Genetic ‘trace’ in ancient genomes suggests previously unknown expansion out of Africa

A new study of human genomic diversity suggests there may have in fact been two successful dispersals out of Africa, and that a “trace” of the earlier of these two expansion events has lingered in the genetics of modern Papuans.  

Three major genetic studies are published today in the same issue of Nature. All three agree that, for the most part, the genomes of contemporary non-African populations show signs of only one expansion of modern humans out of Africa: an event that took place sometime after 75,000 years ago.   

Two of the studies conclude that, if there were indeed earlier expansions of modern humans out of Africa, they have left little or no genetic trace. The third, however, may have found that ‘trace’. 

This study, led by Drs Luca Pagani and Toomas Kivisild from the University of Cambridge’s Department of Archaeology and Anthropology, has found a “genetic signature” in present-day Papuans that suggests at least 2% of their genome originates from an even earlier, and otherwise extinct, dispersal of humans out of Africa.

Papuans and Philippine Negritos are populations that inhabit Papua New Guinea and some of the surrounding islands in Southeast Asia and Oceania. In the genomes of these populations, the researchers discovered more of the African ‘haplotypes’ – groups of genes linked closely enough to be inherited from a single source – than in any other present-day population.   

Extensive analysis on the extra 2% of African haplotypes narrowed down the split between African (Yoruban) and Papuan lineages to around 120,000 years ago – a remarkable 45,000 years prior to the very earliest that the main African expansion could have occurred.  

The study analysed genomic diversity in 125 human populations at an unprecedented level of detail, based on 379 high resolution whole genome sequences from across the world generated by an international collaboration led by the Cambridge team and colleagues from the Estonian Biocentre.  

Lead researcher Luca Pagani said: “Papuans share for most part same evolutionary history as all other non-Africans, but our research shows they may also contain some remnants of a chapter that is also yet to be described.

“While our research is in almost complete agreement with all other groups with regard to a single out-of-Africa event, this scenario cannot fully account for some genetic peculiarities in the Papuan genomes we analysed.”

Pagani says the sea which separates the ‘ecozones’ of Asia and Australasia may have played a part: “The Wallace line is a channel of deep sea that was never dry during the ice ages. This constant barrier may have contributed to isolating and hence preserving the traces of the otherwise extinct lineage in Papuan populations.”

Toomas Kivisild said: “We believe that at least one additional human expansion out of Africa took place before the major one described in our research and others. These people diverged from the rest of Africans about 120,000 years ago, colonising some land outside of Africa. The 2% of the Papuan genome is the only remaining trace of this otherwise extinct lineage.”

The Estonian Biocentre’s Dr Mait Metspalu said: “This endeavour was uniquely made possible by the anonymous sample donors and the collaboration effort of nearly one hundred researchers from 74 different research groups from all over the world.”

Metspalu’s colleague Richard Villems added: “Overall this work provides an invaluable contribution to the understanding of our evolutionary past and to the challenges that humans faced when settling down in ever-changing environments.”

Researchers say the deluge of freely available data will serve as future starting point to further studies on the genetic history of modern and ancient human populations.