Denisovans and extinct sub-Saharan ghost populations

ancient history
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Since the discovery of the first Neanderthal skeleton in 1856 in Germany, we have been curious to find out who exactly they were and how they were related to us. In 2010, geneticists theorized that they had likely interbred with humans when the latter ventured into territory they occupied (this was later confirmed in 2012).

Further excitement was caused and the situation got more complicated with the discovery of skeletal remains of another extinct species in Denisova Cave in the Altai Mountains in Siberia. These are now popularly known as Denisovans. The lineage that developed into Neanderthals and Denisovans is estimated to have separated from the lineage of modern humans around 500,000 to 750,000 years ago.

In the last decade or so, there have been unprecedented advances in DNA extraction and analysis techniques. The results have revealed that Homo sapiens not only interbred with Neanderthals but also with Denisovans, and modern non-African populations carry small amounts of DNA from both. Furthermore, Neanderthals and Denisovans also interbred with each other, as was evident from the DNA of Denny, a 13 year old girl with both Neanderthal and Denisovan parents.

The Denisovan genome suggests that they shared a common ancestor with the Neanderthals but while the latter remained primarily in the cold Eurasian habitat, Denisovans were more mobile, ranging from Siberia to Southeast Asia.

Watch this VLOG on ancient Africans and how our ancestors interbred with other species

Also, while the genome of all non-African modern humans contains portions of Neanderthal DNA ranging from 1.5 to 2 %, Denisovans seem to have contributed a higher share, with about 3% to 5% of the DNA of Melanesians and Aboriginal Australians and around 6% in Papuans deriving from them. Other modern Asia populations also have a smaller percentage of Denisovan DNA.


Distribution of Denisovans.

Downloadable graphical abstract from Cell

A recent analysis published in April 2019, suggests that there may have been three distinct species of Denisovans spread all over Eurasia (from Siberia to Indonesia)and our ancestors interbred with all three. This analysis was done one a new dataset of 161 genomes covering the Indonesia-New Guinea region (spanning 14 island groups) — an area that has been relatively understudied. It shows that modern Papuans carry hundreds of gene variants from two deeply divergent Denisovan lineages that separated over 350 thousand years ago. One of these also interbred with Homo sapiens east of the Wallace line probably as early as 15,000 years ago, while a third lineage occurs in modern East Asians.


a) Distribution of African individuals analysed and b) Signals of interbreeding at population and individual levels.

a) Distribution of African individuals analysed and b) Signals of interbreeding at population and individual levels. Source: GMC

Meanwhile, there have also been new finds in Africa. When we think of the human story, we tend to concentrate on our movement once we left the continent and think of African populations to be lacking in diversity. This is completely at odds with modern genetics, which has shown that there is more genetic diversity in Africa then there is out of it. Now, whole genome sequencing of 15 African populations covering all major continental linguistic groups, ecosystems, and lifestyles reveals archaic gene flow from an extinct ghost population of modern humans into sub-Saharan populations. This sequencing has identified the fingerprint of an interbreeding event in the sub-Saharan populations included in the models (~ 4.0% in Khoisan, ~ 4.3% in Mbuti Pygmies, and ~ 5.8% in Mandenka) with an early divergent and now extinct ghost human lineage.

Both the Denisovan and ancient African admixture shows how mobile human populations have been and how complex our relationships with each other. As DNA extraction techniques become more advanced, enough to enable scientists to extract DNA from hot environments (where chances of disintegration are very high), we can be certain that more such admixtures will be revealed.

Human species have always been mobile and they have always been horny. That is why we are so successful.

Featured image: Ancient human map, Wikepedia

I am a Chartered Environmentalist from the Royal Society for the Environment, UK and co-owner of DoLocal Digital Marketing Agency Ltd, with a Master of Environmental Management from Yale University, an MBA in Finance, and a Bachelor of Science in Physics and Mathematics. I am passionate about science, history and environment and love to create content on these topics.

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