Zooarchaeology by mass spectrometry

Science is continually developing new methods to coax evidence from archaeological finds. Professor of Archaeological Science and Deputy Director of the Oxford Radiocarbon Accelerator Unit Tom Higham explains ZooMS – a technique that has been adapted to identify human bone fragments – and how it has been used with the multiple bone fragments found at the Denisova Cave.

Update

Further to this lecture, the small bone identified as human was confirmed as belonging to a Neanderthal. Read about the process on the PalaeoChron blog or in the published paper Identification of a new hominin bone from Denisova Cave, Siberia using collagen fingerprinting and mitochondrial DNA analysis.

Transcript

PROF TOM HIGHAM

The hunt for fossils goes on, but it’s going on in a really intriguing way. This is my PhD student Samantha Brown, who is working in Oxford, and we’re using a revolutionary technique that was developed by a colleague of mine called Michael Buckley in Manchester University, and it’s called ZooMS, which means zooarchaeology by mass spectrometry. To cut a very long story short, all animal bones contain slightly different sequences of proteins and peptides in them, which correlate to species. So if you can measure these, you can get a kind of a fingerprint. So you can identify bones based on these protein sequences. So here, for example, this one – this sequence here belongs to a human. And this one – you can see it’s very different – belongs to a reindeer, and here, a hyena.

Now at Denisova Cave, 95% of the bones are unidentifiable. They’re tiny fragments because they’ve been chewed up and eaten by animals like hyenas, and as a result, archaeologists can’t identify them. No one can say, “Oh look. This is a piece of a hyena,” because it’s too fragmented. Some of the bones can be identified, but these are the bigger ones, and they’re comparatively rare. So what we’ve been doing is using this technique of ZooMS, which allows you to take a tiny amount of the bone, measure the abundance of these different peptides and put an identification on the bone.

Now why are we doing this? Because the bone is so well preserved, if we can find even a fragment of the bone that could be a human, we can get a genome, and then we can get all this amazing information about the relatedness and the population histories of these people. So 2 months ago, after analysing 2,513 bones – poor Sam, took her months – found this tiny little 2.5 centimetre bone completely unidentifiable. We’ve just got the result from Leipzig. Its mitochondrial DNA analysis tells this is very highly likely to be a Neanderthal. So this tiny little bone, very well preserved, it could give us another genome, which is extremely useful information, because it tells us a lot about the relationships between these people. We’ve dated this, and it’s about – we think it’s about 80,000 years old.

The Science Learning Hub would like to acknowledge: Professor Tom Higham, University of Oxford The Allan Wilson Centre for Molecular Ecology and Evolution Images of Sam in lab, courtesy of Samantha Brown, University of Oxford Bag of bone fragments from Denisova Cave, Professor Tom Higham, University of Oxford Hominin bone fragment image, Identification of a new hominin bone from Denisova Cave, Siberia using collagen fingerprinting and mitochondrial DNA analysis. Samantha Brown, Thomas Higham, Viviane Slon, Svante Pääbo, Matthias Meyer, Katerina Douka, Fiona Brock, Daniel Comeskey, Noemi Procopio, Michael Shunkov, Anatoly Derevianko and Michael Buckley. Scientific Reports 6, Article number: 23559 (2016). doi:10.1038/srep23559