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Author Interview: Justin Adams on a New Digital Fossil Archive (Part 1)

Skull of the ancient cat Dinofelis piveteaui, now digitally available. Modified from Adams et al., 2015, CC-BY.
Skull of the ancient cat Dinofelis piveteaui, now digitally available. Modified from Adams et al., 2015, CC-BY.

As a digital fossil buff, I’m always excited to learn about new efforts for serving 3D fossil data. Thus, a recent PLOS ONE paper by Justin Adams and colleagues definitely caught my attention. In short, they announce the availability of surface and CT scans for a variety of fossil mammals housed at the Ditsong National Museum of Natural History in South Africa. Monkeys, hyraxes, elephants, warthogs, and more are in the database, with a focus on the holotypes and paratypes in the collection.

In an effort to learn a little more about the project, I had an email Q & A with senior author Justin Adams. Part 1 is posted here–Part 2 will be coming up tomorrow.

Q: What spurred your involvement with the project?

A: It really began as one of those ‘Wouldn’t it be great?’ conversations with colleagues during my annual excavation/museum collections fieldwork to South Africa in 2014. I have been conducting excavations and/or working in the country pretty much continuously since 2002, and have been collecting a lot of data (typically a lot of linear metrics, photos, etc.) on non-hominin faunas over that entire period. Prior to the 2014 season I had acquired an Artec Spider surface scanner with funding from my Department (Department of Anatomy and Developmental Biology at Monash University, Australia) and had brought it down to generate some surface data for a research project.

As we progressed through the season with both the surface scanning and acquiring microCT datasets, we realised we had an opportunity to do more than just address our own research goals. As we all know, data collection can be expensive, time consuming, requires specialist equipment, sometimes requires transport of fossils to do tomographic work, etc. Since all of the specimens we were working with have been in the literature for decades, there was really no reason for us to go through this process only to have other research teams have to repeat the same financial and time investment to gather the same type of data.

We ultimately realised that we could accomplish a series of ‘Wouldn’t it be great’ ideas if we took all of the data we were gathering that season and expanded our efforts (quite a bit actually!) into a separate digitisation initiative. For one, there has not been a single catalogue published that listed all of the Plio-Pleistocene mammal type and paratype specimens held in the Ditsong collections; nor has there been a resource that pulled together all the primary and secondary citations on the specimens or the evolving (and occasionally messy) taxonomic attributions of specimens over the decades. For another, many of these specimens have been previously published with only very basic linear metrics, simple line drawings or a few standard photos; and the more fragile specimens have never been molded or cast to facilitate research outside the Museum.

But the biggest impact we felt could come from this is encouraging more integration of the Ditsong collection specimens into research projects at a time when grants in palaeobiology (and overall) are getting harder and harder to obtain. We know that the data we are providing won’t satisfy every research need, but if it can provide pilot data to improve the chances of grant success or improve the impact of a palaeobiological analysis then that’s to the benefit of the entire research community.

Skull of a prehistoric warthog, Phacochoerus antiquus. Modified from Adams et al., 2015, CC-BY.
Skull of a prehistoric warthog, Phacochoerus antiquus. Modified from Adams et al., 2015, CC-BY.

Q: What particular challenges did you face in assembling these data? How did your group overcome them?

A: There were certainly a few bumps along the road. The first big decision was where to draw a line to consider the project ‘complete’ enough to describe and announce. The Ditsong Plio-Pleistocene Section essentially houses the largest collections of fossil mammals in South Africa, so we decided to limit ourselves to producing surface scans of the type and paratype specimens that are currently stored in the Vault (‘The Broom Room’ after Robert Broom) so as to not be collecting data for decades. Because the baseline data for all the specimens was acquired using a surface scanner, there were many specimens with deep undercuts and internal contours that required a lot of very careful data acquisition to ensure we didn’t miss critical anatomy in the final meshes.

The most surprising challenge for me was overcoming a bit of possessiveness about some of the tomographic data in the archive that I originally acquired for my own research (that I haven’t quite finished working with or submitted as manuscripts yet). If anything it’s a good motivation tool to finish up my analyses! But really, it’s been a shift in how I think about data access and it’s informed my practices for my research projects. For example, I lead excavations at a historically primate-rich site in South Africa called Haasgat and last year (thanks to the generosity of the Leakey Foundation) my team recovered some very nice extinct baboon and colobus monkey specimens. We are moving to publish those in early 2016 and we will be making surface and tomographic datasets available with the initial descriptions and photographs so they are immediately accessible to other researchers.

Get ready…Part 2 is coming up tomorrow! In the meantime, you can check out the DNMNH Archive Page or the data posted on MorphoSource.

Adams JW, Olah A, McCurry MR, Potze S (2015) Surface Model and Tomographic Archive of Fossil Primate and Other Mammal Holotype and Paratype Specimens of the Ditsong National Museum of Natural History, Pretoria, South Africa. PLoS ONE 10(10): e0139800. doi:10.1371/journal.pone.0139800

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