The oldest North American genome and what it tells us about the peopling of the Americas

Jennifer Raff —  February 18, 2014 — 6 Comments

Last Wednesday, Dr. Morton Rasmussen of the Natural History Museum of Denmark and his colleagues announced that they had completely sequenced the genome of an infant boy, buried ~12,600 years ago in Montana. A few weeks earlier, I’d been approached by an editor at Nature, who asked me if I and my mentor Deborah Bolnick would be interested in writing a companion paper that would analyze and contextualize their results. We agreed, and the paper was published in last week’s issue, alongside Rasmussen et al.’s work. Because it’s (unfortunately) behind a paywall, I’d like to summarize what we said in that paper for non-scientists. There are a lot of things to talk about with regard to this study, including a consideration of ethical issues and the media’s response, so I’m likely going to do several posts on it. This first post is mainly a discussion of how we interpret the results.

For a TL;DR version of this post, here’s a link to a short interview I did on the subject last week with the BBC World Service.

The infant whose genome was sequenced, referred to as Anzick-1, belonged to the Clovis culture; a widespread and very ancient group of North American hunter-gatherers who made beautiful stone points that are often found in association with mammoth remains. Clovis is the oldest known culture in the Americas, dating to approximately 13,000 to 12,600 years ago. Anzick-1′s DNA isn’t the oldest ever recovered in the Americas*, but his is the first completely sequenced genome from an ancient American** .  This is an extremely important achievement, because it can help us better understand how Native American genetic diversity has evolved, and how the Americas were initially peopled. We don’t have very much genetic information from the very oldest (pre- 5000 years ago) Americans, and Anzick-1 is the only known Clovis burial.

 

Until very recently, Clovis peoples were thought to be the first inhabitants of the Americas. For example, when I took “North American Prehistory” at Indiana University (about 8 years ago), my professor systematically dismissed every single archaeological site thought to be older than Clovis (at the time many of them did have issues with dating and context). But in the years since, we’ve amassed enough evidence to be certain that people were in the Americas before Clovis–they just didn’t leave much in the way of preserved tools or burials.

The earliest sites in the Americas tell us that people were here before 13,000 years ago.  The Monte Verde archaeological site, dating to 14,600 years ago, shows that the earliest peoples made it as far south as Chile at least by then. The extent of the massive glacial ice sheets that once covered North America gives us a bracket on the other side: people could not have moved southward into the Americas from Beringia until 17,000 years ago along the west coast, or ~13,500 years ago through the interior of the continent.***  Both Monte Verde, and patterns of distribution of certain mitochondrial (a maternally inherited, non-nuclear genome) lineages throughout North and South America strongly argue in favor of a coastal migration sometime after 17,000 years ago. But we also know from analysis of Native American mitochondrial and nuclear DNA that there were other, later migrations from Siberia as well–probably two others: one that likely came through the interior after 13,500 years ago, and one much more recent (~1,000 years ago) that gave rise to the modern inhabitants of the Arctic.

This figure summarizes what we currently know from mitochondrial, nuclear, and archaeological evidence. It’s complex, and definitely subject to change as we get more data!

Screen Shot 2014-02-18 at 9.54.37 AM

Figure 1 from Raff and Bolnick, 2014. Nature 506: 162

 

So where does Anzick-1′s genome fit into this picture? First, I should state the obvious: Anzick-1 is indisputably Native American. This is important because there are some who claim, on the basis of some similarity in shape between stone tools, that Clovis peoples were actually descended from migrations across the Atlantic from the Solutrean culture of Europe. I may go into this more extensively in a later post, but I do want to address it briefly here. These similarities in shape between stone tools of both cultures are pretty superficial–not enough to convince most archaeologists that Clovis is actually European in origin. Nor are geneticists convinced: all Native Americans (ancient and modern) genetic lineages studied to date are descended from known founder lineages, and those founders themselves can be traced directly to Siberia (via Beringia). There is currently no genetic data whatsoever supporting a link between ancient Europeans and Native Americans. Could there be some unsampled ancient genetic variation derived from Europe, no longer existing in modern Native American populations because of genetic drift (random loss of genetic diversity)? Possibly, but we can’t argue an entire model from spurious tool associations and non-evidence of genetic lineages. IF proponents of the “Solutrean hypothesis” find evidence for European lineages in securely dated ancient remains, THEN I’ll accept it. Otherwise, as my co-author and I say in the paper “It is time to move on to more interesting questions.”

What’s really neat about Anzick-1′s genome is how many predictions from previous studies it confirms. The figure above is based not on the Anzick-1 results (at least, not entirely), but rather on decades and decades of archaeological, paleoclimate, and genetic research. Anzick-1′s genome fits within this model extremely well. His maternal lineage, D4h3a is very old and rare among living Native Americans, but it seems to have been much more common among ancient populations. This lineage seems to be associated with (or a marker of?) the first “wave” of migration: those individuals who moved from Beringia into the Americas southward along the west coast, and then eastward across the continents. My co-author and I interpret Anzick-1′s possession of the D4h3a lineage as a suggestion that his maternal ancestors (at least) were part of that migration. We think that’s a much better explanation for the close genetic affinities between Anzick-1 and Central/South Americans than saying that Clovis peoples were “ancestral to all Native Americans”, which is how many media organizations are reporting it.

One of the surprising new findings emerging from Rasmussen et al.’s study is that there is additional, previously unrecognized, genetic structure within North American populations. Anzick-1′s genome confirms a previous study’s findings of three “streams” of gene flow from Siberia contributing to Native American ancestry, but it also has a more close affinity with Central/South American populations than with certain North American populations. Although they ruled out an additional “stream” of gene flow to account for this structure, it is hard to distinguish between other possibilities without more North American genomes.

Over the last few decades, mounting genetic and archaeological evidence has led us to develop a very complex model of migrations, admixture, and other evolutionary processes to account for the patterns of genetic diversity we see in ancient and living Native Americans. This paper is another major step towards refining these models, and opens the door for much more sophisticated analyses of Native American genomes. However, the ways in which the media has treated this story have given me some concerns–not the least since I was interviewed for a lot of the stories on it. My next post on this subject will go over my experiences with–and reactions to–some recent articles.

————————————————————————————————————————————–

* The oldest DNA from the Americas, fragments of mitochondrial DNA was recovered from human coprolites (ancient poop) at the Paisley Caves site, dating to 14,100 years ago.

**I’m not counting the Paleo-Eskimo Saqqaq genome as “American”, since it’s from Greenland.

***While there are some suggestions for much earlier migrations pre- 30,000 years ago, I don’t think we currently have enough evidence to accept them

References and further reading:

References to all the points I made in this post are contained in our paper (“Genetic roots of the first Americans”) here: http://www.nature.com/nature/journal/v506/n7487/full/506162a.html.

Rasmussen et al. 2014 (“The genome of a Late Pleistocene human from a Clovis burial site in western Montana”) is here: http://www.nature.com/nature/journal/v506/n7487/full/nature13025.html

And here’s more on how we use ancient DNA to study prehistory, and the precautions we take to ensure that ancient DNA isn’t contaminated. If you’re interested in ancient DNA, or have additional questions, please feel free to contact me.

As I said, I’ll be returning to the Solutrean hypothesis in more depth soon, in particular to discuss why haplogroup X2a is not evidence of European ancestry (a point raised in some of the media articles on this). But in the meantime, here’s another blogger’s take on the death of the Solutrean hypothesis.

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Jennifer Raff

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Scientist, fighter, reader. In pursuit of the extraordinary.

6 responses to The oldest North American genome and what it tells us about the peopling of the Americas

  1. 

    That’s fascinating, and more comprehensible than your Nature piece to people who aren’t expert in genetics. I’ll admit that I had to look up Beringia (to me, the Bering strait always brings to mind Lynne Cox who swam across it without a wetsuit). I’m looking forward to the next episode because I’d never heard of “Solutrean” until I read your Nature article, so please explain.

  2. 

    Thank you! Yes, I plan to dig in much deeper on the Solutrean hypothesis in the next post on the subject, so please stay tuned…

  3. 

    As you are a geneticist, I can’t fault you for accepting unskeptically, in your “Nature” commentary, what appears to be the consensus among archaeologists: that Monte Verde II is a demonstrated site of pre-Clovis human occupation. However, I have been pointing out for the last 15 years that the pathetic MV lithic assemblage (mainly unmodified stream cobbles) and the other claimed indices of human activity there are completely incongruous with what we know about the early peopling of southern South America. The first people appeared in Chile and Argentina about 13,000 years ago (not 14,500!) with a Clovis-derived toolkit including fluted bifaces and well-made bone foreshafts. For an example of an authentic early site, check out the site of Quebrada Santa Julia in coastal Chile, which was reported in Current Anthropology. Also, it’s ironic that you would now derive Clovis from a Pacific coastal population. Only a year or two ago, the proponents of pre-Clovis occupation of Paisley Caves and other Western Stemmed sites were suggesting that the early people of the northern Great Basin were both technologically and biologically distinct from Clovis, and descended from a supposed pre-Clovis coastal migration wave (for which there is no archaeological evidence) while also asserting that Clovis was solely an Eastern US culture. Clovis was an interior-adapted culture specialized in hunting of large terrestrial mammals, and they descended from the interior-adapted Siberian population now known from Malt’a.

  4. 

    I’m just a layman who’s followed this subject as thoroughly as I can, and to add to Stuart Fiedel’s thoughts, I would like to know what “patterns of distribution of certain mitochondrial (a maternally inherited, non-nuclear genome) lineages throughout North and South America strongly argue in favor of a coastal migration sometime after 17,000 years ago”?

    Specifically, the only DNA evidence I’ve seen of a coastal migration is Perego’s use of the D4h3 haplogoup where he noted it was found in California and on down into South America along the Pacific Coast. Yet Deborah Bolnick sequenced D4h3 in those pre-Columbian Hopewell remains in Illinois, and now we have this find as well, which my map tells me is also on the eastern side of the Continental Divide.

    That removes it as “evidence” in favor of the coastal migration, doesn’t it?

  5. 

    I really like this shortcut “_kyr” that saves 2 zeros

Trackbacks and Pingbacks:

  1. Problematic science journalism: Native American ancestry and the Solutrean hypothesis « Violent metaphors - March 10, 2014

    […] This is the second post in a series discussing the recent publication of a 12,500 year old genome from Montana. You can find the first post here. […]

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