Fig. 1.

A simplified example of the impact of unrecognized homoplasy on phylogenetic analysis. Evolutionary changes in each miRNA family are indicated by a different color. (A) If miRNA evolution proceeds without homoplasy, there would be a single origin (indicated by a plus) and no losses for each miRNA family. A simple model can recover true relationships. (B) If there is homoplasy, in this case a single loss (indicated by a minus), and it is not recognized with additional data and robust analysis tools, phylogenetic estimation can provide the wrong answer (C and D are switched).