Frequency distribution of relative rates of A/T → G/C and G/C → A/T substitutions in T. muenninki, mouse, and rat. Each relative rate was estimated from the combined sequences of coding (3rd codon only) and noncoding sites of each gene located on the peritelomeric (a) and pericentromeric (b) regions of T. muenninki neo-sex chromosomes and the corresponding autosomal regions of mouse and rat. The horizontal axis shows the log of the ratio of A/T → G/C substitutions to G/C → A/T substitutions, and the vertical axis shows the number of genes. Black bar: T. muenninki; white bar: M. musculus; and gray bar: R. norvegicus. Figure S2. Comparison of nucleotide sequences of TXNDC11 between T. muenninki neo-X and neo-Y. Single base insertion site in neo-Y–linked sequence was indicated by gray box. The sequences were partially skipped in TMU (2407 bp) and MMU (2410 bp), and the skipped site is shown by double slashes. The accession number for Txndc11 gene from mouse is NM_029582. TMU: T. muenniniki, MMU: M.musculus. Figure S3. The estimation of nucleotide substitution directions in the three species by the maximum parsimony principle. TMU: T. muenninki, MMU: M. musculus, RNO: R. norvegicus. (ZIP 342 kb)

List of BAC clones screened for FISH analysis in this study. Table S2. List of genes located on the three regions of neo-sex chromosomes in T. muenninki. Table S3. Comparison of G + C content and nucleotide substitution frequency in three regions among T. muenninki, mouse, and rat with guinea pig as outgroup. Table S4. Frequencies (%) of nucleotide substitutions in sites preceded by C or followed by G in T. muenninki neo-sex chromosomal segments and their autosomal homologs in mouse and rat. Table S5. Detection of male-specific substitutions in 24 genes located on the neo-sex chromosomes. Table S6. Male-specific substitutions observed in the pericentromeric region of the T. muenninki neo-Y chromosome. Table S7. Resulti of tests of the differences in dN/dS ratios among T. muenninki neo-X, neo-Y, and other branches. Table S8. G + C content and frequency of nucleotide substitutions in T. muenninki neo-sex chromosomes and their homologous region in mouse. Table S9. List of BAC clones identified for neo-sex sequence determination. Table S10. Results of next-generation sequencing on an Illumina HiSeq, using a 100 bp paired-end protocol and de novo assembly. Table S11. Results of next-generation sequencing on an Illumina MiSeq, using a 300 bp paired-end protocol and de novo assembly. (ZIP 110 kb)

List of BAC clones screened for FISH analysis in this study. Table S2. List of genes located on the three regions of neo-sex chromosomes in T. muenninki. Table S3. Comparison of G + C content and nucleotide substitution frequency in three regions among T. muenninki, mouse, and rat with guinea pig as outgroup. Table S4. Frequencies (%) of nucleotide substitutions in sites preceded by C or followed by G in T. muenninki neo-sex chromosomal segments and their autosomal homologs in mouse and rat. Table S5. Detection of male-specific substitutions in 24 genes located on the neo-sex chromosomes. Table S6. Male-specific substitutions observed in the pericentromeric region of the T. muenninki neo-Y chromosome. Table S7. Resulti of tests of the differences in dN/dS ratios among T. muenninki neo-X, neo-Y, and other branches. Table S8. G + C content and frequency of nucleotide substitutions in T. muenninki neo-sex chromosomes and their homologous region in mouse. Table S9. List of BAC clones identified for neo-sex sequence determination. Table S10. Results of next-generation sequencing on an Illumina HiSeq, using a 100 bp paired-end protocol and de novo assembly. Table S11. Results of next-generation sequencing on an Illumina MiSeq, using a 300 bp paired-end protocol and de novo assembly. (ZIP 110 kb)

Frequency distribution of relative rates of A/T → G/C and G/C → A/T substitutions in T. muenninki, mouse, and rat. Each relative rate was estimated from the combined sequences of coding (3rd codon only) and noncoding sites of each gene located on the peritelomeric (a) and pericentromeric (b) regions of T. muenninki neo-sex chromosomes and the corresponding autosomal regions of mouse and rat. The horizontal axis shows the log of the ratio of A/T → G/C substitutions to G/C → A/T substitutions, and the vertical axis shows the number of genes. Black bar: T. muenninki; white bar: M. musculus; and gray bar: R. norvegicus. Figure S2. Comparison of nucleotide sequences of TXNDC11 between T. muenninki neo-X and neo-Y. Single base insertion site in neo-Y–linked sequence was indicated by gray box. The sequences were partially skipped in TMU (2407 bp) and MMU (2410 bp), and the skipped site is shown by double slashes. The accession number for Txndc11 gene from mouse is NM_029582. TMU: T. muenniniki, MMU: M.musculus. Figure S3. The estimation of nucleotide substitution directions in the three species by the maximum parsimony principle. TMU: T. muenninki, MMU: M. musculus, RNO: R. norvegicus. (ZIP 342 kb)