Genetics, Vol 135, 599-607, Copyright © 1993

INVESTIGATIONS

Simple Methods for Testing the Molecular Evolutionary Clock Hypothesis

F. Tajima
Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka-ken 411, Japan

Simple statistical methods for testing the molecular evolutionary clock hypothesis are developed which can be applied to both nucleotide and amino acid sequences. These methods are based on the chi-square test and are applicable even when the pattern of substitution rates is unknown and/or the substitution rate varies among different sites. Furthermore, some of the methods can be applied even when the outgroup is unknown. Using computer simulations, these methods were compared with the likelihood ratio test and the relative rate test. The results indicate that the powers of the present methods are similar to those of the likelihood ratio test and the relative rate test, in spite of the fact that the latter two tests assume that the pattern of substitution rates follows a certain model and that the substitution rate is the same among different sites, while such assumptions are not necessary to apply the present methods. Therefore, the present methods might be useful.


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S. N. Avedisov, I. B. Rogozin, E. V. Koonin, and B. J. Thomas
Rapid Evolution of a Cyclin A Inhibitor Gene, roughex, in Drosophila
Mol. Biol. Evol., November 1, 2001; 18(11): 2110 - 2118.
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A. L. Roca, N. Georgiadis, J. Pecon-Slattery, and S. J. O'Brien
Genetic Evidence for Two Species of Elephant in Africa
Science, August 24, 2001; 293(5534): 1473 - 1477.
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M. Barrier, R. H. Robichaux, and M. D. Purugganan
Accelerated regulatory gene evolution in an adaptive radiation
PNAS, August 17, 2001; (2001) 181257698.
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C. A. Matthee and S. K. Davis
Molecular Insights into the Evolution of the Family Bovidae: A Nuclear DNA Perspective
Mol. Biol. Evol., July 1, 2001; 18(7): 1220 - 1230.
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A. Munte, M. Aguade, and C. Segarra
Changes in the Recombinational Environment Affect Divergence in the yellow Gene of Drosophila
Mol. Biol. Evol., June 1, 2001; 18(6): 1045 - 1056.
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M. Nei, P. Xu, and G. Glazko
Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms
PNAS, February 15, 2001; (2001) 51611498.
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Q. Liu, C. L. Brubaker, A. G. Green, D. R. Marshall, P. J. Sharp, and S. P. Singh
Evolution of the FAD2-1 fatty acid desaturase 5' UTR intron and the molecular systematics of Gossypium (Malvaceae)
Am. J. Botany, January 1, 2001; 88(1): 92 - 102.
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S. Yi and B. Charlesworth
A Selective Sweep Associated With a Recent Gene Transposition in Drosophila miranda
Genetics, December 1, 2000; 156(4): 1753 - 1763.
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J. Kusumi, Y. Tsumura, H. Yoshimaru, and H. Tachida
Phylogenetic relationships in Taxodiaceae and Cupressaceae sensu stricto based on matK gene, chlL gene, trnL-trnF IGS region, and trnL intron sequences
Am. J. Botany, October 1, 2000; 87(10): 1480 - 1488.
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P. S. Schmidt, D. D. Duvernell, and W. F. Eanes
Adaptive evolution of a candidate gene for aging in Drosophila
PNAS, September 19, 2000; (2000) 190338897.
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R. L. Small and J. F. Wendel
Copy Number Lability and Evolutionary Dynamics of the Adh Gene Family in Diploid and Tetraploid Cotton (Gossypium)
Genetics, August 1, 2000; 155(4): 1913 - 1926.
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G. J. Schmidt and E. E. Schilling
Phylogeny and biogeography of Eupatorium (Asteraceae: Eupatorieae) based on nuclear ITS sequence data
Am. J. Botany, May 1, 2000; 87(5): 716 - 726.
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R. C. Cronn, R. L. Small, and J. F. Wendel
Duplicated genes evolve independently after polyploid formation in cotton
PNAS, December 7, 1999; 96(25): 14406 - 14411.
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K. J. Schmid, L. Nigro, C. F. Aquadro, and D. Tautz
Large Number of Replacement Polymorphisms in Rapidly Evolving Genes of Drosophila: Implications for Genome-Wide Surveys of DNA Polymorphism
Genetics, December 1, 1999; 153(4): 1717 - 1729.
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A. Caccone, J. P. Gibbs, V. Ketmaier, E. Suatoni, and J. R. Powell
Origin and evolutionary relationships of giant Galapagos tortoises
PNAS, November 9, 1999; 96(23): 13223 - 13228.
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T. Takano-Shimizu
Local Recombination and Mutation Effects on Molecular Evolution in Drosophila
Genetics, November 1, 1999; 153(3): 1285 - 1296.
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C. Su and M. Nei
Fifty-million-year-old polymorphism at an immunoglobulin variable region gene locus in the rabbit evolutionary lineage
PNAS, August 17, 1999; 96(17): 9710 - 9715.
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R. L. Small, J. A. Ryburn, R. C. Cronn, T. Seelanan, and J. F. Wendel
The tortoise and the hare: choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group
Am. J. Botany, September 1, 1998; 85(9): 1301 - 1315.
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X. Gu and W.-H. Li
Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution
PNAS, May 26, 1998; 95(11): 5899 - 5905.
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C. Vilà, P. Savolainen, J. E. Maldonado, I. R. Amorim, J. E. Rice, R. L. Honeycutt, K. A. Crandall, J. Lundeberg, and R. K. Wayne
Multiple and Ancient Origins of the Domestic Dog
Science, June 13, 1997; 276(5319): 1687 - 1689.
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J. A. Leonard, R. K. Wayne, and A. Cooper
From the Cover: Population genetics of Ice Age brown bears
PNAS, February 15, 2000; 97(4): 1651 - 1654.
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