Figure 1.

Tree reconciliation. (A) Hypothetical host tree showing divergence times (node height intervals, as horizontal bars). While some divergence time intervals span a single time zone, as seen for the mammalian MRCA in zone 4, others can span multiple time zones, as observed for the MRCA of all host species in the host tree, which divergence intervals span the time zones 2 and 3. (B) Hypothetical viral tree, also with divergence time intervals shown as horizontal bars. While this tree resembles the host tree, some mismatches can be observed, especially in terms of divergence times, which in many instances do not coincide. (C) By reconciling both trees, topological and temporal properties of the trees are compared, and cophylogenetic events can be inferred, such as cospeciations (CO), intrahost speciations (IS), host switches (HS), and losses (LO).