More reliable estimates of divergence times in pan using complete mtDNA sequences and accounting for population structure

Anne Stone, Fabia U. Battistuzzi, Laura S. Kubatko, George H. Perry, Evan Trudeau, Hsiuman Lin, Sudhir Kumar

Research output: Contribution to journalArticlepeer-review

57 Scopus citations


Here, we report the sequencing and analysis of eight complete mitochondrial genomes of chimpanzees (Pan troglodytes) from each of the three established subspecies (P. t. troglodytes, P. t. schweinfurthii and P. t. verus) and the proposed fourth subspecies (P. t. ellioti). Our population genetic analyses are consistent with neutral patterns of evolution that have been shaped by demography. The high levels of mtDNA diversity in western chimpanzees are unlike those seen at nuclear loci, which may reflect a demographic history of greater female to male effective population sizes possibly owing to the characteristics of the founding population. By using relaxed-clock methods, we have inferred a timetree of chimpanzee species and subspecies. The absolute divergence times vary based on the methods and calibration used, but relative divergence times show extensive uniformity. Overall, mtDNA produces consistently older times than those known from nuclear markers, a discrepancy that is reduced significantly by explicitly accounting for chimpanzee population structures in time estimation. Assuming the human-chimpanzee split to be between 7 and 5 Ma, chimpanzee time estimates are 2.1-1.5, 1.1-0.76 and 0.25-0.18 Ma for the chimpanzee/bonobo, western/(eastern + central) and eastern/central chimpanzee divergences, respectively.

Original languageEnglish (US)
Pages (from-to)3277-3288
Number of pages12
JournalPhilosophical Transactions of the Royal Society B: Biological Sciences
Issue number1556
StatePublished - Oct 27 2010


  • Divergence time
  • Mitochondrial genome
  • Pan paniscus
  • Pan troglodytes

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)


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