Abstract
A likelihood ratio test is presented for comparing rates of evolutionary change in the paths of descent leading to two species. The test is compared to previous relative rate tests based on variances of estimated numbers of base substitutions. The likelihood approach allows for different transversion and transition rates, and when these rates are actually different, the likelihood ratio test can be much more powerful than the variance-based tests. For single-parameter mutation models, however, the two tests have similar power. The tests are applied to a set of chloroplast sequences from several species of grasses, and additional indications of significantly different rates leading to barley were found with the likelihood ratio test.
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Selected References
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- Bulmer M. Estimating the variability of substitution rates. Genetics. 1989 Nov;123(3):615–619. doi: 10.1093/genetics/123.3.615. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981;17(6):368–376. doi: 10.1007/BF01734359. [DOI] [PubMed] [Google Scholar]
- Felsenstein J. Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet. 1988;22:521–565. doi: 10.1146/annurev.ge.22.120188.002513. [DOI] [PubMed] [Google Scholar]
- Hasegawa M. Phylogeny and molecular evolution in primates. Jpn J Genet. 1990 Aug;65(4):243–266. doi: 10.1007/978-4-431-54011-3_16. [DOI] [PubMed] [Google Scholar]
- Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980 Dec;16(2):111–120. doi: 10.1007/BF01731581. [DOI] [PubMed] [Google Scholar]
- Li W. H., Wu C. I., Luo C. C. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol. 1985 Mar;2(2):150–174. doi: 10.1093/oxfordjournals.molbev.a040343. [DOI] [PubMed] [Google Scholar]
- Sarich V. M., Wilson A. C. Rates of albumin evolution in primates. Proc Natl Acad Sci U S A. 1967 Jul;58(1):142–148. doi: 10.1073/pnas.58.1.142. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Weir B. S., Basten C. J. Sampling strategies for distances between DNA sequences. Biometrics. 1990 Sep;46(3):551–582. [PubMed] [Google Scholar]
- Wu C. I., Li W. H. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc Natl Acad Sci U S A. 1985 Mar;82(6):1741–1745. doi: 10.1073/pnas.82.6.1741. [DOI] [PMC free article] [PubMed] [Google Scholar]