4,000-year-old frozen hair mtDNA sequenced from a Greenlandic Saqqaq settlement

A couple days ago Science published a peopling of the Americas paper. The paper is based on ancient mtDNA analysis of hair from a site in Greenland called, Saqqaq, also known as Qeqertasussuk, Disko Bay. The authors were able to identify a unique haplogroup, not shared by other Native Americans, which suggests that a different group from north Asia settled in what is now Greenland and then disappeared.

The paper is titled, “Paleo-Eskimo mtDNA Genome Reveals Matrilineal Discontinuity in Greenland.” The twigs associated with the site were dated by Carbon-14 to be roughly 4,000 – 3,100 years old. Four human long bones were excavated but were in poor condition. A clump of permafrost-preserved hair was also excavated. While hair is mostly made up of keratin protein polymers, the shaft of hair follicles often are an abundant source of well-preserved ancient DNA.

The authors first honed in on this, first PCR amplifying, cloning and sequencing just the mtDNA HVS1 sequences. It was found that the hair derives from a single clade, Hg D2. D2 is shared with Aleuts of the Commander Islands as well as Sireniki, Yuit, Chukchi, Buryat, Khamnigan, Yakut, and Evenk peoples. Hg D2 is not found in any European and Inuit populations, and that determined that there was no contamination from the excavators.

Unlike the other ancient DNA paper we heard about earlier this week, the authors of this paper decided to sequence the complete ancient human mtDNA genome. The FLX sequencing-by-synthesis developed by 454 Life Sciences and Roche Diagnostics was used primarily, as well as traditional pyrosequencing for shorter segments. The genome was sequenced approximately 11 times over and approximately 16,497 bp of the 16,569 base pairs genome was assembled. All of the Hg-diagnostic SNPs they found in their first pass, the HSV 1 trial, were re-confirmed, further validating no contamination.

Comparing the Saqqaq genome to the Cambridge Reference Sequence indicated the Saqqaq differs at 40 SNPs. At these 40 SNPs, no detectable contamination or mosaic sequence variation was found. Comparing this nearly complete mtDNA genome to 300 complete Native American mtDNA genome sequences indicates that the Saqqaq sample is distinctly different from modern and ancient Neo-Eskimo people. From the paper,

“The sample is closely related to D2a1a, a common mtDNA haplogroup found among Aleuts, in particular those of the Commander Islands, who are descendants of a forced colonization of the Medny and Bering Islands in the mid 19th century. The sample is also closely related to a subset of the Siberian Sireniki Yuit. However, the Saqqaq sequence is unique, and does not share specific mutations with these groups (n.p. 8,910 for D2a1a and n.p.16111-16366 for D2a1b) but rather branches off of the root of D2a1 on the basis of two homoplasmic (n.p.14226-16092) and the putatively heteroplasmic (n.p.11234) private mutations.

Based on the contemporary Sireniki Yuit and Aleutian mtDNA data, the coalescence of the D2a1 clade was estimated to 2,000±3,400 years using the synonymous transition clock (23) or 7,500±4,500 years when the clock is calibrated over all coding region sites.”

This cladogram provided in the original paper documents the differences much better:

The observation that ‘Hg D2 derives from an Asian specific Hg D4e and not from any of the 5 Native American founding haplogroups,’ indicates to the authors that migrations that first lead human populations to colonize the far North of the New World all the way to Greenland first. This is not a crazy claim, we now know there were multiple migrations into the Americas and the current mitochondrial diversity of Native Americans indicates very few ancestral mothers, but with this new study we now know the diversity of Native Americans was at least diverse in at least one more lineage.

    Gilbert, M.T., Kivisild, T., Gronnow, B., Andersen, P.K., Metspalu, E., Reidla, M., Tamm, E., Axelsson, E., Gotherstrom, A., Campos, P.F., Rasmussen, M., Metspalu, M., Higham, T.F., Schwenninger, J., Nathan, R., De Hoog, C., Koch, A., Moller, L.N., Andreasen, C., Meldgaard, M., Villems, R., Bendixen, C., Willerslev, E. (2008). Paleo-Eskimo mtDNA Genome Reveals Matrilineal Discontinuity in Greenland. Science DOI: 10.1126/science.1159750

17 thoughts on “4,000-year-old frozen hair mtDNA sequenced from a Greenlandic Saqqaq settlement

  1. Are you asking about the outer space detail? ‘Cause I noticed that. Or are you asking about the angle of the map?


  2. My best guess is that a bunch of geneticists, biologists, archaeologists, and geologists publishing in one of the most prestigious science journals still feel a need to reaffirm their artistic freedom.


  3. Nice exposition, specially the mtDNA tree. But, as I have mentioned elsewhere (several times already), it is a known archaeological and oral-history fact that the Inuits, who are documented in Alaska only since c. 500 CE, replaced a former arctic population they called the Tuniit. Archaeologically they are described as Dorset culture (and the Inuit as Thule culture) and the replacement happened between 1000 and 1500 CE.

    So while the mtDNA findings are interesting in itself, the fact that some other ethnicity was in the American Arctic before the Inuits is not breaking news at all. Also the mtDNA fits with the model of a Beringian homeland for all succesive waves (the Na-Dene, who are the ones with Y-DNA C3 almost exclusively, could be another secondary wave as well).

  4. Hey Luis,

    Are you saying this Saqqaq culture were Dorset, or predecessors of Dorset peoples? I wanna make sure because the carbon dating from this site is at 3,900-2,500 years old (I rounded up in the blog), which is at least 1,500 years before Dorset artifacts are recognized.


  5. You got me with that, Kambiz. I just noticed that it was well known that Inuit were pretty recent and that some other people (Dorset) were before them – so there is some fallacy in the claim of newly discovered several waves in any case: we knew already that the Inuits were not the first ones over there. But if these are pre-Dorset, that I don’t know. It’s not like I have paid too much attention to arctic archaeology really, sorry.

    Still now that I look at it I am not sure. This site (http://www.civilization.ca/cmc/archeo/cvh/arctic/earc7.htm), for instance, first argues with you that the Dorset culture began c. 1000 BCE and then says that by 1000 CE, their “culture had developed in the isolation of the Canadian Arctic over the previous 3,000 years”, what would mean a beginning c. 2000 BCE instead.

    If so this would agree with your C14 dates.

    But in any case I’m not the one able to clarify this point (if he Saqqaq are proto-Dorset or just pre-Dorset).

  6. It seems my post didn’t make it through. :(

    Anyhow, Kambiz: my real point was to say that there is a fallacy in claiming that these aDNA findings show something we did not know. We already knew that the Inuits were not the first in the American Arctic.

    Now if this Saqqaq people are Dorset, proto-Dorset or pre-Dorset, I don’t know. It’s not my primary area of interest, really. But looking at one site (http://www.civilization.ca/cmc/archeo/cvh/arctic/earc7.htm), I see that they first declared Dorset to begin at c. 1000 BCE but then they claim that by 1000 CE their “culture had developed in the isolation of the Canadian Arctic over the previous 3,000 years”, what would make their initial stages be c. 2000 BCE in agreement with the C-14 dates you mention.

    Can’t clarify anymore, sorry.

  7. “Hey Luis,

    Are you saying this Saqqaq culture were Dorset, or predecessors of Dorset peoples? ”

    I tried yesterday to reply to this but the comment would not make it through (maybe because it included a link?). I really don’t know how old are the Dorset or how could be related to the Saqqaq but I read contradictory dates of both 1000 BCE and 2000 BCE. In the second case it would fit with your C-14 dates fully.

    Anyhow, I see with pleasure that you have posted a second review of the paper’s conclusions, with interesting genetic considerations they seem to have ignored.

  8. “To clarify, Dr. German Dziebel posted the second entry on this study.”

    I meant “you” as in “you” (plural) :)

    Anyhow, I could not find where it says who posted what. Most blogs, and specially muti-author blog state that.

    “Good timeline for Eskimo cultures…”

    Very nice, thanks. :)

  9. Yeah, I know most multi-author blogs distinguish inside the blog post who authored it, but because WordPress.com is running this blog, I don’t have the ability to change this theme and add the feature. Anyways, I know that’s the case and I just wanted to clarify so there’s no confusion.

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