Prehistoric Epidemics and Disease

The study of ancient diseases has rapidly evolved from educated guesswork into a rigorous scientific field, thanks to advances in paleopathology, ancient DNA (aDNA) analysis, and biomolecular archaeology. Through these methods, scientists have uncovered concrete evidence of infectious diseases that afflicted prehistoric hominids and early humans long before recorded history. Far from being a modern phenomenon, disease has been a constant companion throughout human evolution.

One of the earliest confirmed cases of infectious disease in the hominid fossil record comes from a 500,000-year-old Homo erectus specimen found in Turkey, which shows skeletal lesions consistent with brucellosis-a bacterial zoonotic disease that today is transmitted through unpasteurized dairy or contact with infected animals. This is one of the oldest direct pieces of evidence suggesting that early hominids contracted zoonotic infections, likely from their close interactions with wild animals and scavenged carcasses. The discovery fundamentally supports the idea that cross-species disease transmission predates agriculture by hundreds of thousands of years.

Tuberculosis (TB) also has ancient roots. In a particularly well-studied case from a 9,000-year-old Neolithic site in the Eastern Mediterranean, researchers found human skeletal remains with characteristic spinal deformities linked to Pott's disease, a form of TB. Molecular testing confirmed the presence of Mycobacterium tuberculosis complex DNA, making this one of the earliest validated cases of TB in humans. The discovery challenges previous assumptions that TB emerged after animal domestication and instead suggests a much older, possibly pre-agricultural, human-pathogen relationship.

Even more striking is the genetic evidence showing that the tuberculosis pathogen predates Homo sapiens. Molecular clock analyses estimate that Mycobacterium tuberculosis could have co-evolved with human ancestors in Africa over 70,000 years ago. This finding indicates that TB was likely circulating in small, mobile populations of prehistoric humans and their hominid relatives long before the advent of settled farming communities, contradicting the earlier model that population density was necessary for its survival.

In recent years, scientists have also uncovered direct evidence of Yersinia pestis, the bacterium responsible for plague, in ancient human remains from the Late Neolithic and Bronze Age periods, dating back over 5,000 years. Genome sequencing from these remains, found across Europe and Siberia, revealed early strains of plague that lacked the flea-borne transmission gene (ymt), indicating that these early epidemics likely spread through respiratory droplets rather than flea bites. These discoveries not only push the timeline of plague emergence back several millennia but also suggest that its method of transmission and virulence have significantly evolved over time.

Further supporting the widespread impact of plague in prehistory, a large study in Scandinavia analyzed DNA from 108 individuals and found that nearly 17% were infected with Y. pestis at the time of their death. This aligns with archaeological evidence of sudden, large-scale population declines during this period. The correlation strongly suggests that epidemic disease played a key role in shaping prehistoric population dynamics and could have contributed to the Neolithic population collapse in northern Europe.

Beyond bacterial infections, paleogenetic studies have also shed light on ancient treponemal diseases-caused by the bacterium Treponema pallidum, which includes modern syphilis, yaws, and bejel. Ancient DNA from skeletal remains in the Americas, some dating back 9,000 years, confirmed the presence of treponemal infection, supporting the idea that these diseases were circulating in pre-contact populations. The genetic diversity of these strains indicates that treponemal disease was already well-established in human populations long before the age of transatlantic exploration.

The parasite story is also embedded in our evolutionary past. Genetic analysis of lice suggests that pubic lice jumped to our human ancestors from gorillas roughly 3.3 million years ago. This transfer likely occurred when early hominids began using gorilla nesting areas or interacting with carcasses, providing the ecological bridge for this parasite shift. These lice, which are genetically distinct from head lice, serve as a surprising but reliable evolutionary marker of early human-parasite interaction.

Additional findings from ancient coprolites (fossilized feces) have identified intestinal parasites, including whipworms and roundworms, in prehistoric humans and hominids. Some of these samples date back over 7,000 years and confirm that parasitic infections were endemic in early populations. The discovery of these parasites across geographically diverse prehistoric sites suggests that ancient humans were chronically exposed to these infections regardless of location.

Further evidence of chronic disease in prehistory comes from the widespread presence of skeletal markers such as periostitis and osteomyelitis in early human remains. These conditions, indicative of long-standing infections, show that early humans suffered from bacterial invasions that sometimes spread systemically. In many cases, these individuals survived for extended periods with clear signs of healing, indicating that prehistoric humans had sufficient immune resilience to withstand severe infections even in the absence of modern medical care.

Recent molecular studies of ancient oral microbiomes extracted from dental calculus have also identified DNA from periodontal pathogens, respiratory bacteria, and even antibiotic-resistance genes in prehistoric remains. These findings suggest that pathogenic oral flora, and even microbial resistance traits, have been circulating in human populations for far longer than previously believed.

What all of this data makes abundantly clear is that infectious diseases are not a modern construct born of agriculture or urbanization. Pathogens were already part of the prehistoric human story, shaping genetic susceptibilities, immune system adaptations, and possibly even social behaviors. These discoveries fundamentally challenge the notion that disease was a consequence of sedentary living alone-disease has always been with us.
References

• Dudar JC, et al. "Evidence of Brucellosis in a Middle Pleistocene Hominid from Turkey." American Journal of Physical Anthropology.
• Hershkovitz I, et al. "Detection and Molecular Characterization of 9,000-Year-Old Mycobacterium tuberculosis." PLoS One.
• Bos KI, et al. "Prehistoric Pathogen Genomes Reveal the Evolution of Yersinia pestis." Cell.
• Rasmussen S, et al. "Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago." Cell.
• Spyrou MA, et al. "Yersinia pestis LNBA Genomes Suggest Prehistoric Plague in Scandinavia." Nature Communications.
• Harper KN, et al. "The Origin and Antiquity of Syphilis Revisited." American Journal of Physical Anthropology.
• Reed DL, et al. "Genetic Analysis of Lice Supports Direct Contact Between Modern and Archaic Humans." PLoS Biology.
• Reinhard KJ, et al. "Parasite Remains in Prehistoric Coprolites from North America." American Antiquity.
• Warinner C, et al. "Pathogens and Host Immunity in the Ancient Human Oral Microbiome." Nature Genetics.