Using light to describe the ancient world

Archive for the ‘Near Infrared’ Category

Near infrared scanning for ancient DNA

Near infrared spectroscopy could be useful for detecting ancient DNA in fossil bone.

Deoxyribonucleic acid (DNA) is very rarely preserved in fossil bone. The fossil record for soft tissues is incredibly sparse, and the recovery of ancient DNA (aDNA) generally requires highly specific preservation conditions. Like most rare treasures though, the benefits of finding aDNA are immense: relationships between living and extinct groups can be established (e.g. Baker et al. 2005) and reconstructions of once living organisms can be entertained (e.g. Jurassic Park). The importance of aDNA is embodied in the Australian Centre for Ancient DNA, an entire research centre at the University of Adelaide dedicated to its study (prospective PhD students should check out this link). Finding aDNA is a difficult task, and one that would benefit from a rapid, non-destructive technique. Like near infrared spectroscopy.

Near-infrared (NIR) spectroscopy is most useful for characterising compounds constructed from light atoms, like soft tissues, which are mostly carbon, hydrogen, oxygen and nitrogen. In contrast, NIR is less adept at detecting bone mineral, which contains abundant calcium and phosphorus. This combination of these positive and negative biases makes NIR a potentially useful technique for finding aDNA. Bone mineral is essentially invisible with NIR spectroscopy, but soft tissues stand out like beacons. Ancient DNA may be found alongside collagen, the organic scaffold on which bone mineral is deposited, which is readily detectable with NIR. Further, entire surfaces of bones can be analysed with NIR using hyperspectral imaging. In essence, NIR hyperspectral imaging could be used to rapidly screen fossil bones for aDNA: surfaces of fossil bones could be mapped, allowing regions with telltale signs of preserved soft tissues to be identified.

For more detail on the prospective uses of NIR hyperspectral imaging in paleontology, check out my recent article in NIR News.


Thomas DB. 2011. Illuminating fossils by NIR. NIR News 22: 6-8.

Baker AJ, Huynen LJ, Haddrath O, Millar CD, Lambert DM. 2005. Reconstructing the tempo and mode of evolution in an extinct clade of birds with ancient DNA: The giant moas ofNew Zealand. Proceedings of the NationalAcademy of SciencesUSA102: 8257-8262.


Hyperspectral near infrared mapping of fossil bone

Pleistocene horn cores from bovids (like the springbok shown here) were recently analysed using hyperspectral near infrared imaging. We were able to make spectral maps of the horn cores, and determine that the bones had been exposed to a substantial groundwater flow. Might this be bad news for isotope studies of these fossils? We shall have to find out.

Spectra can be richly informative, as I have hopefully shown in earlier entries. Take any fossil, position it under the spectroscopic instrument of your choice, and you will likely be rewarded with some otherwise invisible information. X-ray diffraction will reveal mineralogy, x-ray fluorescence will give chemistry, mid-infrared and Raman will give ionic composition. Most of the time, the information couldn’t be gleaned from that spot on the fossil using any other method. And most of the time, spectroscopic techniques reveal information about a single spot per analysis.

In the surge of every advancing technology, spectroscopic instrumentation is moving beyond single spot analyses and entering an era where entire surfaces are rapidly mapped. An example of this is hyperspectral near infrared imaging. We have recently published results from a SisuChema imaging system, administrated by Professor Alvaro Viljoen of the Tshwane University of Technology in Pretoria, South Africa. Using this instrument, we were able to collect near infrared spectra from the surfaces of Pleistocene bovid horn cores. Thousands of spectra. The instrument collected roughly 1000 spectra every square millimetre, across a 10 mm wide transect. By taking multiple transects we were able to prepare detailed maps of the horn cores that showed exactly where certain near infrared wavelengths were absorbed. Why was that important? The hyperspectral NIR maps revealed the suffusion of ancient groundwater.

A NIR spectrum of fossil bone is generally uninformative. Near infrared is only really useful for materials made from the lightest elements, which fortuitously includes carbonates and clays. The hyperspectral maps revealed that secondary minerals had been deposited deep inside the tiniest pores and cracks in the bovid horn cores, meaning that a substantial amount of groundwater had flowed into and through the bones. Groundwater is the agent of diagenesis, which means that these fossil bones may no longer carry vital information. The fossils we chose to study are from a suite of sites where geochemical signals have been used to understand the ancient environment. If anything, our data show that these sites may not be giving trustworthy answers. Our next step is to study the isotopic compositions and histology of these bones, to determine whether groundwater has stripped away any analytically useful signals.

So, hyperspectral NIR mapping of Pleistocene fossil bones is a great way to assess whether they have been diagenetically altered.

Thomas DB, McGoverin CM, Chinsamy A, Manley M. 2011. Near infrared analysis of fossil bone from the Western Cape of South Africa. Journal of Near Infrared Spectroscopy 19:151-159.

NIR 2011

The 15th International Conference on Near Infrared Spectroscopy is being held in Cape Town this week. Yesterday I presented work from a forthcoming publication, where we used NIR to study burial history. Two other talks describing NIR of minerals were also presented, demonstrating just how powerful this spectroscopy could be for the paleosciences. Part of the reason that NIR has not attracted a lot of attention by the paleoscience community is that bands in the NIR region tend to come from light elements, which are not large components of bone mineral. There are plenty of light elements in secondary minerals though, which I think is where the focus should be. So, instead of studying bone mineral with NIR, we instead study burial history of bone from mineral composition. Given time, I think we will see some interesting fossil applications from NIR spectroscopy

E.T. Stathopoulou, V. Psycharis, G.D. Chryssikos, V. Gionis and G. Theodorou, “Bone diagenesis: new data from infrared spectroscopy and x-ray diffraction”, Palaeogeogr. Palaeocl. 266, 168 (2008). doi: 10.1016/j.palaeo.2008.03.022

Thomas, DB, McGoverin, CM, Chinsamy A. and Manley, M. 2011.Near infrared analysis of fossil bone from the Western Cape of South Africa. Journal of Near Infrared Spectroscopy. In press.


I have just found out that I will be presenting a talk at NIR2011 in Cape Town (13-20 May). NIR2011 is an international conference that will showcase all of the latest research in the field of near infrared spectroscopy, including unusual applications like fossils.  I am going to be talking about Near infrared spectroscopy of fossil antelope bone from South Africa. Find out more from the conference website (, or you can email Professor Marena Manley ( or Ms Deidre Cloete ( for more information, including registration details.

Near infrared spectroscopy of fossil antelope bone from South Africa

Daniel B. Thomas­, Cushla M. McGoverin and Anusuya Chinsamy­

Introduction: Raw materials for constructing bone are supplied by food, water and air, and are ultimately sourced from the external environment. Bone chemistry consequently records the living environment of an animal, and such information may persist after death and into the fossil record. Chemical alteration of bone during burial (diagenesis) may erase the life history signals from fossil bone, however, severely reducing the analytical utility of fossil material. We have used NIR spectroscopy to screen fossil bone for signs of diagenetic alteration.

Materials and methods: Fossil antelope bone from the Western Cape of South Africa was studied using two instruments: 1) large sample volume (bulk) measurements were collected using a Spectrum IdentiCheck FT-NIR, and 2) low sample volume (hyperspectral, chemical imaging) measurements were collected using a sisuChema short wave infrared imaging system.

Results and discussion: Bulk NIR spectroscopy indicated that secondary minerals had been deposited within the fossil bone. Fossils from different sites could be distinguished by secondary mineralogy, where bone from coastal Swartklip 1 featured calcium carbonate (calcite), and inland Elandsfontein Main exhibited clay mineral infill. Hyperspectral NIR spectroscopy allowed the distribution of secondary minerals to be mapped. Both clay and calcite were concentrated in cancellous spaces, as the residue of deeply infiltrating pore water. Water is the primary agent of diagenetic alteration, and NIR data indicated that the fossil antelope bones had been saturated.

Conclusions: NIR spectroscopy provided evidence for ancient pore water movement through fossil antelope bone. Different secondary minerals had accumulated inside bones from different sites, and informed of different palaeoenvironments. We found NIR spectroscopy to be a useful tool when screening fossil bone for evidence of diagenetic alteration.

Novelty statement: NIR data collected from fossil antelope bone provided evidence for ancient pore water suffusion. NIR represents a new, non-destructive tool for studying bone diagenesis.

Summary statement: Large and small sample volume near infrared spectroscopic data were collected from fossil antelope bone. Fossils from different sites were distinguished by secondary mineral deposits, which were found concentrated in cancellous spaces. Secondary minerals represent residues of ancient pore waters that would have suffused the fossil bones.

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