Journal of Molecular Evolution

, Volume 37, Issue 4, pp 347-354

First online:

Toward a more accurate time scale for the human mitochondrial DNA tree

  • Masami HasegawaAffiliated withThe Institute of Statistical Mathematics and Department of Statistical Science, The Graduate University for Advanced Studies
  • , Anna Di RienzoAffiliated withDepartment of Psychiatry, University of California
  • , Thomas D. KocherAffiliated withDepartment of Zoology and Program in Genetics, University of New Hampshire
  • , Allan C. WilsonAffiliated withDivision of Biochemistry and Molecular Biology, University of California

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Several estimates of the time of occurrence of the most recent common mitochondrial DNA (mtDNA) ancestor of modern humans have been made. Estimates derived from noncoding regions based on a model that classifies sites into two categories (variable and invariable) have been consistently older than those derived from the third positions of codons. This discrepancy can be attributed to a violation of the assumption of rate homogeneity among variable sites when analyzing the noncoding regions. Additional data from the partial control region sequences allow us to take into account some of this further heterogeneity. By assigning the sites to three classes (highly variable, moderately variable, and invariable) and by assuming that the last common mtDNA ancestor of humans and chimpanzees lived 4 million years ago, the most recent common mtDNA ancestor of humans is estimated to have occurred 211,000 ±111,000 years ago (±1 SE), consistent with the estimate, 101,000 ± 52,000 years, made from third positions of codons and also with those proposed previously. We used the same technique to estimate when a putative expansion of modern humans out of Africa took place and estimated a time of 89,000 ± 69,000 years ago. Even though the standard errors of these estimates are large, they allow us to reject the multiregional hypothesis of modern human origin.

Key words

Third positions of codons Control region Heterogeneity among sites Molecular clock