Biological Theory

, Volume 5, Issue 1, pp 40–52 | Cite as

The Overlap Feature of the Genetic Equidistance Result—A Fundamental Biological Phenomenon Overlooked for Nearly Half of a Century

  • Shi Huang


The genetic equidistance result shows that different species are approximately equidistant to a simpler outgroup in protein sequence similarity, as first reported by Margoliash in 1963. This result, together with those of Zuckerkandl and Pauling in 1962 inspired the molecular clock and in turn the neutral theory of evolution. Here it is shown that the clock/neutral theory had from the beginning overlooked another characteristic of the equidistance result, the overlap feature, which shows a large number of overlapped mutant amino acid positions where any pair of any three species is different provided that the species concerned differ from one another in complexity as a result of macroevolution. In contrast, when simple organisms of similar complexity and short evolutionary divergence are compared, there are only a small number of overlaps largely consistent with chance or the neutral theory. The full reality of the equidistance result strongly supports the Maximum Genetic Diversity hypothesis, a more complete account of hereditary changes.


evolution First Axiom of Biology First Axiom of Construction genetic equidistance Maximum Genetic Diversity hypothesis molecular clock neutral theory overlap feature 


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  1. Avise JC (1994) Molecular Markers, Natural History, and Evolution. New York: Springer.CrossRefGoogle Scholar
  2. Ayala FJ (1999) Molecular clock mirages. BioEssays 21: 71–75.CrossRefGoogle Scholar
  3. Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461: 1243–1247.CrossRefGoogle Scholar
  4. Chatterjee HJ, Ho SYW, Barnes I, Groves C (2009) Estimating the phylogeny and divergence times of primates using a supermatrix approach. BMC Evolutionary Biology 9: 259; doi:210.1186/1471-2148-1189-1259CrossRefGoogle Scholar
  5. Clarke B (1970) Darwinian evolution of proteins. Science 168: 1009–1011.CrossRefGoogle Scholar
  6. Dobzhansky T, Ayala FJ, Stebbins L, Valentine JW (1977) Evolution. San Francisco, CA: Freeman.Google Scholar
  7. Doolittle RF, Blombaeck B (1964) Amino-acid sequence investigations of fibrinopeptides from various mammals: Evolutionary implications. Nature 202: 147–152.CrossRefGoogle Scholar
  8. Gago S, Elena SF, Flores R, Sanjuan R (2009) Extremely high mutation rate of a hammerhead viroid. Science 323: 1308.CrossRefGoogle Scholar
  9. Goodman M, Moore GW, Barnabas J, Matsuda G (1974) The phylogeny of human globin genes investigated by the maximum parsimony method. Journal of Molecular Evolution 3: 1–48.CrossRefGoogle Scholar
  10. Halabi N, Rivoire O, Leibler S, Ranganathan R (2009) Protein sectors: Evolutionary units of three-dimensional structure. Cell 138: 774–786.CrossRefGoogle Scholar
  11. Huang S (2008a) Ancient fossil specimens are genetically more distant to an outgroup than extant sister species are. Rivista di Biologia 101: 93–108.Google Scholar
  12. Huang S (2008b) Histone methylation and the initiation of cancer. In Cancer Epigenetics (Tollefsbd T, ed), 109–150. New York: CRC Press.CrossRefGoogle Scholar
  13. Huang S (2008c) The genetic equidistance result of molecular evolution is independent of mutation rates. Journal of Computer Science and Systems Biology 1: 92–102.CrossRefGoogle Scholar
  14. Huang S (2009a) Inverse relationship between genetic diversity and epigenetic complexity. Preprint available at Nature Precedings:
  15. Huang S (2009b) Molecular evidence for the hadrosaur B. canadensis as an outgroup to a clade containing the dinosaur T. rex and birds. Rivista di Biologia 102: 20–22.Google Scholar
  16. Jukes TH, Holmquist R (1972) Evolutionary clock: Nonconstancy of rate in different species. Science 177: 530–532.CrossRefGoogle Scholar
  17. Kimura M (1968) Evolutionary rate at the molecular level. Nature 217: 624–626.CrossRefGoogle Scholar
  18. Kimura M (1986) DNA and the neutral theory. Philosophical Transactions of the Royal Society London B 312: 343–354.CrossRefGoogle Scholar
  19. Kimura M, Ohta T (1971) On the rate of molecular evolution. Journal of Molecular Evolution 1: 1–17.CrossRefGoogle Scholar
  20. King JL, Jukes TH (1964) Non-Darwinian evolution. Science 164: 788–798.CrossRefGoogle Scholar
  21. Kumar S (2005) Molecular clocks: Four decades of evolution. Nature Reviews Genetics 6: 654–662.CrossRefGoogle Scholar
  22. Laird CD, McConaughy BL, McCarthy BJ (1969) Rate of fixation of nucleotide substitutions in evolution. Nature 224: 149–154.CrossRefGoogle Scholar
  23. Langley CH, Fitch WM (1974) An examination of the constancy of the rate of molecular evolution. Journal of Molecular Evolution 3: 161–177.CrossRefGoogle Scholar
  24. Li W-H (1997) Molecular Evolution. Sunderland, MA: Sinauer.Google Scholar
  25. Margoliash E (1963) Primary structure and evolution of cytochrome c. Proceedings of the National Academy of Sciences of the USA 50: 672–679.CrossRefGoogle Scholar
  26. Nei M, Kumar S (2000) Molecular Evolution and Phylogenetics. New York: Oxford University Press.Google Scholar
  27. Nevo E (2001) Evolution of genome-phenome diversity under environmental stress. Proceedings of the National Academy of Sciences of the USA 98: 6233–6240.CrossRefGoogle Scholar
  28. Pulquerio MJ, Nichols RA (2007) Dates from the molecular clock: How wrong can we be? Trends in Ecology and Evolution 22: 180–184.CrossRefGoogle Scholar
  29. Richmond RC (1970) Non-Darwinian evolution: A critique. Nature 225: 1025–1028.CrossRefGoogle Scholar
  30. Van Valen L (1974) Molecular evolution as predicted by natural selection. Journal of Molecular Evolution 3: 89–101.CrossRefGoogle Scholar
  31. Zuckerkandl E, Pauling L (1962) Molecular Disease, Evolution, and Genetic Heterogeneity. Horizons in Biochemistry. New York: Academic Press.Google Scholar

Copyright information

© Konrad Lorenz Institute for Evolution and Cognition Research 2010

Authors and Affiliations

  1. 1.State Key Laboratory of Medical Genetics Xiangya Medical SchoolCentral South UniversityChangsha, HunanChina

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