Fig 6. ACR for provinces of Cuba.

To reconstruct the ancestral states for characters annotated at diagnostics dates (such as provinces of Cuba), we added additional nodes to the time-scaled trees at times of diagnostics, named those nodes (on the middle panel, the diagnostics nodes, e.g. a, correspond to the tips with the same names but capitalised, e.g. A), and associated the input annotations for PastML with them. We then reconstructed ancestral and tip characters with PastML based on those annotations (see text for calculation details).