Genetics Suggest Indigenous People Arrived In Americas Earlier Than Some Thought

16:37 minutes

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For years, grade school textbooks have told the story of how the Americas were populated by people crossing a land bridge from Asia and migrating in the safe havens between glaciers. In this version of history, its inhabitants arrived 13,000 years ago. 

But that story needs an update, thanks to both new archaeological evidence, and the increasingly robust tools of genetic analysis—ancient genomes extracted from millennia-old human remains suggest a much longer history of people in the Americas, perhaps by thousands more years, and aligns with the oral histories of Native Americans and other Indigenous peoples. The genetic evidence also brings up new mysteries, including evidence of some groups of ancient peoples with no direct descendants today. 

Producer Christie Taylor talks to University of Kansas anthropological geneticist Jennifer Raff, the author of Origin: A Genetic History of the Americas, about the growing evidence for the need to revise the history of the First Peoples. Plus, why researchers seeking to tell that story need to work directly with contemporary tribes to ensure that exploitative scientific practices of the past are not repeated.

Read an excerpt of Raff’s book Origin: A Genetic History of the Americas.

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Jennifer Raff in the lab. Credit: Devin Clarke

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Segment Guests

Jennifer Raff

Jennifer Raff is a genetic anthropologist and an assistant professor at the University of Kansas in Lawrence, Kansas. and author of Origin: A Genetic History of the Americas.

Segment Transcript

IRA FLATOW: This is Science Friday. I’m Ira Flatow. When you were in elementary school learning about the peopling of the Americas, I’ll bet you heard a story that goes something like this. 13,000 years ago, glaciers from the last Ice Age were just starting to melt across North America. And a group of people from what is now Asia crossed into North America by a land bridge through what is now the Bering Sea, and they found the path through the ice to North America. Anthropologists called them the Clovis people, and we know they were here because they left very distinct spear tips all over the continent. And for a long time, we assumed they were the first people to arrive. And then–

CHRISTIE TAYLOR: Hey. Hey, Ira. Hey, wait. Wait a second.

IRA FLATOW: Oh, hi, SciFri’s Christie Taylor. Am I telling it wrong?

CHRISTIE TAYLOR: Well, so unfortunately, the real picture is actually pretty complicated and involves some disagreements among scientists. But what many archeologists are starting to think is actually that the First peoples, the ancestors of Indigenous people in the Americas, were here much earlier than previously thought. And I’m talking thousands of years before that 13,000 number you just threw out. Also, they think the Clovis people weren’t the first people here.

IRA FLATOW: Really? Where is all this new evidence coming from?

CHRISTIE TAYLOR: Well, some of it is from older archeological sites that have been found recently with evidence of human habitation. But a lot of it is also genetics. We’re getting better and better tools for sequencing DNA and extracting very old DNA from people’s remains.

IRA FLATOW: Wow, this is much more interesting than what I was talking about. Fill us in on the rest of the story.

CHRISTIE TAYLOR: Yeah, I talked to Dr. Jennifer Raff. She’s an anthropological geneticist at the University of Kansas in Lawrence. And she’s the author of the book Origin– A Genetic History of the Americas, which came out earlier this year. We started by talking about how the timeline of human arrival is changing thanks to the introduction of DNA evidence.

JENNIFER RAFF: In the genetic record, we can see that there were splits between populations of ancestral Native Americans that coincide with or date to just after the beginning of the melting of the ice sheet that once covered most of northern North America. So these splits take place after 17,000 years ago. So these branches diverge very, very rapidly, which is a signal of rapid population movement across a landscape that’s likely devoid of other people.

And so the genetic record shows that occurring much earlier than the Clovis peoples. In addition to that, the archeological record shows candidates for early archeological sites that date between 14,000 and 16,000 years ago. What these approaches are telling us is a really fascinating story of a population that emerged from two previous populations, one in East Asia and one in northern Siberia.

There’s a lot of blanks we still have to fill in, but these two populations encountered one another during the peak of the last glacial maximum or just before. And this climate event really peaked between about 26,000 and 20,000 years ago. And so we see evidence for gene flow between these two populations somewhere. We don’t know where exactly they encountered each other. And then they become isolated for a period of a few thousand years, and this period of isolation is when they evolve genetic variants that are unique to the peoples of the Americas. And there are so many aspects to that story that I’ve just told you that we really can’t answer yet.

CHRISTIE TAYLOR: I mean, overall, what can genes tell us that the archeological sites themselves– bones, settlements, spear tips– what can genes tell us that those can’t?

JENNIFER RAFF: So what genetics tells us is biological history. Looking at genomes of individuals can tell us how closely they’re related, how closely they’re related to past populations and to global populations. And we can also look at genetic evidence and use it based on population genetics. We can estimate things like population size changes in the past. We can estimate the dates at which two populations last shared a common ancestor. We can look at how natural selection has affected populations and other forces of evolution, genetic drift and mutation and gene flow.

And so from all of these data, we can build models about the past and use those models as a test of archeological data. So I think that really the most powerful approach is to integrate archeology and genetics as best as one can and try to come up with the most comprehensive story of history that we can that matches both data sets. It’s not easy at all. It really is not.

CHRISTIE TAYLOR: It sounds like it. Well, and you don’t even have just one data set because you’re talking about both ancient remains of people who died thousands of years ago and the DNA from their descendants, Indigenous people in the Americas today. Right? How do those two sets of genealogies complement each other as well?

JENNIFER RAFF: Well, it can be really tricky because, of course, we want to avoid defining who is Native American in genetic terms. And present-day Indigenous peoples of the Americas are genetically variable. They have ancestry from many different populations. A lot of this ancestry comes from European contact and colonization processes that took place after 1492. And so it can complicate trying to reconstruct histories of the deep past, very, very ancient histories.

A lot of times to look at the stories of those ancestors, one has to look mostly at ancient DNA. And right now, we have a very limited sampling of genomes across the Americas from these ancient ancestors. And there are a lot of reasons why that’s the case. It’s a lot of ethics, a lot of history that geneticists really need to take into account and be sensitive to when we’re doing our work.

CHRISTIE TAYLOR: Let’s visit your lab virtually. You have received a new genome. What do you do with it? What happens?

JENNIFER RAFF: The process of our research always starts with the tribe or the descendant community and talking to them about what questions they have, what would they be interested in and looking at and bringing to them the questions that we might be interested in and coming to an agreement before we even bring any ancestral remains into the lab, that we always get that worked out first. What can we do, and how should we handle these remains?

And we bring that sample into our isolation facility at the University of Kansas, and that facility has a positive pressure and all the other attributes of an ancient DNA lab. So everything is covered in bleach. Everything is. And we are very, very careful about what we bring into the lab and how we work in it to preserve as much as possible a DNA-free environment or at least an environment free of contemporary human DNA. And that sample is then bleached, and the surface of it if it’s bone or tooth is removed. And the process of DNA extraction begins, which is a long and complicated and multiday process. It takes a lot of patience on the part of the worker to do this in a way that does not contaminate it with our own DNA.

CHRISTIE TAYLOR: You’re extracting the DNA. You’re sequencing it. What are the things you’re looking for in the sequence?

JENNIFER RAFF: So it again really depends on what kinds of questions that we have agreed to with the community that we’re working with. We are in our lab group also very interested in the very earliest peopling of the Americas. And so if the community finds it appropriate, then we will look for, how does the genome that we’re working with here fit with existing models of the population history of these earliest peoples?

We’re also interested in really small-scale relationships between individuals buried in the same cemetery, relationships between different groups who may have been trading partners and it was their gene flow accompanying that trading relationship. Can we see the effects of European contact in these populations? Do we see evidence for gene flow from European populations or other populations, or can we see the impact of European contact on population size changes in these groups? We are really interested in everything that one can learn from genetic relationships.

CHRISTIE TAYLOR: I want to go back to some of the ethical questions that you talk about in this book, Origin. We’re not talking about a story of people in a vacuum but one that involves people who are still alive today and people who have been exploited both in the process of colonization and by scientists who are looking for exactly the story you’re trying to tell.

JENNIFER RAFF: You know, it was really important to me as I wrote this book that I not only explained what we think we know today but how we came to those scientific understandings and this history of our discipline. And it’s not just genetics. It’s archeology. It’s anthropology. It’s scientific study in general. This history is deeply rooted in colonialism and centuries of exploitation of Indigenous peoples, and it’s really important that the process of consultation is a process of obtaining permission. It’s also a process of making sure the community is aware of all the implications that work can have for them and soliciting from them the parameters for how to do research.

So in the past, many scientists have not understood, I think, that– many non-Native scientists have not understood that these ancestral remains are sacred. They’re people. And doing work in the way that we do it, it can damage the remains. It can actually go against the ways in which some tribes view the dead. And so to do this work respectfully, it’s absolutely necessary that one talks to present-day communities about the ways in which one can handle these ancestral remains and what is OK to do and what is not OK to do.

And throughout the history of our field, unfortunately, that sensitivity has not been there. This field has really changed in the last, I would say, decade really, really changed. And that’s in large part thanks to the leadership of Indigenous peoples who have really educated non-Native scientists on these issues. But we still have a long way to go, I think. And I am hoping that by bringing this discussion to the public, it will be a little bit more accessible and people will understand a little bit more the issues involved.

CHRISTIE TAYLOR: Well, and I guess a follow-up to that, and that is just, why is it important for scientists to establish this story of people arriving in the Americas, how and when humans first made their homes here? Would it materially change the lives of those people’s descendants?

JENNIFER RAFF: That’s a really good question. And it’s one that I think about a lot. There are a couple of different ways to answer it. One way is to say that to understand the genetic history of humans globally is to help inform our understanding of the processes which have shaped genetic variation in present-day communities and understanding that evolutionary history can have real importance for medical research and, again, with caution and with care because Indigenous peoples have had, as other marginalized people, a very long history of exploitive medical research as well.

So that’s one answer to your question, but another one is there is a lot of bad information out there about history. Quite often, this alternative history is extremely racist or at least is used for racist purposes to deny the sovereignty of Indigenous peoples by saying, well, they weren’t the first people in the Americas, or it was really Europeans or ancient people from other parts of the world.

So genetics can show us, for example, that the first peoples of the Americas are the direct ancestors of present-day Indigenous peoples. I mean, that’s one fundamental thing. But it can also in concert with archeology show us that these First peoples got here very early, much, much earlier than I think most people realize– most non-Natives. Let me correct myself because Indigenous peoples will be like, yes, we know our ancestors have been here a long time. But it is actually a shame that we have to confirm this with genetic data for some people to believe it.

But it’s really fascinating, and what’s been interesting to me is in looking at these news stories that are emerging from genetics is how these origins are getting pushed back earlier and earlier. And so very early in the history of archeology, there was an argument about whether the First peoples were even ancestors to Native Americans. And then it was, well, they’ve only been here 5,000 years. And then it was, well, they’ve only been here 13,000 years. And now we’re saying before 15,000 years. And even adding to that now, there’s a site that was just published in New Mexico, the White Sands site, that shows evidence of human footprints potentially dating as early as 21,000 to 23,000 years ago, which means–


JENNIFER RAFF: Yeah. And so we have to now look at that evidence and say, OK. And I will say there are a lot of archeologists who disagree with the dating methods used. But if those dating methods hold up, you know, what does that mean for our field? How do we incorporate that into our models? How does that intersect with genetics right now and how can we reconcile all these different data sets?

And so I think that this study, as long as it’s done carefully and with sensitivity to Indigenous peoples’ perspectives and respect for their own histories, transmitted orally for generations and generations, if we can do this work respectfully and in a good way, I think it can benefit Indigenous communities if only to push back on some of these narratives. And then again, though, they shouldn’t need scientific confirmation of this. Right? But there it is. Yeah.

CHRISTIE TAYLOR: Just a quick reminder, this is Science Friday from WNYC Studios. Talking to Jennifer Raff, author of the book Origin– A Genetic History of the Americas. Your book is called Origin, which refers to the beginning of a people, of a history. Do you think we’ll ever know the entire story?

JENNIFER RAFF: No, I don’t think we’ll ever know the whole story. I really don’t. I mean, I am optimistic that we will get closer and closer. But by far, the majority of archeologists and geneticists including myself interpret the evidence as showing people present in the Americas by at least 16,000, 17,000 years ago or perhaps if White Sands holds up, if the dates hold up, maybe there were people here even as early as 25,000 years ago. How we reconcile those dates is going to be a fascinating conversation over the next few years. And I hope that my book kind of provides a framework for people to understand where that conversation is going and what it implies.

CHRISTIE TAYLOR: So we should all be setting Google Alerts for White Sands.

JENNIFER RAFF: Yes, I think so. It’s one of the most exciting sites that has been published recently, I think.

CHRISTIE TAYLOR: Jennifer, thank you so much for joining me today.

JENNIFER RAFF: Thank you so much.

CHRISTIE TAYLOR: Jennifer Raff is an anthropological geneticist at the University of Kansas in Lawrence and the author of the book Origin– A Genetic History of the Americas. I’m Christie Taylor.

IRA FLATOW: Thank you, Christie. And if you want to hear more about the revolutions in genetics driving our understanding of history, you can read an excerpt of Jennifer’s book Origin on our website, sciencefriday.com/origin. Once again, sciencefriday.com/origin.

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About Christie Taylor

Christie Taylor was a producer for Science Friday. Her days involved diligent research, too many phone calls for an introvert, and asking scientists if they have any audio of that narwhal heartbeat.

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