Deleterious mutations contribute to polymorphism even when selection effectively prevents their fixation. The efficacy of selection in removing deleterious mitochondrial mutations from populations depends on the effective population size (Ne) of the mitochondrial DNA and the degree to which a lack of recombination magnifies the effects of linked selection. Using complete mitochondrial genomes from Drosophila melanogaster and nuclear data available from the same samples, we reexamine the hypothesis that nonrecombining animal mitochondrial DNA harbor an excess of deleterious polymorphisms relative to the nuclear genome. We find no evidence of recombination in the mitochondrial genome, and the much-reduced level of mitochondrial synonymous polymorphism relative to nuclear genes is consistent with a reduction in Ne. Nevertheless, we find that the neutrality index, a measure of the excess of nonsynonymous polymorphism relative to the neutral expectation, is only weakly significantly different between mitochondrial and nuclear loci. This difference is likely the result of the larger proportion of beneficial mutations in X-linked relative to autosomal loci, and we find little to no difference between mitochondrial and autosomal neutrality indices. Reanalysis of published data from Homo sapiens reveals a similar lack of a difference between the two genomes, although previous studies have suggested a strong difference in both species. Thus, despite a smaller Ne, mitochondrial loci of both flies and humans appear to experience similar efficacies of purifying selection as do loci in the recombining nuclear genome.

Deleterious mutations contribute to polymorphism even when selection effectively prevents their fixation. The efficacy of selection in removing deleterious mitochondrial mutations from populations depends on the effective population size (N e) of the mitochondrial DNA and the degree to which a lack of recombination magnifies the effects of linked selection. Using complete mitochondrial genomes from Drosophila melanogaster and nuclear data available from the same samples, we reexamine the hypothesis that nonrecombining animal mitochondrial DNA harbor an excess of deleterious polymorphisms relative to the nuclear genome. We find no evidence of recombination in the mitochondrial genome, and the much-reduced level of mitochondrial synonymous polymorphism relative to nuclear genes is consistent with a reduction in N e. Nevertheless, we find that the neutrality index, a measure of the excess of nonsynon-ymous polymorphism relative to the neutral expectation, is only weakly significantly different between mitochondrial and nuclear loci. This difference is likely the result of the larger proportion of beneficial mutations in X-linked relative to autosomal loci, and we find little to no difference between mitochondrial and autosomal neutrality indices. Reanalysis of published data from Homo sapiens reveals a similar lack of a difference between the two genomes, although previous studies have suggested a strong difference in both species. Thus, despite a smaller N e , mitochondrial loci of both flies and humans appear to experience similar efficacies of purifying selection as do loci in the recombining nuclear genome. KEYWORDS cytoplasmic sweep mtDNA neutrality index tests of selection The effective size of a population (N e) impacts how effectively selection removes deleterious mutations and fixes advantageous mutations. The unique genetics of the mitochondrial genome (mitochondrial DNA; mtDNA) are thought to reduce its N e relative to the nuclear genome, via haploid, uniparental inheritance, the mitochondrial bottleneck in the maternal germline, and a lack of recombination that decreases N e via selection on linked sites (Hill and Robertson 1966; Maynard Smith and Haigh 1974; Gillespie 2000; Meiklejohn et al. 2007; White et al. 2008; Charlesworth 2012). In addition, cytoplasmic transmission can link the mtDNA to selfish cytoplasmic elements (e.g., Wolbachia in insects) that may sweep through populations, further decreasing mito-chondrial N e and possibly increasing mitochondrial substitution rates via the fixation of slightly deleterious mutations (Shoemaker et al. 2004). For these reasons it has been widely hypothesized that selection is less effective in mitochondrial genomes than in their nuclear counterparts and that mitochondrial genomes may accumulate greater numbers of deleterious substitutions (Lynch 1996, 1997). Analyses of sequence data in Drosophila and mammals have largely supported the conclusion that mtDNA harbors significant levels of slightly dele-terious polymorphism (Ballard and