New methods for estimating the numbers of synonymous and nonsynonymous substitutions - PubMed (original) (raw)
. 1995 Feb;40(2):190-226.
doi: 10.1007/BF00167113.
Affiliations
- PMID: 7699723
- DOI: 10.1007/BF00167113
New methods for estimating the numbers of synonymous and nonsynonymous substitutions
Y Ina. J Mol Evol. 1995 Feb.
Abstract
New methods for estimating the numbers of synonymous and nonsynonymous substitutions per site were developed. The methods are unweighted pathway methods based on Kimura's two-parameter model. Computer simulations were conducted to evaluate the accuracies of the new methods, Nei and Gojobori's (NG) method, Miyata and Yasunaga's (MY) method, Li, Wu, and Luo's (LWL) method, and Pamilo, Bianchi, and Li's (PBL) method. The following results were obtained: (1) The NG, MY, and LWL methods give overestimates of the number of synonymous substitutions and underestimates of the number of nonsynonymous substitutions. The major cause for the biased estimation is that these three methods underestimate the number of synonymous sites and overestimate the number of nonsynonymous sites. (2) The PBL method gives better estimates of the numbers of synonymous and nonsynonymous substitutions than those obtained by the NG, MY, and LWL methods. (3) The new methods also give better estimates of the numbers of synonymous and nonsynonymous substitutions than those obtained by the NG, MY, and LWL methods. In addition, estimates of the numbers of synonymous and nonsynonymous sites obtained by the new methods are reasonably accurate. (4) In some cases, the new methods and the PBL method give biased estimates of substitution numbers. However, from the number of nucleotide substitutions at the third position of codons, we can examine whether estimates obtained by the new methods are good or not, whereas we cannot make an examination of estimates obtained by the PBL method. (5) When there are strong transition/transversion and nucleotide-frequency biases like mitochondrial genes, all of the above methods give biased estimates of substitution numbers. In such cases, Kondo et al.'s method is recommended to be used for estimating the number of synonymous substitutions, although their method cannot estimate the number of nonsynonymous substitutions and is time-consuming. These results, particularly result (1), call for reexaminations of some genes. This is because evolutionary pictures of genes have often been discussed on the basis of results obtained by the NG, MY, and LWL methods, which are favorable for the neutral theory of molecular evolution.
Similar articles
- A method for estimating the numbers of synonymous and nonsynonymous substitutions per site.
Comeron JM. Comeron JM. J Mol Evol. 1995 Dec;41(6):1152-9. doi: 10.1007/BF00173196. J Mol Evol. 1995. PMID: 8587111 - Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.
Nei M, Gojobori T. Nei M, et al. Mol Biol Evol. 1986 Sep;3(5):418-26. doi: 10.1093/oxfordjournals.molbev.a040410. Mol Biol Evol. 1986. PMID: 3444411 - Variance and covariances of the numbers of synonymous and nonsynonymous substitutions per site.
Ota T, Nei M. Ota T, et al. Mol Biol Evol. 1994 Jul;11(4):613-9. doi: 10.1093/oxfordjournals.molbev.a040140. Mol Biol Evol. 1994. PMID: 8078400 - A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes.
Li WH, Wu CI, Luo CC. Li WH, et al. Mol Biol Evol. 1985 Mar;2(2):150-74. doi: 10.1093/oxfordjournals.molbev.a040343. Mol Biol Evol. 1985. PMID: 3916709 Review.
Cited by
- Evolution of a minimal cell.
Moger-Reischer RZ, Glass JI, Wise KS, Sun L, Bittencourt DMC, Lehmkuhl BK, Schoolmaster DR Jr, Lynch M, Lennon JT. Moger-Reischer RZ, et al. Nature. 2023 Aug;620(7972):122-127. doi: 10.1038/s41586-023-06288-x. Epub 2023 Jul 5. Nature. 2023. PMID: 37407813 Free PMC article. - Genetic polymorphism of circumsporozoite protein of Plasmodium falciparum among Chinese migrant workers returning from Africa to Henan Province.
He ZQ, Zhang QQ, Wang D, Hu YB, Zhou RM, Qian D, Yang CY, Lu DL, Li SH, Liu Y, Zhang HW. He ZQ, et al. Malar J. 2022 Aug 27;21(1):248. doi: 10.1186/s12936-022-04275-7. Malar J. 2022. PMID: 36030242 Free PMC article. - dN/dS-H, a New Test to Distinguish Different Selection Modes in Protein Evolution and Cancer Evolution.
Gu X. Gu X. J Mol Evol. 2022 Oct;90(5):342-351. doi: 10.1007/s00239-022-10064-2. Epub 2022 Aug 3. J Mol Evol. 2022. PMID: 35920867 - Incorporation of transition to transversion ratio and nonsense mutations, improves the estimation of the number of synonymous and non-synonymous sites in codons.
Aziz R, Sen P, Beura PK, Das S, Tula D, Dash M, Namsa ND, Deka RC, Feil EJ, Satapathy SS, Ray SK. Aziz R, et al. DNA Res. 2022 Jun 25;29(4):dsac023. doi: 10.1093/dnares/dsac023. DNA Res. 2022. PMID: 35920776 Free PMC article. - Two decades of suspect evidence for adaptive molecular evolution-negative selection confounding positive-selection signals.
Chen Q, Yang H, Feng X, Chen Q, Shi S, Wu CI, He Z. Chen Q, et al. Natl Sci Rev. 2021 Dec 3;9(5):nwab217. doi: 10.1093/nsr/nwab217. eCollection 2022 May. Natl Sci Rev. 2021. PMID: 35663241 Free PMC article.
References
- J Mol Evol. 1982;18(6):414-23 - PubMed
- Nature. 1981 Apr 9;290(5806):457-65 - PubMed
- Mol Biol Evol. 1992 Jul;9(4):678-87 - PubMed
- J Mol Evol. 1993 Jan;36(1):96-9 - PubMed
- Proc Natl Acad Sci U S A. 1993 Nov 15;90(22):10676-80 - PubMed
MeSH terms
LinkOut - more resources
Miscellaneous