Fig. 1

Representations of estimated IM models generated by IMa3 and the IMfig program [37] for the three subspecies of house mouse. The phylogeny is depicted as a series of boxes organized hierarchically, with ancestor boxes positioned in between the corresponding descendants, and the width of boxes proportional to estimated N_e. Gray arrows extending to the left and right of the right boundary of each population box depict 95% confidence intervals for N_e values. Splitting times are depicted as solid horizontal lines, with text values on the left. Confidence intervals for splitting times are shown as vertical gray arrows on the left, and parallel dashed lines. Migration arrows (if shown) indicate estimated 2 Nm values from one population to another over the time interval when both populations exist. Arrows are shown only for estimated migration rates that are statistically significant at or above the 0.05 level (^*p < 0.05, ^**p < 0.01, ^***p < 0.001 [33]). (a) without a ghost population (b) with a ghost population included. Estimates assume 1.5 generations/year and 6 × 10⁻⁹ mutations per base pair per generation