Less 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 artefacts left behind reveal nothing about them.
Over the last few years, the silence has been shattered by pioneering research that analyses microbial DNA extracted from very old human skeletons. The latest example of this is a groundbreaking study that identified three viruses in 50,000-year-old Neanderthal bones. These pathogens still afflict modern humans: adenovirus, herpesvirus and papillomavirus cause the common cold, cold sores, and genital warts and cancer, respectively. The discovery may help us resolve the greatest mystery of the Palaeolithic era: what caused the extinction of Neanderthals.
Recent advances in the technology used to extract and analyse ancient DNA has 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 analysed DNA from burial sites across Britain revealed that Stonehenge was built by dark-haired, olive-skinned farmers originating from modern-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 realised that modern humans with European, Asian or Native American ancestry inherited about 2% of their genes from Neanderthals. Then, during the pandemic, it became apparent that several Neanderthal gene variants that are particularly common among South Asians influenced the immune response to novel coronavirus, making carriers much more likely to get very sick and die. It is wild to think that inter-species trysts that occurred tens of thousands of years ago impact the health of people alive 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 came from the mid-14th century, when the Black Death killed around 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 showed – in Somerset and Cumbria. Around this time, northwest Europe’s population fell by as much as 60%. It is likely that a “Neolithic black death” contributed to the demographic crash, which coincided with the disappearance from Britain of the farmers who built Stonehenge and the arrival of another group that contributes more than any other to the DNA of modern Britain.
Ancient microbial DNA also offers tantalising 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 strain with the contemporary one, researchers calculated that their last common ancestor lived about 120,000 years ago. Since this is several hundred millennia after Neanderthals and Homo sapiens diverged, the germ must have been transmitted between the species. The most likely way this happened was through inter-species smooching.
It is technically challenging to extract and analyse viral DNA from ancient bones. As viruses are much smaller than bacteria, they contain less genetic material, and because they are less robust, it degrades more quickly. This 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 hints at a solution to the great mystery of the Palaeolithic era.
Until about 70,000 years ago, Homo sapiens lived in Africa while Neanderthals inhabited western Eurasia. Then everything changed. Our ancestors migrated northwards, spreading quickly across 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 human), the dominant explanation for this transformation is that our ancestors outcompeted other human species using their superior cognitive abilities. This argument has become increasingly untenable, however, thanks to mounting evidence that Neanderthals were capable of all sorts of sophisticated behaviours, including burying their dead, painting cave walls, using medicinal plants and seafaring between Mediterranean islands.
The discovery of the 50,000-year-old viruses points to an alternative explanation for Neanderthals’ demise: deadly infectious diseases carried by Homo sapiens. Having been separated for more than half a million years, the two species would have evolved immunity to different infectious diseases. When they encountered one another during Homo sapiens’ migration out of Africa, pathogens that caused innocuous symptoms in one species would have been deadly to the other, and vice versa.
The reason that 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 is more abundant there. This provides a habitat for more dense and varied animal life, which in turn supports more microbes that are capable of jumping the species barrier and infecting humans. Consequently, Palaeolithic Homo sapiens would have carried more deadly pathogens than Neanderthals.
The ancient DNA revolution is not only transforming our understanding of prehistory – it also has important implications for the present. If infectious diseases played such a critical role in Neanderthals’ disappearance and Homo sapiens’ rise to world domination, then pathogens are far more powerful than we ever realised. Our ancestors 50,000 years ago had germs on their side, but we might not be so lucky in the future.
Jonathan Kennedy teaches politics and global health at Queen Mary University of London and is the author of Pathogenesis: How Germs Made History
