Fig. 3.

Timeline of divergence for archaic and modern human ancestors, and for HPV16. (A) Dated and classification-confirmed Hominin fossil taxa (light green represents uncertain classification, as reviewed by Scally and Durbin 2012). (B) Phylogenetic relationship of modern human, Neanderthal and Denisovan populations. Vertical arrows indicate the proposed interbreeding and subsequent gene flow from the Neanderthal and Denisovan populations to the ancestors of present-day modern humans. The evolutionary relationships between Neanderthals and Denisovans are still unresolved (Sawyer et al. 2015; Stringer and Barnes 2015). (C) Phylogenetic relationships for 118 selection-filtered HPV16 coding genome sequences using maximum clade credibility tree under the Hominin host-switch scenario. Blue bars indicate the 95% probability intervals for the corresponding node age. Arrows indicate the nodes used for calibration.