The Problem of Modern Contamination at Fossil Sites


When uncovering preserved fossils, the idea has been that what is found is indicative of the organism and its ancient environment – if it is studied, the fossil will provide clues to help discern information about the past.  A recent study showed that the remnants can sometimes be contaminated by modern microbes, which should be kept in mind when analyzing the specimen.  The microorganisms can overtake the fossilized structures even while underground, before the digging takes place.

Fossil (illustrated)

There are techniques to deal with contaminated fossils – for instance, radiocarbon dating of the specimen can still be achieved by removing only one of the amino acids from the collagen present in the bone (Malewar, 2019, para. 5).  Human DNA from scientists can also taint the fossilized structures and obfuscate the accuracy of the results.  While there are methods to help clean up the microbial infiltration, removal of human DNA contamination remains a challenging problem (Korlević et al., 2015).

Unfortunately, in most cases, the relative abundance of contaminant DNA is much greater than that of the target organism (Korlević and Meyer, 2019).  To address this problem, the invasive DNA can be taken out of the specimen via chemical or enzymatic processes, and then, the DNA from the fossil can be analyzed separately (Korlević et al., 2015).

The goal is the accuracy of dating and true analysis of the DNA of the fossilized specimen, without corruption from modern-day microbes, which can break down the structures during decomposition, and human DNA, which can contaminate the fossil during excavation and handling.

Amit Malewar (2019, January 30).  Ancient Mongolian skull is the earliest modern human yet found in the region, Tech Explorist, Retrieved from

Petra Korlević, Tobias Gerber, Marie-Theres Gansauge, Mateja Hajdinjak, Sarah Nagel, Ayinuer Aximu-Petri and Matthias Meyer (2015).  Reducing microbial and human contamination in DNA extractions from ancient bones and teeth, Biotechniques, 59 (2), 87-93.

P. Korlević and M. Meyer (2019).  Pretreatment: Removing DNA Contamination from Ancient Bones and Teeth Using Sodium Hypochlorite and Phosphate, Methods Mol. Biol., 1963, 15-19.  

Sanne Boessenkool, Kristian Hanghøj, Heidi M. Nistelberger, Clio Der Sarkissian,  Agata T. Gondek, Ludovic Orlando, James H. Barrett, and Bastiaan Star (2016).  Combining bleach and mild predigestion improves ancient DNA recovery from bones, Mol. Ecol. Resour., 17 (4), 742-751.

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