Artist’s depiction of ancient hominids.

How Ancient Hominid Interbreeding has Shaped Humans Today

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Over the past half-decade, ancient DNA research has revealed some surprising aspects to our evolutionary history during the past 50,000 years. Perhaps the most startling of these has been the extent to which the ancestors of living people across the planet interbred with other closely related species of human. But where in the world did these cross-species mating’s occur? Which archaic species were involved? Just how much of the human genome comprises DNA from these archaic relatives? And what impact did interbreeding have on our evolution and general biology as a species?

These are questions are the core of current research into interbreeding as revealed by DNA sequences obtained from fossils in Europe and Asia, as well as from comparisons with the genomes of living people.

In Africa, interbreeding with an archaic species has left genetic signatures in the genomes of some living sub-Saharan populations.

Roughly two percent of the DNA of these people  derives from an archaic species as a result of mating that occurred around 35,000 years ago.

Neanderthal genes in Europeans and East Asians

The very well-known  Neanderthals – for whom we have hundreds of fossils including near complete skeletons – interbred with the founders of living European and East Asian populations.

Estimates published in 2014 indicate  that 1.5-2% of the genome of living non-Africans  was inherited from Neanderthals.

Yet, East Asians have significantly more Neanderthal genes  than Europeans do indicating that their ancestors interbred with this archaic species perhaps more than once, or in an event separate to that involving the ancestors of western Eurasians.

Models of a Neanderthal man and woman. Neanderthal Museum,

Models of a Neanderthal man and woman. Neanderthal Museum, Dusseldorf. ( Wikimedia Commons  )

Denisovan interbreeding

Another species, the  mysterious ‘Denisovans,’  is known from the fossil record only by a single tooth, finger bone and toe bone.

Yet their fully sequenced genome shows that  they shared their genes  with the ancestors of some Southeast Asians, New Guineans and Aboriginal Australians.

These living people also show the genetic signs of interbreeding with Neanderthals, so have inherited DNA from both of these species.

Not only do we all carry the evidence for these interspecies dalliances, in some cases these genes seem to have provided real benefits for us today.

In 2010, analysis on an upper molar from a young adult revealed it was from a Denisovan.

In 2010, analysis on an upper molar from a young adult revealed it was from a Denisovan. Picture: Max Planck Institute

Benefits from interbreeding

Take for example the finding last year  by Emilia Huerta-Sánchez and her team  that the ability of populations living today in Tibet to thrive at high altitude is the result of a gene inherited from the mysterious ‘Denisovans.’

The gene in question –  EPAS1 – is associated with differences in haemoglobin levels at high altitude underpinning the capacity of the individuals carrying it to pump more oxygen around in their blood.

The Denisovans also seem to have  contributed genes  that bolstered the immune systems of people in New Guinea and Australia.

In Europe, interbreeding with the Neanderthals may also have  provided gene variants associated with lipid catabolism , or the conversion of fat to energy in the body’s cells.

Other examples include genes associated with: sugar metabolism; muscle and nervous system function; skin formation and structure; skin, hair and eye colour; and the female reproductive system, especially the formation of ova.

But of course we would expect natural selection to work in both directions given that these mating events were between different species:  Homo sapiens  x Homo neanderthalensis Homo sapiens  x Denisovans and  Homo sapiens  x mystery African species.

One particularly interesting example  compared the genome of a female Neanderthal with 1,000 contemporary human ones from across the world and found clear evidence for negative selection.

Mapping the DNA of Neanderthals against this large number of human genomes also showed that there were vast ‘deserts’ of Neanderthal ancestry.

One million base pairs compared across the autosomes (i.e. other than the X or Y chromosomes) showed four windows in Europeans and 14 in East Asians where around 0.1% of the DNA was Neanderthal.

The human Y chromosome is also known to be lacking Neanderthal DNA suggesting strong natural selection against hybrid males, who were likely to have been infertile.

Other genes  inherited from the Neanderthals  seem to have conferred greater risk for a range of diseases such as lupus, biliary cirrhosis, Crohn’s disease, altered optic-disc size, smoking behaviour, IL-18 levels (producing inflammation) and type 2 diabetes.

Comparison of Modern Human and Neanderthal skulls.

Comparison of Modern Human and Neanderthal skulls.  (CC BY-SA 2.0)

The mystery of the Denisovans

One of the especially odd things about the evidence for interbreeding with the Denisovans is that the only fossils we have for them were recovered from Denisova Cave in southern Siberia, some 6,000 km northwest of New Guinea.


Thanks for the article – I find this research very exciting as it reveals new insights into how our ancestors evolved and interacted with other hominid species.


Both my parents are from Denmark and i have Neanderthal and Denisovan DNA.

I always thought the disappearance of the Neanderthals was the first true genocide otherwise they'd still be here beside us, two sub-species of human living together. As a white man I can say I suspect it was the early white man who wiped them out.

Neanderthals probably were infected with diseases they had no immunity to and succumbed as a result. It wouldn't be the first or the last time this would happen when strangers move into a new territory.

Check the list of things Europeans inherited from Neanderthals: it includes skin color. Neanderthals WERE the early white man.


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