A high observed substitution rate in the human mitochondrial DNA control region


The rate and pattern of sequence substitutions in the mitochondrial DNA (mtDNA) control region (CR) is of central importance to studies of human evolution and to forensic identity testing. Here, we report a direct measurement of the intergenerational substitution rate in the human CR. We compared DNA sequences of two CR hypervariable segments from close maternal relatives, from 134 independent mtDNA lineages spanning 327 generational events. Ten substitutions were observed, resulting in an empirical rate of 1/33 generations, or 2.5/site/Myr. This is roughly twenty-fold higher than estimates derived from phylogenetic analyses. This disparity cannot be accounted for simply by substitutions at mutational hot spots, suggesting additional factors that produce the discrepancy between very near-term and long-term apparent rates of sequence divergence. The data also indicate that extremely rapid segregation of CR sequence variants between generations is common in humans, with a very small mtDNA bottleneck. These results have implications for forensic applications and studies of human evolution.

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  1. 1

    Vigilant, L., Pennington, R., Harpending, H., Kocher, T.D. & Wilson, A.C. Mitochondria! DNA sequence in single hairs from a southern African population. Proc. Natl. Acad. Sci. USA 86, 9350–9354 (1989).

  2. 2

    Horai, S. & Hayasaka, K. Intraspecific nucleotide sequence differences in the major noncoding region of human mitochondrial DNA. Am. J. Hum. Genet. 46, 828–842 (1990).

  3. 3

    Vigilant, L., Stoneking, M., Harpending, H., Hawkes, K. & Wilson, A.C. African populations and the evolution of human mitochondrial DNA. Science 253, 1503–1507 (1991).

  4. 4

    Di Rienzo, A. & Wilson, A.C. Branching pattern in the evolutionary tree for human mitochondrial DNA. Proc. Natl. Acad. Sci. USA 88, 1597–1601 (1991).

  5. 5

    Ward, R.H., Frazier, B.L., Dew-Jager, K. & Pääabo, S. Extensive mitochondrial DNA diversity within a single Amerindian tribe. Proc. Natl. Acad. Sci. USA 88, 8720–8724 (1991).

  6. 6

    Stoneking, M., Sherry, S.T., Redd, A.J. & Vigilant, L. New approaches to dating suggest a recent age for human mtDNA ancestor. Phil. Trans. R. Soc. Lond. B 337, 167–175 (1992).

  7. 7

    Horai, S. et al. Peopling of the Americas, founded by four major lineages of mitochondrial. DNA. Mol. Biol. Evol. 10, 237ndash;47 (1993).

  8. 8

    Mountain, J.L. et al. Demographic history of India and mtDNA-sequence diversity. Am. J. Hum. Genet. 56, 979–992 (1995).

  9. 9

    Sajantila, A. et al. Genes and languages in Europe: an analysis of mitochondrial lineages. Genome Res. 5, 42–52 (1995).

  10. 10

    Graven, L. et al. Evolutionary correlation between control region sequence and restriction polymorphisms in the mitochondrial genome of a large Senegalese Mandenka sample. Mol. Biol. Evol. 12, 334–345 (1995).

  11. 11

    Cann, R.L., Stoneking, M. & Wilson, A.C. Mitochondrial DNA and human evolution. Nature 325, 31–36 (1987).

  12. 12

    Merriwether, D.A. et al. The structure of human mitochondrial DNA variation. J. Mol. Evol. 33, 543–555 (1991).

  13. 13

    Ruvolo, M. A new Approach to Studying Modern Human Origins: Hypothesis Testing with Coalescence Time Distributions. Mol. Phylo. Evol. 5, 202–219 (1996).

  14. 14

    Chen, Y.-S., Torroni, A., Excoffier, L., Silvana Santachiara-Benerecetti, A. & Wallace, D.C. Analysis of mtDNA variation in African populations reveals the most ancient of all human continent-specific haplogroups. Am.J. Hum. Genet. 57, 133–149 (1995).

  15. 15

    Horai, S., Hayasaka, K., Kondo, R., Tsugane, K. & Takahata, N. African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs. Proc. Natl. Acad. Sci. USA 92, 532–536 (1995).

  16. 16

    Hasegawa, M. & Horai, S. Time of the deepest root for polymorphism in human mitochondrial DNA. J. Mol. Evol.. 32, 37–42 (1991).

  17. 17

    Horai, S. et al. Man's place in Hominoidea revealed by mitochondriaJ DNA genealogy. J. Mol. Evol. 35, 32–43 (1992).

  18. 18

    Pesole, G., Sbisa, E., Preparata, G. & Saccone, C. The evolution of the mitochondrial D-loop region and the origin of modern man. Mol. Biol. Evol. 9, 587–598 (1992).

  19. 19

    Hassegawa, M., Di Rienzo, A., Kocher, T.D. & Wilson, A.C. Toward a more accurate estimate for the human mitochondrial DNA tree. J. Mol. Evol. 37, 347–354 (1993).

  20. 20

    Tamura, K. & Nei, M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10, 512–526 (1993).

  21. 21

    Wakeley, J. Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA. J. Mol. Evol. 37, 613–623 (1993).

  22. 22

    Wills, C. When did Eve live? An evolutionary detective story. Evolution 49, 593–607 (1995).

  23. 23

    Ruvolo, M., Zehr, S., von Dornum, M., Pan, D., Chang, B. & Lin, J. Mitocondrial COII sequences and modern human origins. Mol. Biol. Evol. 10, 1115–1135 (1993).

  24. 24

    Adachi, J. & Hasegawa, M. Tempo and mode of synonymous substitutions in mitochondrial DNA of primates. Mol. Biol. Evol. 13, 200–208 (1996).

  25. 25

    Ginther, C., Issel-Tarver, L. & King, M.-C. Identifying individuals by sequencing mitochondrial DNA from teeth. Nature Genet. 2, 135–138, (1992).

  26. 26

    Piercy, R., Sullivan, K.M., Benson, N. & Gill, P. The application of mitochondrial DNA typing to the study of white Caucasian genetic identification. Int. J. Leg. Med. 106, 85–90 (1993).

  27. 27

    Holland, M.M. et al. Mitochondrial DNA sequence analysis of human skeletal remains: identification of remains from the Vietnam War. J. Forensic Sci. 38, 542–553, (1993).

  28. 28

    Holland, M.M. et al. Mitochondrial DNA sequence analysis of human remains. Crime Lab.Digest 22, 3–8 (1995).

  29. 29

    Wilson, M., DiZinno, J.A., Polanskey, D., Replogle, J. & Budowle, B. Validation of mitochondrial DNA sequencing for forensic casework analysis. Int. J. Leg. Med. 108, 68–74 (1995).

  30. 30

    Gill, P. et al. Identification of the remains of the Romanov family by DNA analysis.. Nature Genet. 6, 130–135, (1994).

  31. 31

    Ivanov, P.L. et al. Mitochondrial DNA sequence heteroplasmy in the grand duke of Russia Georgji Romanov establishes the authenticity of the remains of Tsar Nicholas II. Nature Genet. 12, 417–420 (1996).

  32. 32

    Anderson, S. et al. Sequence and organization of the human mitochondrial genome. Nature 290, 457–465 (1981).

  33. 33

    Holland, M.M. et al. Identification of human remains using mitochondrial DNA sequencing: potential mother-child mutational events, in Advances in Forensic Haemogenetics(eds Bar, W., Fiori, A. & Rossi, U.) 399–406 (Springer Verlag, New York, 1994).

  34. 34

    Nei, M. Age of the common ancestor of human mitochondrial DNA. Mol. Biol. Evol. 9, 1176–1178 (1992).

  35. 35

    Ayala, F. The myth of Eve: molecular biology and human origins. Science 270, 1930–1936 (1995).

  36. 36

    Penny, D., Steel, M., Waddel, P.J. & Hendy, M.D. Improved analyses of human mtDNA sequences support a recent African origin for Homo sapiens . Mol. Biol. Evol. 12, 863–882 (1995).

  37. 37

    Howell, N., Kubacka, I. & Mackey, D.A. How rapidly does the human mitochondrial genome evolve? Am. J. Hum. Genet. 59, 501–509 (1996).

  38. 38

    Nachman, M.W., Brown, W.M., Stoneking, M. & Aquadro, C.F. Nonneutral mitochondrial DNA variation in humans and chimpanzees. Genetics 142, 953–963 (1996).

  39. 39

    Templeton, A.R. Contingency tests of neutrality using inta/interspecific gene trees: the rejection of neutrality for the evolution of the mitochondrial cytochrome oxidase II gene in the homonoid primates. Genetics 144, 1263–1270 (1996).

  40. 40

    Excoffier, L. Evolution of human mitochondrial DNA: evidence for departure from a pure neutral model of populations at equilibrium. J. Mol. Evol. 30, 125–139 (1990).

  41. 41

    Gemmel, N.J., Western, P.S., Watson, J.M. & Marshall Graves, J.A. Evolution of the mammalian mitochondrial control region — comparisons of control region sequences between monotreme and therian mammals. Mol. Biol. Evol. 13, 798–808 (1996).

  42. 42

    Hauswirth, W.W. & Laipis, P.J. Mitochondrial DNA polymorphism in a maternal lineage of Holstein cows. Proc. Natl. Acad. Sci. USA 79, 4686–4690 (1982).

  43. 43

    Laipis, P., Hauswirth, W., O'Brian, T. & Michaels, G. Unequal partitioning of bovine mitochondrial genotypes among siblings. Proc. Natl. Acad. Sci. USA 85, 8107–8110 (1988).

  44. 44

    Solignac, M., Genermont, J., Monnerot, M. & Mounolou, J.C. Genetics of mitochondria in Drosophila: mtDNA in heteroplasmic strains of D. mauritiana. Mol. Gen. Genet. 197, 183–188 (1984).

  45. 45

    Poulton, J. Transmission of mtDNA: cracks in the bottleneck. Am. J. Hum. Genet. 57, 224–226 (1995).

  46. 46

    Bendall, K.E., Macaulay, V.A., Baker, J.R. & Sykes, B.C. Heteroplasmic point mutations in the human mtDNA control region. Am.J. Hum. Genet. 59, 1276–1287 (1996).

  47. 47

    Jenuth, J.P., Peterson, A.C., Fu, K. & Shoubridge, E.A. Random genetic drift in the female germline explains the rapid segregation of mammalian mitochondrial DNA. Nature Genet. 14, 146–151 (1996).

  48. 48

    Comas, D., Pääbo, S. & Bertranpetit, J. Heteroplasmy in the control region of human mitochondrial DNA. Genome Res. 5, 89–90 (1995).

  49. 49

    Howell, N. et al. Mitochondrial gene segregation in mammals: Is the bottleneck always narrow? Hum. Genet. 90, 117–120 (1992).

  50. 50

    Walsh, P.S., Metzger, D.A. & Higuchi, R. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. BioTechniques 10, 506–513 (1991).

  51. 51

    Miller, K.W.P., Dawson, J.L. & Hagelberg, E. A concordance of nucleotide substitutions in the first and second hypervariable segments of the human mtDNA control region. Int. J. Legal Med. 109, 107–113 (1996).

  52. 52

    SAS Procedures Guide, release 6.07, SAS Institute, Carey, NC (1991).

  53. 53

    Wilson, M.R., Stoneking, M., Holland, M.M., DiZinno, J.A. & Budowle, B. Guidelines for the use of mitochondrial DNA sequencing in forensic science. Crime Lab. Digest 20, 68–77 (1993).

  54. 54

    Sullivan, K.H., Hopgood, R. & Gill, P. Identification of human remains by amplification and automated sequencing of mitochondrial DNA. Int. J. Leg. Med. 105, 83–86 (1992).

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Parsons, T., Muniec, D., Sullivan, K. et al. A high observed substitution rate in the human mitochondrial DNA control region. Nat Genet 15, 363–368 (1997). https://doi.org/10.1038/ng0497-363

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