Additional file 1 of Further resolution of the house mouse (Mus musculus) phylogeny by integration over isolation-with-migration histories
Creators: name: Phifer-Rixey, Megan
name: Harr, Bettina
name: Hey, Jody
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: Additional file 1:Supplementary Table 1. Collection information and mapping metrics for samples from Harr et al. [39] included in this study. Supplementary Table 2. Parameter estimates with 95% confidence limits for the most probable model of three subspecies without a ghost population. Supplementary Table 3. Parameter estimates with 95% confidence limits for the most probable model of three subspecies with a ghost population. Supplementary Table 4. Estimated split times (years) with 95% confidence limits. Supplementary Table 5. Estimated effective population sizes (Ne) with 95% confidence limits (no ghost population). Supplementary Table 6. Estimated effective population sizes (Ne) with 95% confidence limits (with a ghost population). Supplementary Table 7. Estimated population migration rates with 95% confidence limits for the most probable topology with and without a ghost population included. Supplementary Table 8. Phylogeny results from the analysis of a second set of 200 random autosomal loci without a ghost population (compare with values from Table 1). Supplementary Table 9. Parameter estimates with 95% confidence limits for the most probable model of three subspecies without a ghost population for a second set of 200 random autosomal loci. Supplementary Table 10. Estimated split times (years) and effective population sizes (Ne) with 95% confidence limits using a second set of 200 random autosomal loci (without a ghost population). Supplementary Table 11. Estimated population migration rates with 95% confidence limits for the most probable topology using a second set of 200 random autosomal loci (without a ghost population). Supplementary Table 12. θ ̂ π $$ {\hat{\theta}}_{\pi } $$ / D ̂ xy $$ {\hat{D}}_{xy} $$ matrix for the 200 randomly selected autosomal loci from the genomic data. Supplementary Table 13. θ ̂ π $$ {\hat{\theta}}_{\pi } $$ / D ̂ xy $$ {\hat{D}}_{xy} $$ matrix for the 4 autosomal loci from Geraldes et al. [27]. Supplementary Table 14. Fst between subspecies was calculated as the mean across loci. Locus specific values of Fst were calculated using pairwise differences between sequences following Hudson, Slatkin, and Maddison [45]. Supplementary Table 15. Phylogeny results from the re-analysis of four autosomal and two X-linked loci included in Geraldes et al., [27]. Supplementary Table 16. Parameter estimates with 95% confidence limits for the most probable model of three subspecies using four autosomal and two X-linked loci included in Geraldes et al. [27]. Supplementary Table 17. Estimated split times (years) and effective population sizes (Ne) with 95% confidence limits for an analysis using four autosomal and two X-linked loci included in Geraldes et al. [27]. Supplementary Table 18. Estimated population migration rates with 95% confidence limits given the most probable topology for an analysis using four autosomal and two X-linked loci included in Geraldes et al. [27]. Supplementary Table 19. Summary information for 200 loci, including location on the chromosome, length, number of variable sites, and recombination rate (cM/Mb). Recombination rates were based on sex-averaged maps [54] as reported at http://cgd.jax.org/mousemapconverter/ . Supplementary Figure 1. A representation of an estimated Isolation with Migration model generated by IMa3 and the IMfig program [37] for house mice using a set of 200 alternative random autosomal loci. Details are as given in Fig. 1. Estimates assume 0.75 generations/year and 6 × 10−9 mutations per base pair per generation. Supplementary Figure 2. SNP density plotted against recombination rate for 200 sampled loci for A) all loci (y = 0.0005x + 0.0272, R2 = 0.0009) and B) all loci excluding outliers with recombination rate greater than 2 cM/Mb (y = 0.0008x + 0.271, R2 = 0.0007; data from Table S19).