Australia: The Land Where Time Began

A biography of the Australian continent 

Ancient Gene Flow Early Modern Humans to Eastern Neanderthals

It has previously been shown that Neanderthals contributed genetically to modern humans outside Africa 47-65 ka. In this paper Kuhlwilm et al. present the results of their study of the genome of a Neanderthal and a Denisovan from the Altai Mountains in Siberia, as well as the sequence of chromosome 21 of 2 Neanderthals from Spain and Croatia. The results of the study show that a population that diverged early from other modern human populations in Africa made a contribution to the genetics of Neanderthals living in the Altai Mountains about 100,000 BP. In contrast to this, the study failed to find such a contribution to the Denisovan or the 2 European Neanderthals. Kuhlwilm et al. concluded that as well as later interbreeding events, ancestral Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than had previously been believed.

It is suggested by the fossil evidence Neanderthals diverged from modern humans at least 430,000 BP (Arsuaga et al., 2014), though analysis of a Neanderthal genome from a fossil recovered from a cave in the Altai Mountains, Siberia, suggests the time of diversion was between 765,000 and 550,000 BP (Prüfer et al., 2014). When a Denisovan genome was recovered from a fossil in the same cave in the Altai Mountains analysis suggested that Neanderthals and Denisovans diverged from each other between 481,000 and 473,000 BP (Prüfer et al., 2014). Following this divergence admixture among archaic and modern human populations, which included gene flow from Neanderthals into modern humans outside Africa (Prüfer et al., 2014; Green et al., 2010; Fu et al., 2014; Fu et al., 2015), Denisovan gene flow into ancestral modern humans of the present in Oceania and mainland Asia (Reich et al., 2010; Meyer et al., 2012), gene flow into the Denisovans from Neanderthals, and possibly an archaic group that has yet to be identified, which had diverged from the other lineages more than 1 million BP (Prüfer et al., 2014). What has remained elusive is gene flow from modern humans into Neanderthals or Denisovans.

Archaic genomes – divergence and heterozygosity

The Neanderthal genome from the Altai Mountains shares more than 5.4 % derived alleles with Africans of the present than does the Denisovan genome.  For derived alleles found at >0.9 % frequency in Africans, this excess is particularly pronounced. These observations have been interpreted as evidence that gene flow from an unknown archaic hominin, that was more deeply diverged, into the Denisovan lineage (Prüfer et al., 2014). In this study Kuhlwilm et al. examined whether the gene flow from modern humans into the ancestral Altai Neanderthal may have also taken place.

Kuhlwilm et al. examined the divergence of these archaic genomes to 504 African genomes (The 1000 Genome Project Consortium, 2015) in 15,881 sequence windows of 100 kb (supplementary information section 9), noting that regions in the Denisovans genome introgressed from a deeply divergent archaic hominin should have unusually high divergence to Africans of the present, and that in the Altai Neanderthal genome regions introgressed from modern humans should have unusually low divergence to them, the use of only derived alleles at >0.9 frequency in the combined African genomes, archaic alleles that had been brought by Eurasians to Africa about 3,000 BP Pickrell et al., 2014; Llorente et al., 2015) were excluded from these windows. Kuhlwilm et al. calculated their divergence to Africans using the archaic alleles in each window that give the minimum number of differences, to allow introgressed segments from modern humans to be identified more easily, if they exist. Also noting that in the Denisovan or Altai Neanderthal genomes introgressed regions should have divergence to the other archaic genome that should be unusually high, Kuhlwilm et al. calculated the divergence that existed between the archaic genomes in the same window by the use of alleles that give the maximum number of differences.

Windows of the Denisovan genome that have high divergence to Africans have also a high divergence to the Altai Neanderthal, whereas in the Altai Neanderthal genome widows that have high divergence to Africans tend to not have a high divergence to the Denisovan, which is consistent with gene flow from a hominin that is deeply diverged into the Denisovan ancestors. On the other hand it was found that windows of the Altai Neanderthal genome that have low divergence to Africans have higher divergence to the Denisovan than the Denisovan windows that have low divergence to Africans. These windows in the Altai Neanderthal genome have higher heterozygosity than in the Denisovan genome, and 40.7 % of their heterozygous sites share a derived allele with Africans, whereas 24.2 % share a derived allele in the Denisovan. The possibility of gene flow from modern humans into Neanderthals is raised by these observations.

See Source1


It is suggested by the integrated demographic analysis of multiple archaic and present-day human genomes by Kuhlwilm et al. a scenario of decline over a long term of the Neanderthal and Denisovan populations which possibly reflects a long period of isolation in the Altai Mountains. This study also provides evidence of modern human introgression into the ancestors of this Neanderthal population, and no evidence was found of introgression into the European Neanderthals. According to Kuhlwilm et al. these modern humans may represent a population that diverged from other modern humans in Africa and at a later time met the ancestors of the Altai Neanderthal. Kuhlwilm et al. suggest that the finding of ‘African’ haplotypes as young as 100,000 years old in the genome of the Altai Neanderthal is consistent with interbreeding around that age.

It has been proposed by Hablin (Hablin, 1998) that Neanderthals expanded to the east from Europe during an interglacial about 125,000 BP (Mercier et al., 1993; Grün et al., 2005) (Oxygen Isotope Stage 5e). As early as 120,000 BP the presence of modern humans at Skhul and Qafzeh and Neanderthals at Tabun in the Levant provides a place where gene flow from early modern humans to Neanderthals could possibly have occurred. There is also a place in Southern Arabia and the area around the Persian Gulf where modern humans may also have settled early (Armitage et al., 2011) and where Neanderthals may also have been present (Rose & Marks, 2014). The suggestion that modern humans may have migrated out of Africa early is supported by the recent demonstration that modern humans may have been in China as early as 120,000 BP (Liu et al., 20156). This suggests early modern humans may have had the opportunity to admix with archaic hominins prior to the migration of ancestral of modern non-African humans if the present.

Sources & Further reading

  1. Kuhlwilm, M., I. Gronau, M. J. Hubisz, C. de Filippo, J. Prado-Martinez, M. Kircher, Q. Fu, H. A. Burbano, C. Lalueza-Fox, M. de la Rasilla, A. Rosas, P. Rudan, D. Brajkovic, Ž. Kucan, I. Gušic, T. Marques-Bonet, A. M. Andrés, B. Viola, S. Pääbo, M. Meyer, A. Siepel and S. Castellano (2016). "Ancient gene flow from early modern humans into Eastern Neanderthals." Nature 530(7591): 429-433.



Author: M. H. Monroe
Last Updated 06/03/2016
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