Detecting the presence of hominins in ancient soil samples

Out on the plains countless herbivores fertilise the ground by continual urination and defecation. A friend’s sheep are doing just that in the small field that came with my current home while they are keeping the grass under control.  Millions of hectares of prime agricultural land in China are kept fertile through disposal of human night soil from ‘honey wagons’ every day; it is even fed to fishes in small ponds. Such a nice economy also donates the DNA of the animal and plant inhabitants to the soil system. In 2015 analysis of environmental DNA from permafrost in Siberia and Alaska produced ‘bar codes’ for the now vanished ecosystems of what was  mammoth steppe during the climate decline to the last glacial maximum and the subsequent warming. The study revealed mammoth and pre-Columbian horse DNA and changes in the steppe vegetation, from which it was concluded that the steppe underwent regional extinction pulses of its megafauna linked to rapid climate ups and downs connected with Dansgaard-Oeschger cycles. It was but a small step to see the potential for studying distribution and timing of various hominins’ occupation of caves from the soils preserved within them, without depending on generally very rare occurrences of human skeletal remains.

Tourists at the entrance to Denisova Cave, Rus...

Tourists at the entrance to Denisova Cave, Russia (credit: Wikipedia)

The Max Planck Institute for Evolutionary Anthropology in Leipzig, now famous for extracting DNA from Neanderthal, Denisovan and possibly H. antecessor fossils, has applied the environmental DNA approach to sediments from 7 caves in France, Belgium, Spain, Croatia and Russia that span the period from 550 to 14 ka (Slon, V. and 30 others 2017.  Neandertal and Denisovan DNA from Pleistocene sediments. Science, v. 356 (online publication); doi:10.1126/science.aam9695). The sites had previously yielded fossils and/or artefacts. All of them contained mitochondrial DNA from diverse large mammals, four including archaic human genetic material supplied by Neanderthal individuals and Denisovans in the case of the Denisova cave. A key finding was Neanderthal mtDNA in one sedimentary layer that contained no skeletal remains – decay of a body was probably not involved. In two cases the DNA was from more than one individual. A variety of tests showed that surprisingly large quantities of DNA survive in soil and that it is spread evenly in sediment rather than being present in spots – an indication of derivation from urine, excreta or decayed soft tissue.

Although the study does not add to knowledge of hominin genetics, it confirms that the methodology is sufficiently advanced and efficient to detect hominin presence in fossil-free sediment. So this approach seems set to become a standard for many sites, such as that from California reported in the previous post, which suggest a human influence, or any cave sediments for that matter. Although skeletal remains are essential for reconstruction of bodily characteristics, hominin phylogeny seems set to cut loose from fossils. Hitherto suspected species’ presence in the time period where DNA analysis is feasible may be detected, such as Asian H. erectus. It may become possible to map or extend the geographic ranges of Denisovans and Neanderthals. Perhaps species new to science will emerge.

More on late Pleistocene hominin genetics here

Wade, E. 2017. DNA from cave soil reveals ancient human occupants. Science, v. 356, p. 363.

Wade, E. 2017. DNA from cave soil reveals ancient human occupants. Science, v. 356, p. 363.

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One response to “Detecting the presence of hominins in ancient soil samples

  1. Hello Steve, I wonder if you could help me. I’m from austwick and doing a drawing project on Norber. I used to teach for the open university. One summer when I was lecturing on a summer school an open lecture caught my eye. It was about the geology of the North Yorkshire Dales. The lecturer talked about Malham and the surrounding dales having once been part of Africa, breaking off and joining on to the British Isles. Does this make sense?. Do you have any idea who this geology lecturer could have been at the open university in about 1984 and what I could read about this? many thanks, sue

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