Out of Africa: DNA Analysis Points to a Single Major Exodus

Posted on September 27, 2016 by Dr. Francis Collins

Credit: NASA

If you go back far enough, the ancestors of all people trace to Africa. That much is clear. We are all Africans. But there’s been considerable room for debate about exactly when and how many times modern humans made their way out of Africa to take up residence in distant locations throughout the world. It’s also unclear what evolutionary or other factors might have driven our human ancestors to set off on such a perilous and uncertain journey (or journeys) in the first place.

By analyzing 787 newly sequenced complete human genomes representing more than 280 diverse and understudied populations, three new studies—two of which received NIH funding—now help to fill in some of those missing pages of our evolutionary history. The genomic evidence suggests that the earliest human inhabitants of Eurasia came from Africa and began to diverge genetically at least 50,000 years ago. While the new studies differ somewhat in their conclusions, the findings also lend support to the notion that our modern human ancestors dispersed out of Africa primarily in a single migratory event. If an earlier and ultimately failed voyage occurred, it left little trace in the genomes of people alive today.

In one of the three studies published in Nature [1], NIH grantee David Reich of Harvard Medical School, Boston, and colleagues report on the genome sequences of 300 people from 142 different populations around the globe. The DNA samples, part of the Simons Genome Diversity Project, were carefully chosen to span much of the variation in human genetics, language, and culture. In a stroke of good timing, David spoke at NIH this past week, so I had a chance to query him about these results.

The new analysis of this diverse DNA dataset suggests that the ancestors of all present-day humans had slowly begun to split into distinct populations as long as 200,000 years ago. By 100,000 years ago, the ancestors of some contemporary human populations, including various populations of hunter-gatherers within Africa, already showed substantial differences at the genetic level. That’s well before the archaeological evidence shows signs of more modern human behavior, including use of more complex tools and ornaments, such as necklaces.

As for people outside of Africa, the researchers estimate that the most ancient genetic differences go back about 50,000 years. That’s consistent with earlier evidence that modern humans made their way from Africa into Eurasia at about that time.

All three studies weigh in on the long-standing debate among experts over whether the ancestors of Aborigines in Australia and Papuans in New Guinea might have departed Africa some 120,000 or 130,000 years ago, well prior to the event that brought the first people to Eurasia. Reich and his colleagues report no evidence in their sequence data for such an earlier dispersal of modern humans.

That’s the general conclusion also of a second Nature report led by Eske Willerslev of the University of Copenhagen in Denmark [2]. Willerslev and colleagues generated high quality genomes for 83 Aborigines and 25 individual Papuans covering most of the Australian continent and the New Guinea Highlands. They estimated that Aborigines and Papuans have been separated for the last 37,000 years, long before the physical split of their shared ancient continent known as Sahul. The researchers further concluded that Australian Aborigines and Papuans from New Guinea diverged from Eurasians about 58,000 years ago, consistent with the hypothesis of a single out-of-Africa excursion.

In the third Nature study [3], Luca Pagani and Mait Metspalu of the Estonian Biocentre in Tartu and their colleagues analyzed 483 human genomes (including 379 newly generated genome sequences). Collectively, the genomes represented 125 populations from around the world.

They propose a slightly different model, including echoes of a potential earlier migration. While their analyses suggest that the genomes of modern Papuans derive primarily from a single migration of humans out of Africa, they report traces of DNA—accounting for at least 2 percent of the Papuan genome—reflecting a perhaps earlier and otherwise extinct out-of-Africa migration. These results lead them to suggest that modern humans living outside of Africa more than 75,000 years ago may have contributed a little bit of ancestry to non-Africans living today.

As for what might have driven our ancestors to make such an uncertain voyage all those years ago, of course we’ll never have the full story. But Reich and colleagues say they see no evidence that one or a few major genetic mutations would have produced any shift in human traits and behavior since the time of that fateful departure. Instead, they contend it’s more likely that cultural and environmental changes exerted a selective influence on mating and survival, and so were most likely to be the ultimate driving forces spurring the transformations that made Homo sapiens who we are today.

References:

[1] The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Mallick S et al. Nature. 21 September 2016. [Epub ahead of print]

[2] Genomic analyses inform on migration events during the peopling of Eurasia. Pagani L et al. Nature. 21 September 2016. [Epub ahead of print]

[3] A genomic history of Aboriginal Australia. Malaspinas AS et al. Nature. 21 September 2016. [Epub ahead of print]

Links:

Simons Genome Diversity Project (Simons Foundation, New York, NY)

Reich Lab (Harvard Medical School, Boston)

Estonian Biocentre (Tartu, Estonia)

Eske Willerslev (Natural History Museum of Denmark)

NIH Support: National Institute of Environmental Health Sciences; National Institute of Diabetes and Digestive and Kidney Diseases; National Institute of General Medical Sciences