Restricted access
Articles
Articles
The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them
Published:12 August 2009https://doi.org/10.1098/rstb.2009.0032
Abstract
Debates over the status of the tree of life (TOL) often proceed without agreement as to what it is supposed to be: a hierarchical classification scheme, a tracing of genomic and organismal history or a hypothesis about evolutionary processes and the patterns they can generate. I will argue that for Darwin it was a hypothesis, which lateral gene transfer in prokaryotes now shows to be false. I will propose a more general and relaxed evolutionary theory and point out why anti-evolutionists should take no comfort from disproof of the TOL hypothesis.
References
-
Bapteste E.& Boucher Y. . 2008 Lateral gene transfer challenges principles of microbial systematics. Trends Microbiol. 16, 200–207. (doi:10.1016/j.tim.2008.02.005). Crossref, PubMed, ISI, Google Scholar -
Bapteste E., Boucher Y., Leigh J.& Doolittle W. F. . 2004 Phylogenetic reconstruction and lateral gene transfer. Trends Microbiol. 12, 406–411. (doi:10.1016/j.tim.2004.07.002). Crossref, PubMed, ISI, Google Scholar -
Beiko R. G., Harlow T. J.& Ragan M. A. . 2005 Highways of gene sharing in prokaryotes. Proc. Natl Acad. Sci. USA 102, 14332–14337. (doi:10.1073/pnas.0504068102). Crossref, PubMed, ISI, Google Scholar -
Charlebois R. L.& Doolittle W. F. . 2004 Computing prokaryotic gene ubiquity: rescuing the core from extinction. Genome Res. 14, 2469–2477. (doi:10.1101/gr.3024704). Crossref, PubMed, ISI, Google Scholar -
Ciccarelli F. D., Doerks T., von Mering C., Creevey C. J., Snel B.& Bork P. . 2006 Toward automatic reconstruction of a highly resolved tree of life. Science 311, 1283–1287. (doi:10.1126/science.1123061). Crossref, PubMed, ISI, Google Scholar -
Coleman M. L., Sullivan M. B., Martiny A. C., Steglich C., Barry K., Delong E. F.& Chisholm S. W. . 2006 Genomic islands and the ecology and evolution of Prochlorococcus. Science 311, 1768–1770. (doi:10.1126/science.1122050). Crossref, PubMed, ISI, Google Scholar -
Cracraft J.& Donoghue M. J. . 2004 Assembling the tree of life. Oxford, UK: Oxford University Press. Google Scholar -
Dagan T.& Martin W. . 2006 The tree of one percent. Genome Biol. 7, 118. (doi:10.1186/gb-2006-7-10-118). Crossref, PubMed, ISI, Google Scholar -
Darwin C. . 1859 On the origin of species by mean of natural selection, 1st edn. London, UK: John Murray. Google Scholar -
De Queiroz K. . 1988 Systematics and the Darwinian revolution. Phil. Sci. 55, 238–259. (doi:10.1086/289430). Crossref, ISI, Google Scholar -
Deurenberg R. H., Vink C., Kalenic S., Friedrich A. W., Bruggeman C. A.& Stobberingh E. E. . 2007 The molecular evolution of methicillin-resistant Staphylococcus aureus. Clin. Microbiol. Infect. 13, 222–235. (doi:10.1111/j.1469-0691.2006.01573.x). Crossref, PubMed, ISI, Google Scholar -
Diamond J.& Bishop D. K. . 1999 Ethno-ornithology of the Ketengban People, Indonesian New Guinea. Folkbiology (eds, Medin D. L.& Aran S. ), pp. 17–45. Cambridge, MA: The MIT Press. Google Scholar -
Donoghue M. J.& Gauthier J. A. . 2004 Implementing the PhyloCode. Trends Ecol. Evol. 19, 281–282. (doi:10.1016/j.tree.2004.04.004). Crossref, PubMed, ISI, Google Scholar -
Doolittle W. F. . 2005 If the tree of life fell, would it make a sound? In Microbial phylogeny and evolution: concepts and controversies (ed.& Sapp J. ), pp. 119–133. Oxford, UK: Oxford University Press. Google Scholar -
Doolittle W. F.& Bapteste E. . 2007 Pattern pluralism and the tree of life hypothesis. Proc. Natl Acad. Sci. USA 104, 2043–2049. (doi:10.1073/pnas.0610699104). Crossref, PubMed, ISI, Google Scholar -
Doolittle W. F., Nesbø C. L., Bapteste E.& Zhaxybayeva O. . 2007 Lateral gene transfer. Evolutionary genomics and proteomics (eds, Pagel M.& Pomiankowski A. ), pp. 45–79. Sunderland, MA: Sinauer. Google Scholar -
Ereshefsky M. . 1992 Eliminative pluralism. Phil. Sci. 59, 671–690. (doi:10.1086/289701). Crossref, ISI, Google Scholar -
Galtier N.& Daubin V. . 2008 Dealing with incongruence in phylogenomic analysis. Phil. Trans. R. Soc. B. 363, 4023–4029. (doi:10.1098/rstb.2008.0144). Link, ISI, Google Scholar -
Hacking I. . 2007 Natural kinds: rosy dawn, scholastic twilight. R. Inst. Phil. Suppl. 82, 203–239. Crossref, Google Scholar -
Hein J. . 2004 Human evolution: pedigrees for all humanity. Nature 431, 518–559. (doi:10.1038/431518a). Crossref, PubMed, ISI, Google Scholar -
Isaak M. . 2005 The counter-creationism handbook. Berkeley, CA: University of California Press. Google Scholar -
Jain R., Rivera M. C.& Lake J. A. . 1999 Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl Acad. Sci. USA 96, 3801–3806. (doi:10.1073/pnas.96.7.3801). Crossref, PubMed, ISI, Google Scholar -
Jeffroy O., Brinkmann H., Delusc F.& Philippe H. . 2006 Phylogenomics: the beginning of incongruence? Trends Genet. 22, 225–231. (doi:10.1016/j.tig.2006.02.003). Crossref, PubMed, ISI, Google Scholar -
Lerat E., Daubin V.& Moran N. A. . 2003 From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-proteobacteria. PLoS Biology 1, E19. Crossref, PubMed, ISI, Google Scholar -
Marri P. R., Hao W.& Golding G. B. . 2007 The role of laterally transferred genes in adaptive evolution. BMC Evol Biol. 7((Suppl. 1)), S8. Crossref, PubMed, ISI, Google Scholar -
Maynard Smith J. (ed.) 1982 Evolution now. San Francisco, CA: W.H. Freeman and Co. Crossref, Google Scholar -
Mayr E. . 1981 Biological classification: towards a synthesis of opposing methodologies. Science 214, 510–516. (doi:10.1126/science.214.4520.510). Crossref, PubMed, ISI, Google Scholar -
Nelson K. E., 1999 Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of. Thermotoga maritima. Nature 399, 323–329. PubMed, ISI, Google Scholar -
Pace N. R. . 2006 Time for a change. Nature 441, 289. (doi:10.1038/441289a). Crossref, PubMed, ISI, Google Scholar -
Padian K. . 1999 Charles Darwin's views of classification in theory and practice. Syst. Biol. 48, 352–364. (doi:10.1080/106351599260337). Crossref, PubMed, ISI, Google Scholar -
Panchen A. L. . 1992 Classification, evolution and the nature of biology. Cambridge, UK: Cambridge University Press. Crossref, Google Scholar -
Rasko D. A., Rosovitz M. J., Myers G. S., Mongodin E. F., Fricke W. F., Gajer P., Crabtree J., Sperandio V.& Ravel J. . 2008 The pan-genome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J. Bacteriol. In press. Crossref, ISI, Google Scholar -
Soria-Carrasco V.& Castresana J. . 2008 Estimation of phylogenetic inconsistencies in the three domains of life. Mol. Biol. Evol. Epub ahead of print. Crossref, PubMed, ISI, Google Scholar -
Susko E., Leigh J., Doolittle W. F.& Bapteste E. . 2006 Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the gamma-proteobacteria. Mol. Biol. Evol. 23, 1019–1030. (doi:10.1093/molbev/msj113). Crossref, PubMed, ISI, Google Scholar -
Vestigian K., Woese C.& Goldenfield N. . 2006 Collective evolution and the genetic code. Proc. Natl Acad. Sci. USA 103, 10696–10701. Crossref, PubMed, ISI, Google Scholar -
Vilas-Boas G. T., Peruca A. P. S.& Arantes O. M. N. . 2007 Biology and taxonomy of Bacillus cereus, Bacillus anthracis, and Bacillus thuringiensis. Can. J. Microbiol. 53, 673–687. (doi:10.1139/W07-029). Crossref, PubMed, ISI, Google Scholar -
Walsh D. A., Boudreau M. E., Bapteste E.& Doolittle W. F. . 2006 The root of the tree: lateral gene transfer and the nature of the domains. In Archaea: evolution, physiology and molecular biology (eds, Garrett R. A.& Klenk H. P. ), pp. 29–38. Oxford, UK: Blackwell Publishing. Google Scholar -
Wells J. . 2006 The politically incorrect guide to darwinism and intelligent design. Washington, DC: Regnery Publishing Inc. Google Scholar -
Woese C. R. . 1987 Bacterial evolution. Microbiol. Rev. 51, 221–271. Crossref, PubMed, Google Scholar -
Woese C. . 2005 Evolving biological organization. Microbial phylogeny and evolution: concepts and controversies (ed.& Sapp J. ), pp. 99–118. Oxford, UK: Oxford University Press. Google Scholar -
Zuckerkandl E.& Pauling L. . 1965 Evolutionary divergence and convergence in proteins. Evolving genes and proteins (eds, Bryson V.& Vogel H. J. ), pp. 97–166. New York, NY: Academic Press. Crossref, Google Scholar
