extinct organisms such as dinosaurs, often due to a very small sample size. Having a few fossil skulls with different morphologies (crest or horns) and relating them to sexual differences thus appears quite hasty. For instance, hypothesized males and females of hadrosaurs (Parasaurolophus or Lambeosaurus) were later shown to be species separated in time and in space. Variation in the number of chevron bones (wishbone-shaped bones under the tail vertebrae) in Tyrannosaurus, previously attributed to sex differences between males and females, are instead the product of non-sexual variation.

Ceratopsians, popularly known as “horned dinosaurs”, represent another group for which paleontologists have inferred sexual dimorphism. Protoceratops andrewsi is a well know ceratopsian from the Late Cretaceous of the Gobi Desert, Mongolia, discovered almost a century ago during the American Museum Expeditions of the 1920s. Protoceratops is a small (<2 m total body length) quadrupedal animal, characterized by a skull with a thin, bony frill projecting over the neck and lacking the prominent horns that characterized ceratopsids such as Triceratops. More than one hundred well-preserved skulls and skeletons (many from various life stages) have been unearthed, providing a lot of information on its paleoecology and paleobiology. This large sample size allows a statistical test on whether shape differences of skulls could be truly related to sex.

Variation in Protoceratops skulls; the skull on the left has been previously hypothesized as male, whereas the skull on the right has been suggested as female. Scale bars equal 10 cm. Image from Maiorino et al. 2015, modified from original by Brown and Schlaikjer 1940.

Variation in Protoceratops skulls; the skull on the left has been previously hypothesized as male, whereas the skull on the right has been suggested as female. Scale bars equal 10 cm. Image from Maiorino et al. 2015, modified from original by Brown and Schlaikjer 1940.

Back in 1975, Peter Dodson used skull measurements from 24 specimens to investigate growth changes in Protoceratops as well as possible sexual dimorphism. He assigned the sex to each specimen on the basis of its position on scatter plots (above or below a trend line). Based on this analysis, Dodson hypothesized that male Protoceratops had a broader and taller frill, broader skull above the eyes, and taller nasal bump than seen in females. This analysis was quite advanced for its time, but given advances in statistical methods, morphometrics, and computing power, as well as the discovery of many new fossils, we decided to look at the problem again.

Geometric morphometrics is a suitable method to analyze shape and size differences among groups of animals. Where previous work used basic measurements, we digitized the shape of 29 skulls in top and side views, based on photographs. We assigned skulls to male or female using the previously outlined criteria. Geometric morphometrics allows the study of shape variation within sampled specimens and capturing the overall geometry (instead linear measurements) of biological structures by means of simple analyses. How can we detect shape information? It is easy: just digitizing spots on images (called landmark) on homologous anatomical features for the all skulls (in our case) in top and side view. By so doing, we have now a large sample constituted by geometries that represent the shape of the skull.

We asked ourselves, if males and females have different skull shape, are we able to distinguish the two groups using geometric morphometrics and statistical tests?

We plotted all specimens in a X-Y graph. One graph for the Protoceratops individuals in side view, and one other for the individuals in top view. We refer to those X-Y graphs as “morphospace” because they represent the shape variation of the specimens in the space. Those two graphs highlighted that males and females overlap each other; the two groups are not well separated in the plots. This suggests that males and females possess similar skull shape. Moreover, we used statistical tests to verify if what we can see in the graphs is statistically reliable and thus if the shape difference between males and females is well-founded.

Note the overlap between "male" and "female" Protoceratops; if there is sexual dimorphism, it is fairly week. Image from Maiorino et al. 2015.

A plot of morphospace for Protoceratops skulls in side view. Note the overlap between “male” and “female” Protoceratops; if there is sexual dimorphism, it is fairly weak. Image from Maiorino et al. 2015.

No matter how we plotted or analyzed the data, we weren’t able to find a clear, statistically significant difference between males and females. Therefore, we think that the previously hypothesized criteria are not suitable to distinguish the two sexes in Protoceratops andrewsi easily. Frill height and width as well as the width of the skull over the eyes do not represent sex-discriminant features in our sample. The occurrence of the horn above the nose would seem partially related to sexual dimorphism, even if this evidence is not well-rendered.

We suggest that cranial shape variation previously interpreted as sexual dimorphism is related instead to shape changes occurring during the animal growth and perhaps also related to the shape variation occurring among the adults of this ceratopsian dinosaur. Maybe, new fossils will give the chance to confirm our results or reject them.

Citation
Maiorino, L., A. A. Farke, T. Kotsakis, and P. Piras. 2015. Males resemble females: re-evaluating sexual dimorphism in Protoceratops andrewsi (Neoceratopsia, Protoceratopsidae). PLoS ONE 10:e0126464.

Category: Dinosaurs, Paleontology, PLOS ONE, Zoology | Tagged , , , , | Leave a comment

International Museum Day

Today is International Museum Day. Today (and every day) I’m grateful for museums and the people who work in them. Natural history museums (especially The Field Museum in Chicago) were key inspirations that got me on my path to a career in evolutionary biology. It’s no stretch to say that museums helped make me who I am today – they opened my eyes to the amazing planet we live on and got me excited to learn about it. More than any teacher, museums encouraged me to explore the world and to add to our understanding of it.

The Field Museum inspired me to become a scientist.

The Field Museum inspired me to become a scientist.

Perhaps because of this, I think about museums as an equalizing force. A leg up for kids who weren’t born into money. A path to change. Just 150 years ago, most museums were private, essentially curio cabinets for wealthy people to display their collections. The idea of museums as a public good –that the beauty and wonder of the world should be accessible and inspiring to all– is one of the great cultural advances we have seen in that time.

Museums preserve our natural and cultural heritage, remind us of humanity’s greatest achievements and its lowest moments. They expose us to beauty and darkness, and challenge our assumptions about ourselves and others. Like all educational institutions, museums are a democratizing force. Their very existence proves that the world is bigger than our particular circumstances, that there are better things out there than what we observe from day to day, and that there are other ways of doing things than those we were taught.

Museums are powerful; they give us hope, question the status quo, and inspire us to be better versions of ourselves. This really is a revolutionary concept; if these ideas weren’t threatening, the existence of museums would never be at risk. Invading forces wouldn’t destroy them when they took over new area. Politicians would not be so keen to defund them.

So, today (and every day), I encourage you to support and protect your local, state, and national museums. Visit, volunteer, and become a member. Donate to funds that get kids in the door. Combat their defunding. Don’t elect politicians or school boards who think museums aren’t valuable. Support school districts, principals, and programs who advocate student access to museums. Museums preserve our past, but they also have the power to change the future.

Be like Patrick. Support museums.

Be like Patrick. Support  museums. Become powerful.

Category: Miscellaneous, Museums, Navel Gazing, Uncategorized | Tagged | Leave a comment

Sharing Paleodata (Part 4): MorphoSource

Today I continue my series highlighting repositories for paleontological raw data. Previous posts in this series can be found here, here, and here.

 

Welcome to the MorphoSource

MORPHOSOURCE (http://morphosource.org/)

MorphoSource is a data repository for 3D data – raw CT and microCT data, but also surface models, slice movies, and 2D images. It’s the brainchild of Doug Boyer, an Evolutionary Anthropology professor at Duke. While there are plenty of data repositories for 2D images (e.g., MorphoBank and MorphBank), there really isn’t an equivalent for raw 3D data. Yes, some sites like Dryad or Figshare can host CT datasets (as Andy and I did for our 2013 “Dinosaur Joe” paper), and the website DigiMorph hosts these data in a more limited format, but currently there’s no dedicated repository for raw CT data.

CT has been an increasingly common tool in paleontological research for the last two decades, but for most of that time, CT datasets were too large to host online. Early on, Tim Rowe and his UT Austin colleagues set up DigiMorph as a central online repository for hosting the data, albeit in smaller file formats. DigiMorph has long been the only site focused on paleo/morphology CT data; they currently host an impressive 1ooo+ datasets. I’m a big fan of DigiMorph and use it regularly in both teaching and research, but it has some limitations. First, nearly all of the DigiMorph data comes in video form (movies that cycle through CT slices or show spinning rendered volumes) or annotated 2D images. Only ~50 have associated downloadable STL files (surface meshes/models), and none of the raw data (projections or slices) are downloadable. There’s also a backlog of specimens that have yet to be uploaded, because they only have so many techs and they all have many other responsibilities. MorphoSource answers these concerns by allowing users to upload their own raw data and STL files, in addition to movies and 2D images.

Full Disclosure: The statements about MorphoSource in the “Nitty Gritty” section were checked for accuracy by Doug Boyer (site director). The impressions are my own. I’ve used the site for a couple months now, and have submitted, shared, viewed,  and downloaded data.

 

Lemur tooth

3D surface mesh of a ring-tailed lemur molar. Image from: http://morphosource.org/index.php/Detail/MediaDetail/Show/media_id/307

 

Impressions: Two weeks ago, University of Texas sent me some fossils. I opened the box on Wednesday night, photographed and measured my specimens on Thursday, and on Friday morning at 7:30AM, I scanned all 8 bones. By noon, I had made some surface meshes in Avizo, created a MorphoSource project, uploaded all the dicom and STL files (the raw data and my interpretations of it), and shared the whole shebang with the collections manager. In two days I went from a sealed box to having returned all the data to the lending institution. Yes, it’s highly unlikely that anyone will need to see this particular right femur of a juvenile false gharial in the few months I have these guys on loan, but if they do, Texas already has the data and a surface model they can share with people who need it. So, yeah, I really like MorphoSource and find it beneficial even prior to publishing anything publically on the site. It’s now my go-to site for 3D data management.

Part of its appeal is that it sticks to functionality and doesn’t get bogged down in unnecessary features – no social media stuff; it’s all business and functionality. In several months of use, I’ve never had problems with the site; no crashes, stalled downloads, or errors. I was able to figure out the site without needing to consult the User Guide, although it took me a couple hours to become comfortable navigating and uploading. If I had read the directions first, I probably wouldn’t have found some aspects clunky (see below), because I would have anticipated what information I needed to have on hand before uploading.

To begin, you create a project, and then add taxa and specimens before uploading media files. It auto-searches to see if someone has previously entered a taxon or specimen number, which is pretty handy. You determine who can view/download the media before the project is published by adding collaborators. Collaborators can see all specimens within a project, but you can also choose to share a given specimen with people outside your collaboration group (if you didn’t want to give them access to every specimen). Outside of collaborators, nobody can see your data until you publish it. Upon publication, you can decide whether everyone can download it without contacting you, or if they need to email you for permission before access is granted. You can also elect to be notified passively when people download your data. After publication, people can view your surface meshes in the browser, but if they want to download data, they need to register to do so.

So far, I’ve included collections managers as collaborators on projects that involve their museum’s specimens. One nice feature: if I want to, I can give them sole access to the project/media/specimen (i.e., transfer the project to them) after publication. I like this idea a lot; most museums ask for the raw CT data upon publication anyway, and this is a good way to both give them the data and allow them to control and track its use down the road.

In addition to sharing the tiff or dicom stack, you can also share movies and surface meshes, duplicating a major and minor feature of DigiMorph, respectively. An especially helpful tool is the ability to view and rotate surfaces in-browser, without having to download the file or requiring sophisticated 3D software. This has already proved useful in sharing data with my colleagues; they can view and manipulate the specimen virtually while we chat about it over the phone. As a tool for real-time collaborative research, this is pretty great. It also has a lot of promise as an outreach and education tool – for example, the Florida Museum of Natural History has uploaded surface meshes for two K-12 educational projects on Horse Evolution and the megasnake Titanoboa. I can see MorphoSource as a great supplement for in-class activities or virtual lab assignments; for example, using this incredible dataset of primate skulls in the Harvard MCZ collection.

3D surface mesh viewer

Screenshot of the 3D surface mesh viewer

If you want “official” credit for these open-data efforts, you can request a DOI for projects or media items. The first time, you’ll need approval as a DOI user and then it’s a simple request each time you need a DOI after that.  They’ve also included some pretty cool features that make downloading files and managing metadata easier. If a large dataset is available for immediate download, you can choose specific specimens to download using a shopping cart button. Once you get to the “check out” page, you can opt to download only part of the data, say, only the meshes or tiff stacks. You can also download all the metadata for every specimen in your cart as a CSV – all the specimen data and scan parameters in one file, so you don’t have to hunt for the information later.

Another strong positive is Doug Boyer himself. I’ve been testing the site for a couple months now, and have sent him several suggestions by email. Each time, he took the time to read and respond, indicating which were already planned, which weren’t practical, and which were good ideas. Some of these have already been incorporated. He’s really invested in the functionality of the site, and wants to ensure that every feature directly relates to the primary goals of storing and sharing data.

There aren’t many negatives. I find searching a little clunky (they’re working on improving this), but browsing is ok once you get used to using in-window forward and back arrows to navigate. Initially I thought it was a little annoying to have to enter and save taxonomy, specimen, and scan information before uploading can begin, but really, it’s no more cumbersome than the same process on MorphoBank. One advantage over MorphoBank is that basic museum, specimen, and taxonomic information are accessible to the whole site once one person enters it – nobody will ever have to go through the trouble of entering the higher taxonomy of Tomistoma schlegelii again. Currently, each specimen requires entering a genus and species, which for my critters is not always possible (my best workaround is entering g: Phytosauria, sp: indet, or g: Incertae, sp: sedis). Future improvements will include the ability to search using higher taxonomy, which will get around this problem to some extent.

Bottom Line: MorphoSource is functional and fairly easy to use. Currently, it’s probably the best option for sharing raw CT data. Grant writers should feel comfortable listing MorphoSource in their Data Management Plan. Reviewers should feel comfortable asking authors post data to MorphoSource.

 

A Titanoboa vertebra used in a K-12 project published on MorphoSource.

3D surface mesh of a Titanoboa vertebra, published as part of an education/outreach project aimed for K-12 teachers and students. Image from: http://morphosource.org/index.php/Detail/MediaDetail/Show/media_id/5943

 

MORPHOSOURCE: THE NITTY GRITTY

What it is: 3D data repository for CT and microCT data

What it is, in their words: “a project-based data archive that allows researchers to store and organize, share, and distribute their own 3D data”; also “an image-sharing resource designed to allow users to upload, search, and browse high quality 3D images”

Who runs it: Doug Boyer, Duke University

Who funds it: Duke University (directly and by hosting the site), NSF (BCS 1317525; BCS 1304045)

Who uses it: Researchers who use, download, or submit 3D data.

Cost to submit: Free (registration required).

Cost to access: Free (registration required to download).

Data and file types supported: 2D images: JPEG, PNG, TIFF, DICOM and PSD. Video: MPEG-2, MPEG-4/H.264, FLV, QuickTime, and Windows Media. Surfaces: PLY and STL. You can also submit zipped archives of TIFF and DICOM files. I included Avizo files within my zipped archive with no uploading issues.

File sizes allowed: No limit

Copyright status: You choose whether or not the data is copyrighted and who owns the copyright. You select among Creative Commons licenses (CC0 and CC/BY/NC/SA/ND) or release the data for one-time use on MorphoSource. No option (yet) to upload a copyright permissions document, but you can copy text from those documents into the notes. Nifty feature: you can opt to receive a notification email when your data are downloaded, or require users to contact you for permission before data are downloaded.

Data available during peer review? Kinda, in that you can make the data live at submission rather than upon publication of the paper.

Allowed to post data from previous pubs? Yes, even publications published before MorphoSource existed, and they invite and encourage this practice.

Accession numbers provided? Every project, specimen, and media item gets their own accession number (similar to GenBank) as you upload them. You can also request a DOI.

Data goes live when: You choose to publish the project. Data can stay as an unpublished project forever, or you can publish it when you like – before or after the manuscript is accepted, when embargo is lifted, when the paper is published, etc.

Data is backed up? There are 4 copies (RAID1 drives in 2 separate physical locations). Currently applying for funding to expand physical storage, add additional cloud storage, and expand the archival system.

Stats provided? Number of views and downloads for each specimen and media item. You can also see which registered users have viewed/downloaded your files.

How to cite your data in your manuscript? Cite the MorphoSource software. Right now there are two extended abstracts (Boyer et al. 2014; Kaufman & Boyer 2014 , but there’s also a formal paper in the works

Boyer DM, Kaufman S, Gunnell GF, Gomes E, and Thostenson J. 2014. MorphoSource: A currently active project-based 3D digital web-accessible data archive for museums and individuals at Duke University USA. In: Mallison H, Vogel J, and Belvedere M, editors. Digital Specimen 2014 – Abstracts of Presentations. pp 8-12.

Kaufman S, and Boyer DM. 2014. Developing Platforms for Management and Distribution of Digital Specimen Data. In: Mallison H, Vogel J, and Belvedere M, editors. Digital Specimen 2014 – Abstracts of Presentations. p47.

You should also cite your data, something like: “TIFF stacks and STL files are available on MorphoSource (http://www.morphosource.org): Project XXX (DOI: ). Media accession numbers are listed in Table X.”

How to cite data you download from someone else’s project? DOI, if they have one. Otherwise cite the site, project and media numbers.

Can update after publication? Yes. In their words: “You always have the option of removing materials from public view, and adding new media to longstanding projects.” *This may not be the case for DOI-assigned media.

Benefits in a nutshell:

  • Secure cloud storage of 3D surfaces and raw microCT and CT scan data
  • Accessible to your collaborators before publication
  • View and rotate 3D surface meshes in your browser
  • Add new citations to a project as you/others re-use the data
  • Notification when people view/download your dataset
  • You can require people to ask permission before downloading data

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. MorphoSource data example: media S1312, a presacral vertebra. YOU CAN DOWNLOAD YOUR OWN BEELZEBUFO, PEOPLE!

Chester, SGB, JI Bloch, DM Boyer, WA Clemens. 2015. Oldest known euarchontan tarsals and affinities of Paleocene Purgatorius to Primates. PNAS 112(5): 1487-1492. MorphoSource data example: media S1405, an astragalus.

Boyer, DM and ER Seiffert. 2013. Patterns of astragalar fibular facet orientation and their evolutionary implications in extant and fossil primates. American Journal of Physical Anthropology 151(3): 420-447. MorphoSource data example: media S1083, a different astragalus.

Category: Digitization, Open Data, Paleontology | Tagged , , | 4 Comments

Romer’s Gap and the Four-Limbed Critters of Nova Scotia

The fossil record is a window into the past, but much of that window is boarded over. This situation spurs paleontologists to look in new places and new rocks, in an attempt to pry some of those boards off that window into our planet’s history. This is a great example of how paleontology is a testable science. Missing fossils from a certain time span? Look in rocks from that time span, and you should find them!

Romer’s Gap” presents a classic case of the incomplete fossil record. We know quite reliably that tetrapods–the four-limbed vertebrates including amphibians, reptiles, and us–originated around 370 million years ago. Fossils from 365 million years ago show distinct arms, legs, fingers, and toes on animals such as Acanthostega, leaving no doubt as to their tetrapod status. And we also know that tetrapods were pretty successful after that, because I’m using my tetrapod forelimbs (arms, hands, and fingers) to type out this blog post. But frustratingly, a time slice from around 360 to 345 million years ago yields precious few tetrapod fossils. This phenomenon was first noted by paleontologist Al Romer, hence its nickname of “Romer’s Gap“. The gap frustrates scientists because it is so soon after the origin of tetrapods, immediately before many important groups appear in the fossil record. That interval probably includes many events central for the transformation of tetrapods from leggy fish into truly terrestrial organisms. Tetrapods must have been around during Romer’s Gap, but where were they?

Romer's Gap is a ~15 million year interval, during which a whole bunch of tetrapod evolution presumably happened. Sites such as Blue Beach help to fill this gap. Eoherpeton at top modified from original by Nobu Tamura (CC-BY). Ichthyostega at bottom modified from public domain original by Scott Hartman.

Romer’s Gap is a ~15 million year interval, during which a whole bunch of tetrapod evolution presumably happened. Sites such as Blue Beach help to fill this gap.
Eoherpeton at top modified from original by Nobu Tamura (CC-BY). Ichthyostega at bottom modified from public domain original by Scott Hartman, phylopic.org.

Various ideas have been proposed to explain the gap. Two front runners include:

  • Low atmospheric oxygen levels put a damper on land animals. No oxygen, no animals. But, it turns out that oxygen wasn’t that much lower than other times in history, and were actually higher than times just before the “gap”. Furthermore, marine waters should have had even lower oxygen (long story–I’ll just wave my hands and say “Chemistry!”), providing extra pressure for tetrapods to move onto land.
  • Artifact of collection and/or preservation. Is there a genuine gap in the fossil record? For any number of reasons, the fossil record is patchy. You might not have rocks from the type of environments to preserve particular organisms, or paleontologists just haven’t gotten around to studying the appropriate rocks yet.

As more paleontologists seek out more fossils, the latter hypothesis is starting to gain ground. A new study by Jason Anderson and colleagues, just published in PLOS ONE, provides additional support along these lines.

Rocks from the Horton Bluff Formation in Nova Scotia that yield fossils filling "Romer's Gap". CC-BY, modified from Anderson et al. 2015.

Rocks from the Horton Bluff Formation in Nova Scotia that yield fossils filling “Romer’s Gap”. CC-BY, modified from Anderson et al. 2015.

Blue Beach, rimming an estuary on the Bay of Fundy, has a long history of producing fossils from the time span including the base of Romer’s Gap. But, these rocks are notoriously hard to work. Wide swings in tidal levels limit working time to only a few hours a day, and most fossils are isolated bones difficult to assign to a particular kind of animal. Unless the finds are collected soon after exposure, they are lost to wave action. Thankfully, discoveries by local amateur paleontologists, in concert with fieldwork by external researchers, have slowly and steadily produced a stream of fossils.

The fossils described in the new study are nearly all isolated bones–individual limb, pelvic, and shoulder girdle pieces. But, by comparing them to more complete finds from elsewhere, it is possible to identify the specimens to varying degrees of precision.

Humerus (arm bone) of an early tetrapod from the Blue Beach locality. CC-BY, from Anderson et al. 2015.

Humerus (arm bone) of an early tetrapod from the Blue Beach locality; multiple views of the same fossil. CC-BY, from Anderson et al. 2015.

Let’s face it–the limb bones of early tetrapods are pretty clunky objects, lacking the sweeping and elegant lines of today’s salamanders, lizards, or mammals. The above image is a great example of a typical early tetrapod arm bone. But, each awkward ridge and bump points to the bone’s original owner. For instance, the bone shown here is similar to that of an animal called Pederpes, which belongs to a family of early tetrapods called Whatcheeriidae. Imagine something that looked like an ugly salamander, and you’ve got Pederpes.

All together, 37 different specimens (including isolated limb bones, skull bones, and even a handful of specimens with multiple bones from the same individual) were studied by Anderson and colleagues. The fossils could be referred to six or seven different groups of early tetrapods, showing that tetrapods were going strong even in the middle of Romer’s Gap. Some of these (closely related to Ichthyostega, shown below) are forms that are most closely associated with earlier times in earth’s history; one way or another, they made it through a big extinction just prior to Romer’s Gap. Maybe, then, the extinction didn’t hit tetrapods as hard as previously thought.

An ominous Ichthyostega. Silhouette by Scott Hartman via phylopic.org, public domain.

An ominous Ichthyostega. Bones from a closely related animal were found at Blue Beach. Silhouette by Scott Hartman via phylopic.org, public domain.

Blue Beach isn’t the only locality to plug Romer’s Gap–another recently described set of fossils from Scotland shows a similarly rich tetrapod ecosystem. Together, these localities in disparate parts of the world suggests that the purported gap in the fossil record is more a collecting artifact than the result of genuine rarity of these animals during their time. Anderson and colleagues perhaps summarize it best:

“It now seems that, whenever we discover rare windows into this time period, we find numerous fossil tetrapods reflecting a rich diversity of forms.” — Anderson et al. 2015

In other words, Romer’s Gap probably isn’t a real phenomenon! With more fossils, it’s getting shorter and shorter. This is so often the case in paleontology–and that’s a good part of what keeps us all out looking for fossils. A “gap” in the fossil record is just a challenge to overcome.

Citation
Anderson JS, Smithson T, Mansky CF, Meyer T, Clack J (2015) A diverse tetrapod fauna at the base of ‘Romer’s Gap’. PLOS ONE 10(4): e0125446. doi:10.1371/journal.pone.0125446

Category: Paleontology | Tagged , , , | 5 Comments

Brontosaurus thunders back!

Pretty much every person who ever read a dinosaur book or went to a natural history museum learned that Brontosaurus is just an outdated name for a big long-necked dinosaur that should be called Apatosaurus. Two different names were applied to the same type of animal, but Apatosaurus wins out because it was named first.

But…it’s just not that simple. It’s never that simple! In a move that is sure to generate considerable discussion by scientists and non-scientists alike, Brontosaurus is back. This topic is being covered in immense detail by many other writers, so I’m going to give just a quick tutorial here. In the interests of full disclosure, I should also note that I was the volunteer editor who handled this paper for the open access journal PeerJ. The opinions expressed here are solely my own.

An old school Brontosaurus, as envisioned in the late 1800s. After Marsh 1896.

An old-school Brontosaurus, as envisioned in the late 1800s. After Marsh 1896.

So, how do we resurrect Brontosaurus? It’s not just a matter of arbitrary scientific opinion–the authors of the new study, Emanuel Tschopp, Octávio Mateus, and Roger Benson–didn’t wake up one morning and say, “Hmm…let’s mess with people.” The work entailed a ridiculously awesome amount of hands-on study of specimens around the world, as well as detailed analysis of the features of the fossils to determine their evolutionary relationships.

Evolutionary relationships are the key–erecting, demolishing, or maintaining species and genera requires an understanding of how these organisms are related. Basically, if species of Brontosaurus are all mixed in with species of Apatosaurus, then the two animals should be recognized under one name (Apatosaurus). If, on the other hand, what used to be called Brontosaurus is evolutionarily well separated from species of Apatosaurus, then Brontosaurus stands up.

In order to see how the species are related, Tschopp and colleagues built a massive database documenting the anatomical features for numerous relatives of Apatosaurus–at the individual specimen level. This was the largest-scale study of its type ever done; most other studies (with few exceptions) have lumped specimens together under species, or have lumped species together into genera. A fine-scale approach, looking at individual specimens, turns out to be key. Once all of the specimens were coded, they were subjected to a phylogenetic analysis to determine which possible evolutionary trees best fit the data. In other words, a computer algorithm took the data and found which possible arrangement of evolutionary relationships made the most sense in light of the anatomical evidence. Animals that share more features changed from the ancestral condition (“derived features” in paleontological parlance) are assumed to be more closely related.

In the diagram below, which is roughly similar to a previously published analysis by Paul Upchurch and colleagues, note that the original Brontosaurus species (Brontosaurus excelsus) is in the middle of a whole bunch of Apatosaurus. Species more closely connected are more closely related–and here, the original Brontosaurus species is more closely related to the original Apatosaurus species than anything else. Unless one wanted to name each of those other species its own genus (a practice  employed for many other dinosaur groups), it made the most sense to keep Brontosaurus the same as Apatosaurus.

Tentative evolutionary tree of Brontosaurus and Apatosaurus

A hypothetical  view of the evolutionary relationships of Apatosaurus and Brontosaurus, based in part on a previously published analysis by Upchurch and colleagues. The dates at right indicate when each species was named. If this arrangement is correct, then Brontosaurus should be called Apatosaurus.

In their own analysis, Tschopp and colleagues found that Brontosaurus excelsus is well separated from the two species most traditionally considered Apatosaurus. Not only does the shape of the evolutionary tree show this, but the sheer quantity of differences also supported Brontosaurus as something different from Apatosaurus. By the paper’s standard of a “genus”, Brontosaurus fits the bill.

A new evolutionary hypothesis showing Apatosaurus and Brontosaurus as different genera.

In this arrangement, based on that found by Tschopp and colleagues, Apatosaurus and Brontosaurus are two different genera. As an interesting side-note, Brontosaurus parvus originally got its own name, Elosaurus. But, because it is “nested” within Brontosaurus, it keeps that name. As another side-note, Brontosaurus yahnaphin has also been called Eobrontosaurus. So, one could make an argument that BrontosaurusElosaurus, and Eobrontosaurus are all valid! This is where things can get a little subjective, but Tschopp et al. posit that the differences are few enough so that they should also be Brontosaurus.

So, Brontosaurus lives again! In terms of pop cultural significance, this is a pretty big deal–but in terms of scientific nomenclature, these kinds of things happen all of the time. In fact, the real treasure of the paper by Tschopp and colleagues is its in-depth approach to unraveling the evolutionary relationships of ApatosaurusBrontosaurus, and their relatives. This level of detail is becoming increasingly common for dinosaur research, and as demonstrated here can be a pretty handy tool for unraveling long-standing problems in identifying and naming species.

Brontosaurus has an unparalleled hold on the public imagination–its name aptly means “thunder lizard,” after all. As such, it’s a prime example for showing how scientists classify and reclassify organisms in light of new information.  Papers such as this, beyond taking care of naming species and genera, provide an important backbone for other analyses. If we want to understand the migrations and interchanges of dinosaurs between continents, we have to know how the various species are related. If we want to correlate the origination or extinction of species to climate changes or other global events, we have to have a solid grasp on these same relationships. Scientific progress thunders onward!

Citation
Tschopp E, Mateus O, Benson RBJ. (2015) A specimen-level phylogenetic analysis and taxonomic revision of Diplodocidae (Dinosauria, Sauropoda) PeerJ 3:e857 https://dx.doi.org/10.7717/peerj.857

[post edited to add clarification on shared derived features, add links to other blog posts, fixed a typo or two]

Category: Dinosaurs, Paleontology | Tagged , , , , | 4 Comments

A digital head for Acanthostega

What has 16 fingers and a digital skull? Acanthostega, that’s what!

Acanthostega was one of the first limbed (rather than strictly “finned”) vertebrates, living around 365 million years ago in the shallow waters of modern day Greenland. Imagine something that looked roughly like a two foot long cross between a salmon and a salamander. As an odd evolutionary quirk, perhaps representing early experimentation in tetrapods (limbed vertebrates), Acanthostega had eight fingers on each of its hands. This critter is known from the nicely preserved fossils of several individuals, which has deservedly given it the title of “iconic” for our understanding of the transition from water onto land, for everything from feeding to locomotion.

<i>Acanthostega</i> in the flesh. "

Acanthostega in the flesh. “Acanthostega BW” by Nobu Tamura (http://spinops.blogspot.com) – Own work. Licensed under CC BY 2.5 via Wikimedia Commons.

Of course, we paleontologists are never satisfied with beautiful fossils. There always seems to be something that isn’t quite preserved, or is preserved in the wrong orientation for easy viewing, or is crushed in such a way as to render opinions on anatomy equivocal. Frustratingly, these kinds of details can be important for nailing down the finer points of evolutionary relationships as well as behavior and function. During the last two decades, non-invasive medical imaging techniques have been adapted for digital preparation and reconstruction of many fossils. Thus, it is increasingly easy to pull out previously inaccessible details of ancient anatomy.

Laura Porro and colleagues just published a paper detailing their new digital reconstruction of the skull of Acanthostega, based on CT (computed tomography) scanning of three different specimens. Each fossil had some degree of crushing or incompleteness, but together they essentially added up to a whole skull. The trick, of course, was getting them to all fit together.

The first step is to digitally remove the rock from the fossils. This process involves making a judgment in the grayscale CT scans as to where one ends and the next begins. When there is high contrast (perceived by us humans as sharp color differences in the scan), this can be done fairly automatically by the computer; in less clear cases, a human has to make this decision. Anatomical knowledge as well as a “feel” for the scan are key.

Although we often think of a “skull” as a single unit of bone, the head is in fact made up of a number of separate but interlocking bones. Thus, each bone digitally was separated from its neighbor. The result is a bunch of colored bones floating in space, which are in their original position as preserved but not necessarily life position.

The original "squished" skull of <i>Acanthostega</i>. Modified from Porro et al. 2015, CC-BY.

The original “squished” skull of Acanthostega. Modified from original figure in Porro et al. 2015, CC-BY.

The next step is to fill in missing pieces and restore the skull to its life condition. Missing or incomplete bones could be replaced by scans from more complete fossils, scaled appropriately. Removing the post-death displacement of bones was a little more challenging. For animals with loosely-knit skull bones, individual bones tend to “sag” relative to each other after death, squishing some parts that weren’t originally squished. In the fossils, this can be evidenced through big gaps that obviously weren’t there in life, or through disturbingly overlapping bones that once again don’t look like anything in a living animal. Through digital manipulation, each bone can be scooted back to its life position relative to the other bones. Even in the best case this is a long and tedious process, and the authors clearly sank a lot of work into getting it right with Acanthostega. The result (below) is pretty dramatically different from the “as-is” fossil.

The "unsquished" skull of <i>Acanthostega</i>. Modified from Porro et al. 2015, CC-BY. I have combined two figures to better show the overall anatomy.

The “unsquished” skull of Acanthostega. Modified from Porro et al. 2015, CC-BY. I have combined two figures to better show the overall anatomy.

Although this isn’t the first attempt to “undeform” the skull of Acanthostega (previous pen-and-paper versions have been published), it is perhaps the best supported and most constrained by the fossil data. A quick glance at the original fossil as well as the digital reconstruction shows a number of difference between the two–the overall shape of the snout, position and size of the eye sockets, angulation of the back half of the skull relative to the front half, etc. The overall skull shape wasn’t the only thing that was newly revealed–the anatomy of some bones closely related to feeding (the quadrate bone, connecting the upper part of the skull to the lower jaws, for example) are also known for the first time.

There are no massive reinterpretations of the life, appearance or evolutionary history for Acanthostega in this paper, but that is okay. Nonetheless, descriptions of previously unseen bones and relationships between bones help generate refined hypotheses for future testing. For instance, Porro and colleagues further confirmed a previously suspected gap between bones on the top of the snout called the midline rostrals and nasals. This gap wasn’t immediately visible on the fossils themselves, but was unavoidably open when reassembling the skull on the computer. Some other early tetrapods also show this feature, and thus it might be handy for clarifying evolutionary relationships between these species.

Porro and colleagues also were able to describe the shape and texture of the contacts between individual bones (typically called sutures) at a new level of detail. The nature of these sutures–whether they are tightly linked from bone to bone, broad, narrow, sinuous, or whatever–can be correlated with feeding style. Something chowing down on actively wriggling prey might want to have a beefy skull with sturdy attachments between bones, for instance. If different parts of the skulls are used differently, this might also be reflected in the sutures. Some arrangements show resistance to being pushed together or pulled apart, and others show resistance to twisting. In the case of Acanthostega, it is hypothesized that the front of the skull was used for nabbing live prey (based on the teeth as well as the sturdy connections between bones on the front and roof of the skull). In contrast, the mid-section (as shown by the more loosely connected bones on the roof of the mouth and in the cheek) was more of a “stabilizer”, holding prey in place as Acanthstega swallowed. These interpretations can now be worked out in more detail using computer models.  Overall, the evidence from this and other studies points towards Acanthostega feeding underwater (perhaps as a suction feeder), rather than on land.

The field of digital paleontology is no longer as new and shiny as it once was–indeed, CT scanning is now a fairly standard technique for many scientists. But, the case of Acanthostega once again shows how digital fossils have moved from “gee whiz we scanned a specimen” into “here’s a whole bunch of new anatomy and behavior.” Although it would have been pretty cool to see this animal devour live prey, I just as much like the fact that it’s now devouring internet bandwidth as I read the open access paper and soak in the beautiful imagery!

explodostega

“Explodostega”. Modified from Porro et al. 2015, CC-BY.

Soapbox Addendum
On a final note, I particularly commend the authors for including this phrase in their paper:

It should be noted that the 3D model represents our hypothesis of the reconstructed skull of Acanthostega, based on available specimens, scan resolution and personal interpretation.

When I read that sentence, I practically wept sweet tears of replicable science joy. As I have stated elsewhere, even in the best cases CT reconstructions require a certain level of finesse, practice, and personal judgment, with the strong possibility of alternative interpretations. It is wonderful to see that fact acknowledged in the literature–this is pretty rare otherwise. Additionally, although I strongly prefer that raw scans themselves be made available whenever possible, the authors have done a good thing by indicating that the scans are archived at the institution housing the original fossil specimens. I’m glad that there are more and more people thinking about reproducibility in digital reconstructions.

Citation
Porro LB, Rayfield EJ, Clack JA (2015) Descriptive anatomy and three-dimensional reconstruction of the skull of the early tetrapod Acanthostega gunnari Jarvik, 1952. PLOS ONE 10(3): e0118882. doi:10.1371/journal.pone.0118882

Category: Digitization, Paleontology, PLOS ONE | Tagged , , , , , | 4 Comments

Beefy Bones and a Big Bite for the Ancient Whale Basilosaurus

Basilosaurus life restoration by Dmitry Bogdanov, CC-BY.

Basilosaurus life restoration by Dmitry Bogdanov, CC-BY.

Although its name sounds rather dinosaurian, Basilosaurus was in fact one of the first extinct whales to make a splash in humanity’s perception of the past.

When its bones were first described back in the early 19th century, the anatomy of the backbone was thought to most closely resemble that of some Mesozoic marine reptiles. Later work, and examination of other parts of the skeleton, revealed Basilosaurus to be an early whale that lived around 34 million years ago. Of course, more recent discoveries have since produced older whales with even more “primitive” features, but Basilosaurus and its close relatives remain important for piecing together the details of whale evolution. This past week, two papers in PLOS ONE added more information on the internal anatomy of the bones of Basilosaurus as well as its strong bite.

The first paper, by Alexandra Houssaye and colleagues, used computed tomography (CT) scans to peek inside the limb bones, vertebrae, and ribs of a number of early whales. For the purposes of this post, I’ll just focus on Basilosauruscheck out the paper for the story with the other species, which is pretty interesting in its own right.

Rib of Basilosaurus--note its high density, a common feature of whale ribs. Modified from Houssaye et al., 2015. CC-BY.

Rib of Basilosaurus–note its high density (gray is bone tissue, black is empty space), a common feature of whale ribs. Modified from Houssaye et al., 2015. Scale bar equals 10 mm. CC-BY.

Two distinct adaptations are common in the bones of aquatic amniotes (birds, reptiles, and mammals) that forage underwater. The first is Bone Mass Increase (BMI); this is achieved by making bone denser (getting rid of spongy bits) as well as by adding more bone tissue to an individual bone. The second adaptation is, by contrast, creating spongy bones with internal struts to hold up to the forces of swimming. Presumably, both of these adaptations evolved in order to maintain optimal buoyancy while enabling effective locomotion.

Basilosaurus had ribs largely made of compact bone, typical of whales (even those today). Its arm and thigh bones were also quite compact and dense, unlike the condition in some other early whales. This is actually a bit of a puzzle, because it is fairly different from close relatives of Basilosaurus that have less dense arm bones (presumably tied to swimming style), and doesn’t match with the overall picture of Basilosaurus as a predatory animal that lived in open waters. Because the hind limbs were fairly useless, it doesn’t make a lot of sense that they would have such dense bone (no need to stand up to big muscular forces). The basic conclusion: more research is needed. The study by Houssaye and colleagues provides some important data points to launch future investigations.

Blue Skull of Death. Computer reconstruction of the skull of Basilosaurus, with jaw muscles added. Modified from Snively et al. 2015. CC-BY.

Blue Skull of Death. Computer reconstruction of the skull of Basilosaurus, with jaw muscles added. Modified from Snively et al. 2015. CC-BY.

The next paper under consideration turned to the business end of Basilosaurus–its skull. Fossilized stomach contents showed that Basilosaurus chowed down on fish, wear patterns on the teeth suggested at least some shellfish in the diet, and tooth marks on the bones of other whales indicate a habit of chomping anything willing (or unwilling) to be eaten. Presumably Basilosaurus had the bite force to dent bone–could this be confirmed?

Eric Snively and colleagues constructed a computer model of the skull of Basilosaurus, complete with simulated musculature. After crunching all of the numbers, they estimated that this long-dead whale packed over 16,000 N of force in its bite (and potentially even more, depending upon the conditions invoked). This blows the bone-crushing hyena out of the water–our poor terrestrial pal weighs in at a “paltry” 3,500 N for measurements of bite force in captive animals.

The bite of Basilosaurus sounds impressive–and it certainly is–but context is everything. With a skull measuring over a meter long, Basilosaurus was far larger than hyenas. Big head, big bite. Modern crocodilians have a bite force well beyond that of Basilosaurus, and ancient marine reptiles and the “land shark” Tyrannosaurus also would have won in the cranial equivalent of an arm wrestling contest. Differences in skull size as well as muscular configuration are probably in play here. As Snively and colleagues suggest, it would also be nice to see how the bites of modern whales stack up (e.g., orcas). We’re only beginning to understand the evolution of whale bites.

So…we have a lot more information on Basilosaurus, but not much in the way of explanations or answers. Perhaps that is frustrating for some. As for me, I like these new mysteries. Science is at its best when it has questions to investigate!

Citations
Houssaye A, Tafforeau P, de Muizon C, Gingerich PD (2015) Transition of Eocene whales from land to sea: evidence from bone microstructure. PLOS ONE 10(2): e0118409. doi:10.1371/journal.pone.0118409

Snively E, Fahlke JM, Welsh RC (2015) Bone-breaking bite force of Basilosaurus isis (Mammalia, Cetacea) from the Late Eocene of Egypt estimated by finite element analysis. PLOS ONE 10(2): e0118380. doi:10.1371/journal.pone.0118380

Category: Paleontology, PLOS ONE | Tagged , , , , , , | 3 Comments

What is the scientific literature used for?

For better or for worse, we paleontologists (and many other scientists) view the use and importance of the literature in terms of citations. Citations are what drives the ever-beloved impact factor, as well as other metrics such as the h-index. Indeed, this focus on citations colors many discussions on access to the literature, such as the relative importance of rapid electronic access. You’ll hear lots of statements along these lines: “If you are in the business of writing a manuscript, but don’t have access to a particular piece of literature, you can always use interlibrary loan or a similar service. Or just got to the university library next door. Patience is a virtue. It won’t kill you (or science) to wait a few extra days.”

Oh, for everyone to have a library like this on their doorstep! Or at least the electronic equivalent. Stockholm Public Library, photo by Samantha Marx, CC-BY.

Oh, for everyone to have a library like this on their doorstep! Or at least the electronic equivalent. Stockholm Public Library, photo by Samantha Marx, CC-BY.

Although I don’t completely discount this idea (indeed, we all have seen our share of PDF requests that could have been fulfilled with a few extra seconds of Googling), I think it reflects a rather anemic view of how the scientific literature is used by scientists. Citations are certainly an easily trackable mode of literature use, but (as noted time and time again by advocates of “alternative metrics”) the literature is used for more than just writing papers. Particularly in a field like paleontology, which has a strong record of public interest and public engagement, these non-citeable uses can be myriad.

So, I decided to put together a quick list of the different ways that I use the scientific literature on a day-to-day basis. In particular, I’ve noted some areas where timely (i.e., near-immediate) access is highly desirable.

How do I use the literature?

  • Background research for teaching. I teach a one month introduction to paleontology / evolution in the fossil record course for high school freshmen, and this is a topic for which there isn’t a good textbook for all of the content we cover (although Neil Shubin’s Your Inner Fish does an excellent job with talking about homology, development, and the fossil record). And even if there was a comprehensive textbook, I still want to sprinkle my lectures with examples from the literature, images from papers, and the like, as well as bring in relevant material from recent publications. Thus, I not infrequently turn to the primary literature.
  • Background research for a media interview. Every once in awhile, I’m contacted by a member of the news media to provide an opinion on a piece of new research. Although I do not generally accept interview requests for topics outside my area of expertise, even for topics within my area of expertise I sometimes want to brush up on a particular fact or research some of the context behind a particular story. For instance, I’m quite comfortable talking about horned dinosaurs–but if it’s a horned dinosaur from a place I don’t know much about, I might head to the literature to brush up on the overall context. This may or may not come up in the interview, but I want to be prepared to represent the science as accurately and completely as possible. Time is of the essence here!
  • Research for public talk. When developing a talk for a public audience (I give between 5 and 10 annually, for museums, community groups, and other events), I sometimes need to delve into a new topic. Maybe it’s to see what else has been found in a particular formation (it’s always nice to throw in “local color”), or just to understand a particular point on a related topic.
  • Reviewing manuscripts. Although I only accept review requests for manuscripts within my area of expertise, I frequently refer back to the literature to double-check claims made by the authors, suggest additional references, and refresh my memory on relevant details of anatomy, statistics, or geology. Review turnarounds are usually between 10 and 30 days, and it is not uncommon to be polishing a review a few days (or hours) before it is due. Waiting two weeks for an ILL isn’t a good use of time, or fair to the authors and editors who expect timely reviews. I’m certainly not going to drop $40 for a PDF in this case, either (particularly because publishers don’t reimburse for these kinds of expenses).
  • Reviewing grant applications. The same logic as for reviewing manuscripts applies to reviewing grants.
  • Writing manuscripts. I’ve buried this one in the middle of the list to emphasize that it is only one of many uses. There are few things more frustrating than being in the final push to finish a manuscript, and finding out there is a seemingly critical paper tantalizingly out of reach behind a paywall.
  • Identifying specimens in a museum collection. In the process of curating a museum collection, I am called upon to ensure that all of our cataloged specimens are identified as precisely and accurately as possible. In some cases, past experience guides me and others who work in the collections. However, parts of our collections (particularly historically collected ones) are somewhat outside my expertise (e.g., oreodonts and trilobites). Off to the literature! A well-illustrated paper can be invaluable for pinning down an identification. (how well some papers achieve this, though, is the topic of another post)
  • Providing information on a topic to a colleague or member of the public. At our museum, we’ll sometimes have folks drop by for a fossil identification, or we might get a question about a particular paleontological topic. If it’s something that’s outside the realm of popular books (and let’s face it, if it’s not a dinosaur, it’s probably not in a book), off to the literature!
  • Writing museum exhibit text. I am fortunate to have the opportunity to assemble temporary exhibits for my museum sometimes, focusing on fossils from our collection that tell a story about Earth’s history and our connection to it. But, I am not necessarily an expert on every fossil that I think is exhibit-worthy. So, off to the literature I go! Temporary exhibits here are frequently the result of reading or skimming at least a few papers on the topic.
  • Reference for artistic project. Every once in awhile, I’m lucky enough to work with an artist to illustrate a new discovery made by my museum and colleagues, or I am contacted by an artist who wants an opinion on a particular piece of work. My extensive photo library comes in handy, but I also rely extensively on the literature. If there’s a question about the plants found in a particular environment, or the scale pattern on the skin in a particular group, or the types of non-dinosaurs that lived at a relevant time in history, I’ll often turn to previously published work.

I’m sure I’ve probably missed something–how do you use the literature? Sound off in the comments section!

Category: Open Access, Publishing | Tagged , , , , | 5 Comments

The Open Access Dinosaurs of 2014

As we enter 2015, it’s a good time to reflect on the state of paleontology and the state of open access. Because I’m a dinosaur paleontologist (my apologies to the other 99% of life that ever lived), this post will of course address that clade in particular!

<i>Ziapelta</i>, one of the new open access dinosaurs named in 2014. Illustration by Sydney Mohr, from Arbour et al. 2014. CC-BY.

Ziapelta, one of the new open access dinosaurs named in 2014. Illustration by Sydney Mohr, from Arbour et al. 2014. CC-BY.

Thirty-eight new genera or species of dinosaur were announced in 2014 (according to my count based on a list at Wikipedia and the Dinosaur Genera List), spanning everything from sauropods to tyrannosaurs to horned dinosaurs. Seventeen of these were published in open access or free-to-read journals. This works out to around 45%.

PLOS ONE continues to dominate the world of open access dinosaur species–9/17 were published here. I will be very interested to see if this trend continues into future years, particularly as more open access journals enter publication. Seven other journals hosted open access or free-to-read papers on new taxa. These included publications hosted by professional societies, “big publishers,” museums, and the like.

You’ve probably noted by now that I’ve been parsing a difference between “open access” and “free to read.” The former category includes those that are fully BOIA-compliant; usually this means publication under a Creative Commons Attribution (CC-BY) license. This freely allows redistribution, repurposing, translation, and other uses, as long as the author is credited (interestingly, I note that many critics of CC-BY conveniently forget that authors must always be attributed). 11 out of 17 species were published under a CC-BY license. The remainder were under a variety of licenses (e.g., CC-BY-NC-SA). I will confess a certain amusement at the “NC” (non-commercial) clause, particularly when used by very much for-profit and very much commercial publishers (to their credit, a strict CC-BY license is now the default offering for NPG’s Scientific Reports).

Overall, 2014 (17/36 new taxa are free-to-read) doesn’t reflect a big change from 2013 (16/38 free to read). I would be interested to see what percentage of the overall paleontology literature (not just alpha taxonomy) is freely available–anyone up to collating this?

Full disclosure: I was an author on one of the papers naming a new dinosaur this year, and was handling editor for some of the other papers naming new dinosaurs. 

Appendix: The Data

Taxon Freely readable CC-BY? Journal
Adelolophus No No
Arcovenator No No
Augustynolophus No No
Changyuraptor No No
Daurosaurus No No
Eousdryosaurus No No
Gobivenator No No
Gongpoquansaurus No No
Kulindadromeus No No
Kulindapteryx No No
Laquintasaura No No
Mercuriceratops No No
Panguraptor No No
Pentaceratops aquilonius No No
Plesiohadros No No
Qianzhousaurus No No
Quetecsaurus No No
Rhinorex No No
Vahiny No No
Zaraapelta No No
Zby No No
Allosaurus lucasi Yes No Volumina Jurassica
Datanglong Yes No Acta Geological Sinica
Dreadnoughtus Yes No Scientific Reports
Fosterovenator Yes No Volumina Jurassica
Rukwatitan Yes No Journal of Vertebrate Paleontology
Huangshanlong Yes No? Vertebrate PalAsiatica
Anzu Yes Yes PLOS ONE
Aquilops Yes Yes PLOS ONE
Chuanqilong Yes Yes PLOS ONE
Leinkupal Yes Yes PLOS ONE
Nanuqsaurus Yes Yes PLOS ONE
Tachiraptor Yes Yes Royal Society Open Access
Tambatitanis Yes Yes Zootaxa
Torvosaurus gurneyi Yes Yes PLOS ONE
Yongjinglong Yes Yes PLOS ONE
Zhanghenglong Yes Yes PLOS ONE
Ziapelta Yes Yes PLOS ONE

Note: The taxa Camarillasaurus and Oohkotokia were published “officially” in 2014, but made their initial (pre-print) appearance in past years, so I don’t include these open access dinosaurs on the list.

Category: Dinosaurs, Open Access, PLOS ONE, Publishing | Tagged , , , , | 5 Comments