How did diseases influence human evolutionary processes in Africa? And what is the ‘Pleistocene disease baseline’?

Methods

Challenges

While advances in the field of aDNA and the detection of prehistoric pathogens has advanced our understanding of the antiquity of human-pathogen interactions, the likelihood of detecting ancient diseases poses significant complications. Individuals who succumb to death shortly after disease onset generally do not display skeletal indications of infection, while those that do survive long after the onset of symptoms might, on rare occasions, exhibit skeletal indications of disease. Essentially, most diseases leave no definite signs of their existence on human osseous remains, and even those that do affect human skeletal morphology (e.g. Yersinia pestis, Mycobacterium tuberculosis, M. leprae, Treponema pallidum, Brucella melitensis, Plasmodium falciparum, Trypanosoma cruzi etc.) are frequently misdiagnosed. Taphonomic alterations also mimic disease conditions which can induce interpretation errors (pseudo-pathologies), even for experienced palaeo-pathologists. Thus, and on account of this ‘osteological paradox’, disease incidence is often unnoticed or misconstrued, which leads to unverified statements that some diseases were either rare or non-existent in prehistory. But, on a molecular level, human remains have proven increasingly valuable in providing information concerning the prevalence of human diseases in the past. 

While the DNA of bacteria and fungi and the remains of parasitic eggs are likely to be detected in ancient African cave sediments, viral DNA is not as likely to be preserved. Unlike the double-stranded DNA structures of bacteria, viral genetic information is encoded in a variety of structures, including double- or single-stranded DNA or RNA genomes. Viral aDNA is more likely to preserve than viral aRNA because DNA degrades more slowly over time than RNA, except when integrated in their host’s genome, as for example Human Herpesvirus 6 (HHV-6). Ancient single-stranded or RNA genome viruses in archaeological samples may occur when preservation conditions are exceptional, for example in caves with cool and constant temperatures or where soft tissue has been preserved (Maixner et al., 2016). While the Hepatitis B virus (HBV) has been recovered from human mummified remains, and may be much older than previously estimated, the likelihood of recovering ancient viral RNA is largely predicted as there is currently little data to support this theory. Yet, despite its single-stranded RNA genome, Hepatitis C virus (HCV) has been detected in the tooth pulp of living humans with HCV, and HCV RNA may therefore be preserved in human teeth after death.