Simple diagnostic statistical tests of models for DNA substitution - PubMed (original) (raw)

Simple diagnostic statistical tests of models for DNA substitution

N Goldman. J Mol Evol. 1993 Dec.

Abstract

The accuracy of models for DNA substitution used in phylogenetic analyses is becoming more important with the increasing availability and analysis of molecular sequence data. It is natural to look for ways of improving these models, and to do this in a planned manner it is useful to be able to identify features of sequences that may not be described adequately. In this paper, I describe three statistics which may give useful diagnostic information on departures from models' predictions. The statistical distributions of these statistics are discussed and simple significance tests are derived. These tests are based on the (estimated) phylogeny of the sequences and so have the advantage of using the information contained in this tree. Examples are given of the application of the new tests to Markov chain models describing the evolution of primate pseudogene sequences and small-subunit RNA sequences.

PubMed Disclaimer

Similar articles

• Statistical tests of models of DNA substitution.
  Goldman N. Goldman N. J Mol Evol. 1993 Feb;36(2):182-98. doi: 10.1007/BF00166252. J Mol Evol. 1993. PMID: 7679448
• Estimating the pattern of nucleotide substitution.
  Yang Z. Yang Z. J Mol Evol. 1994 Jul;39(1):105-11. doi: 10.1007/BF00178256. J Mol Evol. 1994. PMID: 8064867
• Pseudogenes.
  Wilde CD. Wilde CD. CRC Crit Rev Biochem. 1986;19(4):323-52. CRC Crit Rev Biochem. 1986. PMID: 2421975 Review.
• A discrete Fourier analysis for evolutionary trees.
  Hendy MD, Penny D, Steel MA. Hendy MD, et al. Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):3339-43. doi: 10.1073/pnas.91.8.3339. Proc Natl Acad Sci U S A. 1994. PMID: 8159749 Free PMC article.
• Models of coding sequence evolution.
  Delport W, Scheffler K, Seoighe C. Delport W, et al. Brief Bioinform. 2009 Jan;10(1):97-109. doi: 10.1093/bib/bbn049. Epub 2008 Oct 29. Brief Bioinform. 2009. PMID: 18971241 Free PMC article. Review.

Cited by

• The build-up of the present-day tropical diversity of tetrapods.
  Quintero I, Landis MJ, Jetz W, Morlon H. Quintero I, et al. Proc Natl Acad Sci U S A. 2023 May 16;120(20):e2220672120. doi: 10.1073/pnas.2220672120. Epub 2023 May 9. Proc Natl Acad Sci U S A. 2023. PMID: 37159475 Free PMC article.
• Impact of model assumptions on the inference of the evolution of ectomycorrhizal symbiosis in fungi.
  Sheikh S, Khan FK, Bahram M, Ryberg M. Sheikh S, et al. Sci Rep. 2022 Dec 21;12(1):22043. doi: 10.1038/s41598-022-26514-2. Sci Rep. 2022. PMID: 36543862 Free PMC article.
• Analysis and Allocation of Cancer-Related Genes Using Vague DNA Sequence Data.
  Aslam M, Albassam M. Aslam M, et al. Front Genet. 2022 Apr 19;13:858005. doi: 10.3389/fgene.2022.858005. eCollection 2022. Front Genet. 2022. PMID: 35518359 Free PMC article.
• AliSim: A Fast and Versatile Phylogenetic Sequence Simulator for the Genomic Era.
  Ly-Trong N, Naser-Khdour S, Lanfear R, Minh BQ. Ly-Trong N, et al. Mol Biol Evol. 2022 May 3;39(5):msac092. doi: 10.1093/molbev/msac092. Mol Biol Evol. 2022. PMID: 35511713 Free PMC article.
• On the Need for New Measures of Phylogenomic Support.
  Thomson RC, Brown JM. Thomson RC, et al. Syst Biol. 2022 Jun 16;71(4):917-920. doi: 10.1093/sysbio/syac002. Syst Biol. 2022. PMID: 35088868 Free PMC article.

References

1. 1. Biochem Genet. 1967 Jun;1(1):65-71 - PubMed
2. 1. J Mol Evol. 1993 Feb;36(2):182-98 - PubMed
3. 1. Am J Hum Genet. 1973 Sep;25(5):471-92 - PubMed
4. 1. Mol Biol Evol. 1989 May;6(3):301-16 - PubMed
5. 1. J Mol Evol. 1985;22(2):160-74 - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources

• Medical

  • MedlinePlus Health Information