Natural taxonomy in light of horizontal gene transfer

Biology and Philosophy

Volumn 25, Issue 4, 2010, Pages 589-602

  Andam, Cheryl P ^a   Williams, David ^a   Gogarten, J Peter ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

Cladistics; Horizontal gene transfer; Net of life; Reticulate evolution; Shared ancestry; Tree of life

Indexed keywords

BACTERIUM; CLADISTICS; GENE TRANSFER; PHYLOGENETICS; PHYLOGENY; POPULATION GENETICS; TAXONOMY;

BACTERIA (MICROORGANISMS);

EID: 77956010582     PISSN: 01693867     EISSN: 15728404     Source Type: Journal    
DOI: 10.1007/s10539-010-9212-8     Document Type: Article

References (71)

1. Acinas SG, Marcelino LA, Klepac-Ceraj V, Polz MF (2004) Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186: 2629-2635.
2. Adams KL, Song K, Roessler PG, Nugent JM, Doyle JL, Doyle JJ, Palmer JD (1999) Intracellular gene transfer in action: dual transcription and multiple silencings of nuclear and mitochondrial cox2 genes in legumes. Proc Natl Acad Sci U S A 96: 13863-13868.
3. Asai T, Zaporojets D, Squires C, Squires CL (1999) An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria [see comments]. Proc Natl Acad Sci U S A 96: 1971-1976.
4. Bapteste E, Boucher Y (2009) Epistemological impacts of horizontal gene transfer on classification in microbiology. In: Gogarten M, Gogarten J, Olendzenski L (eds) Horizontal gene transfer: genomes in flux, vol 532. Humana Press, New York.
5. Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupré J, Dagan T, Boucher Y, Martin W (2009) Prokaryotic evolution and the tree of life are two different things. Biol Direct 4: 34.
6. Beiko RG, Harlow TJ, Ragan MA (2005) Highways of gene sharing in prokaryotes. Proc Natl Acad Sci U S A 102: 14332-14337.
7. Blankenship RE, Raymond J, Lince M, Larkum AWD, Jermiin LS, Lockhart PJ, Zhaxybayeva O, Gogarten JP (2001) Evolution of photosynthetic antennas and reaction centers. In: Proceedings of the 12th international congress on photosynthesis Melbourne, Australia, CSIRO Publishing, PL13.
8. Boussau B, Gueguen L, Gouy M (2008) Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of Aquificales in the phylogeny of bacteria. BMC Evol Biol 8: 272.
9. Brochier C, Philippe H, Moreira D (2000) The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome. Trends Genet 16: 529-533.
10. Chan CX, Darling AE, Beiko RG, Ragan MA (2009) Are protein domains modules of lateral genetic transfer? PLoS One 4: e4524.
11. 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.
12. Dagan T, Martin W (2007) Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc Natl Acad Sci U S A 104: 870-875.
13. Dagan T, Artzy-Randrup Y, Martin W (2008) Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci U S A 105: 10039-10044.
14. Daubin V, Gouy M, Perriere G (2002) A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res 12: 1080-1090.
15. Doolittle WF (2004) W. Ford Doolittle. Curr Biol 14: R176-R177.
16. Doolittle WF (2009) 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. Philos Trans R Soc Lond B Biol Sci 364: 2221-2228.
17. Farahi K, Pusch GD, Overbeek R, Whitman WB (2004) Detection of lateral gene transfer events in the prokaryotic tRNA synthetases by the ratios of evolutionary distances method. J Mol Evol 58: 615-631.
18. Fournier GP, Gogarten JP (2008) Evolution of acetoclastic methanogenesis in Methanosarcina via horizontal gene transfer from cellulolytic Clostridia. J Bacteriol 190: 1124-1127.
19. Franklin-Hall L (2010) Trashing the tree: bad reasons and good reasons. Biol Philos (this issue) [details to follow].
20. Frost LS, Leplae R, Summers AO, Toussaint A (2005) Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 3: 722-732.
21. Geach P (1967) Identity. Rev Metaphys 21: 3-12.
22. Gogarten JP (1995) The early evolution of cellular life. Trends Ecol Evol 10: 147-151.
23. Gogarten JP, Hilario E (2006) Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements. BMC Evol Biol 6: 94.
24. Gogarten JP, Townsend JP (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 3: 679-687.
25. Gogarten JP, Doolittle WF, Lawrence JG (2002) Prokaryotic evolution in light of gene transfer. Mol Biol Evol 19: 2226-2238.
26. Gray GS, Fitch WM (1983) Evolution of antibiotic resistance genes: the DNA sequence of a kanamycin resistance gene from Staphylococcus aureus. Mol Biol Evol 1: 57-66.
27. Hennig W (1966) Phylogenetic systematics. University of Illinois Press, Urbana.
28. Hilario E, Gogarten JP (1993) Horizontal transfer of ATPase genes-the tree of life becomes a net of life. Biosystems 31: 111-119.
29. House CH (2009) The tree of life viewed through the contents of genomes. Methods Mol Biol 532: 141-161.
30. Huang J, Gogarten JP (2006) Ancient horizontal gene transfer can benefit phylogenetic reconstruction. Trends Genet 22: 361-366.
31. Huang J, Gogarten JP (2007) Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids? Genome Biol 8: R99.
32. Huang J, Gogarten JP (2008) Concerted gene recruitment in early plant evolution. Genome Biol 9: R109.
33. Huang J, Gogarten JP (2009) Ancient gene transfer as a tool in phylogenetic reconstruction. Methods Mol Biol 532: 127-139.
34. Huang J, Xu Y, Gogarten JP (2005) The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic. Mol Biol Evol 22: 2142-2146.
35. Hyde D (2008) Sorites Paradox http://plato. stanford. edu/archives/fall2008/entries/sorites-paradox/. In: Zalta EN (ed) The Stanford encyclopedia of philosophy (Fall 2008 Edition).
36. Igarashi N, Harada J, Nagashima S, Matsuura K, Shimada K, Nagashima KVP (2001) Horizontal transfer of the photosynthesis gene cluster and operon rearrangement in purple bacteria. J Mol Evol 52: 333.
37. Jain R, Rivera MC, Lake JA (1999) Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci U S A 96: 3801-3806.
38. Koonin EV, Wolf YI (2009) The fundamental units, processes and patterns of evolution, and the tree of life conundrum. Biol Direct 4: 33.
39. Lawrence JG, Hendrickson H (2005) Genome evolution in bacteria: order beneath chaos. Curr Opin Microbiol 8: 572-578.
40. Lynch M, Conery JS (2003) The origins of genome complexity. Science 302: 1401-1404.
41. Margulis L (2009) Genome acquisition in horizontal gene transfer: symbiogenesis and macromolecular sequence analysis. Methods Mol Biol 532: 181-191.
42. Margulis L, Sagan D (2002) Acquiring genomes: a theory of the origin of species. Basic Books, New York.
43. Martin W, Brinkmann H, Savonna C, Cerff R (1993) Evidence for a chimeric nature of nuclear genomes: eubacterial origin of eukaryotic glyceraldehyde-3-phosphate dehydrogenase genes. Proc Natl Acad Sci U S A 90: 8692-8696.
44. McCann A, Cotton JA, McInerney JO (2008) The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods. BMC Evol Biol 8: 312.
45. Miller SR, Augustine S, Olson TL, Blankenship RE, Selker J, Wood AM (2005) Discovery of a free-living chlorophyll d-producing cyanobacterium with a hybrid proteobacterial/cyanobacterial small-subunit rRNA gene. Proc Natl Acad Sci U S A 102: 850-855.
46. Mongodin EF, Nelson KE, Daugherty S, Deboy RT, Wister J, Khouri H, Weidman J, Walsh DA, Papke RT, Sanchez Perez G, Sharma AK, Nesbo CL, MacLeod D, Bapteste E, Doolittle WF, Charlebois RL, Legault B, Rodriguez-Valera F (2005) The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc Natl Acad Sci U S A 102: 18147-18152.
47. Morandi A, Zhaxybayeva O, Gogarten JP, Graf J (2005) Evolutionary and diagnostic implications of intragenomic heterogeneity in the 16S rRNA gene in Aeromonas strains. J Bacteriol 187: 6561-6564.
48. O'Malley MA, Dupré J (2007) Size doesn't matter: towards a more inclusive philosophy of biology. Biol Philos 22: 155-191.
49. Olendzenski L, Gogarten JP (2009) Gene transfer: who benefits? Methods Mol Biol 532: 3-9.
50. Olendzenski L, Liu L, Zhaxybayeva O, Murphey R, Shin DG, Gogarten JP (2000) Horizontal transfer of archaeal genes into the Deinococcaceae: detection by molecular and computer-based approaches. J Mol Evol 51: 587-599.
51. Olendzenski L, Zhaxybayeva O, Gogarten J (2001) What's in a tree? Does horizontal gene transfer determine microbial taxonomy? In: Seckbach J (ed) Cellular origin and life in extreme habitats, vol 4. Kluwer, Dordrecht, pp 67-78.
52. Olendzenski L, Zhaxybayeva O, Gogarten JP (2002) Horizontal gene transfer: a new taxonomic principle? In: Syvanen M, Kado CI (eds) Horizontal gene transfer. Academic Press, New York, pp 427-435.
53. Papke RT (2009) A critique of prokaryotic species concepts. Methods Mol Biol 532: 379-395.
54. Plutarch (75) Theseus, translated by John Dryden. The Internet Classics Archive. Retrieved 7 Oct 2009.
55. Puigbò P, Wolf YI, Koonin EV (2009) Search for a 'tree of life' in the thicket of the phylogenetic forest. J Biol 8: 59.
56. Sawyer S (1989) Statistical tests for detecting gene conversion. Mol Biol Evol 6: 526-538.
57. Schouls LM, Schot CS, Jacobs JA (2003) Horizontal transfer of segments of the 16S rRNA genes between species of the Streptococcus anginosus group. J Bacteriol 185: 7241-7246.
58. Sheppard SK, McCarthy ND, Falush D, Maiden MC (2008) Convergence of Campylobacter species: implications for bacterial evolution. Science 320: 237-239.
59. Sorek R, Zhu Y, Creevey CJ, Francino MP, Bork P, Rubin EM (2007) Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318: 1449-1452.
60. Stoltzfus A (1999) On the possibility of constructive neutral evolution. J Mol Evol 49: 169-181.
61. Swithers KS, Gogarten JP, Fournier GP (2009) Trees in the web of life. J Biol 8: 54.
62. Wang Y, Zhang Z (2000) Comparative sequence analyses reveal frequent occurrence of short segments containing an abnormally high number of non-random base variations in bacterial rRNA genes. Microbiology 146: 2845-2854.
63. Wang Y, Zhang Z, Ramanan N (1997) The actinomycete Thermobispora bispora contains two distinct types of transcriptionally active 16S rRNA genes. J Bacteriol 179: 3270-3276.
64. Wolf YI, Rogozin IB, Grishin NV, Koonin EV (2002) Genome trees and the tree of life. Trends Genet 18: 472-479.
65. Yap WH, Zhang Z, Wang Y (1999) Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J Bacteriol 181: 5201-5209.
66. Zhaxybayeva O, Gogarten JP (2004) Cladogenesis, coalescence and the evolution of the three domains of life. Trends Genet 20: 182-187.
67. Zhaxybayeva O, Lapierre P, Gogarten JP (2004) Genome mosaicism and organismal lineages. Trends Genet 20: 254-260.
68. 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.
69. Zhaxybayeva O, Nesbo C, Doolittle WF (2007) Systematic overestimation of gene gain through false diagnosis of gene absence. Genome Biol 8: 402.
70. Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP (2009a) Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus. Genome Biol Evol 1: 325-339.
71. Zhaxybayeva O, Swithers K, Lapierre P, Fournier G, Bickhart D, DeBoy R, Nelson K, Nesbo C, Doolittle W, Gogarten J, Noll K (2009b) On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proc Natl Acad Sci USA 106: 5865-5870.