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Table 1 The topology that places M. m. castaneus sister to M. m. musculus was sampled most frequently, whether a ghost population was included or not. The three subspecies are numbered from 0 to 2 (corresponding to M. m. castaneus, M. m. domesticus, and M. m. musculus, respectively). Ancestral populations are numbered beginning with 3 and are ordered numerically in time (i.e. 4 is the ancestor of all populations). When a ghost population is included, it is an outgroup to the sampled subspecies and has not been included in the species tree notation

From: Further resolution of the house mouse (Mus musculus) phylogeny by integration over isolation-with-migration histories

Model Species Tree Count Frequency
Without ghost (1,(0,2)3)4 237,697 0.758636
(2,(0,1)3)4 45,610 0.145753
(0,(1,2)3)4 29,919 0.095610
With ghost (1,(0,2)3)4 227,602 0.920739
(2,(0,1)3)4 12,363 0.050013
(0,(1,2)3)4 7230 0.029248