A new approach to estimate parameters of speciation models with application to apes

Precision and accuracy for the five parameters of the isolation-migration model (using the mode as a point estimate). MIMAR was applied to 20 simulated multilocus data sets under parapatric and allopatric models (for details, see Methods). When M = 0, the mean estimate of θ_A is significantly lower than the true value (P = 0.0003, using a Wilcoxon signed rank test). This can be explained as follows: The prior on M does not include 0 (the true value) so is necessarily an overestimate and consequently, θ_A tends to be underestimated slightly. This problem is likely to apply to IM as well, since the prior on M is likewise exclusive of 0. When M = 1, the mean estimate of T is significantly lower than the true value (P = 0.005, using a Wilcoxon signed rank test). This can be explained by the fact that, whenever M and/or θ_A are slightly underestimated, T tends to be underestimated (see Supplemental Fig. S4)

^aA significant bias in the estimates at the 5% level, after Bonferroni correction.