Gene Expression

Interesting that I just pointed to Neandertal DNA, a really big story just came out on ancient Greenlander genetics, Whole Genome of Ancient Human Is Decoded:

The genome of a man who lived on the western coast of Greenland some 4,000 years ago has been decoded, thanks to the surprisingly good preservation of DNA in a swatch of his hair so thick it was originally thought to be from a bear.

This is the first time the whole genome of an ancient human has been analyzed, and it joins the list of just eight whole genomes of living people that have been decoded so far. It also sheds new light on the settlement of North America by showing there was a hitherto unsuspected migration of people across the continent, from Siberia to Greenland, some 5,500 years ago.

The Greenlander belonged to a Paleo-Eskimo culture called the Saqqaq by archaeologists. Using his genome as a basis, a team of researchers from the University of Copenhagen determined that the Saqqaq man’s closest living relatives were the Chukchis, people who live at the easternmost tip of Siberia. His ancestors split apart from Chukchis some 5,500 years ago, according to genetic calculations, implying that the Saqqaq people’s ancestors must have traveled across the northern edges of North America until they reached Greenland.

One of the interesting aspects of this nearly total genome sequencing is that with the current state of knowledge of the loci which control skin and eye color and hair form, i.e., extremely salient phenotypic traits, you can reconstruct the general appearance of deceased individuals who are sequenced. The practical application of this in criminal forensics is obvious in its utility, but when applied to “historically sensitive” topics it will likely be more fraught. Because of the relative completeness of the genome a lot of functional information was extracted, but there’s also very interesting phylogenetic information. It looks like the that the Saqqaq culture is an instance of geographical “leapfrogging.” They skirted the northern margins of North America to settle in Greenland, with their ultimate provenance being the far eastern tip of Asia. Here’s the abstract, Ancient human genome sequence of an extinct Palaeo-Eskimo:

We report here the genome sequence of an ancient human. Obtained from ~4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20×, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.

Here’s some of the panels from figure 3, which shows the location of various populations sequenced and compared to this individual (he’s “starred” in the second two panels).

i-6dc4b1ce5c1316d8ad1a39e84c1ed2ae-chuck1.png

i-d268225947179afad2b996af04a6a5ce-chuck2.png

i-e3f1d4bd87de04635f641dddd841eacf-chuck3.png

The second panel is a straightforward PC plot, showing the top two dimensions of variation within the genetic data. In the third panel you have the characterization of the genomes of individuals assuming a K number of ancestral populations generating the extant variation (e.g., three colors of equal proportion in the bar plot individual 1/3 ancestry from three populations). So for example the Uygurs are a mix of east and west Eurasian genes, which is what the history would lead us to expect. The ADMIXTURE program assumed K = 5, so 5 putative ancestral populations.

These types of studies are going to revolutionize our understanding of population movements and deep history at higher latitudes. In particular I am excited by the potential they have in elucidating the more complicated network structure of the flow of genes, and by inference, cultural information.

Related: Edward Yong also has a post up.

Citation: Nature 463, 757-762 (11 February 2010) | doi:10.1038/nature08835

Comments

  1. #1 agnostic
    February 10, 2010

    Any word on if he was lactose tolerant? In Chukchis, 88% are homozygous for the intolerant allele. In Alaskan Eskimos, 80% are intolerant phenotypically. Doesn’t sound like he was a pastoralist, but you never know what Greenlanders 5500 years ago were up to.

  2. #2 Clark
    February 10, 2010

    Out of curiosity are the laplanders of Scandanavia also this same group? I believe they are genetically different from the Chukchis but I believe are far more Asian than European.

  3. #3 John Emerson
    February 10, 2010

    Individuals and peoples can travel long distances over empty space relatively quickly. Historically (and prehistorically) what kept peoples from moving far was typically resistance from a different people standing in the way, along with the temptations along the way of comfortable places to settle. Where neither was a factor (on the steppe during the early period, on the ocean, in the arctic) travel and migration can be rapid.

    Also, of course, arctic distances are shorter than they look on maps. From Nome Alaska to Thule Greenland is 2080 miles.

  4. #4 razib
    February 10, 2010

    the sami might be part of this story, but i would bet against it right now. their mtDNA looks really ancient in europe (u5). also, they are, i believe, closer to siberians than any other european group, but they are not closer to siberians than to europeans (specifically, finns, and even other scandinavians).

  5. #5 vasha
    February 11, 2010

    A correction for your post title: Kalaalisut is the name of the main Greenlandic language. The Eskimo population there is called “Kalaallit”, the country is “Kalaallit Nunaat”.

    With that out of the way: thank you for this in-depth post. It adds a lot to what I’ve seen elsewhere.

  6. #6 frog
    February 11, 2010

    Wow — those “relatedness” patterns are curious.

    They don’t seem to fit with the concensus patterns. Why are Aleuts and Greenlanders grouped so much with Europeans? What’s with the Mayas, and the Chukchis?

    How many migrations were there, and in how many different directions?

  7. #7 frog
    February 11, 2010

    Oh — the non-Saqqaq data is contemporary, so it includes post-Columbian migrations. Makes it much less useful — I thought it was pre-Columbian data, since we already know about migrations in the last 500 years.

    But still, where the hell does the “American” tree come from?

  8. #8 John Emerson
    February 11, 2010

    From the archaeological and linguistic evidence, it has been concluded that the Aleut and Inuit are the most recent arrivals from Asia, with the Na-Dene (Athabaskans, mostly in Arctic Canada, but also Navajo and Apache in NM and AZ and others in California) coming before them, and the great body of Amerinds before that. The third “Amerind” group is just a lumping group, no one knows how many migrations it represents.

    From what I could Google, the Inuit reached Greenland pretty late, about 1400 AD. The Dorset culture which preceded them arrived after 500 BC. So this evidence was from still a third people, which could have been Athabaskan or Amerind, or simply an otherwise unattested migration from Asia.

    Google does not tell me when the Athabaskans arrived. A recent theory which seems to be well-grounded has found linguistic relationships between the Athabaskan languages and Ket in Siberia, previously thought of as an isolate.

    There are a number of isolate languages in NE Siberia, as well as languages whose relationships outside the region are few. And the Bering strait isn’t very intimidating to the people who live near it, though I wouldn’t want to cross it in a skin boat. Some Inuit remain in Asia.

  9. #9 John Emerson
    February 11, 2010

    I just looked more carefully at the graph. Taking the color coding as accurate, this means that the Saqqaq were entirely unrelated with Europeans and Early Amerinds, has some relationship to East Asian (Chinese and Japanese), had the next closest relationship to misc. Siberian peoples, and had the closest relationship to Chukchees. Greenlanders, Aleuts, and Na-Dene share the relationship with Chukchis but not with the other Siberians, with the Na-Dene having the most Amerind kinship.

    It seems to me that given the data, the Saqqaq could have been close to either the original Inuit-Aleut migration or the INa-Dene migration, once allowance is made for interbreeding recently with Europeans and over a long period with Amerinds.

  10. #10 doug l
    February 11, 2010

    There are quite a few interesting aspects to this story. One thing that it brings to mind was something that is not often considered when discussing these people of the far north which is that they can travel such long distances. Prior to the recent introduction of modern technology in transportation, even people in so-called advanced civilizations, for the most part didn’t travel all that far, but the people of the north, using both skin boats and sleds pulled by dogs and reindeer regularly travelled long distances; hundreds of miles across landscape the rest of the world’s cultures would find unimaginable and yet through their technologies these same landscapes, frozen rivers and the teeming waters of the ice-edge, became avenues for seasonal migrations and means by which they could exploit vast areas for their animal resources, far beyond what the rest of the world could undertake prior to modern mechanization.
    In the warm weather and 24 hour daylight of summer, when the rest of us might think it would be the right time to be out and about, northern people become sedentary, whereas in the winter, once the land is frozen solid the people of the arctic start to travel over long distances.

  11. #11 doug l
    February 11, 2010

    One more note: if you look at a north polar projection of the world it becomes evident that to the people of the north, with their dog-sleds and skin boats, the resources for which they were perfectly adapted to exploit and the region across which they travelled actually connected them to Europe, Asia, Greenland and North America; all of it being exploitable and accessible and even inviting; one big coastal system without any of it being seperated by any insurmountable barrier.

  12. #12 Alan Kellogg
    February 12, 2010

    I had a different thought than most others in this thread; since the cost of genome sequencing has come down so much in the past few years, and we’ve gotten such useful results from human hair, I was wondering if maybe somebody could do sequencing on purported sasquatch hair. Sequence the genome found in the cells of the hair to see how closely, and how distantly, it is related to other primates.

    Yes, I am well aware that I am … different.

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