What an ancient Paleoindian girl tells us about Native American prehistory

Photo by Paul Nicklen/National Geographic from http://www.nature.com/news/mexican-skeleton-gives-clue-to-american-ancestry-1.15226?WT.mc_id=TWT_NatureNews



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.



17 thoughts on “What an ancient Paleoindian girl tells us about Native American prehistory

  1. empressluna May 15, 2014 / 6:16 pm

    Looking forward to seeing if you post about his comments.
    As always, great post. I have only thus far studied science…recreationally, for lack of a better word. But I have recently begun working on an academic path towards a PhD in a field of biology (still exploring my interests). I just wanted to say that even though I have a great understanding and comprehension of most scientific writing, it sometimes gets a bit confusing. Your blog doesn’t and that’s one of the reasons I LOVE following your posts. Even if the content isn’t something I’m very familiar with, you write concisely and the context isn’t all mumblyjumblymuddlemess (ha, see what I did there?)
    Keep up the awesome work 🙂

    • Jennifer Raff May 15, 2014 / 6:19 pm

      Thank you so much for your kind words! I’m trying to learn how to write in a less stilted, “sciency” way, and you guys are my guinea pigs to practice on 🙂

      Best of luck on your PhD!

      • empressluna May 15, 2014 / 6:21 pm

        Awesome! I actually started college as an English and creative writing major so that’s where my more natural talents lie. But biology and science in general have stolen my heart.
        Thank you! I expect it will be a long road but definitely worth it 🙂

    • Tina September 5, 2016 / 2:20 pm

      Ifbthey can’t get her DNA from the father’s line or from anyone in between why even classify her as anything until they can grind her brother or Amway to test what all 400,000 of her ancestors were each time you go back it doubles. They are looking at one line and making a conclusion as to keep the normal thought of only one nation was here I beg to differ and hope they can find the rest of that girls dna because she had a father, grand parents greats and so on. DNA can be faked now as it’s told and I’m pretty sure most of these scientist are trying to stay on good grace and not upset the masses. Just saying

  2. gewisn May 16, 2014 / 12:26 am

    I’m developing an idea (as I write this, so please keep expectations very low) that we need to change scientific publication style manuals. With internet access to journal publications and the movement for free access, we may need to change the style of jounal article writing so that the messages and conclusions are more easily understood and less easily misrepresented by those who are not already experts in the field.
    I am not suggesting we dumb down the journals.
    I am suggesting we get serious about making the writing clear and concise, and not just for the in-crowd of a small circle of other researchers working on the same specific topic.
    1) At the end of the introduction, each article must answer, “What exactly is the question answered by this research?” If you cannot state the question addressed, how can we know if you answered it?
    2) There must be a discussion of why this method of answering the question was chosen over alternative options to answer it.
    “The people who published on this topic before me used this same type of analysis,” is not a sufficient answer.
    3) There must be discussion of the advantages and disadvantages of the particular methods chosen to arrive at the conclusion. If this has been addressed previously, it must be at least referenced.
    We cannot help students and developing researchers learn to think about the topic if we do tell them what we were thinking.

    Referees will also have to get more serious about reining in authors abstracts, conclusions, and discussions. If authors are permitted to use buzzwords in the abstract solely to increase search hits and are not held accountable for conclusions and discusssions that are not directly resulting from the research, then there is little hope of improving the science literacy of the population, or even just the next generation of researchers.

    So, how can this be done?
    I think this kind of tightening of requirements and raising expectations is best done by outside groups – but not by a single monopoly on the certification process. I’m suggesting that there should be several journals that review the quality of scientific journals articles. Competition will develop the most effective and most useful Journal journals. There might even be Journal journals based on how the journals are used. For example, The Journal of High School Science Education References, which would examine the usefulness of particular publicartions for science educators. Another might be Biology Researcher’s Chemistry Journal Review. Over time, good reviews in such meta journals would become a useful marketing tool for the publishers of the original research, and their own editors will encourage assist authors to write in ways that garner such attention and the avenue for revenue moves from hard copy advertisements to internet hit-mining.

    Currently, in medicine, there is greater and greater competition among such journal review newsletters and it is forcing the authors of original research to be aware that conclusions that are not warranted by the data and presumptions of relevance will both be challenged and mindless mining of data from previous studies will not get you noticed by these meta journals (I’m sorry, I just couldn’t keep writing “Journal journals” no matter how clever it looked to me at first).
    So I’m hoping this trend will continue and force a new standard of relevance and lucidity on scientific journal writing.

    What started this?
    Oh, yeah. It was paleoindian girl, and the absurd comments of one of the authors, and Jennifer Raff’s attempts to make science communication clearer and even more interesting.
    Dr Raff is winning.
    If I can’t even remember why I started writing, I’m clearly losing.

    • Jennifer Raff May 16, 2014 / 6:55 am

      Do you mean this guy?

      All journals need to be open-access, definitely. Not only do our results belong to taxpayers, but it would also save us a lot of aggravation when trying to get people to read a paper to bolster a point we’re trying to make.

      As for the rest, I don’t know if the problem is in the writing of the papers, per se. Writing for other scientists, as opposed to writing for the public, is not an inherently bad thing, and there are conventions (like jargon) that are actually quite useful in this context. But I do think that important papers (at the very least) need to be “translated” better than many journalists are doing. Having been (somewhat peripherally) involved in the process of the release of major papers, I can tell you that editors and journalists do their best but can be way more influenced by what the authors say at press conferences than they are by the paper itself. That’s a big problem that I don’t think many people may be aware of.

      So my solution is this! More scientists need to blog about papers in their field, with the intention of making them intelligible to non-scientists, not just have discussions with each other.

  3. Anonymous May 16, 2014 / 4:21 pm

    I don’t expect an exact number, within an order of magnitude would be fine, but roughly how many paleoindian remains have they gotten any aDNA from? Is there a good primer online on haplogroups and the migration(s?) into the Americas for people like me who are interested in this sort of research? And yes, I recognize that just like Scott’s brief description of the immune system, nothing like that would make me any sort of expert, but it would help me follow along more easily.

    • Joe Seatter May 16, 2014 / 4:22 pm

      Ugh, hate it when I forget to log in before hitting post comment…

    • Jennifer Raff May 18, 2014 / 6:53 am

      I would estimate that ancient DNA has been published from approximately 20-25 Paleoindian individuals. Most reports just consist of a few diagnostic fragments of the mitochondrial genome. There have been two complete genomes published; one from a Paleoeskimo (~4,000 YBP, which is much younger than Paleoindians), and the most recent Clovis child from the Anzick site.

  4. K Ann Horsburgh May 16, 2014 / 11:10 pm

    Interesting post. But Chatters comments. Wow. I suppose we can hope he was misquoted, but good grief. The equating of feminine with juvenile – ever such a popular technique of the misogynist!

    • Jennifer Raff May 18, 2014 / 6:54 am

      Hi Ann! Right? I was taken aback (to put it mildly). Thankfully, that doesn’t seem to be what the news reports are focusing on.

  5. Quinn May 17, 2014 / 10:40 pm

    In my more cynical moments, I wonder whether academics like Chatters really believe their outlandish hypotheses are plausible, or whether they’re just making provocative claims in the hopes of bagging more citations. Are they, in a word, trolling?

    • Jennifer Raff May 18, 2014 / 6:56 am

      Quinn, I don’t think he’s trolling….but it’s possible that he’s floating hypotheses to gauge reaction? I don’t know Chatters, so I want to give him the benefit of the doubt. (But still, he should know better.)

  6. Patrick McDonald May 19, 2014 / 1:18 pm

    I saw a piece about this find in our “national newspaper”, THE GLOBE AND MAIL, on May 16th. One aspect of it that struck me was how sharply topography can change in relatively short period of Geological time. Who’d have thought that mitochondrial DNA would have turned out to be so important?

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