Figure 6.

Errors in tree estimation with one sample per species, four-species-trees. When using one sample per species, a value for the within-species variability $\theta$ has to be specified by the user. The Y axis is the error in species tree estimation calculated as BSD between the normalized simulated species tree and the normalized estimated tree. The X axis is the ratio of the guessed input $\theta$ with the simulated one. Each boxplot includes 10 independent replicates. Different colors represent different methods (see legend). a) $1N_e$ tree height and scenario with trichotomy. b) $1N_e$ tree height and ILS scenario. c) $1N_e$ tree height and anomalous species tree. d) $1N_e$ tree height and recent population radiation. e) $10N_e$ tree height and trichotomy. f) $10N_e$ tree height and ILS. g) $10N_e$ tree height and anomalous species tree. h) $10N_e$ tree height and recent population radiation. The PoMo estimates are depending on the quality of the guess for $\theta$. We therefore do not recommend to use PoMo in this situation.