Success of phylogenetic latency detection in critical simulation scenarios. Detection of latency-affected lineages was done by pair-wise comparisons of all taxa, testing whether the shorter lineage was significantly shorter according to a Poisson test. (A) Sensitivity results from simulations with 100 taxa and one random branch affected by latency at flatent = 0.1–0.9 of the corresponding original non-latent genetic distance. Lines show moving average for general trends (flatent = 0.9–0.1, left to right). Individual simulation results are shown in the Supplement (Additional file 1: Figure S2). (B) The minimum latency fraction on an affected branch to achieve 95% sensitivity as a function of the mean height of non-latent taxa from the MRCA of all taxa. The height is in log10-units to facilitate reading short tree height performance. (C) Specificity as a function of the mean height of non-latent taxa from the MRCA of all taxa. Panels B and C have loess curves fitted to show general trends.