Inside the Archaeology of Paleofeces

Ancient Poop Science: Inside the Archaeology of Paleofeces

Alasdair Wilkins 

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The invention of the toilet accomplished many good things, but it did rob us of the chance at immortality - through our poop. Ancient humans have revealed some of their greatest secrets through paleofeces, the study of the waste they left behind.


Image via Democratic Underground

In studying ancient humanity, there's no more powerful resource than preserved DNA... theoretically. While DNA has evolved to be the molecule of life, it's not built nearly as well to stick around after its organism is dead and gone. There are a few ways to preserve DNA for up to as much as a million years without complete degradation, but these mostly involve being frozen in ice or permafrost. Since most of humanity historically has stayed away from extremely cold climates, that naturally limits our sources of usable ancient human DNA.

That's where poop enters the picture. As one of the great works of Western literature once so cogently observed, everybody does it — and in the 99% or so of human history without sanitation services, humans pretty much just pooped wherever there was space. These "nonhardened fossils", as archaeologists have euphemistically referred to them, account for a shockingly high percentage of the material found in ancient cave sites. There's such a ridiculously high quantity of preserved human poop — paleofeces, if we're being technical — that being able to extract any amount of DNA would make them a massively useful resource.

Luckily, the dry, cool conditions of these caves provide workable conditions to preserve DNA for posterity, and the paleofeces provide the carrier that protects the DNA on its journey into history. The ancient dung can hold onto recoverable DNA through a process known as the Maillard reaction. As the feces dried out all those thousands of years ago, the sugars from the digested plant material began to react with surrounding amino acids, forming larger sugar compounds that formed around and encased the DNA, preserving it for future extraction. This same chemical reaction is crucial today in the coloring and flavoring of a bunch of foods, including French fries, biscuits, maple syrup, and brioche.

A 2005 article in Current Science recounts the simple, five-step process to extract DNA from poop. All you need is some liquid nitrogen, a diabetes drug, and a polymerase chain reaction machine... oh, and some preserved dung, of course. Freezing the samples in the liquid nitrogen allows them to be ground down to a fine powder, although the individual grains are still significantly bigger than the individual sugar and DNA fragments.

Next, the diabetes drug, which is designed to help people control their high blood sugar, is used to break down the sugar compounds surrounding the DNA. The chain reaction machine is used to make millions of copies of the recovered DNA, which can then be sequenced and compared to other DNA fragments from different sources, such as bones found at the same site. This is useful in establishing the accuracy of the sequencing and ensuring that degradation hasn't robbed the DNA of the useful information it once contained.


The first successful recovery of DNA from poop came in 1998, when Hendrik Poinar and Svante Paabo, at the time scientists at the Max Planck Institute in Munich, released DNA left by now-extinct ground sloths some 20,000 years ago. Poinar, who has since become one of, if not the leading expert in the archaeology of poop — though I'm guessing he wouldn't phrase it quite like that — then had similar success with dung samples from an extinct goat species and another ground sloth species. But these were all just examples of animal crap, which are called coprolites to distinguish them from the human paleofeces.

The big breakthrough in human DNA extraction came with the arrival of Kristin Sobolik, and archaeologist at the University of Maine Orono, who proposed Poinar and his colleagues test some of the thousands of paleofeces specimens found in Hinds Cave (pictured up top), an ancient dwelling in southern Texas whose preserved poop samples date from 8,500 to just 500 years ago. Using the method outlined above, the researchers tested five small samples dating between 400 and 100 BCE.

Their remarkable results are recounted in a July 2000 article in Science:

Poinar pulled out human mitochondrial DNA and found sequences, called haplogroups, that are known to be Native American. (An independent lab has replicated the findings.) The group next extracted chloroplast DNA, from which they matched sequences to buckthorn, acorns, sunflower, a shrub called ocotillo, and a kind of nightshade, probably wild tobacco. Sobolik examined the samples under a microscope but could see no remnants of these plants. (On the other hand, cacti and rodents found by Sobolik did not show up in the molecular analysis.) Both the DNA and visual methods identified traces of legumes, yuccas, and elm, which may have been used to brew tea.

The paleofeces also contain visible bones of pack rats and mice, as well as fish scales. Poinar didn't find DNA from these, perhaps because the samples that he tested lacked the tiny bone fragments. However, he did find sequences for sheep and pronghom antelope, bones of which have not been found in Hinds Cave. That suggests that the large game was killed and eaten elsewhere, Poinar says.

That's just an absurd amount of information, and it's almost all from the poop. Indeed, this is part of why paleofeces are such a powerful archaeological tool - they don't just reveal the DNA of a single organism, as bones would, but instead they give you the DNA of the organism and all the things it ate. In this case, it helped reveal the incredible diversity of foods eaten by these ancient hunter-gatherers, which is a vital fact of their existence that would have otherwise remain hidden from the view of archaeologists.

Indeed, the prevailing view before Poinar and Sobilik's work was that these ancient humans subsisted on a poor diet heavily dependent on foraged berries. On the contrary, one of the samples contained evidence of four different animals and three different plants, all of which had been eaten in the two days or so before defecation — I suspect a worrying percentage of modern poop couldn't match that kind of nutritional diversity. And thus, an ancient truth was poop.

There's really only one final, vital question left to consider, at least as far as I'm concerned — does ancient poop smell? Kristin Sobilik addressed this all-important question in a 2008 interview with the magazine Odyssey. The dried poop itself has no particular smell. The organic compounds that give poop its odor are encased inside the sugar compounds alongside the DNA — which means that the process of extracting the DNA can also mean releasing the poop smell of somebody who lived thousands of years ago. Now if that isn't leaving a legacy to future generations, I really don't know what is.

Hinds Cave and Coprolite images by TAMU Anthropology Archives and Glenna Williams-Dean.


"Extraction of DNA from Paleofeces" by Melanie Kuch and Hendrik Poinar
"Divining Diet and Disease From DNA" by Erik Stokstad, Science
"Poop Sleuth" by Mark Witten, Current Science
"Mysteries of ancient people poop: Vaughn Bryant and Kristin D. Sobolik" by Geoff Williams,Odyssey