Why does my tree produced by TreeAnnotator have negative branch lengths?

MCC trees produced by TreeAnnotator can have a descendent node that is older than its direct ancestor (a negative branch length). This may seem like an error but it is actually the correct behaviour. The MCC tree is, by default, generated with average node heights across all trees in the sample which contain that clade. The negative branch lengths result when a clade is at low frequency and tends not to occur in those trees that have the MCC tree’s ancestral clade (or vice versa). This means the average heights for the adjacent nodes are derived from different sets of trees and may not have any direct ancestor-descendent relationship.

Note: The Common Ancestor heights option will never produce negative branch lengths.

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Bayesian evolutionary analysis by sampling trees