More than 12,000 years ago, a young teenage girl walking through a deep cave (known today as Hoyo Negro) fell down a massive pit. The fall fractured her pelvis, and she died among the remains of giant ground sloths and saber-toothed cats who had met a similar fate. Over the next few millennia, the pit filled with water and their bones were covered with cave formations. They were left undisturbed until discovered in 2007 by cave divers, who named the girl “Naia” in a reference to Greek mythology.
Today, a team of archaeologists and geneticists announced the results from sequencing her mitochondrial genome. She possessed a haplogroup (D1) that evolved in Beringia and is seen in modern Native Americans.
So why is this result so important? The Hoyo Negro girl, like other Paleoindians (the oldest inhabitants of the Americas), had a skull shape that was distinctive from later (younger than 9,000 years before present) ancient Americans, who more closely resembled modern Native Americans.
This cranial distinctiveness has long presented a puzzle to archaeologists: if the most ancient inhabitants of the Americas looked so different, did that mean they had different ancestry from later inhabitants? Geneticists have long insisted that all Native Americans derived from a single source population in Beringia, including the Paleoindians. And the recent sequencing of the Clovis-period infant, Anzick-1 confirmed this finding. But Anzick-1’s skull was not preserved, so we don’t know if he was actually morphologically distinct from contemporary Native Americans. Might he have descended from Beringians, while the morphologically distinctive Paleoindians have descended from a different population?
The sequencing of the Hoyo Negro girl’s mitochondrial DNA says exactly what geneticists would have predicted: she was closely related to all other ancient and modern Native Americans. I was asked by Michael Balter, a writer for Science, to share my thoughts on the significance of this finding. Since the article he wrote (containing a few quotes from me) is paywalled, I thought I’d share my complete response here with you:
This study is a very simple and direct test of two competing hypotheses about Paleoindian ancestry. If Paleoindians’ distinct cranial and tooth morphology is a reflection of non-Berigian ancestry, as has been hypothesized by some archaeologists, then we would expect them to possess genetic lineages that did not evolve in the Americas.
In contrast, our genetic models about the peopling of the Americas hypothesize that all modern and ancient indigenous Americans are descended from several migrations from a Beringian ancestral population. These models offer a clear prediction: all Paleoindian individuals should show the closest genetic affinity to contemporary Native Americans, and secondarily show more shared ancestry with Siberians than any other Old World population.
The Hoyo Negro girl possessed one of the founder mitochondrial lineages that are unique to descendents of Berigians. She therefore shares the same maternal ancestry as later Native American populations, and upholds the prediction of genetic models of Native American prehistory. We would expect to find similar results in future tests of other Paleoindian remains, if our models are a good approximation of history.
It’s important to recognize the limitations on what we can say from the Hoyo Negro results, however. This study presents only one genetic marker—the mitochondrial genome—and without characterizing the variation in the nuclear genome we can’t completely exclude other contributions to her ancestry. Nor should we extrapolate her results to all Paleoindian individuals. But we can confidently say that there is currently not a shred of genetic evidence to support a separate origin for Paleoindians and more recent Native Americans. The most parsimonious interpretation, therefore, is that these morphological differences are there result of evolutionary change, not distinct ancestry.
In order to better refine our models of Native American prehistory, and the relationship between Paleoindians and more recent (<9000 YBP) Native American populations, we need two things: 1) additional markers from the Hoyo Negro girl’s genome to understand more components of her ancestry, and 2) genetic characterization of more Paleoindian individuals. Based on the amelogenin results, it seems unlikely that her nuclear genome is well enough preserved for extensive genome sequencing, and we are very fortunate to have a complete mitochondrial genome sequenced from this individual. People should not have unrealistic expectations based on the recent spectacular publications of complete ancient genomes—that level of preservation is extremely unusual. For every ancient individual’s genome sequenced, there are dozens to hundreds that fail to work, or yield only limited sequence. But I am hopeful that there are additional skeletons out there that will yield enough genetic information that will help us continue to improve our understanding about early Native American genetic history.
There’s already a bunch of stories coming out about this paper. Here are a few (I’ll update this as I get more):
The original article (unfortunately behind a paywall): http://www.sciencemag.org/content/344/6185/750
I really encourage anyone who is interested in this subject to read stories from multiple sources, as each journalist tends to contact different archaeologists and geneticists for their comments–you’ll get a diversity of perspectives on the findings.
So this raises the question: how did these changes to cranial morphology occur? Note that forensic anthropologists use skull shape all the time to infer ancestry, and they would (at least some of them) argue that such dramatic differences in skull shape must mean that the Paleoindians have distinct ancestry. So what does this finding mean? Are their inferences about the relationship between cranial morphology and ancestry off base? We can’t really definitively answer that question until we have more information, as I said above, from the nuclear genome of a (or ideally, several) Paleoindian with this distinctive cranial morphology. We need to rule out any additional ancestral contribution. But I’m going to boldly predict that all Paleoindians, like Anzick, will show exclusively Beringian ancestry, like all ancient and modern Native Americans studied to date. It will be interesting to see if I’m right or wrong in the coming years.
I do wish to note, however, that I think these comments of the lead author of the Hoyo Negro study, Jim Chatters, are absurd:
Chatters, the lead author, said he is working on another paper in which he will lay out his theory of the “Human Wild Style” population.
He believes that these early migrants were an aggressive breed — risk-takers and novelty-seekers. They chased wild game, including megafauna like mastodons and saber-toothed cats, into unpopulated lands far from their ancestral hunting grounds.
But later, as their descendants settled down, and adopted agriculture, natural selection favored a gentler sort of personality, and men and women took on softer, more feminine features, Chatters argues. This tendency toward “neotony,” or natural selection of more childlike features, has been seen across much of the world, he said.
But that’s a subject for another post.