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).