Mitochondrial sequences show diverse evolutionary histories of African hominoids

Phylogenetic trees for the four extant species of African hominoids are pre sented, based on mtDNA control region-1 sequences from 1,158 unique haploty pes. We include 83 new haplotypes of western chimpanzees and bonobos. Phylo genetic analysis of this enlarged database, which takes intraspecific geogr aphic variability into account, reveals different patterns of evolution amo ng species and great heterogeneity in species-level variation. Several chim panzee and bonobo clades (and even single social groups) have retained subs tantially more mitochondrial variation than is seen in the entire human spe cies, Among the 811 human haplotypes, those that branch off early are predo minantly but not exclusively African. Neighbor joining trees provide strong evidence that eastern chimpanzee and human clades have experienced reduced effective population sizes, the latter apparently since the Homo sapiens-n eanderthalensis split. Application of topiary pruning resolves ambiguities in the phylogenetic tree that are attributable to homoplasies in the data s et. The diverse patterns of mtDNA sequence variation seen in today's homino id taxa probably reflect historical differences in ecological plasticity, f emale-biased dispersal, range fragmentation over differing periods of time, and competition among social groups. These results are relevant to the ori gin of zoonotic diseases, including HIV-1, and call into question some aspe cts of the current taxonomic treatment and conservation management of goril las and chimpanzees.