Fig. 1

Phylogenetic relationships and population structure of mice. a Phylogenetic tree of mice. Wild M. m. domesticus (blue), M. m. musculus (yellow), and M. m. castaneus (green) are clustered with their wild-derived inbred mice relatives (with gray background) and separated from classical inbred mice (purple). SPRET/EiJ representing M. spretus is set as outgroup. All the bootstrap values are 100 except for the 3 bootstrap values marked in the panel. b Population structure analysis of the mice by ADMIXTURE. CV errors are low when K = 4 to 7 (see Additional file 1: Fig. S2). Wild M. m. domesticus, M. m. musculus, M. m. castaneus and classical inbred mice are clustered from each other when K = 4. c Principal component analysis (PCA) of wild mice, wild-derived mice, and classical inbred mice. The components with the percentage of eigenvalue > 5% (PC1–PC3, see Additional file 1: Fig. S3) are included. The strain names of the wild-derived strains are marked by arrows