June 12, 2024

LMore than a decade ago, the American anthropologist James C Scott described infectious diseases as the “loudest silence” in the prehistoric archaeological record. Epidemics must have devastated human societies in the distant past and changed the course of history, but, Scott lamented, the artifacts left behind reveal nothing about it.

Over the last few years, the silence has been broken by pioneering research analyzing microbial DNA extracted from very ancient human skeletons. The latest example of this is a groundbreaking study who identified three viruses in 50,000-year-old Neanderthal bones. These pathogens continue to plague modern humans: adenovirus, herpesvirus, and papillomavirus cause the common cold, cold sores, and genital warts and cancer, respectively. The discovery could help us solve the greatest mystery of the Paleolithic era: what caused the extinction of Neanderthals.

Recent advances in the technology used to extract and analyze ancient DNA have given us incredible insights into the ancient world. With the exception of time travel, it is difficult to imagine a technology capable of so profoundly changing our understanding of prehistory.

The first major developments in the ancient DNA revolution came from human genetic material. A study that analyzed DNA from cemeteries across Britain reveals that Stonehenge was built by brunette farmers with olive skins originating from present-day Turkey, and that their descendants died out a few centuries after the megaliths were raised.

When a team led by Nobel laureate Svante Pääbo sequenced the Neanderthal genome, they realized that modern humans of European, Asian, or Native American ancestry inherited about 2% of their genes from Neanderthals. Then, during the pandemic, it became clear that several Neanderthal gene variants that were particularly common among South Asians affected the immune response to novel coronavirus, making carriers much more likely to get very sick and die. It’s wild to think that interspecies testing that took place tens of thousands of years ago is affecting the health of people living today.

When scientists extract human DNA from human skeletons, they also pick up traces of the microbes that were in the bloodstream at the time of death. Some of the most interesting research in this field focuses on Yersinia pestis, the bacteria responsible for the plague. Not long ago, the oldest evidence of Y pestis comes from the middle of the 14th century, when the Black Death killed about 60% of Europe’s population.

We now know that the plague goes back much further. Between 4,000 and 5,000 years ago it was widespread across Europe and Asia, including – as a recent study shown – in Somerset and Cumbria. Around this time, Northwestern Europe’s population dropped by as much as 60%. It is likely that a “Neolithic Black Death” contributed to the demographic collapse, which coincided with the disappearance from Britain of the farmers who built Stonehenge and the arrival of another group that contributes more to the DNA than any other of modern Britain.

Ancient microbial DNA also offers tantalizing insights into the private lives of our distant ancestors.

Scientists have found Methanobrevibacter oralis, a bacteria-like organism associated with gum disease in modern humans, in the calcified plaque on 50,000-year-old Neanderthal teeth. By comparing the prehistoric tribe with the contemporary one, researchers calculated that their last common ancestor lived about 120,000 years ago. Since it is several hundreds of millennia after Neanderthals and Homo sapiens diverged, the germ must have been transferred between the species. The most likely way this happened was through inter-species smooching.

It is technically challenging to extract and analyze viral DNA from ancient bones. Since viruses are much smaller than bacteria, they contain less genetic material, and because they are less robust, they are broken down more quickly. That’s what makes the recent news that scientists have sequenced 50,000-year-old viral DNA so exciting.

While the discovery that Neanderthals were infected by adenovirus, herpesvirus and papillomavirus will not on its own change our understanding of the distant past, it does suggest a solution to the great mystery of the Paleolithic era.

Until about 70,000 years ago, Homo sapiens lived in Africa while Neanderthals inhabited Western Eurasia. Then everything changed. Our ancestors migrated northward and quickly spread over much of the world. Not long after, Neanderthals disappeared.

Since the late 19th century, when the German zoologist Ernst Haeckel proposed calling Neanderthals Homo stupidus to distinguish them from Homo sapiens (wise man), the dominant explanation for this transformation has been that our ancestors outwitted other human species through their superior use cognitive abilities. However, this argument has become increasingly untenable, thanks to mounting evidence that Neanderthals were capable of all sorts of sophisticated behaviour, including to bury their dead, painting cave walls, the use of medicinal plants and sea ​​voyage between Mediterranean islands.

The discovery of the 50,000-year-old viruses suggests an alternative explanation for Neanderthals’ demise: deadly infectious diseases carried by Homo sapiens. After being separated for more than half a million years, the two species would have developed immunity to different infectious diseases. When they encountered each other during Homo sapiens’ migration out of Africa, pathogens that caused harmless symptoms in one species would have been fatal to the other, and vice versa.

The reason why Homo sapiens survived while Neanderthals disappeared is simple. Our ancestors lived closer to the equator. As more of the sun’s energy reaches the Earth, plant life there is more abundant. This provides a habitat for denser and more varied animal life, which in turn supports more microbes capable of jumping the species barrier and infecting humans. Consequently, Paleolithic Homo sapiens would have carried more deadly pathogens than Neanderthals.

The ancient DNA revolution is not only changing our understanding of prehistory – it also has important implications for the present. If infectious diseases played such a critical role in the extinction of Neanderthals and the rise of Homo sapiens to world domination, then pathogens are far more powerful than we ever realized. Our ancestors 50,000 years ago had germs on their side, but we may not be so lucky in the future.

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