Phylogenetic Classification and the Universal Tree
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E. Mayr The Growth of Biological Thought (Belknap Press Cambridge MA 1982).
A. L. Panchen Classification Evolution and the Nature of Biology (Cambridge Univ. Press Cambridge 1992)
M. T. Ghiselin Metaphysics and the Origin of Species (State Univ. of New York Press Albany NY 1997).
E. Zuckerkandl and L. Pauling in Evolving Genes and Proteins V. Bryson and H. J. Vogel Eds. (Academic Press New York 1965) pp. 97–166; J. Theor. Biol. 8 357 (1965).
Doolittle W. F., Brown J. R., ibid. 91, 6721 (1994);
; N. Iwabe K. Kuma M. Hasegawa S. Osawa T. Miyata ibid. p. 9355; J. R. Brown and W. F. Doolittle ibid. 92 2441 (1995); S. L. Baldauf J. D. Palmer W. F. Doolittle ibid. 93 7749 (1996);
. Organisms in all major groups bear genes encoding elongation factors EF-1α (EF-Tu) and EF-2 (bacterial EF-G). These homologous (more precisely paralogous) genes thus must be products of a gene duplication that had already occurred before the time of the last common ancestor of all organisms alive today. A tree made of EF-1α and EF-2 sequences should comprise two subtrees (one for each of these paralogs) each of which (barring LGT or artifacts) should have the topology of the true universal organismal tree. The point at which each subtree attaches to the other will be its root and will correspond to the last common organismal ancestor. Neither subtree is rootable without the other. Because rRNA genes all seem to be orthologous (derived from a single ancestral gene in the last common ancestor) such a rooting is not possible with rRNA sequences alone.
M. J. Kates D. J. Kushner A. T. Matheson Eds. The Biochemistry of Archaea (Archaeobacteria) (Elsevier Science Amsterdam 1993)
W. F. Doolittle in Evolution of Microbial Life D. M. Roberts P. Sharp G. Alderson M. Collins Eds. (Cambridge Univ. Press Cambridge 1996) pp. 1-21.
; D. E. Edgell and W. F. Doolittle ibid. p. 995; J. N. Reeve K. Sandman C. J. Daniels ibid. p. 999; P. P. Dennis ibid. p. 1007;
; H. Phillippe and A. Adoutte in Evolutionary Relationships Among Protozoa G. H. Coombs K. Vickerman M. A. Sleigh A. Warren Eds. (Systematics Association London 1998) pp. 25–26;
Prominent among sources of error or uncertainty in establishing branching patterns are mutational saturation “long-branch attraction ” and “among-site rate variation.” Mutationally saturated sequences are maximally diverged so that further changes are as likely to make them more similar as they are to make them more different and tree topology is based on noise. Long-branch attraction [
] occurs when rates of sequence change differ substantially between taxa (even without saturation). Lineages with higher rates of sequence change artifactually associate with each other and with out-groups except with maximum likelihood methods. Even with these methods [
; Trends Ecol. Evol. 11 367 (1996)] long-branch attraction occurs when there is a substantial rate variation among different sites in a gene.
Stiller J. W., Duffield E. C., Hall B. D., ibid. 95, 11769 (1998).
P. J. Gogarten E. Hilario L. Olenzenski in Evolution of Microbial Life D. M. Roberts P. Sharp G. Alderson M. Collins Eds. (Cambridge Univ. Press Cambridge 1996) pp. 267–292.
Miyamoto M. M., Fitch W. M., Mol. Biol. Evol. 12, 513 (1995).
Brown J. R., Doolittle W. F., Microbiol. Mol. Biol. Rev. 61, 456 (1997);
Sonea S., Paniset M., Rev. Can. Biol. 35, 103 (1976);
; D. C. Reanney in Aspects of Genetic Action and Evolution suppl. 8 of International Review of Cytology G. H. Bourne J. F. Danielli K. W. Jeon Eds. (Academic Press New York 1978) pp. 1–67.
S. A. Baldauf and W. F. Doolittle in preparation.
D. M. O'Neil
___, Traub P., Bechmann H., Nature 219, 793 (1968).
J. Xiong K. Inoue C. C. Bauer ibid. p. 14851.
I thank J. Logsdon A. Roger D. Faguy O. Feeley and Y. Inagaki for critical discussions and the Medical Research Council of Canada and the Canadian Institute for Advanced Research for support. I am indebted to J. P. Gogarten and W. Martin for persuading me of the importance of LGT.