Comparative nuclear and mitochondrial genome diversity in humans and chimpanzees

Restriction mapping and sequencing have shown that humans havesubstantially lower levels of mitochondrial genome diversity (d) thanchimpanzees. In contrast, humans have substantially higher levels ofheterozygosity (H) at protein-coding loci, suggesting a higher level ofdiversity in the nuclear genome. To investigate the discrepancy further, wesequenced a segment of the mitochondrial genome control region (CR) from 49chimpanzees. The majority of these were from the Pan troglodytes versussubspecies, which was underrepresented in previous studies. We alsoestimated the average heterozygosity at 60 short tandem repeat (STR) lociin both species. For a total sample of 115 chimpanzees, d = 0.075 +/00.037, compared to 0.020 +/- 0.011 for a sample of 1,554 humans. Theheterozygosity of human STR loci is significantly higher than that ofchimpanzees. Thus, the higher level of nuclear genome diversity relative tomitochondrial genome diversity in humans is not restricted toprotein-coding loci. It seems that humans, not chimpanzees, have an unusuald/H ratio, since the ratio in chimpanzees is similar to that in othercatarrhines. This discrepancy in the relative levels of nuclear andmitochondrial genome diversity in the two species cannot be explained bydifferences in mutation rate. However, it may result from a combination offactors such as a difference in the extent of sex ratio disparity, thegreater effect of population subdivision on mitochondrial than on nucleargenome diversity, a difference in the relative levels of male and femalemigration among subpopulations, diversifying selection acting to increasevariation in the nuclear genome, and/or directional selection acting toreduce variation in the mitochondrial genome.