Additional file 1 of Mitochondrial-nuclear coadaptation revealed through mtDNA replacements in Saccharomyces cerevisiae

Additional file 1: Table S1. Strain table. Table S2. SNP table for mitochondrial coding sequences for the 15 parental strains. Allzle numbering is arbitrary. Table S3. Mitochondrial coding sequence statistics. Table S4. Mitochondrial × nuclear interactions (mt × n) within single environments. To determine the significance of each term, ANOVAs comparing the full model with a model lacking the indicated term were evaluated. Each factor was treated as a random effect. Full model: n + mt + (mt × n). Table S5. Phenotypic variance analysis to show the amount of variance contributed by mitochondrial, nuclear background, and mitonuclear interactions in all growth conditions. Table S6. Mitochondrial × nuclear × environment interactions (mt × n × e). To determine the significance of each term, ANOVAs comparing the full model with a model lacking the indicated term were evaluated. Each factor was treated as a random effect. Full model: n + mt + e + (mt × n) + (n × e) + (mt × e) + (mt × n × e). Table S7. Phenotypic variance of strains with original, synthetic, and all possible mitonuclear combinations across all growth conditions. Student’s t-test were performed to determine whether the difference among strains with original and synthetic combinations is statistically significant. Table S8. Fixed effect model, two-way ANOVA table showing mt × n interactions for each mtDNA exchange between two strains. The P values for genetic terms (nuclear, mitochondrial, mitonuclear epistasis), type of epistasis, and estimated strength of epistasis were provided for each pairwise mtDNA exchange. Table S9. Numbers of significant mitonuclear tests following mtDNA exchanges within and between clades. Table S10. Mitochondrial genotype-phenotype association tests.