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. 1995 Dec;141(4):1641–1650. doi: 10.1093/genetics/141.4.1641

A New Method of Inference of Ancestral Nucleotide and Amino Acid Sequences

Z Yang 1, S Kumar 1, M Nei 1
PMCID: PMC1206894  PMID: 8601501

Abstract

A statistical method was developed for reconstructing the nucleotide or amino acid sequences of extinct ancestors, given the phylogeny and sequences of the extant species. A model of nucleotide or amino acid substitution was employed to analyze data of the present-day sequences, and maximum likelihood estimates of parameters such as branch lengths were used to compare the posterior probabilities of assignments of character states (nucleotides or amino acids) to interior nodes of the tree; the assignment having the highest probability was the best reconstruction at the site. The lysozyme c sequences of six mammals were analyzed by using the likelihood and parsimony methods. The new likelihood-based method was found to be superior to the parsimony method. The probability that the amino acids for all interior nodes at a site reconstructed by the new method are correct was calculated to be 0.91, 0.86, and 0.73 for all, variable, and parsimony-informative sites, respectively, whereas the corresponding probabilities for the parsimony method were 0.84, 0.76, and 0.51, respectively. The probability that an amino acid in an ancestral sequence is correctly reconstructed by the likelihood analysis ranged from 91.3 to 98.7% for the four ancestral sequences.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. 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]
  2. Goldman N. Simple diagnostic statistical tests of models for DNA substitution. J Mol Evol. 1993 Dec;37(6):650–661. doi: 10.1007/BF00182751. [DOI] [PubMed] [Google Scholar]
  3. Jermann T. M., Opitz J. G., Stackhouse J., Benner S. A. Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily. Nature. 1995 Mar 2;374(6517):57–59. doi: 10.1038/374057a0. [DOI] [PubMed] [Google Scholar]
  4. Jones D. T., Taylor W. R., Thornton J. M. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 1992 Jun;8(3):275–282. doi: 10.1093/bioinformatics/8.3.275. [DOI] [PubMed] [Google Scholar]
  5. Libertini G., Di Donato A. Reconstruction of ancestral sequences by the inferential method, a tool for protein engineering studies. J Mol Evol. 1994 Aug;39(2):219–229. doi: 10.1007/BF00163811. [DOI] [PubMed] [Google Scholar]
  6. Malcolm B. A., Wilson K. P., Matthews B. W., Kirsch J. F., Wilson A. C. Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing. Nature. 1990 May 3;345(6270):86–89. doi: 10.1038/345086a0. [DOI] [PubMed] [Google Scholar]
  7. Stackhouse J., Presnell S. R., McGeehan G. M., Nambiar K. P., Benner S. A. The ribonuclease from an extinct bovid ruminant. FEBS Lett. 1990 Mar 12;262(1):104–106. doi: 10.1016/0014-5793(90)80164-e. [DOI] [PubMed] [Google Scholar]
  8. Stewart C. B., Schilling J. W., Wilson A. C. Adaptive evolution in the stomach lysozymes of foregut fermenters. 1987 Nov 26-Dec 2Nature. 330(6146):401–404. doi: 10.1038/330401a0. [DOI] [PubMed] [Google Scholar]
  9. Swanson K. W., Irwin D. M., Wilson A. C. Stomach lysozyme gene of the langur monkey: tests for convergence and positive selection. J Mol Evol. 1991 Nov;33(5):418–425. doi: 10.1007/BF02103133. [DOI] [PubMed] [Google Scholar]
  10. Yang Z. A space-time process model for the evolution of DNA sequences. Genetics. 1995 Feb;139(2):993–1005. doi: 10.1093/genetics/139.2.993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Yang Z. Estimating the pattern of nucleotide substitution. J Mol Evol. 1994 Jul;39(1):105–111. doi: 10.1007/BF00178256. [DOI] [PubMed] [Google Scholar]
  12. Yang Z. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol. 1993 Nov;10(6):1396–1401. doi: 10.1093/oxfordjournals.molbev.a040082. [DOI] [PubMed] [Google Scholar]
  13. Yang Z., Roberts D. On the use of nucleic acid sequences to infer early branchings in the tree of life. Mol Biol Evol. 1995 May;12(3):451–458. doi: 10.1093/oxfordjournals.molbev.a040220. [DOI] [PubMed] [Google Scholar]

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