Evolutionary history of chimpanzees inferred from complete mitochondrial genomes

Investigations into the evolutionary history of the common chimpanzee, Pan troglodytes, have produced inconsistent results, due to differences in the types of molecular data considered, the model assumptions employed, and the quantity and geographical range of samples used. We amplified and sequenced 24 complete P. troglodytes mitochondrial genomes from fecal samples collected at multiple study sites throughout sub-Saharan Africa. Using a ‘relaxed molecular clock,’ fossil calibrations, and 12 additional complete primate mitochondrial genomes, we analyzed the pattern and timing of primate diversification in a Bayesian framework. Our results support the recognition of four chimpanzee subspecies. Within P. troglodytes, we report a mean (95% highest posterior density (HPD)) time since most recent common ancestor (tMRCA) of 1.026 (0.811-1.263) MYA for the four proposed subspecies, with two major lineages. One of these lineages (tMRCA = 0.510 [0.387-0.650] MYA) contains P. t. verus (tMRCA = 0...