Fig 7. ACR for DRMs.

To reconstruct the ancestral character states, resistant (violet) or sensitive (light-green), for a DRM (e.g. RT:M41L), we cut the time-scaled tree at the date of introduction to Cuba of the first ARV (as, for example, AZT for the DRM RT:M41L, used in Cuba since 1987) that can provoke this DRM (left panel), obtaining the pre-treatment-introduction tree (upper part of the tree) and a forest of post-treatment-introduction subtrees (bottom part). For the trees in the forest we then marked their roots as sensitive (middle left panel). We performed the ACR with PastML on the forest (middle right panel) and combined the results with the the all-sensitive annotation for the pre-treatment-introduction tree nodes (right panel).