Archeologists and Molecular Biologists debate evidence of early human habitation of North America

Last year, some ancient excrement made headlines when an international team claimed they had found the earliest definitive evidence of human habitation of North America in the form of fossilized feces, known to archeologists by the cryptic name “coprolites.” These findings are now disputed by two groups. It all comes down to the crux of good experimental science: proper controls and unbiased interpretation of results. This is a complicated debate, the research lies at the intersection of geology, anthropology, and molecular biology, and its outcome has far-reaching consequences for our understanding of human migration and archeology.

During an archeological dig of a cave in southern Oregon, a team led by Dennis Jenkins of the University of Oregon uncovered 14 coprolites that, in their words, “are morphologically human (based on size, shape, constituents, and color).” They also found animal bones and some possible rock tools. The archeologists thought that the coprolites might contain trace amounts of the DNA of the species that left them behind, so they gave the samples to Thomas Gilbert and Eske Willerslev, two molecular biologists at the University of Copenhangen in Denmark who specialize in ancient DNA.

Gilbert and Willerslev set out to see if any of the feces contained DNA characteristic of Native Americans. While all humans have very similar DNA, descendants of a particular population have characteristic differences in their DNA that can be read out in the sequence of the DNA. The results of their work, published in 2008 in Science, seemed definitive. Six of the 14 coprolites contained human DNA characteristic of Native Americans. Dating methods established that at least 3 of the coprolites are at least 1,000 years older than the earliest evidence of human habitation of North America.

The authors of this paper were aware that contamination of Native American DNA either in modern times or ancient times can be a real problem with such studies. Indeed, they found modern human DNA in all 14 of the coprolites, probably from handling during excavation and lab work. The group tried to rule out the possibility of Native American DNA contamination. First, they screened all of the members of the research team and showed that none of them had the Native American DNA found in the coprolites. This, they argue, rules out modern contamination as the source of the DNA. Secondly, they sampled soil in the cave for Native American DNA and couldn’t detect any. They argue that this is proof that there was not ancient Native American DNA “leaching” from higher (younger) layers of soil down into the older soil and coprolites.

The result of this study added to circumstantial evidence that humans existed in the Americas before the so-called “Clovis Culture,” a well-studied ancient human population with characteristic arrowheads and other tools that spread quickly across the Americas about 13,000 years before present (BP). The new DNA evidence also increased the likelihood that the earliest American humans did not cross through an inland “ice-free” corridor through modern-day Alberta and British Columbia. Instead, it became more likely that they were aided in parts by boat, hopping along the ice-free and habitable coast of Alaska and down the Western coast of the Americas.

In rebuttals published this month in Science, two groups question the scientific basis for the claims that the coprolites are human and move back the date of human habitation of the Americas. The first comment was written by three Boston University (BU) scientists who were asked by the original team to inspect one of the three most-ancient coprolites (containing Native American DNA) to assess its origin. The group at BU used microscopic methods to analyze the contents of the feces and determined that it is likely of herbivore origin – that is, not from a human. They hint that the authors of the original study were aware of their conclusions: “the authors of the study asked us to perform…[analyses]…but our results were not included in the published report.” This implies that the original authors chose not to provide negative evidence that would need to be explained.

The second group, from McMaster University in Canada, disputes the methods that were used to assess the origin and date of the coprolites, and argues that the evidence is not sufficient that the feces are from pre-Clovis humans. Ancient DNA is routinely amplified by the Polymerase Chain Reaction (PCR), a method that allows for the exponential amplification of specific DNA molecules in a reaction tube. This method is extremely sensitive, which makes it great for amplifying a minute amount of ancient, degraded DNA. One downfall of this approach is that it is so sensitive that it can amplify contaminating DNA fragments.

The crux of the argument against the DNA evidence of ancient habitation is this: PCR is so exquisitely sensitive (it is capable of detecting a single molecule of DNA), that the Native American DNA detected in the samples could be from a modern or ancient source of contamination. Remember that a crucial control in the original experiments was to test all of the team members for Native American DNA? The Canadian group argues that this isn’t sufficient: trace amounts of DNA could have come from other individuals who never had contact with the samples.

PCR can also be inhibited by a range of chemicals, or it might be more sensitive to one type of DNA than another. Recall that in the original work, soil samples from the caves tested negative for Native American DNA. They argued that this meant that DNA couldn’t have “leached” through the soil into the coprolites. However, the critics argue that the test might have been inhibited by something in the soil samples, which can be checked with control experiments to see if PCR is still sensitive under such conditions.

The list of critiques goes on, addressing possible disruptions to the original layers of soil by rats, and disputing the dates of the samples. The original group responded to the long lists of critiques in Science the same week, with new data and more details about their methods. From my naïve perspective, although concerns have been brought up about the original work, there is still a chance that the coprolites were from pre-Clovis humans, and more investigation is needed.

Such debate is healthy and crucial to good science. Viewing any discovery, however earth-shattering or mundane, with a skeptical eye, keeps us honest. For those of us who “do science” every day, it highlights the value of objective interpretation of all of the data before us, the need for extreme care with controls, and an understanding of the strengths and limitations of every experiment.