Figures:
Figure 1. Competition experiment to reveal genomic regions involved in mitonuclear incompatibilities and their genomic architecture. Experimental hybridization results in F1 hybrids with the same nuclear composition but fixed alternative mitochondrial backgrounds (SD in red and SC in blue). Experimental evolution starts with F2 hybrids where recombination generated matched and mismatched mitonuclear complexes, leading to a decrease in average fitness of the starting population. Variation of individual fitness at multiple life history traits favors matched mitonuclear genotypes, leading to a recovery of life history traits and census size of the evolved populations. Comparison of allelic frequency change between lines evolving under alternative mitochondrial backgrounds allows distinguishing between genomic regions affected by uniform selection (e.g. adaptation, purging of deleterious mutations or nuclear-nuclear incompatibilities) from those affected by divergent selection related to the mitochondria (i.e. symmetric and asymmetric mitonuclear incompatibilities). In a fourth less likely scenario (not pictured here) a nuclear allele is favored in a mismatched mitochondrial background.
Figure 2. Variation of proxies for fitness during experimental evolution of hybrid lines under two alternative mitochondrial backgrounds (SC in blue, and SD in red). A. Population size expressed as the number of adult individuals. B. Female fecundity as the number of nauplii in the first clutch. C.Nauplii survivorship during 14 days of development. D. Temporal change in nauplii survivorship in the lines selected for sequencing (see Fig. S1 for other lines). Dark grey bars and rectangles refers to initial F2 hybrids (mean ±1SE), and light grey refers to the reference parental population. Lines selected for sequencing are marked in darker colors. Significant differences (P-values < 0.05) are marked with *.
Figure 3. Consistent allele frequency changes identify genomic regions involved in mitonuclear incompatibilities. Genomic windows skewed towards the SC allele are demarked in blue, while windows skewed towards the SD allele are in red. The dotted lined mark P-value thresholds assuming a z-score of 2, based on the variation observed within the SC lines (blue) and within the SD lines (red). Colored squares on the chromosomes mark genomic regions consistent with: uniform selection (green), mitonuclear incompatibilities favoring coadaptation (blue for SC and red for SD), and mitonuclear antagonistic selection (red lines).