The genetic prehistory of the North American Arctic

I’ve been waiting for this paper for months! The Willerslev group has just published the results of their study on ancient DNA from Paleo-Eskimos in the North American Arctic. Unfortunately, this article is behind a paywall at the journal Science, but I’ll give you a brief summary of the results, and talk a bit about why this paper matters and what it means for our understanding of the peopling of the Americas.

First a bit of context. The North American Arctic (consisting of North Alaska, Canada, and Greenland) was the last region on earth to be colonized (unless you count Antarctica, I guess). Our understanding from archaeology is that the first peoples to inhabit it, collectively referred to as the “Paleo-Eskimos”, migrated eastward into the region about 4,000 years before present (YBP)–considerably later than the earliest migrations that peopled the rest of North and South America. The Paleo-Eskimos (we don’t know their name(s) for themselves, unfortunately) didn’t leave many burials, but we do know that they hunted terrestrial and marine mammals and developed regional cultural variants (e.g. Dorset, Ipiutak) in Alaska, Canada, and Greenland.

Beginning around 800YBP, however, there was a rapid eastward expansion of a group of people practicing a different type of subsistence–whale hunting–and utilizing new technologies (such as the bow and arrow, dog sled, and umiaq). This culture, which archaeologists refer to as the “Neo-Eskimos” appeared to originate in Siberia and was carried extremely rapidly from the North Slope of Alaska to Greenland in the space of just a few generations. The Neo-Eskimo Thule expansion has been widely interpreted to be a population replacement event, as Paleo-Eskimo traditions disappear from the archaeological record immediately after the appearance of Thule culture in their regions.  I’ve glossed over a lot of the archaeological details, but you can find more in the following figure from Raghavan et al. 2014:

 

Screen Shot 2014-08-29 at 9.05.36 AM
Figure 1 from Raghavan et al. 2014, showing a detailed chronology of the different prehistoric cultures of the North American Arctic.

 

But–and this is a big but–we should always be careful about using culture as a proxy for people. People can (and do!) adopt new cultural practices without changing biologically. Looking at such events many years later, it might seem as though one population replaced another, but if we test this by comparing the two populations genetically (or one population before and after a cultural change) we can see that this isn’t the case. In the Americas, genetically comparing ancient populations with contemporary populations in the same region has shown us examples of both population replacement and continuity (I published a paper on this back in 2011). So it’s important to not make assumptions about biological relationships in the absence of biological data.

In the case of the North American Arctic, genetic studies on contemporary Inuit populations have shown that they have reduced genetic diversity compared to other Native American populations, and that their mitochondrial lineages (on which most of the work has been done) are sister clades of Native American ones (haplogroups A2a, A2b, a basal A2, and D4b1, if anyone cares about the specifics). That suggests a separate expansion of Arctic peoples from a Beringian ancestral population that was distinct from, but closely related to the population that gave rise to other Native American groups (both being descended from a Siberian ancestral population). Interestingly, the peoples of the Aleutian Islands have a mitochondrial haplogroup that hasn’t been reported from any Inuit populations–haplogroup D2–but has been found in the single Paleo-Eskimo genome that’s been sequenced so far (Gilbert et al. 2008). So there has been some evidence that the Paleo-Eskimos and Aleuts are indeed genetically distinct from the Neo-Eskimo/Inuit peoples, but in order to really test this hypotheses more rigorously more ancient DNA is needed.

Some of the outstanding questions about Arctic prehistory (at least from a genetic perspective) are:
1. Who are the Siberian ancestors of the Paleo-Eskimos?
2. What is the genetic relationship between the Paleo-Eskimos, Neo-Eskimos, and modern Inuit (and Aleut)? Are they genetically distinct (replacement hypothesis), or were the Paleo-Eskimos the ancestors to the Neo-Eskimos (continuity), or were they distinct with some degree of gene flow between them? Some have thought that the Sadlermiut, a group of people living in Southampton Island who were wiped out by European-introduced diseases at the beginning of the 20th century, were possibly descended from both Paleo-Eskimo Dorset and Neo-Eskimo Thule, because their culture was distinct from other contemporary Inuits and had some possible pre-Thule attributes.
3. What is the relationship between Arctic peoples and other Native American groups? How does this fit with or change our understanding of the peopling of the Americas more broadly?

That brings us up to yesterday, when Maanasa Raghavan and her colleagues published ancient DNA from numerous Paleo-Eskimo and Neo-Eskimo individuals, as well as some from contemporary individuals:

“we generated mitochondrial DNA (mtDNA) data from 154 and low-coverage whole genome data sets from 26 of the ancient samples (up to 0.3× depth)….We also sequenced two high-coverage genomes from present-day North American Native Americans belonging to the NaDene family (the
Dakelh of British Columbia, hereafter referred to as Athabascans) and unrelated, present-day Greenlandic Inuit (n = 2), Aleutian Islander (n = 1) and Siberian Nivkhs (n=2) to average depths of 20 to 40×.”

(They also, somewhat randomly, published mitochondrial DNA from a number of ancient Norse individuals to see if they were maternally related to the Inuit. Spoiler alert: they weren’t, nor should this be a surprise, as there really isn’t any archaeological evidence of admixture. I guess it was worth testing, though!)

I don’t want to go into the technical details too much, as this site is aimed at a more general audience. So I’ll just summarize the methods by saying that the authors used various statistical tests (Admixture analysis, ABBA-BABA, D-statistics, f3 statistics, TreeMix, and neighbor joining analyses for those of you who care) to look at relationships between the populations for which they had genetic data.

So what did they find? First of all, the ancient DNA was poorly preserved. For the samples they were able to get genome-wide markers from, they could only get 0.3x coverage. Coverage at that low level means that we should should be cautious about any inferences drawn from these samples. To their credit, the authors were very explicit about the limitations of their results, and they did (in my opinion) the best job they could have to take into account damage patterns and missing data. The authors speculated that the reason the DNA was so poorly preserved in these remains was because of their burial conditions; the (very few) Paleo-Indian remains found were all on the surface, not buried in the ground, and so were exposed to repeated cycles of temperature changes over many years. That’s not good for DNA!

The authors found that all the Paleo-Eskimo remains from all time periods were very closely related. All possessed mitochondrial haplogroup D2 which is also found in Aleut populations, but in none of the Neo-Eskimos or contemporary Inuit*, and analysis of genome-wide nuclear markers (from those that were preserved) showed all Paleo-Eskimos clustered together, but not with Neo-Eskimos, contemporary Inuit, or other Native Americans. The authors did detect a signal of ancient admixture between the ancestors of the Greenlandic Inuit and the Paleo-Eskimos.

 

Screen Shot 2014-08-29 at 9.30.34 AM
Figure 2 from Raghavan et al. 2014, showing supported and unsupported models for the peopling of the Arctic

 

Figure 2 from Raghavan et al. shows the different scenarios for the peopling of the Arctic that the authors tested, with those supported by their results marked by S, and those rejected marked by R.  This study shows that all Paleo-Eskimos that have been genetically characterized, from Canada to Greenland, share ancestry from a common population that is distinct from that which gave rise to Neo-Eskimo populations. The ancestors of the Paleo-Eskimos and the Neo-Eskimos appear to have become genetically isolated from each other sometime prior to the Paleo-Eskimo migration (4000 YBP), although this new study provides evidence for at least some limited gene flow between the Paleo-Eskimos and the Neo-Eskimo ancestors of the Greenlandic Inuit (presumably in Beringia).  These results continue to support the hypothesis of a replacement of Paleo-Eskimo populations by the Neo-Eskimos, who appear to be ancestral to all contemporary Inuits. Interestingly the Sadlermiut are unambiguously most closely related to the Neo-Eskimo/Thule, with no evidence for Paleo-Eskimo ancestry.

I think overall this study emphasizes that the peopling of the Americas shouldn’t be conceptualized as a simple, successive series of discrete steps. Rather, we have evidence of a complex and dynamic history; there were likely multiple groups of people, all descended from an ancestral population from Siberia, who lived in Beringia for a long period of time. Their movements into the Americas at different times contributed to the pattern of genetic diversity that we can see today. As we fill in information from the genomes of ancient and living people from different geographic regions—for example, much of the northern coastal regions of Alaska are uncharacterized**—a clearer, more detailed picture of this history will emerge.

—————————————————————————————————————————————-

*The authors of this study reported finding haplogroup D3 (and sub-haplogroups) in their Neo-Eskimo individuals, but that’s actually an error–since Derenko et al. 2010 those haplogroups have been reclassified as sub-haplogroups of D4. Hopefully this won’t cause too much confusion!

**I’m working on this! Hopefully I can talk about my results soon.

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2 thoughts on “The genetic prehistory of the North American Arctic

  1. Randy Wright August 30, 2014 / 4:12 pm

    Thank you, Jennifer,

    I don’t have access to the science journals you do (and while I champion “open sourcing,” I recognize the reality somebody has to foot the bill for these things), but I saw the following summary in the New York Times a few days ago. I sent a link to a friend of mine with the sub-line “Willerslev is a Busy Man.” This was in reply to a link he’d sent me about a new volume on “Kennewick Man” that is slated for a mid-September release. On that one, the Army Corps of Engineers–probably bowing to pressure from the Native American tribes involved–has refused permission to perform additional extractions for DNA sequencing (and other scientific testing such as early diet, etc.) on KM’s teeth and longer bones, but Willerslev et al are trying to extract it from the earlier samples. I wish them the best of luck.

    http://www.nytimes.com/2014/08/29/science/study-offers-clues-to-arctic-mystery-paleo-eskimos-abrupt-extinction.html?ref=science

    Scientists and science writers–I consider myself the latter and generally defer to the former unless it’s something particularly outlandish–are often at odds, so any contrasts between your write-up and author Krisch’s work may be illuminating. Usually the NY Times is particularly credible, but there have been some howlers.

    I’m looking forward to more debate and conversation here from you on the subject of Kennewick Man. The September issue of the Smithsonian magazine has this article:

    http://www.smithsonianmag.com/history/kennewick-man-finally-freed-share-his-secrets-180952462/?all&no-ist

    I’m troubled by the claim that this is “new” when it comes from forensic studies done almost a decade ago, and the reliance on Douglas Owlsley’s claims don’t square with my own views (or the strong evidence linking Native Americans to their Siberian origins).

    Near the end Owlsley states, “A trace of their DNA [ancient east Asian Homo sapiens who were also ancestral to Polynesians, etc.] still can be detected in some Native American groups, though the signal is too weak to label the Native Americans ‘descendants.’”

    I’m certain there are alternative and credible explanations for those “DNA traces,” and I’m reminded of just how big the Pacific Ocean is and the improbability of Paleolithic “mariners” making such voyages. I note Japan was originally settled via land bridges and not ocean-going craft.

    I also note that Owlsley–and Dennis Stanford–raised considerable ire among Native Americans with their lawsuits (although I’m foursquare in favor of DNA testing of the 9,000 year old remains), and there is an interesting and illuminating contrast between the actions Sarah Anzick took in securing the cooperating of local tribes involving the Anzick Clovis Child.

    Finally, back to the subject of geography and a huge pet peeve of mine involving the “distortion” of maps of Alaska, the Arctic, and Greenland where “Mercator Projections” are involved. Greenland’s map is far out of scale, and Alaska is way too small, and I suggest those distortions contribute significantly to misinterpreting the evidence and offering flawed hypotheses that don’t take into account the actual distances involved.

    In point-of-fact, Alaska is 80% as large as Greenland.

    http://mapfight.appspot.com/us.ak-vs-gl/alaska-us-greenland-size-comparison

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