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Proc Natl Acad Sci U S A. Nov 21, 1995; 92(24): 11317–11321.
PMCID: PMC40623

Inferring phylogenies from DNA sequences of unequal base compositions.

Abstract

A new method for computing evolutionary distances between DNA sequences is proposed. Contrasting with classical methods, the underlying model does not assume that sequence base compositions (A, C, G, and T contents) are at equilibrium, thus allowing unequal base compositions among compared sequences. This makes the method more efficient than the usual ones in recovering phylogenetic trees from sequence data when base composition is heterogeneous within the data set, as we show by using both simulated and empirical data. When applied to small-subunit ribosomal RNA sequences from several prokaryotic or eukaryotic organisms, this method provides evidence for an early divergence of the microsporidian Vairimorpha necatrix in the eukaryotic lineage.

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  • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. [PubMed]
  • Studier JA, Keppler KJ. A note on the neighbor-joining algorithm of Saitou and Nei. Mol Biol Evol. 1988 Nov;5(6):729–731. [PubMed]
  • Jukes TH, Bhushan V. Silent nucleotide substitutions and G + C content of some mitochondrial and bacterial genes. J Mol Evol. 1986;24(1-2):39–44. [PubMed]
  • Bernardi G. The vertebrate genome: isochores and evolution. Mol Biol Evol. 1993 Jan;10(1):186–204. [PubMed]
  • Montero LM, Salinas J, Matassi G, Bernardi G. Gene distribution and isochore organization in the nuclear genome of plants. Nucleic Acids Res. 1990 Apr 11;18(7):1859–1867. [PMC free article] [PubMed]
  • Loomis WF, Smith DW. Molecular phylogeny of Dictyostelium discoideum by protein sequence comparison. Proc Natl Acad Sci U S A. 1990 Dec;87(23):9093–9097. [PMC free article] [PubMed]
  • Hasegawa M, Hashimoto T, Adachi J, Iwabe N, Miyata T. Early branchings in the evolution of eukaryotes: ancient divergence of entamoeba that lacks mitochondria revealed by protein sequence data. J Mol Evol. 1993 Apr;36(4):380–388. [PubMed]
  • Saccone C, Pesole G, Preparata G. DNA microenvironments and the molecular clock. J Mol Evol. 1989 Nov;29(5):407–411. [PubMed]
  • Weisburg WG, Giovannoni SJ, Woese CR. The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction. Syst Appl Microbiol. 1989;11:128–134. [PubMed]
  • Steel MA, Lockhart PJ, Penny D. Confidence in evolutionary trees from biological sequence data. Nature. 1993 Jul 29;364(6436):440–442. [PubMed]
  • Sueoka N. Directional mutation pressure and neutral molecular evolution. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2653–2657. [PMC free article] [PubMed]
  • Tamura K. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Mol Biol Evol. 1992 Jul;9(4):678–687. [PubMed]
  • 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. [PubMed]
  • Tajima F, Nei M. Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol. 1984 Apr;1(3):269–285. [PubMed]
  • Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981;17(6):368–376. [PubMed]
  • Olsen GJ, Matsuda H, Hagstrom R, Overbeek R. fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput Appl Biosci. 1994 Feb;10(1):41–48. [PubMed]
  • Woese CR. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221–271. [PMC free article] [PubMed]
  • Olsen GJ, Overbeek R, Larsen N, Marsh TL, McCaughey MJ, Maciukenas MA, Kuan WM, Macke TJ, Xing Y, Woese CR. The Ribosomal Database Project. Nucleic Acids Res. 1992 May 11;20 (Suppl):2199–2200. [PMC free article] [PubMed]
  • Sogin ML, Gunderson JH, Elwood HJ, Alonso RA, Peattie DA. Phylogenetic meaning of the kingdom concept: an unusual ribosomal RNA from Giardia lamblia. Science. 1989 Jan 6;243(4887):75–77. [PubMed]
  • Vossbrinck CR, Maddox JV, Friedman S, Debrunner-Vossbrinck BA, Woese CR. Ribosomal RNA sequence suggests microsporidia are extremely ancient eukaryotes. Nature. 326(6111):411–414. [PubMed]
  • Cavalier-Smith T. Kingdom protozoa and its 18 phyla. Microbiol Rev. 1993 Dec;57(4):953–994. [PMC free article] [PubMed]

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