mtDNA diversity in rhesus monkeys reveals overestimates of divergence time and paraphyly with neighboring species

Reconstructions of the human-African great ape phylogeny by usingmitochondrial DNA (mtDNA) have been subject to considerable debate. Oneconfounding factor may be the lack of data on intraspecific variation. Totest this hypothesis, we examined the effect of intraspecific mtDNAdiversity on the phylogenetic reconstruction of another Plio- Pleistoceneradiation of higher primates, the fascicularis group of macaque (Macaca)monkey species. Fifteen endonucleases were used to identify 10 haplotypesof 40-47 restriction sites in M. mulatta, which were compared with similardata for the other members of this species group. Interpopulational,intraspecific mtDNA diversity was large (0.5%- 4.5%), and estimates ofdivergence time and branching order incorporating this variation weresubstantially different from those based on single representatives of eachspecies. We conclude that intraspecific mtDNA diversity is substantial inat least some primate species. Consequently, without prior information onthe extent of genetic diversity within a particular species, intraspecificvariation must be assessed and accounted for when reconstructing primatephylogenies. Further, we question the reliability of hominoid mtDNAphylogenies, based as they are on one or a few representatives of eachspecies, in an already depauperate superfamily of primates.