Gomphotheriid Toes and Woes: A Call for More Proboscidean Postcrania Studies


A herd of Rhynchotherium make their way across the landscape (Wikimedia Commons)

In 1999 the partial left and right manus of an extinct gomphotheriid, a relative of modern elephants (Order: Proboscidea), was discovered in a silty sandstone layer in Arizona from the 111 Ranch locality. The fauna from this site are between 2.3 and 2.47 Ma, making this find early Pleistocene in age.

Figure 1: Location of 111 Ranch, from Pasenko 2014

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Holding Hands with Plateosaurus

“Holding Hands with Plateosaurus” is a guest post brought to us by Heinrich Mallison, who recently published an article in PE along with co-author Stefan Reiss. Mallison has also been a long time contributor to the PE blog and my thanks go out to him for helping me get set up with the PE blog. You can find this piece and more by Mallison at his personal blog, dinosaurpalaeo.

Articulated, CT-scan based digital scans of the left hand of Plateosaurus engelhardti specimen "GPIT Skelett 2" in the PLSST in dorsal view. From Reiss and Mallison, 2014.

Although I did not start my professional career in palaeontology as a dinosaur researcher, but (can you believe it?) as a palaeobotanist, the Upper Triassic basal sauropodomorph dinosaur Plateosaurus engelhardti from Central Europe has been accompanying me for a very long time. When I started my studies of geology/palaeontology at the University of Tübingen, two mounted skeletons stood in a second floor hall of the institute, which triples as a lecture hall, office and museum building. These mounts, erected under the direction of Friedrich von Huene, still stand there today, although (thanks to a new curator) the room looks much nicer: the window had been bricked over, but has by now been restored.

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A Fossil Bird from Poland: Another Piece in the Passerine Evolutionary Puzzle

Specimen ZPALWr. A/4005 from SE Poland

  Look out the nearest window and try and spot a bird. While the PE blog audience is joining me from multiple continents and environments, it’s likely that no matter where you are, the bird you see is in the order Passeriformes. This order includes more than half of all extant bird species in the world, including the well-known songbirds.  What makes a bird a member of the Passeriformes order? There are a bunch of technical, complicated characters that distinguish passerines from other birds, but one feature that is significant has to do with the arrangement of the toes. Passerines have an anisodactyl arrangement of toes, meaning that three digits point forward while one lone digit (hallux) points backward.

Toe arrangements in birds (anisodactyl in upper left corner).

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Camel Ankle Bones: The Secret to Productive Procrastination and Understanding Global Processes

Back in December Edward Davis and Brianna McHorse published a paper in Palaeo-Electronica (PE) about using astragali to identify camel genera from the Thousand Creek locality in Nevada. They have written their own blog post about this research, which can (and should) be read here; though I’ve included an excerpt from their blog to introduce their research to the PE blog audience:

“Many Miocene fossil sites are full of camel ankle bones (and ankle bones of other animals, too, but you have to start somewhere!). Ankle bones are small, compact, and extremely durable. They are also in a part of the animal that doesn’t have much tasty, tasty meat. As a result, they often escape significant damage from banging against rocks during transport before burial or by scavenging…

…Most fossil mammals are identified by looking at details of the skulls and teeth. At some sites, like Thousand Creek in Nevada, skulls are extremely rare but ankles and other foot bones are super common. If we want to know what camels lived in Thousand Creek 8 million years ago, skulls are not enough. Instead, we need to be able to identify all of these ankle bones. At a basic level, this lets us know what kind of camels lived there, but that’s important for more than just paleontological trivia. Those little bits of data go into larger-scale studies of evolutionary and ecological dynamics. Each time we increase our knowledge of a single fossil site, we add another brick to the foundation of our largest-scale analyses, improving our ability as a species to predict how our earth’s fragile ecosystems will behave as we turn up the thermostat.”

So how do you identify ankle bones?

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The last of a lineage of giants: A blog post in both Spanish and English

This is a piece about the recent Iberian gomphothere paper published earlier this month in Palaeo-Electronica. This is Amy Atwater’s  first post as the new publicity editor for PE and she is pleased to share the following guest post by authors Guiomar Garrido and Alfonso Arribas. Seeing as the authors are both Spanish speakers, it was decided to post their blog piece in both Spanish and English.

El último de un linaje de gigantes: historia del descubrimiento de Anancus arvernensis mencalensis

El contexto geográfico y geológico

Como suele ocurrir, también en esta ocasión el azar, o la conjunción de casualidades, resultó ser uno de los factores más decisivos a la hora de avanzar en el conocimiento de los seres vivos que poblaron nuestro planeta hace miles o millones de años. Corría el mes de julio del año 2006 cuando, bajo un sol abrasador, los paleontólogos del Proyecto Fonelas realizábamos una campaña de prospección con el fin de localizar nuevos yacimientos en el desierto de Guadix, situado en el sureste de España.

Desierto de Guadix (en el sureste de España)

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zotero style updated

The new zotero 3.0 comes with updated styles, but the conversion caused some errors. Furthermore, the changes we made to the PE style had not been implemented. That’s all fixed now, and you can get the new, correct style here (zip file, 9 kb). On the zotero site it will also soon be available.



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SPIERS and VAXML – lowering barriers to the adoption of Virtual Palaeontology

This post is a 3-in-1 on Carboniferous arthropods, CT data of them, and a free program for handling such data. It covers three papers just published in PE, and was written by two of the the authors, Mark Sutton and Russell Garwood. I have added a comment on the text (in italics and inset paragraphs), regarding the Virtual Palaeontology computer program described in one of the papers.

Virtual Palaeontology is a set of techniques for working with three-dimensionally preserved fossils in the digital domain – essentially as three-dimensional interactive on-screen models (virtual fossils). Fossils can be digitised into three-dimensional models in a variety of ways, but the most important of these are tomographic (based on serial slices, either from machines such as CT scanners or from more traditional techniques such as serial grinding). Turning slices into three-dimensional models is not a straightforward process, and requires dedicated software – while appropriate packages do exist, few are free, and none are tuned to the needs of palaeontological data, which is often noisy and complex. In a new PE paper published in May 2012, Sutton et al. introduce the SPIERS package (software website) which is aimed at filling this gap with a free, multi-platform software toolkit for converting slice-images from any source into three-dimensional models. SPIERS is carefully and extensively documented, flexible in approach, and designed to run on everyday computers. It has already seen extensive use in the study of the invertebrate fauna of the Silurian Herefordshire Lagerstatte (see e.g., Briggs et al. 2008, Sutton et al. 2011), as well as for micro-CT based studies (e.g., Garwood et al. 2011, Sutton & Sigwart 2012). SPIERS has already made informal inroads within the palaeontological community through a process of osmosis and direct contact with its authors; its formal launch should help increase the uptake of these techniques within our science.

Figure 2 of Garwood and Sutton (2012), showing fossil examples of the genus Camptophyllia, the guinea pigs for the presentation of SPIERS.

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Blog downtime is over

This place has been quite as a grave for a long time. That downtime was caused by a number of factors, most significantly the simple fact that I was totally overworked, and that my blogging time went to my own, personal blog.

Additionally, PE was totally revamped, and a lot of papers came out of our backlog caused by last year’s special issue. Add to that a number of papers where authors’ revisions took a long time, which also made it to publication, and there simply was very much work to do for all involved, including the style editors, Daniela Schwarz-Wings and me.

Now, though, I hope to revive the blog, with a series of overdue articles.


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The Systematics of Strange Turtles

This is a guest post by Natasha S. Vitek, author of the article Giant fossil soft-shelled turtles of North America that recently was published in PE. For some reason, the scheduling feature didn’t work, and I didn’t notice, thus the late publication.

Soft-shelled turtles are strange. Over the long course of evolution, they’ve lost the outer, keratinous, layer of their shell. With the exception of one clade they’ve lost the peripheral bones on the outer ring of their shell. These and other morphological oddities make soft-shelled turtles a compelling study animal.

Florida softshell turtle (Apalone ferox),
image from wikipedia under license specified there.

A look into previous research about the fossil record of soft-shelled turtles reveals a lot of confusion. Parallel evolution and high levels of variation within species are common. Although these features might someday make soft-shelled turtles ideal for studying particular evolutionary patterns, they pose a serious challenge for scientists seeking to untangle the history of the group.

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Art, science, and early tetrapods

This is a guest post by Julia Molnar, lead author of the latest technical article in PE.

In this blog post, I summarize our recent paper for Palaeontologica Electronica, write a little bit about my research, and show some pretty pictures of tetrapods.

The paper

In this methodology paper, I explain a 3D modeling technique and how it can be applied to paleontology. Have you ever thought to yourself, “Wow, these scan data look terrible. I wish I knew some way to fix my data up a little bit without making it all up”? If so, you should take a look at our article on idealized models from scan data. The technique is borrowed from 3D animators, who know an awful lot about manipulating meshes. To give you an idea of what it’s about, here’s an image of the scan data, a 2D reconstruction by Coates (1996) showing what it’s supposed to look like, and a picture of the 3D model I made from the scan data.  The procedure is really simple, and anyone can learn to do it.

Micro-CT scan of Acanthostega vertebra segmented in Materialise Mimics software


2D reconstruction (Coates 1996)

Idealized model created in Autodesk Maya


Our research

This modeling technique was actually an unexpected outgrowth of my research on early tetrapod biomechanics with my co-authors, Stephanie Pierce, Jenny Clack, and John Hutchinson. Readers who are familiar with the field will know that decent (three-dimensionally preserved and complete) early tetrapod fossils are hard to come by, especially for postcranial anatomy. This helps to explain why so few people are working on early tetrapods in 3D! I pursued this topic in order to solve the problem of making good bone models to put into our other software for biomechanical analyses we’re doing.

Regardless of the difficulties, our long term aim is to build complete 3D models and simulations of the biomechanics of locomotion in early tetrapods. The goal is to examine how their musculoskeletal functions changed as they transitioned from aquatic to terrestrial modes of life. What was the first vertebrate to walk on land? How did it move? Did it resemble any modern animal(s), and if so, which one(s)?

To do this, we needed a method that would make 3D objects from partial scan data (often 2D-ish, from flattened or obscured slab specimen), and we needed to test how reproducible that method was—do subjective errors and investigator biases mean that no one can reproducibly reconstruct 3D morphology from such limited data (even, in the worst case, the same person if they repeat the whole process 5 times)?

Here’s the method we came up with: First, pick important points on the scan data that you want to make sure are reproduced faithfully in the model. Second, draw a grid on the surface of the model connecting your points. Third, use your grid to construct a smooth spline surface that follows the contours of the scan data while smoothing over any holes or rough bits. Finally, adjust your model to your heart’s content using a few control points. Simples!

We tested the method by having myself, Stephanie, and John each repeat the process 5 times, and used geometric morphometrics software to compare the resulting models made by each investigator. Thankfully, it worked out great for all investigators—we produced models that were statistically identical and repeatable. What’s more, the morphometrics were almost identical to the original data. Hurrah! That’s no small feat for paleontology; our colleagues in our lab even had scoffed about the poor likelihood of such an outcome. So I guess we showed them, and that’s a nice bonus for paleobiologists interested in 3D visualization methods. We encourage more researchers to check the biases in their 3D methods to ensure their morphology-based models are on sound footing. We all win by doing that—and the results are quite publishable!

Scientific visualization

Having spent two years studying medical illustration before entering the research field, I am passionate about the importance of good visuals. I believe that it’s important to try to make illustrations that are as accurate as possible, and to make it clear to the viewer which parts are made up. Scientific illustrations are more than just window dressing for papers and presentations – they are a very effective way of communicating our ideas, especially to people working in different disciplines.

The great thing about Palaeontologica Electronica is that it actively encourages scientists to share images, animations, and 3D models in a peer-reviewed journal. Publishing in PE allowed me to include lots and lots of colorful images and animations, including videos to make the procedures clear to people who aren’t familiar with the software.

OK, thanks for sticking with me to this point. As an extra reward, here are some gratuitous illustrations of early tetrapods. Enjoy!

Life reconstruction of Acanthostega

Life reconstruction of Pederpes

Life reconstruction of Crassigyrinus

Life reconstructions of various microsaurs

(All images ©Julia Molnar 2011)


Coates, M. 1996. The Devonian tetrapod Acanthostega gunnari Jarvik: Postcranial anatomy, basal tetrapod interrelationships and patterns of skeletal evolution. Transactions of the Royal Society Edinburgh Earth Sciences, 87:363–421.


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