A Single Migration from Africa Populated the World, Studies Find

Carl Zimmer, New York Times, September 21, 2016

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In a series of unprecedented genetic analyses published on Wednesday in the journal Nature, three separate teams of researchers conclude that all non-Africans 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.

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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 non-Africans 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.

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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 century-old 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 non-Africans 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 genome-gathering 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 high-quality 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, hunter-gatherers 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.

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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.

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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 non-Africans 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 75,000-year-old 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.

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[Editor’s Note: Below is the abstract of one of the studies, which includes other interesting facts.]

Abstract
Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

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