Ancient DNA points to additional New World migration

A 4,000-year-old Greenland man just entered the scientific debate over the origins of prehistoric populations in the Americas.

A nearly complete sequence of nuclear DNA extracted from strands of the long-dead man’s hair — the first such sequence obtained from an ancient person — highlights a previously unknown and relatively recent migration of northeastern Asians into the New World about 5,500 years ago, scientists say.

An analysis of differences, or mutations, at single base pairs on the ancient Greenlander’s nuclear genome indicates that his father’s ancestors came from northeastern Siberia, report geneticist Morten Rasmussen of the Natural History Museum of Denmark in Copenhagen and his colleagues in the Feb. 11 Nature. Three modern hunter-gatherer groups in that region — the Nganasans, Koryaks and Chukchis — display a closer genetic link to the Greenland individual than do Native American groups living in cold northern areas of North America, Rasmussen says.

A largely complete mitochondrial DNA sequence from the ancient man’s hair, extracted by the same researchers in 2008, places his maternal ancestry in northeastern Asia as well.

Danish-led excavations more than 20 years ago unearthed four fragmentary bones and several hair tufts belonging to this ancient man, dubbed Inuk. His remains were found at a site from the Saqqaq culture, the earliest known people to have inhabited Greenland. Saqqaq people lived in Greenland from around 4,750 to 2,500 years ago. One popular hypothesis traces Saqqaq ancestry to Native American groups that had settled Arctic parts of Alaska and Canada by 11,000 years ago.

Inuk’s strong genetic ties to Siberian populations raise a different scenario. “We’ve shown that this ancient individual was not related to Native Americans but derived from an expansion of northeastern Asians into the New World and across to Greenland,” says geneticist and study coauthor Eske Willerslev of the University of Copenhagen.

The team’s new comparative analysis of Inuk’s previously sequenced mitochondrial DNA indicates that the Saqqaqs diverged from their closest present-day relatives, Siberian Chukchis, an estimated 5,400 years ago. That calculation implies that ancestral Saqqaqs separated from their Asian relatives shortly before departing for the New World and rapidly traversing that continent to reach Greenland. No land bridge connected Asia to North America at that time, so migrants probably crossed the Bering Strait from what’s now Russia to Alaska by boat, Willerslev speculates.

His group also identified base pair patterns on Inuk’s nuclear DNA that are associated in modern populations with type A-positive blood and brown eyes, as well as thick, dark hair and large, flat front teeth typical of Asians and Native Americans. Inuk also possessed DNA signatures for an increased susceptibility to baldness, dry earwax characteristic of Asian populations, and a relatively slow metabolism and broad, short body commonly found in residents of cold climates.

DNA analyses of ancient humans and their ancestors usually face enormous technical challenges. Fossil bones get contaminated with the DNA of those who unearth these finds as well as with fungal and bacterial DNA. Measures to enrich ancient DNA include generating multiple samples of the same genetic sequences and isolating genetic fragments that show no signs of contamination.

Because DNA from hair contains little contamination from fungi or bacteria, Rasmussen’s team focused on Inuk’s locks. Frozen conditions following death also helped to preserve Inuk’s DNA and prevent significant contamination. The team generated 20 copies of his genome to confirm that significant contamination had not occurred.

About 84 percent of the DNA extracted from Inuk’s hair was his. Rasmussen’s team then sequenced 79 percent of Inuk’s nuclear DNA and identified more than 353,000 base pair mutations.

“It is amazing how well-preserved this ancient genetic sample is, presumably due to its rather young age and the permafrost in which it was found,” remarks geneticist Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

In contrast, 40,000- to 70,000-year-old Neandertal bones studied by Pääbo’s team have yielded genetic sequences that, because of substantial contamination, generally include no more than 4 percent Neandertal DNA. Pääbo and his colleagues recently extracted and sequenced 63 percent of the total Neandertal genome from a bone (SN: 3/14/09, p. 5).  “I am envious,” Pääbo says, referring to the completeness and quality of Inuk’s recovered DNA.

Rasmussen and Pääbo agree that a major challenge will be to sequence ancient human genomes from places where remains have not been permanently frozen and most preserved genetic material consists of microbial, rather than human, DNA.

Another challenge is to gain a firmer grasp of genetic variation in modern Arctic populations, so that scientists can more precisely trace Inuk’s geographic roots. “It will become easier to make sense of the genetic data from Greenland as more and more present-day humans become sequenced over the next few years,” Pääbo says.