DOI: 10.1098/rstb.1986.0010. The estimate of total nucleotide substitutions from pairwise differences is biased

The estimate of total nucleotide substitutions from pairwise differences is biased

10.1098/rstb.1986.0010

Crossref journal-article

The Royal Society

Philosophical Transactions of the Royal Society of London. B, Biological Sciences (175)

Abstract

A nomographic method is presented that estimates the number of nucleotide substitutions since the common ancestor of two nucleotide sequences with no assumption about the proportion of transition and transversion substitutions except that it is constant over time. Of two previous methods of estimating this number, that of M. Kimura ( Proc. natn. Acad. Sci. U. S. A. 78, 454-458 (1981)) obtains the same result, and is thus confirmed by this work, while that of W. M. Brown, E. M. Prager, A. Wang & A. C. Wilson ( J. molec. Evol. 18, 225-239 (1982)) does not get the same result. The method presented here also obtains the fraction of all substitutions that are transitions. If one has three or more homologous sequences to compare, one can test the validity of the model by examining the constancy of the estimated proportion of substitutions that are transitions across the various pairs of sequences in a simple visual way. The method is general for any pair of mutually exclusive nucleotide substitutional categories, not just transitions and transversions. Mitochondrial data provide evidence that, for this and probably other current models correcting for superimposed substitutions, one or more of the underlying assumptions is incorrect. This is because there is some unknown systematic bias affecting this evolutionary process. It is suggested that at least part of the bias arises from incorrectly assuming that all sites are variable. In the absence of evidence that this bias is not present in other data, all estimates of the number of substitutions based upon pairs of sequences and current methods of estimating superimposed substitutions at a single site should be viewed as uncertain.

Bibliography

The estimate of total nucleotide substitutions from pairwise differences is biased. (1986). Philosophical Transactions of the Royal Society of London. B, Biological Sciences, 312(1154), 317â324.

Authors 0

None

References 9 Referenced 31

{'key': 'p_1', 'first-page': '225', 'article-title': 'Mitochondrial DNA sequences of primates: tempo and mode of evolution. J.molec', 'volume': '18', 'author': 'Brown W. M.', 'year': '1982', 'journal-title': 'Evol.'} / Evol. / Mitochondrial DNA sequences of primates: tempo and mode of evolution. J.molec by Brown W. M. (1982)
Cantor C. R. & Jukes T. H. 1969 Evolution of protein molecules. In Mammalian protein metabolism (ed. H. N. Munro) vol. Il l pp. 21-132. New York: Academic Press. (10.1016/B978-1-4832-3211-9.50009-7)
10.1007/BF00485794
{'key': 'p_4', 'first-page': '153', 'article-title': 'Estimating the total number of nucleotide substitutions since the common ancestor of a pair of homologous genes: comparison of several methods and three beta hemoglobin messenger RNAs. molec', 'volume': '16', 'author': 'Fitch W. M.', 'year': '1980', 'journal-title': 'Evol.'} / Evol. / Estimating the total number of nucleotide substitutions since the common ancestor of a pair of homologous genes: comparison of several methods and three beta hemoglobin messenger RNAs. molec by Fitch W. M. (1980)
{'key': 'p_5', 'first-page': '60', 'article-title': 'The old REH theory remains unsatisfactory and the new REH theory is problematical. J. molec', 'volume': '18', 'author': 'Fitch W. M.', 'year': '1981', 'journal-title': 'Evol.'} / Evol. / The old REH theory remains unsatisfactory and the new REH theory is problematical. J. molec by Fitch W. M. (1981)
10.1007/BF00487738
10.1007/BF00486096
{'key': 'p_8', 'first-page': '134', 'article-title': 'Transitions and transversions in evolutionary descent. J. molec', 'volume': '19', 'author': 'Holmquist R.', 'year': '1983', 'journal-title': 'Evol.'} / Evol. / Transitions and transversions in evolutionary descent. J. molec by Holmquist R. (1983)
Holuiquist* R. & Pearl D. 1980 Theoretical foundations for quantitative paleogenetics. Part III: the molecular divergence of nucleic acids and proteins for the case of genetic events of unequal probability. molec. Evol. (10.1007/BF01804977)

Dates

Type	When
Created	18 years, 8 months ago (Dec. 18, 2006, 5:33 p.m.)
Deposited	4 years, 6 months ago (Feb. 17, 2021, 11:36 p.m.)
Indexed	3 months ago (May 26, 2025, 5:06 a.m.)
Issued	39 years, 7 months ago (Jan. 29, 1986)
Published	39 years, 7 months ago (Jan. 29, 1986)
Published Online	28 years, 7 months ago (Jan. 1, 1997)
Published Print	39 years, 7 months ago (Jan. 29, 1986)

Funders 0

None

BibTeX

@article{1986, volume={312}, ISSN={2054-0280}, url={http://dx.doi.org/10.1098/rstb.1986.0010}, DOI={10.1098/rstb.1986.0010}, number={1154}, journal={Philosophical Transactions of the Royal Society of London. B, Biological Sciences}, publisher={The Royal Society}, year={1986}, month=jan, pages={317–324} }

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