February 10, 2010

Paleo-Eskimo whole genome sequenced

From a related NY Times story:
The Greenlander belonged to a Paleo-Eskimo culture called the Saqqaq by archaeologists. On the basis of his genome, the Saqqaq man’s closest living relatives are 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 the Saqqaq people’s ancestors must have traveled across the northern edges of North America until they reached Greenland.

...

The Saqqaq man’s genome is so complete that the Danish researchers have been able to reconstruct his probable appearance and susceptibility to disease from the genetic information in his genome. They predict he would have had brown eyes because of variations, at four positions along his DNA, that are associated with brown eye color in East Asians.

He has the East Asian version of a gene known as EDAR, which endows people with hair that is thicker than that of most Europeans and Africans. Another gene suggests he would have had dry earwax, as do Asians and Native Americans, not the wet earwax of other ethnic groups.

Perhaps reflecting the so far somewhat limited reach of personal genomics, the researchers note that the ancient Greenlander was at risk for baldness, a surprising assessment given that all that remains of him is his hair. Dr. Rasmussen said he assumed the man died young.
The importance of this sequence is that it offers us a glimpse into a man who lived before 4,000 years of recent evolution. Obviously we will need to sample more individuals before we can speak about evolutionary change across this time span, and doing so for anyone living in more southernly latitudes where most of humankind have always lived will be tricky.

Nature 463, 757-762 doi:10.1038/nature08835

Ancient human genome sequence of an extinct Palaeo-Eskimo

Morten Rasmussen

Abstract

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.

Link

24 comments:

marnie said...

http://www.atanarjuat.com/

timmers0 said...

This kind of post, describing genetic links and related phenotype is exactly why I regularly visit your blog.

Thank you for all the amazing posts, you're motivating me to actually learn what a "diploid" is.

Crimson Guard said...

This doesnt make complete sense to me as I was reading this early today on news.yahoo.com.

http://news.yahoo.com/s/ap/20100210/ap_on_sc/us_sci_ancient_dna


I do not think Eskimos go bald,lol. But granted I do not know to much about those people nor how Siberians would've marched all the way across the other side of the world to Greenland. However it is known that Mongoloids seldom go bald. Dry earwax percentages exist in Europeans and in areas not touched by Mongoloids or semi-Mongoloid peoples. Also why do they give Blood type A(ok in this case more specific A+)? That isnt very common among Mongoloids, but more common among Scandinavians and such. They shouldve gave the legit Y chromo./mtDNA/Autosomal.

PS

Dienekes the person over at The spittoon has a decent write on this story to(Plus an illustration):

http://spittoon.23andme.com/2010/02/10/researchers-use-snp-analysis-to-paint-picture-of-an-ancient-human/

Ebizur said...

Crimson Guard said,

"I do not think Eskimos go bald,lol."

It is true that indigenous populations of the Americas are known for having extremely low rates of baldness. I suppose even some Native Americans must go bald, though, just as there must be at least a few raven-haired, brown-eyed Swedes among all the blondes.

"Also why do they give Blood type A(ok in this case more specific A+)? That isnt very common among Mongoloids, but more common among Scandinavians and such."

A+ is not only the most common blood type among Northern Europeans, but also among Japanese, for example. It is certainly not a powerful indicator of an individual's ancestry.

terryt said...

"nor how Siberians would've marched all the way across the other side of the world to Greenland".

According to Dienekes 'the Saqqaq man’s closest living relatives are the Chukchis, people who live at the easternmost tip of Siberia'. Presumably he or his ancestors entered when it was relatively easy to cross the American continent's far north. And I'm sure I've read before that an early Arctic population died out and were replaced by the modern Inuit.

eurologist said...

They shouldve gave the legit Y chromo./mtDNA/Autosomal.

Not sure what you mean by that. The autosomal comparison indicates virtually no European admixture, and also no Native American one. Basically, just East Asian, Siberian, and one that may be best described as Beringian. At any rate, the Y-haplogroup is Q1a, mtDNA is D2a1 (from a previous publication).

marnie said...

Dienekes:

Is there any data on distribution of the EDAR thick hair fiber gene in Europe or SW Asia?

Ponto said...

You have to take some of those SNP results on advisement. For example, according to 23andMe, deCODEme and Promethease, I have every SNP version for baldness. I am not bald, don't even have the typical male hair pattern that young men have which shows the start of male pattern baldness. Obviously the SNPs are indicators, and are not 100%. I am fully intact with your are thinking about that, four children (adults,I was a child husband), and I am 57 years old. I have grandchildren also. My sons are not bald either.

The SNPs tested were printed in 23andMe. They applied to everyone, the higher BMI SNPs, the cold adaptation SNPs, the eye color SNPs (they are the same for all races, ethnic groups whether Chinese, Greek or Ethiopian) and the SNP used for hair color occurs in Caucasians who have pale white skins combined with black or black/brown hair. Some are East Asian specific: the ear wax, the stiffness/thickness of hair which also indicates shoveled shaped incisor teeth. So overall, little is specific to East Asians.

I found the picture of Inuk amusing especially his receding hairline. It is less likely for East Asians to be bald as often as Europeans even with the same baldness SNPs.

terryt said...

"mtDNA is D2a1 (from a previous publication)".

That's intersting. From old data I have the Greenland Eskimos are almost exclusively A. Supports the replacement scenario.

eurologist said...

I just googled "shoveled shaped incisor teeth" and found this in forensicdentistryonline.org :

Shovel shaped incisors display enhanced marginal ridges and present with a distinctive shovel-shaped appearance on the lingual aspect. They appear frequently in many persons of Asian origin, including many Native American Indians. They are especially prominent in Eskimo/Inuit who are descendants of Siberians about 4,000 years ago.

No idea were they came up with this - but nevertheless interesting convergence of conclusions. I am still worried a bit about the time line, though. Are 4,000 to 5,000 years enough to broadly change today's Inuits to include significant Amerindian autosomal material?

eurologist said...

Terry,

The papers reference for mtDNA (Paleo-Eskimo mtDNA Genome Reveals Matrilineal Discontinuity in Greenland; Science 27 June 2008: Vol. 320. no. 5884, pp. 1787 - 1789) gives D3 as a related "NeoEskimo" line. No idea how prevalent that is.

這一定 said...

嫉妒能使人得到短暫的快感,但也能使不幸更辛酸。 ..................................................

pconroy said...

这就是神秘,你是什么意思?

marnie said...

http://www.nature.com/nature/
journal/v449/n7164/full/
nature06250.html

terryt said...

Thanks eurologist.

"They appear frequently in many persons of Asian origin, including many Native American Indians".

Also Neanderthals I think, especially the eastern ones.

"Are 4,000 to 5,000 years enough to broadly change today's Inuits to include significant Amerindian autosomal material?"

Possibly, if just a small group came in and mixed with the locals to the south.

terryt said...

I can't read pconroy's last comment, nor the one before. Anyone else having that problem?

Ebizur said...

terryt said,

"I can't read pconroy's last comment, nor the one before. Anyone else having that problem?"

Please ignore those comments. You can't read them because they are written in Chinese. The first one is nothing but porn spam, anyway.

eurologist said...

Possibly, if just a small group came in and mixed with the locals to the south.

I agree for some parts - like Alaska (you can even see tendencies of that when you drive through). But Greenland is pretty isolated. I mean, it's not like there is a superhighway going in from the mainland. Of course, the area is also affected by periodic climate fluctuations (even during historic times) - so it is possible that there were several waves that almost displaced or replaced previous occupations.

Paul_Johnsen said...

I agree for some parts - like Alaska (you can even see tendencies of that when you drive through). But Greenland is pretty isolated. I mean, it's not like there is a superhighway going in from the mainland. Of course, the area is also affected by periodic climate fluctuations (even during historic times) - so it is possible that there were several waves that almost displaced or replaced previous occupations.

Total displacement during the last 1,000 years at least: The Norse texts doesn't mention Inuits at all. So there were no Eskimos in Greenland 1200 AD.

eurologist said...

The Norse texts doesn't mention Inuits at all. So there were no Eskimos in Greenland 1200 AD.

Does archaeology agree with this?

pconroy said...


there were no Eskimos in Greenland 1200 AD.


The Western Greenland Norse colony may have encountered Inuit in the 1450's AD, that had spread North to South from the Disko Bay area.

There is still debate whether the Medieval Cold Period killed off the Norse, or whether their end came at the hands of the Inuit. Whatever happened, they left their settlement in a hurry, leaving most of their possessions behind them...

terryt said...

"like Alaska (you can even see tendencies of that when you drive through). But Greenland is pretty isolated".

The mixing may have happened in Alaska on their way to Greenland though.

"it is possible that there were several waves that almost displaced or replaced previous occupations".

That seems pretty likely judging from this post and the comments.

"There is still debate whether the Medieval Cold Period killed off the Norse, or whether their end came at the hands of the Inuit".

Jared Diamond, in his book "Collapse", argues a pretty strong case that it was inappropriate over-exploitation of resources combined with the effects of the Medieval Cold Period. He mentions instances of starving Inuit visiting Norse farms looking for food, so the climate change was difficult for them too.

Andrew Oh-Willeke said...

"The Norse texts doesn't mention Inuits at all. So there were no Eskimos in Greenland 1200 AD.

Does archaeology agree with this?"

The archaeology suggests that this civilization died around 800 BC, around 2000 years before the Norse showed up, and that they inhabited Greenland (mostly on the West Coast) for many centuries. The archaeology also supports the idea that they had at least some ability to travel by water.

But, the lack of extant survivors suggests that they didn't admix much with the Inuit and stayed pretty narrow in range.

There is a fair amount of pre-historic evidence that ancient humans at similar levels of technology avoided encroaching on each other's turf. They may have skirted Inuit territory until they reached then uninhabited Greenland.

Given the length of their civilization's survival, one would think that the Greenland population quickly reached a population of at least a few hundred. But, Greenland wouldn't have supported all that many people in what appears to have been a hunter-gatherer society, albeit a rather prosperous one, largely confined to the coasts. The whole coastal region is a few thousand square miles and most of the archeological evidence comes from areas on the Western coast with perhaps a tenth of that area. So, there probably weren't more than a few thousand of them at the peak.

Perhaps, if they followed the stars closely, they were driven to go East by the belief that this could take them home on the circle route and then got stuck when they hit the Greeland Sea, sort of the Columbus story in reverse, and then decided it wasn't worth the trouble to try to make their way home. Other cultures were developing pretty detailed star charts by then.

terryt said...

"The Norse texts doesn't mention Inuits at all. So there were no Eskimos in Greenland 1200 AD".

According to Diamond, 'Incredibly, during the centuries that those people shared Greenland, Norse annals include only two or three brief references to the Inuit'. He then quotes from three, the first of which he suggests 'may refer to either the Inuit or else Dorset people because it describes an incident from the 11th or 12th century, when a Dorset population still survived in Northwest Greenland, and when the Inuit were just arriving'.

On checking I find his comments about starving Inuit refers to a later period. 'In Danish colonial times it happened often that an Inuit would stagger into a Danish settlement, saying that he or she was the last survivor of some Inuit settlement all of whose other members had died of starvation'.