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Denisovan Admixture and the First Modern Human Dispersal into Southeast Asia and Oceania

Recent genetic research has shown that the ancestors of the native population of New Guinea and the people of Bougainville have inherited part of their genetic material from Denisovans. There has been only sparse sampling of Southeast Asian and Oceanian populations for analysis. In this paper Reich et al. quantify the admixture of Denisovan genetic material in 33 additional populations from Asia and Oceania. Genetic material from Denisovans has been inherited by Australian Aboriginals, Near Oceanians, Polynesians, Fijians, east Indonesians (west New Guineans), and Mamanwa (a “Negrito” group from the Philippines), though populations from mainland East Asia, western Indonesia, Jehai (a Negrito group from Malaysia), and Onge (a negrito group from the Andaman Islands), have not inherited Denisovan genetic material. It is indicated by these results that the flow of genes from Denisovans occurred into common ancestors of New Guineans, Australians, and Mamanwa, though not into the ancestors of the Jehai and Onge which also indicates that relatives of East Asians of the present were not in Southeast Asia when the genes from Denisovans entered the genomes of those who received the Denisovan genes. The findings of this study, the descendants of the earliest inhabitants of Southeast Asia do not all have the admixture of Denisovan genetic material is not consistent with a history in which the interbreeding with Denisovans took place in mainland Asia after which it spread over Southeast Asia, leading to all of the earliest modern human inhabitants of Southeast Asia having the admixture. Instead of this the most parsimonious interpretation of the data suggests the Denisovan gene flow actually occurred in Southeast Asia. According to this scenario archaic Denisovans must have occupied an extraordinary extensive territory stretching from Siberia to tropical Asia.


It has been shown by this study that modern humans settled Southeast Asia in waves: The ancestors of the present-day Onge, Jehai, Mamanwa, New Guineans, and Australians, some of whom admixed with Denisovans, and a second wave that contributed much of the ancestry of the present East Asians and Indonesians. Reich et al. suggest that this scenario in which the human dispersals are broadly consistent with the archaeologically-motivated hypothesis that there was an early migration by the southern route that led to the colonisation of Southeast Asia (2) though it also clarifies this scenario. In particular, no evidence of multiple dispersals of modern humans out of Africa is provided by the data of Reich et al., as all non-Africans have amounts of Neanderthal DNA that are statistically indistinguishable (12,18). The data produced by this study are instead consistent with a single dispersal out of Africa (as has been proposed by some southern route hypotheses (1), from which there were then multiple dispersals to South and East Asia.

According to Reich et al. this study also provides a clue concerning the geographic location of the flow of Denisovan genes. It is difficult to use genetic data from populations of the present to infer the location of demographic events in the past with a high degree of confidence, given the high mobility of human populations. It has been found that Denisovan genetic material is present in eastern Southeast Asians and Oceanians, which includes Mamanwa, Australian Aboriginals and New Guineans, but not in west Asians, the Onge and Jehai, or from the northwest, the Eurasian continent, which suggests that the location of the interbreeding may have been in Southeast Asia. The results from the study reported in this paper uncovered further evidence from locations in Southeast Asia of ancient gene flow from relatives of the Onge and Jehai into the common ancestors of Australian Aboriginals and New Guineans following the initial flow of genes from Denisovans; and it is suggested by this that the ancestors of both these groups, though not East Asians, were present in the region at the time. Reich et al. suggest that an alternative history in which some genetic material of Denisovans was initially present throughout Southeast Asia – which was subsequently displaced by subsequent migrations of populations related to populations of present-day East Asians – though such a history cannot, according to Reich et al., parsimoniously explain the absence of Denisovan genetic material in the Onge and Jehai. It is therefore suggested by the evidence from Southeast Asian locations for the Denisovan admixture, which has been presented in this paper, that the Denisovans were spread throughout a wider ecological and geographic region, stretching from the deciduous forests of Siberia to the tropics, than any hominin other than modern humans.

Reich et al. suggest this study is methodically important as it shows that there is much to learn about the relationships among modern humans by the analysis of patterns of genetic material that was contributed by archaic humans. Archaic genetic material is easily detected in the genomes of a modern human, even if only a small proportion of the ancestry is contributed, as the archaic genetic material is highly divergent; this makes possible the use of archaic genetic material to study the ancient gene flow in the same manner as dye material that has been injected into a medical patient allows the tracing of blood vessels. Reich et al. suggest a priority for future research should be to obtain direct dates for the gene flow from Neanderthals and Denisovans, as these will provide a better understanding of interactions among Neanderthals, Denisovans and ancestral populations of the modern human populations of the present.

Sources & Further reading

  1. Reich, D., N. Patterson, M. Kircher, F. Delfin, Madhusudan R. Nandineni, I. Pugach, Albert M.-S. Ko, Y.-C. Ko, Timothy A. Jinam, Maude E. Phipps, N. Saitou, A. Wollstein, M. Kayser, S. Pääbo and M. Stoneking "Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania." The American Journal of Human Genetics 89(4): 516-528.


Author: M. H. Monroe
Last updated: 01/06/2016
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