Table 3 Summary statistics of the MK table for mitochondrially encoded OXPHOS complexes and nuclear genes
SpeciesGenomeGene SetaNIbNITGcZbPFETd
D. melmtDNAeComplex I1.731.59 (0.94, 3.17)−0.2380.070
mtDNAComplex IV0.560.55 (0, 1.30)0.2550.750
mtDNAComplex V9.929.64 (undef)−0.9970.007
mtDNAAll coding1.59 (1.97,3.57,3.89)1.67 (1.03, 2.86)−0.201 (-0.28,-0.33,0.36)0.041
NuclearAutosomes1.16 (1.52,2.83,4.25)1.39 (1.35, 1.43)−0.064 (-0.13,-0.15,0.42)<1e-6
NuclearX chrom0.91 (1.17,2.21,3.24)1.02 (0.94, 1.10)0.041 (-0.07,-0.06,0.41)0.001
H. sapmtDNAComplex I1.191.20 (0.56, 2.40)−0.0740.475
mtDNAComplex IV1.982.00 (0.86, 3.61)−0.2960.402
mtDNAComplex V1.621.66 (0.79, 2.42)−0.2090.127
mtDNAAll coding1.46 (1.38,1.95,1.38)1.48 (0.90, 2.24)−0.165 (-0.23,-0.23,0.32)0.034
NuclearAll coding1.51 (1.39,2.28,2.85)1.57 (1.51, 1.63)−0.180 (-0.12,-0.13,0.40)<1e-6
  • MK, McDonald-Kreitman; OXPHOS, oxidative phosphorylation; NI, neutrality index; D. mel, D. melanogaster; mtDNA, mitochondrial DNA; undef, undefined; X chrom, X chromosomes; H. sap, H. sapiens.

  • a Complex I (ND) seven loci; Complex IV (CO) three loci; Complex V (ATPase), two overlapping loci. Complex II is nuclear encoded and Complex III has only a single mitochondrial locus, Cyt-b.

  • b NI and Embedded Image were calculated using counts of PN, PS, DN, and DS summed across genes within gene sets. Median, mean, and SD provided for whole genome.

  • c Embedded Image with confidence intervals from 5000 bootstrap samples (Stoletzki and Eyre-Walker 2011).

  • d P-value from Fisher’s exact test of the MK table.

  • e D. melanogaster mtDNA data from the “more-inclusive” method. Values from other methods are in Table S3.