Neanderthal genes are everywhere

We seek them here, we seek them there,

We met them often – but when? And where?

They are in our skins and in our hair,

Neanderthal genes are everywhere

There is an explosion of work following up from the genome sequence of the 50,000 year old Neanderthal recreated and published by Svante Pääbo and his team. Two new papers – one in Science and one in Nature – are just out and are contributing to the huge growth of data and nformation now building up. The old paradigm of Neanderthals being a completely separate species to modern humans which became extinct some 30,000 years ago no longer holds. Not only did Neanderthals interact and interbreed with modern humans, it now seems likely that their genes made some critical contributions in our evolution.

A process of many admixture (interbreeding) events followed by selection is the picture that emerges. The admixture events took place at many times and both in Asia and Europe. Neanderthals may have provided the genes favourable to cold resistance which were then selected forin Northern climes. They may also have thus provided the genes for skin and hair colour changes. But they also provided the genes which increased the susceptibility to some new diseases. Hybrid Neanderthal – modern human males may have been infertile and so the assimilation of Neanderthal genes may primarily have been through the hybrid females. All this probably between 80,000 years ago and 40,000 years ago – a span of about 2,000 generations.

And so the story of human evolution must go back to at least when the predecessors of Neanderthals left Africa and not start with the later emergence of modern humans from Africa about 100,000 years ago.

From, Sriram Sankararaman, Swapan Mallick, Michael Dannemann, Kay Prüfer, Janet Kelso, Svante Pääbo, Nick Patterson, David Reich. The genomic landscape of Neanderthal ancestry in present-day humansNature, 2014; DOI:10.1038/nature12961

Harvard Press Release: Remnants of Neanderthal DNA in modern humans are associated with genes affecting type 2 diabetes, Crohn’s disease, lupus, biliary cirrhosis and smoking behavior. They also concentrate in genes that influence skin and hair characteristics. At the same time, Neanderthal DNA is conspicuously low in regions of the X chromosome and testes-specific genes.

…. a legacy of interbreeding between humans and Neanderthals that the team previously showed occurred between 40,000 to 80,000 years ago. (Indigenous Africans have little or no Neanderthal DNA because their ancestors did not breed with Neanderthals, who lived in Europe and Asia.) …..

Reich and colleagues—including Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Germany—analyzed genetic variants in 846 people of non-African heritage, 176 people from sub-Saharan Africa, and a 50,000-year-old Neanderthal whose high-quality genome sequence the team published in 2013. ……. some areas of the modern non-African human genome were rich in Neanderthal DNA, which may have been helpful for human survival, while other areas were more like “deserts” with far less Neanderthal ancestry than average.

…. The barren areas were the “most exciting” finding, said first author Sriram Sankararaman of HMS and the Broad Institute. “It suggests the introduction of some of these Neanderthal mutations was harmful to the ancestors of non-Africans and that these mutations were later removed by the action of natural selection.”

The team showed that the areas with reduced Neanderthal ancestry tend to cluster in two parts of our genomes: genes that are most active in the male germline (the testes) and genes on the X chromosome. This pattern has been linked in many animals to a phenomenon known as hybrid infertility, where the offspring of a male from one subspecies and a female from another have low or no fertility.

“This suggests that when ancient humans met and mixed with Neanderthals, the two species were at the edge of biological incompatibility,” said Reich, …….

The team also measured how Neanderthal DNA present in human genomes today affects keratin production and disease risk.

Neanderthal ancestry is increased in genes affecting keratin filaments. This fibrous protein lends toughness to skin, hair and nails and can be beneficial in colder environments by providing thicker insulation, said Reich. “It’s tempting to think that Neanderthals were already adapted to the non-African environment and provided this genetic benefit to humans,” he speculated.

The researchers also showed that nine previously identified human genetic variants known to be associated with specific traits likely came from Neanderthals. These variants affect diseases related to immune function and also some behaviors, such as the ability to stop smoking. The team expects that more variants will be found to have Neanderthal origins.

The second paper is in Science, Benjamin Vernot and Joshua M. Akey. Resurrecting Surviving Neandertal Lineages from Modern Human GenomesScience, 29 January 2014 DOI:10.1126/science.1245938

Washington University Press Release: A substantial fraction of the Neanderthal genome persists in modern human populations. A new approach applied to analyzing whole-genome sequencing data from 665 people from Europe and East Asia shows that more than 20 percent of the Neanderthal genome survives in the DNA of this contemporary group …..

To check the accuracy of their approach, Vernot ran their analysis before comparing the suspected Neanderthal sequences they found in modern humans to the recently mapped Neanderthal genome obtained from DNA recovered from bone. This genome came from the paleogenetics laboratory of Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Germany. … The results suggest that significant amounts of population-level DNA sequences might be obtained from extinct groups even in the absence of fossilized remains, because these ancient sequences might have been inherited by other individuals from whom scientists can gather genomic data, according to Akey. Therein lies the potential to discover and characterize previously unknown archaic humans that bred with early humans.

The picture that builds up in my mind then is of:

(diagram from The complete genome sequence of a Neanderthal from the Altai MountainsKay Prüfer et al, Nature 505, 43–49 (02 January 2014).

  • The predecessors of Neanderthals splitting away from the main branch of homo erectus in Africa.
  • Some of these then moving out of Africa perhaps some 500,000 years ago.
  • Those remaining in Africa having contact with and continuing to interbreed occassionally with the main branch of homo erectus but eventually dying out (or being superceded by) the predecessors of modern humans
  • Outside of Africa the evolution of the predecessors into the Neanderthals. 
  • A genetic split in this line – outside of Africa – of the Neanderthal line giving rise to the Denisovans around 300,000 years ago and perhaps even to another unknown branch.
  • The Neanderthals  and Denisovans – and any contemporaries – then peopling most of Asia and Europe with the Neanderthals largely in the West and the Denisovans mainly in the East but with a great deal of overlap in the middle.
  • The emergence of modern humans from Africa about 100,000 years ago and a genetic split here between Africa and the rest.
  • Modern humans then spreading across Europe and Asia all the way to Oceania and in contact with and interbreeding – where viable – with the peoples already present.
  • Hybrid males were then mainly infertile but the descendants through female hybrids showing particular advantage in surviving in cold climates and who tended to have lighter skin and hair colour. Perhaps the male progeny of a female hybrid were not completely infertile.
  • The Neanderthals and Denisovans then disappearing (for still unknown reasons) except through their female hybrids with modern humans and their progeny.

The story will surely get much more complicated before the real picture eventually emerges.

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About ktwop

Scientist, technologist, salesman, manager, executive and now a consultant and author.
This entry was posted in AMH, Ancestors, Denisovans, Homo Erectus, Homo Neanderthalensis, Peopling the world and tagged , , , , , . Bookmark the permalink.

3 Responses to Neanderthal genes are everywhere

  1. Pingback: Neanderthals genes are everywhere | The k2p blog

  2. Pingback: Study reveals why Neanderthals never faced brain disordersBig Online News | Big Online News

  3. Pingback: 23andMe and Grams | On a Quasi-Related Note

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