Figure 2. Performance of the MFBD approximation under the four genotype model.

(A) Simulated phylogeny showing the genotype of each lineage through time. (B) Joint likelihood of the phylogeny and tip genotypes under different values of $\sigma$ using the the approximate MFBD (solid line) or the exact MTBD model (dotted line). The vertical blue line marks the true parameter value. (C) The normalized probability of a single hypothetical lineage being in each genotype back through time based on the MFBD approximation (solid line) versus the exact MTBD model (dotted line) with $\sigma =0.5$. Note that the probabilities for genotypes 10 and 01 are identical. All parameters besides $\sigma$ were fixed at $\lambda =0.25$, $d=0.05$, $s=0.05$. The mutation rate $\gamma$ was symmetric between forward and backwards mutations and fixed at 0.05.