The effective gene number (the number of genes that can be inherited) of mitochondrial DNA (mtDNA) is one-fourth of that of nuclear DNA (ncDNA) in idealized populations. Therefore, mtDNA haplotype diversity (h) is predicted to be lower than ncDNA heterozygosity (H-E) because of the higher effect of genetic drift on mtDNA. This prediction has not yet been systematically tested. To this end, in this study, published data for 739 populations of 108 mammalian species (66 terrestrial and 42 marine species) revealed the following patterns: (a) h was higher than H-E in 54.9% of populations, (b) the variance of h (0.097) was significantly higher than that of H-E (0.018) and (c) the frequency distribution of h differed between terrestrial and marine species. The terrestrial species exhibited a U-shaped distribution, whereas the marine species exhibited a right triangle shape. H-E showed a unimodal distribution for both groups. (d) The mean of H-E was similar between the terrestrial (0.668) and marine (0.672) species, whereas the mean of h was significantly lower for the terrestrial species (0.578) than for the marine species (0.740). Two hypotheses were considered to explain the above-described patterns, one of which was based on the higher mutation rates of mtDNA, while the other was based on a nested subpopulation structure in which an ncDNA-based population includes several mtDNA-based subpopulations. Herein, the plausibility of these two hypotheses was discussed with a focus on the higher intraspecific variation of h.
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