By Carl Zimmer (NYT)
Did humans flood out of Africa in a single diaspora, or did we trickle from the continent in waves spread out over tens of thousands of years? The question, one of the biggest in human evolution, has plagued scientists for decades.
Now they may have found an answer.
In a series of unprecedented genetic analyses published on Wednesday in the journal Nature, three separate teams of researchers conclude that all nonAfricans today trace their ancestry to a single population emerging from Africa between 50,000 and 80,000 years ago.
“I think all three studies are basically saying the same thing,” said Joshua M. Akey of the University of Washington, who wrote a commentary accompanying the new work. “We know there were multiple dispersals out of Africa, but we can trace our ancestry back to a single one.”
The three teams sequenced the genomes of 787 people, obtaining highly detailed scans of each. The genomes were drawn from people in hundreds of indigenous populations around the world — Basques, African pygmies, Mayans, Bedouins, Sherpas and Cree Indians, to name just a few.
The DNA of older indigenous populations may be essential to understanding human history, many geneticists believe. Yet until now scientists have sequenced few whole genomes from people outside population centers like Europe and China. The new findings already are altering scientific understanding of what human DNA looks like, experts said, adding a rich diversity of variation to our map of the genome.
Each team of researchers used sets of genomes to tackle different questions about our origins, such as how people spread across Africa and how others populated Australia. But all aimed to settle the question of human expansion from Africa.
In the 1980s, a group of paleoanthropologists and geneticists began championing a hypothesis that modern humans emerged only once from Africa, roughly 50,000 years ago. Skeletons and tools discovered at archaeological sites clearly indicated the existence of modern humans in Europe, Asia and Australia.
Early studies of bits of DNA also supported this scenario. All nonAfricans are closely related to one another, the studies found, and they all branch from a genetic tree rooted in Africa.
Yet there are also clues that at least some modern humans lived outside of Africa well before 50,000 years ago, perhaps part of an earlier wave of migration.
In Israel, for example, researchers found a few distinctively modern human skeletons that are between 120,000 and 90,000 years old. In Saudi Arabia and India, they discovered sophisticated tools dating back as far as 100,000 years.
Some scientists have argued from these finds that there was a human expansion from Africa earlier than 50,000 years ago. In 2011 Eske Willerslev, a renowned geneticist at the University of Copenhagen, and his colleagues reported evidence that some living people descended from this early wave.
Dr. Willerslev and his colleagues reconstructed the genome of an Aboriginal Australian from a centuryold lock of hair kept in a museum — the first reconstruction of its kind. The DNA held a number of peculiar variants not found in Europeans or Asians.
He concluded that the ancestors of Aboriginals split off from other nonAfricans and moved eastward, eventually arriving in East Asia 62,000 to 75,000 years ago. Tens of thousands of years later, a separate population of Africans spread into Europe and Asia.
It was a big conclusion to draw from a single fragile genome, so Dr. Willerslev decided to contact living Aboriginals to see if they’d participate in a new genetic study. He joined David W. Lambert, a geneticist at Griffith University in Australia, who was already meeting with Aboriginal communities about beginning such a study.
Their new paper also includes DNA from people in Papua New Guinea, thanks to a collaboration with scientists at the University of Oxford. All told, the scientists were able to sequence 83 genomes from Aboriginal Australians and 25 from people in Papua New Guinea, all with far greater accuracy than in Dr. Willerslev’s 2011 study.
Meanwhile, Mait Metspalu of the Estonian Biocentre was leading a team of 98 scientists on another genomegathering project.
They picked out 148 populations to sample, mostly in Europe and Asia, with a few genomes from Africa and Australia. They, too, sequenced 483 genomes at high resolution.
David Reich, a geneticist at Harvard Medical School, and his colleagues assembled a third database of genomes from all five continents. The Simons Genome Diversity Project, sponsored by the Simons Foundation and the National Science Foundation, contains 300 highquality genomes from 142 populations.
Dr. Reich and his colleagues probed their data for the oldest evidence of human groups genetically separating from one another.
They found that the ancestors of the KhoiSan, huntergatherers living today in southern Africa, began to split off from other living humans about 200,000 years ago and were fully isolated by 100,000 years ago.
Earlier studies had estimated that the split between living groups of humans occurred much more recently. The new findings indicate that our ancestors already had evolved behaviors seen in living humans, such as language, 200,000 years ago.
Dr. Reich and his colleagues then investigated whether people in Australia and Papua New Guinea descended from an early wave of humans from Africa. They could find no evidence supporting that idea in the genomes.
The people of Australia and Papua New Guinea descended from the same expansion of Africans that produced Europeans and Asians, Dr. Reich’s team decided
Working with a separate set of genomes, Dr. Willerslev and his colleagues came to much the same conclusion. “The vast majority of their ancestry — if not all of it — is coming from the same outofAfrica wave as Europeans and Asians,” said Dr. Willerslev.
Dr. Metspalu and his colleagues ended up with a somewhat different result when they looked at the Estonian Biocentre data.
They compared chunks of DNA from different genomes to see how long ago people inherited them from a common ancestor.
Almost all the DNA from nonAfricans today could be traced back to one population that lived about 75,000 years ago — presumably a group of Africans who eventually left the continent and settled the rest of the world. That squares with the conclusions of the other two studies.
But in Papua New Guinea, Dr. Metspalu and his colleagues found, the story was a little different. They could trace 98 percent of each person’s DNA to that 75,000yearold group. But the other 2 percent was much older.
Some people in Papua New Guinea — but no one else in the analyses — may carry a trace of DNA from a much older wave of Africans who left the continent as long as 140,000 years ago, and then vanished.
The second wave — the one from which the rest of the world descends — departed over 60,000 years later, the researchers suggest. The ancestors of the people of Papua New Guinea interbred with those first pioneers on their way east, which is why their descendants carry remarkable DNA.
Why leave Africa at all? Scientists have found some clues as to that mystery, too.
In a fourth paper in Nature, researchers described a computer model of Earth’s recent climatic and ecological history. It shows that changing rainfall patterns periodically opened up corridors from Africa into Eurasia that humans may have followed in search of food.
Huw Groucutt, an archaeologist at the University of Oxford, criticized the new studies as too simplistic. It’s incorrect, he said, to try to split nonAfricans into just two distinct groups — one 120,000 years ago, and one closer to 50,000 years ago.
He suspects that there were several early waves from Africa, whose descendants combined into a complex gene pool. “It’s probably much more about populations expanding and contracting, fusing and separating,” said Dr. Groucutt.
Luca Pagani, a coauthor of Dr. Metspalu at the University of Cambridge and the Estonian Biocentre, said that their findings suggest a population of early human pioneers were able to survive for tens of thousands of years.
But when the last wave came out of Africa, descendants of the first wave disappeared. Why?
“They may have not been technologically advanced, living in small groups,” Dr. Pagani said of the people of the early wave. “Maybe it was easy for a major later wave that was more successful to wipe them out.”