PMID: 6167733Jan 1, 1981Paper

Statistical properties of the Jukes-Holmquist method of estimating the number of nucleotide substitutions: reply to Holmquist and Conroy's criticism

Journal of Molecular Evolution
M Nei, Y Tateno

Abstract

Conducting computer simulations, Nei and Tateno (1978) have shown that Jukes and Holmquist's (1972) method of estimating the number of nucleotide substitutions tends to give an overestimate and the estimate obtained has a large variance. Holmquist and Conroy (1980) repeated some parts of our simulation and claim that the overestimation of nucleotide substitutions in our paper occurred mainly because we used selected data. Examination of Holmquist and Conroy's simulation indicates that their results are essentially the same as ours when the Jukes-Holmquist method is used, but since they used a different method of computation their estimates of nucleotide substitutions differed substantially from ours. Another problem in Holmquist and Conroy's Letter is that they confused the expected number of nucleotide substitution with the number in a sample. This confusion has resulted in a number of unnecessary arguments. They also criticized our X2 measure, but this criticism is apparently due to a misunderstanding of the assumptions of our method and a failure to use our method in the way we described. We believe that our earlier conclusions remain unchanged.

References

Jul 18, 1979·Journal of Molecular Evolution·M Nei, Y Tateno
May 12, 1978·Journal of Molecular Evolution·Y Tateno, M Nei
Oct 6, 1978·Journal of Molecular Evolution·R Holmquist
Jan 1, 1972·Journal of Molecular Evolution·R Holmquist
Feb 28, 1972·Journal of Molecular Biology·T H Jukes, R Holmquist
Jan 1, 1981·Journal of Molecular Evolution·R Holmquist, T Conroy

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Citations

Dec 24, 2010·PloS One·Delphine PasseriniPascal Le Bourgeois
Aug 25, 2007·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Elena ZaytsevaGeorgy P Somov

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