It may have been something very much like what happened when European diseases hit the Americas, resulting the transmission of diseases resulting in massive mortality.
This is not definitive proof, and I'm inclined to believe that the cause was a function of greater fecundity for H. Sapiens Sapiens as versus H. Sapiens Neanderthalis, but we may never know the truth:
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.
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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.
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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.
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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.
This is no smoking gun, but it does raise interesting questions.
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