Unbiased estimation of the rates of synonymous and nonsynonymous substitution - PubMed

• PMID: 8433381
• DOI: 10.1007/BF02407308

Unbiased estimation of the rates of synonymous and nonsynonymous substitution

W H Li. J Mol Evol. 1993 Jan.

Abstract

The current convention in estimating the number of substitutions per synonymous site (KS) and per nonsynonymous site (KA) between two protein-coding genes is to count each twofold degenerate site as one-third synonymous and two-thirds nonsynonymous because one of the three possible changes at such a site is synonymous and the other two are nonsynonymous. This counting rule can considerably overestimate the KS value because transitional mutations tend to occur more often than transversional mutations and because most transitional mutations at twofold degenerate sites are synonymous. A new method that gives unbiased estimates is proposed. An application of the new and the old method to 14 pairs of mouse and rat genes shows that the new method gives a KS value very close to the number of substitutions per four-fold degenerate site whereas the old method gives a value 30% higher. Both methods give a KA value close to the number of substitutions per nondegenerate site.

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

• New methods for estimating the numbers of synonymous and nonsynonymous substitutions.

  Ina Y. Ina Y. J Mol Evol. 1995 Feb;40(2):190-226. doi: 10.1007/BF00167113. J Mol Evol. 1995. PMID: 7699723

• 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.

• On transition bias in mitochondrial genes of pocket gophers.

  Xia X, Hafner MS, Sudman PD. Xia X, et al. J Mol Evol. 1996 Jul;43(1):32-40. doi: 10.1007/BF02352297. J Mol Evol. 1996. PMID: 8660427

Cited by

• Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets.

  Porter TM, Hajibabaei M. Porter TM, et al. BMC Bioinformatics. 2021 May 19;22(1):256. doi: 10.1186/s12859-021-04180-x. BMC Bioinformatics. 2021. PMID: 34011275 Free PMC article.

• Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing.

  Baek D, Green P. Baek D, et al. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12813-8. doi: 10.1073/pnas.0506139102. Epub 2005 Aug 25. Proc Natl Acad Sci U S A. 2005. PMID: 16123126 Free PMC article.

• How the global structure of protein interaction networks evolves.

  Wagner A. Wagner A. Proc Biol Sci. 2003 Mar 7;270(1514):457-66. doi: 10.1098/rspb.2002.2269. Proc Biol Sci. 2003. PMID: 12641899 Free PMC article.

• Inventing a sex-specific gene: a conserved role of DMRT1 in teleost fishes plus a recent duplication in the medaka Oryzias latipes resulted in DMY.

  Lutfalla G, Roest Crollius H, Brunet FG, Laudet V, Robinson-Rechavi M. Lutfalla G, et al. J Mol Evol. 2003;57 Suppl 1:S148-53. doi: 10.1007/s00239-003-0021-4. J Mol Evol. 2003. PMID: 15008411

• SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis.

  Liang H, Zhou W, Landweber LF. Liang H, et al. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W382-4. doi: 10.1093/nar/gkl272. Nucleic Acids Res. 2006. PMID: 16845032 Free PMC article.

References

Publication types

MeSH terms

Substances

LinkOut - more resources

• Other Literature Sources

  • The Lens - Patent Citations Database

• Medical

  • MedlinePlus Health Information