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The attempt on the life of the Tree of Life: science, philosophy and politics

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Abstract

Lateral gene transfer (LGT), the exchange of genetic information between (primarily prokaryotic) lineages, not only makes construction of a universal Tree of Life (TOL) difficult to achieve, but calls into question the utility and meaning of any result. Here I review the science of prokaryotic LGT, the philosophy of the TOL as it figured in Darwin’s formulation of the Theory of Evolution, and the politics of the current debate within the discipline over how threats to the TOL should be represented outside it. We could encourage a more realistic and supportive public understanding of evolution by admitting that what we believe in is not a unified meta-theory but a versatile and well-stocked explanatory toolkit.

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References

  • Ambler RP, Daniel M, Hermoso J, Meyer TE, Bartsch RG, Kamen MD (1979) Cytochrome c2 sequence variation among the recognized species of purple nonsulphur photosynthetic bacteria. Nature 278:559–560

    Google Scholar 

  • Anonymous (2007) National Center for Science Education. Introduction to a review of Explore Evolution, online at http://www.ncse.com/book/export/html/2007

  • Behe M (2007) The edge of evolution: the search for the limits of Darwinism. Free Press, New York

    Google Scholar 

  • Boussau B, Guéguen L, Gouy M (2008) Accounting for horizontal gene transfer explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria. BMC Evol Biol 8:272

    Article  Google Scholar 

  • Charlebois RL, Doolittle WF (2004) Computing prokaryotic gene ubiquity: rescuing the core from extinction. Genome Res 14:2469–2477

    Article  Google Scholar 

  • Charlebois RL, Beiko RG, Ragan MA (2003) Microbial phylogenomics: branching out. Nature 421:217

    Article  Google Scholar 

  • Chen K, Roberts E, Luthey-Schulten Z (2009) Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4. BMC Evol Biol 9:179

    Article  Google Scholar 

  • Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283–1287

    Article  Google Scholar 

  • Comfort R (2009) Special introduction, in Darwin C, the origin of species: 150th anniversary edition. Bridge Logos Foundation, Alachua

    Google Scholar 

  • Coyne J (2009) Why evolution is true. Oxford University Press, Oxford

    Google Scholar 

  • Creevey CJ, Fitzpatrick DA, Philip GK, Kinsella RJ, O’Connell MJ, Pentiny MM, Travers SA, Wilkinson M, McInerney JO (2004) Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proc Biol Sci 271:2551–2558

    Article  Google Scholar 

  • Dagan T, Martin W (2006) The tree of one percent. Genome Biol 7:118

    Article  Google Scholar 

  • Darwin C (1859) In the origin of species by means of natural selection. John Murray, London

    Google Scholar 

  • De Querioz K (1988) Systematics and the Darwinian revolution. Philos Sci 55:238–259

    Article  Google Scholar 

  • Dennett D, Coyne J, Dawkins R, Myers P (2009) Darwin was right. New Sci 201(2696):24

    Article  Google Scholar 

  • Doolittle WF, Bapteste E (2007) Pattern pluralism and the tree of life hypothesis. Proc Natl Acad Sci USA 104:2043–2049

    Article  Google Scholar 

  • Eldredge N (2005) Darwin: discovering the tree of life. WW Norton and Company, Inc, New York

    Google Scholar 

  • Fox GE, Stackebrandt E, Hespell RB, Gibson J, Maniloff J, Dyer TA, Wolfe RS, Balch WE, Tanner RS, Magrum LJ, Zablen LB, Blakemore R, Gupta R, Bonen L, Lewis BJ, Stahl DA, Luehrsen KR, Chen KN, Woese CR (1980) The phylogeny of prokaryotes. Science 209:457–463

    Article  Google Scholar 

  • Galtier N, Daubin V (2008) Dealing with incongruence in phylogenetic analyses. Phil Trans R Soc Lond B Biol Sci 363:4023–4029

    Article  Google Scholar 

  • Gilbert W (1987) The exon theory of genes. Cold Spring Harbor Symp Quant Biol 52:901–905

    Google Scholar 

  • Gribaldo S, Brochier C (2009) Phylogeny of prokaryotes: does it exist and why should we care? Res in Microbiol 160:513–521

    Article  Google Scholar 

  • House C (2009) The tree of life viewed through the content of genomes. Methods Mol Biol 523:141–161

    Article  Google Scholar 

  • Iggers GG (1997) Historiography in the twentieth century: from scientific objectivity to the postmodern challenge. Wesleyan University Press, Middletown

    Google Scholar 

  • Koonin EV, Wolf YI, Puigbo P (2009) The phylogenetic forest and the quest for the elusive tree of life. Cold Spring Harbor Symp Quant Biol 74 (epub, Aug 17)

  • Kurland CG, Canback B, Berg OG (2003) Horizontal gene transfer: a critical view. Proc Natl Acad Sci USA 100:9658–9662

    Article  Google Scholar 

  • Kyrpides N, Overbeek R, Ouzounis C (1999) Universal protein families and the functional content of the last universal common ancestor. J Mol Evol 49:413–423

    Article  Google Scholar 

  • Lapierre P, Gogarten JP (2009) Estimating the size of the bacterial pangenome. Trends Genet 25:107–110

    Article  Google Scholar 

  • Lawrence JG, Ochman H (1998) Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci USA 95:9413–9417

    Article  Google Scholar 

  • Lawton G (2009) Axing Darwin’s tree. New Sci 201(2692):34–39

    Article  Google Scholar 

  • Lerat E, Daubin V, Moran NA (2003) From gene trees to organismal phylogeny in prokaryotes: the core of the gamma-Proteobacteria. PLoS Biol 1:E19

    Google Scholar 

  • Lerat E, Daubin V, Ochman H, Moran N (2005) Evolutionary origins of genomic repertoires in bacteria. PLoS Biol 3:e130

    Article  Google Scholar 

  • Mallet J (2008) Hybridization, ecological races and the nature of species: empirical evidence for the ease of speciation. Philos Trans R Soc Lond B Biol Sci 363:2971–2986

    Article  Google Scholar 

  • Margulis L (1983) Forward to Sonea S, Panisset M (1983) A new bacteriology. Jones and Bartlett, Boston

  • McInerney JO, Cotton JA, Pisani D (2008) The prokaryotic tree of life: past, present … and future? Trends Ecol Evol 23:276–281

    Article  Google Scholar 

  • Nishihara H, Hasegawa M, Okada N (2006) Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions. Proc Natl Acad Sci USA 103:9929–9934

    Article  Google Scholar 

  • Ogura Y, Ooka T, Iguchi A, Toh H, Asadulghani M, Oshima K, Kodama T, Abe H, Nakayama K, Kurokawa K, Tobe T, Hattori M, Hayashi T (2009) Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli. Proc Natl Acad Sci USA 106:17939–17944

    Article  Google Scholar 

  • Panchen A (1992) Classification, evolution, and the nature of biology. Cambridge University Press, Cambridge

    Google Scholar 

  • Popper K (2002) Unended quest; an intellectual autobiography. Routledge Classics, New York

    Google Scholar 

  • Ragan MA, Beiko RG (2009) Lateral genetic transfer: open issues. Phil Trans R Soc B 364:2241–2251

    Article  Google Scholar 

  • Saap J (2009) The new foundations of evolution: on the tree of life. Oxford University Press, Oxford

    Google Scholar 

  • Schwartz RM, Dayhoff MO (1979) Origins of prokaryotes, eukaryotes, mitochondria, and chloroplasts. Science 199:395–405

    Article  Google Scholar 

  • Scott E (2009) Evolution vs. creationism: an introduction. University of California Press, Berkeley

    Google Scholar 

  • Snyder LA, Loman NJ, Fütterer K, Pallen MJ (2009) Bacterial flagellar diversity and evolution: seek simplicity and distrust it? Trends Microbiol 17:1–5

    Article  Google Scholar 

  • Sonea S, Panisset M (1983) A new bacteriology. Jones & Bartlett, Boston

    Google Scholar 

  • Stanier RY, Doudoroff M, Adleberg EA (1957) The microbial world. Prentice Hall, Engelwood Cliffs

    Google Scholar 

  • Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, Calteau A, Chiapello H, Clermont O, Cruveiller S, Danchin A, Diard M, Dossat C, Karoui ME, Frapy E, Garry L, Ghigo JM, Gilles AM, Johnson J, Le Bouguénec C, Lescat M, Mangenot S, Martinez-Jéhanne V, Matic I, Nassif X, Oztas S, Petit MA, Pichon C, Rouy Z, Ruf CS, Schneider D, Tourret J, Vacherie B, Vallenet D, Médigue C, Rocha EP, Denamur E (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 5:e1000344

  • Watanabe T, Fukasawa T (1961) Episome-mediated transfer of drug resistance in Enterobacteriaceae. I. Transfer of resistance factors by conjugation. J Bacteriol 81:679–683

    Google Scholar 

  • Woese CR (1987) Bacterial evolution. Microbiol Revs 51:221–271

    Google Scholar 

  • Woese CR, Gibson J, Fox GE (1980) Do genealogical patterns in purple photosynthetic bacteria reflect interspecific gene transfer? Nature 283:212–214

    Article  Google Scholar 

  • Xing J, Witherspoon DJ, Ray DA, Batzer MA, Jorde LB (2007) Mobile DNA elements in primate and human evolution. Am J Physiol 45:2–19

    Google Scholar 

  • Zhaxybayeva O, Gogarten JP, Charlebois RL, Doolittle WF, Papke RT (2006) Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res 16:1099–1108

    Article  Google Scholar 

  • Zhaxybayeva O, Swithers KS, Lapierre P, Fournier GP, Bickhart DM, DeBoy RT, Nelson KE, Nesbø CL, Doolittle WF, Gogarten JP, Noll KM (2009) On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proc Natl Acad Sci USA 106:5865–5870

    Article  Google Scholar 

  • Zuckerkandl E, Pauling L (1965) Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ (eds) Evolving genes and proteins. Academic Press, New York, pp 97–166

    Google Scholar 

Download references

Acknowledgments

This paper was first presented at the workshop, Perspectives on the Tree of Life, sponsored by the Leverhulme Trust and held in Halifax, Nova Scotia, July, 2009.

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Correspondence to W. Ford Doolittle.

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Ford Doolittle, W. The attempt on the life of the Tree of Life: science, philosophy and politics. Biol Philos 25, 455–473 (2010). https://doi.org/10.1007/s10539-010-9210-x

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