PAINT-BY-BASE PAIR: Thanks to speedy sequencing (and some nearly forgotten hair and bone fragments), researchers have for the first time been able to decode a thorough genome for an ancient human. Image: NUKA GODFREDSEN
When a man died some 4,000 years ago in what is now western Greenland, he probably had no idea that his remains would provide the first genetic portrait of people of his era. This man, known now as "Inuk" (a Greenlandic term for "human" or "man") left for posterity just four hairs and a few small fragments of bone frozen in permafrost, but that is now all researchers need to assemble a thorough human genome.
And Inuk has just had his code cracked.
The researchers were able to sequence about 80 percent of the ancient genome, which is "comparable to the quality of a modern human genome," Eske Willerslev, director of the Center for Ancient Genetics at the University of Copenhagen, said at a press conference held in the England February 9. He and his team, led by Morten Rasmussen, an assistant professor at the University, were able to sequence about three billion base pairs (the human genome includes just over this amount), which is a finer resolution than that of previous genetic work on Neandertals and mammoths. Their findings will be published February 11 in the journal Nature. (Scientific American is part of Nature Publishing Group.)
At this level of resolution, the researchers noted, individual features and traits began to emerge. "The guy had most likely brown eyes, brown skin" as well as a genetic predisposition for baldness, Willerslev said. The presence of hair, then, might signal that he was rather young when he died and had yet to lose most of his hair, they noted. The genome also tells us Inuk had the recessive gene for dry earwax (as opposed to the more common wet form) and "a metabolism and body mass index commonly found in those who live in cold climates," David Lambert and Leon Huynenboth of the School of Biomolecular and Physical Sciences at Griffith University in Queensland, Australia, wrote in a commentary that accompanies the study.
Aside from painting a detailed picture of the individual the base pairs belonged to, the ancient code can tell scientists a lot about early human migration, much of which has so far been gleaned from archaeological sites and genetic studies of more contemporary people.
The researchers estimate that Inuk's forbearers arrived in the northern New World (which includes Alaska, Canada and Greenland) some 5,500 years ago, but neither they nor he are closely related to the populations of people that inhabit that part of the globe today, as many have proposed.
"People have been puzzled by the relation of these inhabitants," Willerslev said. Two subsequent waves of cultures arrived in the Arctic area, and this new genetic study shows that Inuk's group, of the Saqqaq culture, was of the earliest and does not appear to have intermixed with later inhabitants. "We can show that this individual was neither a direct relative of Inuits or Native Americans," Willerslev said. In fact, Rasmussen noted, "their closest living relatives are [a population] in Siberia now." Such a definitive finding might clear up some of the mystery surrounding this culture's origins, which Lambert and Huynen described as "hotly debated." But it still does not reveal just how or why the Saqqaq came to Greenland in the first place—or what caused their eventual demise.
Inuk's remains were originally retrieved in the 1980s, the researchers noted, but then largely forgotten. This period of obscurity actually helped to render them good candidates for sequencing, as it minimized the potential for contamination with contemporary human genetic material. "The main difficulty with such work is that almost all excavated ancient tissues are contaminated with modern human DNA, not to mention substantial numbers of fungal and bacterial colonies," Lambert and Huynen wrote in their commentary. To overcome this challenge, the researchers studying Inuk found that everyone who was known to have handled the samples was of European descent, so they could test for contamination by looking for traces of modern European DNA. If it had been handled by someone with a similarly Asian background, the results might have been a little hazier, the researchers explained at the press conference. Hair, as opposed to bone or other biological materials, is also typically less prone to fungal or bacterial growth, they said.
Although Inuk's genome is the first ancient sample to be thoroughly sequenced, the researchers do not expect that it will be the last. More rapid and accessible sequencing is feeding the field, Rasmussen noted. "As prices go down, it will be easier to do these types of projects," he said. Indeed, noted Lambert and Huynen in their commentary: "We have an increasingly powerful forensic tool with which to 'reconstruct' extinct humans and the demographics of populations."