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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.<\/jats:p>","DOI":"10.3390\/genes9070317","type":"journal-article","created":{"date-parts":[[2018,6,26]],"date-time":"2018-06-26T10:40:50Z","timestamp":1530009650000},"page":"317","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["The Role of aDNA in Understanding the Coevolutionary Patterns of Human Sexually Transmitted Infections"],"prefix":"10.3390","volume":"9","author":[{"given":"Ville N.","family":"Pimenoff","sequence":"first","affiliation":[{"name":"Department of Cancer Epidemiology and Prevention, Bellvitge Institute of Biomedical Research, Catalan Institute of Oncology, 08908 Barcelona, Spain"},{"name":"Department of Archaeology, University of Helsinki, 00014 Helsinki, Finland"},{"name":"Department of Epidemiology, University of Tampere, FI-33014 Tampere, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1833-5285","authenticated-orcid":false,"given":"Charlotte J.","family":"Houldcroft","sequence":"additional","affiliation":[{"name":"Department of Medicine, Addenbrookes Hospital, University of Cambridge, Cambridge CB2 0QQ, UK"},{"name":"Department of Archaeology, University of Cambridge, Cambridge CB2 3QG, UK"},{"name":"Parasites and Microbes, Wellcome Sanger Institute, Hinxton CB10 1SA, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Riaan F.","family":"Rifkin","sequence":"additional","affiliation":[{"name":"Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa"},{"name":"Human Origins and Palaeo-Environments Research Group, Department of Anthropology and Geography, Oxford Brookes University, Oxford OX3 0BP, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6056-2353","authenticated-orcid":false,"given":"Simon","family":"Underdown","sequence":"additional","affiliation":[{"name":"Human Origins and Palaeo-Environments Research Group, Department of Anthropology and Geography, Oxford Brookes University, Oxford OX3 0BP, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2018,6,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1093\/molbev\/msw214","article-title":"Transmission between archaic and modern human ancestors during the evolution of the oncogenic human papillomavirus 16","volume":"34","author":"Pimenoff","year":"2017","journal-title":"Mol. 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