Despite having an unusual skull, DNA suggests that ancient people like Brazil’s “Luzia” were related to Native Americans.

Despite having an unusual skull, DNA suggests that ancient people like Brazil’s “Luzia” were related to Native Americans.

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Mysterious link emerges between Native Americans and people half a globe away

The Americas were the last great frontier to be settled by humans, and their peopling remains one of the great mysteries for researchers. This week, two major studies of the DNA of living and ancient people try to settle the big questions about the early settlers: who they were, when they came, and how many waves arrived. But instead of converging on a single consensus picture, the studies, published online in Science and Nature, throw up a new mystery: Both detect in modern Native Americans a trace of DNA related to that of native people from Australia and Melanesia. The competing teams, neither of which knew what the other was up to until the last minute, are still trying to reconcile and make sense of each other’s data.

“Both models … see in the Americas a subtle signal from” Australo-Melanesians, notes Science co-author David Meltzer, an archaeologist at Southern Methodist University in Dallas, Texas. “A key difference is when and how it arrived in the New World.” The Nature team concludes it came in one of two early waves of migration into the continent, whereas the Science team concludes it came much later, and was unrelated to the initial peopling.

For the Science paper, nearly 4 years in the making, researchers sequenced 31 complete and 79 partial genomes from people in North and South America, Siberia, and Oceania. They compared these with previously sequenced genomes of three ancient skeletons: the 24,000-year-old Mal’ta child from Siberia, the 12,600-year-old Anzick child from Montana, and the 4000-year-old Saqqaq individual from Greenland. The team examined the genetic differences among their samples to determine how long ago various populations diverged, using the ancient genomes to calibrate this DNA clock. They concluded that all Native Americans, ancient and modern, stem from a single source population in Siberia that split from other Asians around 23,000 years ago and moved into the now-drowned land of Beringia. After up to 8000 years in Beringia—a slightly shorter stop than some researchers have suggested (Science, 28 February 2014, p. 961)—they spread in a single wave into the Americas and then split into northern and southern branches about 13,000 years ago (see map, below).

Adapted from Rhagavan et al., Science

That’s a largely familiar picture of the migration, albeit with much more precise dating. But the Science team also found a surprising dash of Australo-Melanesian DNA in some living Native Americans, including those of the Aleutian Islands and the Surui people of Amazonian Brazil. Some anthropologists had previously suggested an Australo-Melanesian link. They noted that certain populations of extinct Native Americans had long, narrow skulls, resembling those of some Australo-Melanesians, and distinct from the round, broad skulls of most Native Americans. In the so-called Paleoamerican model, Walter Neves of the University of Sao Pãolo in Brazil and Mark Hubbe of Ohio State University, Columbus, argue that these people descended from an early wave of migration that was separate from the one that gave rise to today’s Native Americans, and drew on a different source population in Asia. A similar claim was made for the Kennewick Man, the iconic 8500-year-old skeleton from Washington state, but was refuted when his genome was published by this team last month: He is related only to Native Americans (see http://scim.ag/ancientone).

The Science results also counter the Paleoamerican model. When the team sequenced the DNA of 17 individuals from the extinct South American populations with the distinctive skulls, they found no trace of Australo-Melanesian ancestry. “The analysis refutes a very simplistic view of [skull] variation,” comments anthropologist Rolando Gonzalez-Jose of the National Scientific and Technical Research Council in Puerto Madryn, Argentina.

So how did living South Americans get a dose of this Australo-Melanesian DNA? “A possible explanation is that the connection reflects more recent gene flow,” says Science co-lead author Eske Willerslev of the University of Copenhagen. By that he doesn’t mean boats crossing the Pacific, as some researchers had earlier speculated. Instead, Willerslev contends that the ancestors of some of today’s South Americans might have mixed with Asian populations related to today’s Australo- Melanesians and carried those genes into the Americas during a well-established later wave of migration from Asia that also peopled the Aleutian Islands (Science, 13 January 2012, p. 158).

Hubbe, however, counters that the study could have missed telltale DNA in the ancient populations because its sample size is “extremely small.” geneticist David Reich of Harvard Medical School in Boston and leader of the Nature team, agrees, noting that the genomes from the 17 ancient relict populations are incomplete and provide very low coverage.

His own paper also finds this mysterious Australo-Melanesian DNA in some of the same modern populations but reaches a different conclusion about its source. His team analyzed partial genome sequences of 106 Native Americans from 25 populations in Central and South America, and compared them with DNA data from 197 populations from outside the Americas. They found that some Amazonians, including the Surui people, shared about 1% to 2% of their ancestry with present-day native people from Australia, New Guinea, and the Andaman Islands. Differences in the shared DNA suggest this ancestry did not come directly from these populations, the team concluded, but through a now extinct population they call “Population Y” that may have lived somewhere in East Asia and contributed genes to both very early Paleoamericans and to Australo-Melanesians. Because the Amazonian groups are only distantly related to Population Y, the team concludes that this represents an ancient rather than recent genetic contribution that arrived in an early “pulse of migration” to the Americas.
 
And yet Reich says his data, like those of the Science team, clash with the classic Paleoamerican model, which postulates a major, more direct genetic contribution from Australo-Melanesians. In that sense, Reich says, “the two papers are not in disagreement.”

Researchers agree that more genomes from modern and ancient Native Americans are needed to unravel the mysteries. For now, says anthropologist Jennifer Raff of the University of Texas, Austin, the two papers throw open an “incredibly exciting” window on the ancestors of today’s Native Americans, as they sat poised to enter the New World.