Genome-Wide Patterns of Differentiation Among House Mouse Subspecies

Supporting Information

Supporting Information

Supporting Information - Figures S1-S6, Files S1-S4, and Tables S1-S14 (PDF, 1 MB)
Figure S1 - Fixed differences and shared polymorphisms across the genome for all pairwise comparisons of subspecies of Mus. (PDF, 770 KB)
Figure S2 - The ratio of fixed differences (FDs) to topologically informative sites, fixed differences and shared polymorphisms (SPs), across the genome for all pairwise comparisons of Mus musculus subspecies. (PDF, 972 KB)
Figure S3 - The distribution of values of δ in the observed data and in simulations based on demographic parameters from Table S7. (PDF, 479 KB)
Figure S4 - The distribution of values of δ in the observed data and in simulations based on demographic parameters from Table S9. (PDF, 479 KB)
Figure S5 - The distribution of values of δ in the observed data and in simulations based on demographic parameters from Table S7, but with a divergence time of 425 Kya. (PDF, 480 KB)
Figure S6 - The distribution of values of δ in the observed data and in simulations based on demographic parameters from Table S7, but with a divergence time of 825 Kya.
File S2 - Supplementary Methods and Results (PDF, 163 KB)
Table S1 - Sampling localities for all wild-derived inbred laboratory strains used in this study. (PDF, 154 KB)
Table S2 - Short read transcriptome sequencing yields in megabases for all wild-derived inbred lines included in the study. (PDF, 153 KB)
Table S3 - Summary data from comparisons of genotype data in coding regions collected by this study and data collected by the Wellcome Trust. (PDF, 129 KB)
Table S4 - The results of a STRUCTURE analysis to determine the probability of different numbers of populations (K) within wild-derived inbred lines sampled from the three subspecies of M. musculus after the removal of lines found to be highly admixed in previous runs of STRUCTURE. (PDF, 160 KB)
Table S5 - Summary statistics describing runs of fixed differences in pairwise comparisons among subspecies of Mus musculus. (PDF, 183 KB)
Table S6 - Summary statistics describing runs of fixed differences on chromosome 2 in all pairwise comparisons of the subspecies of Mus musculus as well as the percentile rank of those statistics in 10,000 coalescent and recombination simulations. (PDF, 183 KB)
Table S7 - Demographic parameters used in ms (Hudson 2002) simulations. (PDF, 183 KB)
Table S8 - Average values of δ for different classes of sites in all pairwise comparisons between subspecies of M. musculus. (PDF, 188 KB)
Table S9 - Demographic parameters used in ms (Hudson 2002) simulations intended to more closely match the number of SNPs surveyed in the observed data. (PDF, 153 KB)
Table S10 - Demographic parameters used in ms (Hudson 2002) simulations. (PDF, 184 KB)
Table S11 - Overlap between inversions and runs of fixed differences identified between each pair of subspecies of Mus musculus. (PDF, 182 KB)
Table S12 - Average measures of differentiation in regions containing testis specific genes and all other regions for all pairwise comparisons of Mus musculus subspecies. (PDF, 189 KB)
Table S13 - Genes identified in regions of overlap between the results of QTL mapping and our study in comparisons between M. m. castaneus and M. m. domesticus. (PDF, 194 KB)
Table S14 - Genes identified in regions of overlap between the results of QTL mapping, a study of the hybrid zone, and our study in comparisons between M. m. musculus and M. m. domesticus. (PDF, 195 KB)
File S1 - SNP Table (.txt, 2 MB)
File S3 - Testis Specific Expression Table (.txt, 477 KB)
File S4 - Genes identified as significantly differentially expressed in each pairwise comparison among subspecies of M. musculus. (.xlsx, 279 KB)