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

Jennifer Raff —  February 18, 2014 — 12 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.

About these ads

Jennifer Raff

Posts

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

12 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

  6. 

    “It is time to move on to more interesting questions.”
    You seem to imagine that the sequencing of one body is a home run. I see in the MAMMOTH TRUMPET for April 2014 an article (pg 6-10) which ends with DNA analysis team member Eske Willerslev asserting that “Now we have to assume, with this result, that all early skeletons in the Americas…are related to contemporary Native American groups.” Presumably Mr. Willerslev would have no problem with turning the 168 Windover Lake human remains to some Amerindian group or other for “repatriation”. Such a move would certainly make the lives of scientists adhering to Beringia-only theories easier. In fact there would be no reason to sequence any prehistoric skeletal remains. Some of us, in view of the rather murky situation around the Windover DNA, still consider that to be an “interesting question”.

  7. 

    Thank you so much for your post. I know this is WAY after the fact (I note you first published this post about 6 months ago), but I was curious as to your opinion on something.

    In my own independent research of Clovis genetic background, I found the same article you reference here by Rasmussen et al., which is how I found this post. In sum, Rasmussen et al. found no European genetic link in the Clovis infant’s genome.

    In another study published just one month prior to Rasmussen et al.’s, the study authors (Raghavan et al.) found what they concluded was a European genetic link in 24,000-year-old Siberian remains. Raghavan et al. concluded that western European admixture occurred prior to the Beringia crossing and not only post-Columbian, as they say was previously believed to be the only source of European blood in Native Americans.

    It’s my understanding that Rasmussen et al did not find a European genetic link in Clovis remains. I also understand that the paleolithic Siberians are believed to be the ancestors to those Paleo-Indians who crossed Beringia. Is it possible that the European genetic link found by Raghavan et al. in the Siberian remains was passed on to Paleo-Indians?

    You stated that you are unaware of any European genetic links found in fossils within the Americas, and neither am I. But I wonder whether one genetic lineage descended from such a Siberian individual as examined by Raghavan et al. might have made it across Beringia and we just have not yet extracted DNA proving the link.

    Since I’m not even a student of anthropology (my areas are midwifery and nursing), I defer to your knowledge on this matter. I am curious to know your thoughts.

    Thanks!

    Raghavan, M., Skoglund, P., Graf, K.E., Metspalu, M., Albrechtsen, A., Moltke, I., … Willerslev, E. (02 Jan 2014). “Upper Paleolithic Siberian genome reveals dual ancestry of Native Americans.” Nature, 505, 7481:87-91. Accessed 15 August 2014. doi:10.1038/nature12736

  8. 

    what about the d.n.a. from the mummies found in the Windover bog in fla.? at first (before the coverup people showed up, they were Eurpoean. hid it for years, then it got defunded right quick. their sewing/cloth was world class European when it was 1st dug up. now I see these people are not even mentioned in these discussions. and how about the Kenniwick man, another cover up attempt? Indians trying to make sure they bury any European evidence to keep the free stuff, 1st people train running? convenient how they get to rebury any pre-Columbus remains due to a treaty, huh? wonder how many they have already hid/buried in some secret location? they didn’t even want the scientist who discovered the Kenniwick man to ever get another look at what he called an obvious European, and he never did. heard the gov. even buried the site in rocks.

    settled science, again?

    don’t care who was 1st. just don’t bury the truth (and science) to kiss some butt.

    • 

      There was no cover-up in either case.

      Just out of curiosity, if you were doing the DNA work and you got a “European” sequence out of ancient Native American remains, how would you distinguish between contamination and genuine ancient DNA?

      • 

        Me,my friend(john linehan who’s mentioned in jason’s blog) and a fellow youtuber who used to go by the name salsassin have all contacted Joseph Lorenz regarding the windover remains.Pretty much the media pulled another fast one on the public like they did with K-man.

        http://www.jasoncolavito.com/blog/review-of-america-unearthed-s02e11-swamp-mammoth

        In Seguchi et al,2011 craniometric study the Windover skulls clustered with the Paleoindian Lagoa Santa skulls from Brazil.In Stojanowski et al, 2011 paper on teeth of the archaic Windover bog remains clearly shows the figs they showed as having shovel shaped incisors.

        THE RECOVERY AND FIRST ANALYSIS OF AN EARLY HOLOCENE
        HUMAN SKELETON FROM KENNEWICK, WASHINGTON, Chatters
        American Antiquity, 65(2), 2000, pp. 291-316

        “Cranial characteristics, femoral morphology and stature together led me, in the forensic venue, to suggest an affiliation with modem Euroamericans. Once the skeleton’s age was known, however, I referred to the remains as “Caucasoid-like” (Preston 1997).~ I did not state, nor did I intend to imply, once the skeleton’s age became known, that he was a member of some European group (Chatters 1998).”

        “It is possible, however, to compare the specimen with modern groups in search of the population with the closest statistical similarity and thus a possible common ancestry.

        This can be done using the craniofacial morphometry of Howells (1973, 1989) (e.g., Jantz and Owsley 1997, 1998; Neves and Pucciarelli 1989; Steele and Powell 1992, 1994). Applying this approach, Chatters et al. (1999) used principal components analysis to compare craniometrics of the Kennewick skull cast (Table 3) with the Ainu and the 18 modem populations that Howells (1989) believes comprise most of the metric variability of modem Homo sapiens.A graphic comparison of the first two components, which included size (Figure ll), placed him nearest the Pacific Islanders and Ainu-Brace and Hunt’s (1990) Jomon-Pacific cluster. When size was factored out, he was an extreme outlier, with no close relationship to any modem population. Powell and Rose (1999) reached the same conclusion using a wider array of techniques and a variety of human databases. These results are consistent with previous analyses, which find that the closest craniofacial morphometric affinity of northern Paleoamericans is generally to the Pacific Islanders and South Asians (Steele and Powell 1992, 1994), and that when size is factored out, they are often far removed from modem peoples (Jantz and Owsley 1998). In general appearance, the Kennewick skull does somewhat resemble Polynesians, particularly Easter Islanders, and Jomon/Ainu.”

        “Dental discrete traits (Table 5) echo this Jomon-Pacific affinity. Turner (1985,1990)”

        “Thus, craniofacial and dental evidence converge to suggest an affinity-a common origin-with some modern coastal and maritime peoples of east Asia and the Pacific.”

        “His physical features, teeth, and skeletal measurements show him to be an outlier relative to modern human populations, but place him closer to Pacific Islanders and Ainu than to Late Prehistoric Amerinds or any other modern group. Despite his uniqueness relative to modern peoples, he is not significantly different from other Paleoamerican males in most characteristics.”

        Anna Roosevelt’s brief lecture on Paleoindians and Kennewick starts around 20:14

        New Light on the Peopling of South America

        Of course this will all eventually come to fruition as Stojanowski et al 2014 paper “Sinodonty and beyond” shows how dental anthropologist are moving beyond the “sinodont/sundadont” dichotomy.

        Well that’s that :)

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. […]

  2. What an ancient Paleoindian girl tells us about Native American prehistory « Violent metaphors - May 15, 2014

    […] 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 […]

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s