Abstract
Analysis of pathogen genome data sequenced from clinical and historical samples has made it possible to perform phylogenetic analyses of sexually transmitted infections on a global scale, and to estimate the diversity, distribution, and coevolutionary host relationships of these pathogens, providing insights into pathogen emergence and disease prevention. Deep-sequenced pathogen genomes from clinical studies and ancient samples yield estimates of within-host and between-host evolutionary rates and provide data on changes in pathogen genomic stability and evolutionary responses. Here we examine three groups of pathogens transmitted mainly through sexual contact between modern humans to provide insight into ancient human behavior and history with their pathogens. Exploring ancient pathogen genomic divergence and the ancient viral-host parallel evolutionary histories will help us to reconstruct the origin of present-day geographical distribution and diversity of clinical pathogen infections, and will hopefully allow us to foresee possible environmentally induced pathogen evolutionary responses. Lastly, we emphasize that ancient pathogen DNA research should be combined with modern clinical pathogen data, and be equitable and provide advantages for all researchers worldwide, e.g., through shared data.
Highlights
Every human carries infectious agents during their lifetime, including sexually transmitted microbes
Mammalian reproductive behaviors can be quite complex, it is commonly assumed that human sexual behaviors are ubiquitous [9,10]
It is very likely that archaic hominins carried several sexually transmitted infections (STIs), and some of them were inherited from their ancestors [1,11,12,13]
Summary
Every human carries infectious agents during their lifetime, including sexually transmitted microbes. This new understanding of a more complex human evolutionary history challenges prevailing epidemiological hypotheses that human infectious diseases only started to severely impact humans after the emergence of agriculture and sedentary lifestyles [33,41] Instead, it advocates an ancient pathogen origin and transmission scenario, including host-switch events typical of pathogen evolution, between ancestral hominin groups and the African great apes (Figure 2) [1,12,42,43,44,45,46,47]. We especially focus on the Papillomaviridae, Herpesviridae, and ectoparasitic pathogen families
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