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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