An analysis of 14,000 year old DNA from crap found in Oregon’s Paisely Caves

Perhaps the biggest anthropology news of this week has been the analysis of ancient DNA from fossilized human poop found in 14,000 year old cave in Oregon. The paper, “DNA from Pre-Clovis Human Coprolites in Oregon, North America,” was published in this recent issue of Science. Even though the study is literally based off of crap, it is a significant find for those interested in the peopling of the Americas.

The current consensus, that the Americas was originally populated by peoples from Siberia and north east Asia, has been based off of comparing and contrasting sequences of DNA from modern day people. While the evidence for this conclusion is overwhelming, it does have one flaw — if there were people from other origins, say from Europe, who died off and did not integrate into the original gene pool, their genetic impact may not be detectable by comparing and contrasting modern DNA sequences. This is where this brand new study really shines.

By studying ancient DNA, the authors potentially had the possibility of detecting any impact of non-Siberian DNA which may have not made it into modern day populations. But that wasn’t found. Instead, the null hypothesis was confirmed — the DNA extracted from coprolites links these people from prehistoric Oregon to two genetic groups of early Americans that moved from east Asia 18,000 years ago. mtDNA was only screened in this study, and not Y-chromosomal or other nuclear DNA loci for several reasons. First off, there’s many more mitochondria in a cell than a nuclei and since discarded red blood cells (who have no nuclei) are found in fecal material, that’s the primary reason it was the only genetic loci screened. mtDNA is also circular, and many think that physical confirmation make it more stable, and less prone, to degradation compared to linearized nuclear DNA which has ends exposed to the elements.

The study actually involved extracting mtDNA from 14 coprolites, which were found in the Paisley caves in 2002 and 2003. Dennis Jenkins led the excavations, he is also one of the co-authors of this current paper. I’m curious in looking deeper into how the researchers purified their ancient DNA. If you don’t remember, there was a recent paper that used ion-exchange columns to purify DNA and remove inhibitors that affect downstream amplification and sequence comparison. Anyways, I’m sure they did a good job.

The coprolites resembled human crap, but unfortunately, according to Thomas Dillehay, they may have not been excavated under sterile conditions and coulda definitely been contaminated by modern human DNA. This is a serious issue to consider when dealing with ancient DNA studies. The DNA of any persons who handled the fossilized crap coulda been inadvertently placed on the sample. I don’t know if any Native American’s were part of the dig, or handled the poop, but since no European DNA signatures were detected and six signatures were confirmed to be Native American only, I think it is safe to conclude that the excavators/curators probably did not contaminate the fossil poo. A similar concern was raised last August, when ancient DNA was analyzed from 2,000 year old chewing gum.

But what about people who occupied the site for the last 14,000 years? Gary Haynes also raises a criticism… Anyone who chose to urinate in the Paisely caves may have contaminated the samples too. Very vivid imagination, Dr. Hayes. Surely that’s a possibility. Over 14,000 year it coulda happened… anyone spitting in the saves and on these samples woulda also done the same. But I imagine there would have to have been a lot of peeing and spitting events that to contaminate 6 spatially separated samples (only 6 coprolites yielded DNA). If they caves were occupied, which I don’t know much about them, over time that possibility becomes more real.

John Noble Wilford, of the New York Times, writes that this find supports an earlier date of people in the Americas. I think that’s a bit misleading… like I mentioned very recent studies, such as this one and this one, have already estimated a temporal distribution of people across Beringia and into the Americas. They did so based upon coalescent theory, which is an indirect method. This study also relied on coalescent theory, but used much more ancient samples, therefore making it a bit more direct.

So, what about Clovis? How does this find affect the understandings of origins of the Clovis culture? The Clovis culture is thought to have emerged in the Americas around 13,000 years ago. If these fossilized crap piles aren’t contaminated, this shows that people where on the North American continent at least 1,000 years before the well-known Clovis people. During this time, it is possible these people could have been indirect or direct ancestors of the Clovis people and influenced the emergence of new archaeological technology associated with Clovis peoples. I suggested that recently.

    Balter, M. (2008). ARCHAEOLOGY: DNA From Fossil Feces Breaks Clovis Barrier. Science, 320(5872), 37-37. DOI: 10.1126/science.320.5872.37
    Gilbert, M.T., Jenkins, D.L., Gotherstrom, A., Naveran, N., Sanchez, J.J., Hofreiter, M., Thomsen, P.F., Binladen, J., Higham, T.F., Yohe, R.M., Parr, R., Cummings, L.S., Willerslev, E. (2008). DNA from Pre-Clovis Human Coprolites in Oregon, North America. Science DOI: 10.1126/science.1154116

2 thoughts on “An analysis of 14,000 year old DNA from crap found in Oregon’s Paisely Caves

  1. Yes, the Clovis-First hypothesis is dead. However, because most of the sites that hypothetically would support the Northwest Coast route are underwater, we have not been able to find any real empirical proof. This site does just that – now there is archaeological data and genetic data supporting an earlier entry into the Americas then Clovis.

  2. I’ve been poking around for fascinating early inhabitant info, since I’m heading out to explore the Fort Rock area with an OSU group. Thanks for the great beta, and the links.

    What fascinates me most about this discovery is that, if I’m not mistaken, it was pretty cold in the Arctic during this time. How did these people migrate from Asia? Land, or even sea?

    I know I’ve got plenty to learn. I’ll start with the links. Thanks again,

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