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.

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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.

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