Philosophy and evolution: Minding the gap between evolutionary patterns and tree-like patterns

Methods in Molecular Biology

Volumn 856, Issue , 2012, Pages 81-110

  Bapteste, Eric ^a   Bouchard, Frédéric ^b   Burian, Richard M ^c  

^a UPMC ^*  (France)

^b UNIVERSITÉ DE MONTRÉAL   (Canada)

^c VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

Evolution; Horizontal gene transfer; Lateral gene transfer; Network; Philosophy of biology; Prokaryotes; Units of evolution

Indexed keywords

ANTIINFECTIVE AGENT;

ADAPTATION; ANTIBIOTIC RESISTANCE; ARCHAEON; ARTICLE; BACTERIUM; DRUG EFFECT; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY;

ADAPTATION, PHYSIOLOGICAL; ANTI-BACTERIAL AGENTS; ARCHAEA; BACTERIA; DRUG RESISTANCE, BACTERIAL; EVOLUTION, MOLECULAR; PHYLOGENY;

EID: 84860155555     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-585-5_4     Document Type: Article

References (103)

1. Hennig, W. (1966) Phylogenetic systematics. Urbana.
2. Daubin, V., Moran, N.A., and Ochman, H. (2003) Phylogenetics and the cohesion of bacterial genomes. Science 301, 829-832.
3. Galtier, N., and Daubin, V. (2008) Dealing with incongruence in phylogenomic analyses. Philos Trans R Soc Lond B Biol Sci 363, 4023-4029.
4. Ciccarelli, F.D., Doerks, T., von Mering, C., Creevey, C.J., Snel, B., and Bork, P. (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311, 1283-1287.
5. Kurland, C.G., Canback, B., and Berg, O.G. (2003) Horizontal gene transfer: A critical view. Proc Natl Acad Sci USA 100, 9658-9662.
6. Lawrence, J.G., and Retchless, A.C. (2009) The interplay of homologous recombination and horizontal gene transfer in bacterial speciation. Methods Mol Biol 532, 29-53.
7. Retchless, A.C., and Lawrence, J.G. (2010) Phylogenetic incongruence arising from fragmented speciation in enteric bacteria. Proc Natl Acad Sci USA 107, 11453-11458.
8. Retchless, A.C., and Lawrence, J.G. (2007) Temporal fragmentation of speciation in bacteria. Science 317, 1093-1096.
9. Halary, S., Leigh, J.W., Cheaib, B., Lopez, P., and Bapteste, E. (2010) Network analyses structure genetic diversity in independent genetic worlds. Proc Natl Acad Sci USA 107, 127-132.
10. Brilli, M., Mengoni, A., Fondi, M., Bazzicalupo, M., Lio, P., and Fani, R. (2008) Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network. BMC Bioinformatics 9, 551.
11. Dagan, T., Artzy-Randrup, Y., and Martin,W. (2008) Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci USA 105, 10039-10044.
12. Dagan, T., and Martin, W. (2006) The tree of one percent. Genome Biology 7, 118.
13. Dagan, T., and Martin, W. (2009) Getting a better picture of microbial evolution en route to a network of genomes. Philos Trans R Soc Lond B Biol Sci 364, 2187-2196.
14. Doolittle, W.F., Nesbo, C.L., Bapteste, E., and Zhaxybayeva, O. (2007) Lateral Gene Transfer. In: Evolutionary Genomics and Proteomics: Sinauer.
15. Doolittle, W.F., and Bapteste, E. (2007) Pattern pluralism and the Tree of Life hypothesis. Proc Natl Acad Sci USA 104, 2043-2049.
16. Lima-Mendez, G., Van Helden, J., Toussaint, A., and Leplae, R. (2008) Reticulate representation of evolutionary and functional relationships between phage genomes. Mol Biol Evol 25, 762-777.
17. Ragan, M.A., McInerney, J.O., and Lake, J.A. (2009) The network of life: genome beginnings and evolution. Introduction. Philos Trans R Soc Lond B Biol Sci 364, 2169-2175.
18. Boucher, Y., Douady, C.J., Papke, R.T., Walsh, D.A., Boudreau, M.E., Nesbo, C.L., Case, R.J., and Doolittle, W.F. (2003) Lateral gene transfer and the origins of prokaryotic groups. Annu Rev Genet 37, 283-328.
19. Bapteste, E., O'Malley, M., Beiko, R.G., Ereshefsky, M., Gogarten, J.P., Franklin-Hall, L., Lapointe, F.J., Dupré, J., Dagan, T., Boucher, Y., and Martin, W. (2009) Prokaryotic evolution and the tree of life are two different things. Biology Direct 4, 34.
20. Lopez, P., and Bapteste, E. (2009) Molecular phylogeny: reconstructing the forest. C R Biol 332, 171-182.
21. Brussow, H. (2009) The not so universal tree of life or the place of viruses in the living world. Philos Trans R Soc Lond B Biol Sci 364, 2263-2274.
22. Zhaxybayeva, O., Swithers, K.S., Lapierre, P., Fournier, G.P., Bickhart, D.M., DeBoy, R.T., Nelson, K.E., Nesbø, C.L., Doolittle, W.F., Gogarten, J.P., and Noll, K.M. (2009) On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proc Natl Acad Sci USA 106, 5865-5870.
23. O'Hara, R.J. (1997) Population thinking and tree thinking in systematics. Zoologica Scripta 26, 323-329.
24. Kuntner, M., and Agnarsson, I. (2006) Are the linnean and phylogenetic nomenclatural systems combinable? Recommendations for biological nomenclature. Syst Biol 55, 774-784.
25. Mayr, E. (1987) The ontological status of species. Biology and Philosophy 2, 145-166.
26. Ghiselin, M.T. (1987) Species concepts, Individuality, and Objectivity. Biology and Philosophy 4, 127-143.
27. Doolittle, W.F., and Zhaxybayeva, O. (2009) On the origin of prokaryotic species. Genome Res 19, 744-756.
28. Tsvetkova, K., Marvaud, J.C., and Lambert, T. (2010) Analysis of the mobilization functions of the Vancomycin resistance transposon Tn1549, a member of a new family of conjugative elements. J Bacteriol 192, 702-713.
29. D'Auria, G., Jimenez-Hernandez, N., Peris-Bondia, F., Moya, A., and Latorre, A. (2010) Legionella pneumophila pangenome reveals strain-specific virulence factors. BMC Genomics 11, 181.
30. Barlow, M. (2009) What antimicrobial resistance has taught us about horizontal gene transfer. Methods Mol Biol 532, 397-411.
31. Manson, J.M., Hancock, L.E., and Gilmore, M.S. (2010) Mechanism of chromosomal transfer of Enterococcus faecalis pathogenicity island, capsule, antimicrobial resistance, and other traits. Proc Natl Acad Sci USA 107, 12269-12274.
32. Davies, J., and Davies, D. (2010) Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 74, 417-433.
33. Krakauer, D.C., and Komarova, N.L. (2003) Levels of selection in positive-strand virus dynamics. J Evol Biol 16, 64-73.
34. Lee, H.H., Molla, M.N., Cantor, C.R., and Collins, J.J. (2010) Bacterial charity work leads to population-wide resistance. Nature 467, 82-85.
35. Dupre, J., and O'Malley, M.A. (2007) Metagenomics and biological ontology. Stud Hist Philos Biol Biomed Sci 38, 834-846.
36. Shah, S.A., and Garrett, R.A. (2010) CRISPR/Cas and Cmr modules, mobility and evolution of adaptive immune systems. Res Microbiol.
37. Lyon, P. (2007) From quorum to cooperation: lessons from bacterial sociality for evolutionary theory. Stud Hist Philos Biol Biomed Sci 38, 820-833.
38. Koonin, E.V., and Wolf, Y.I (2009) Is evolution Darwinian or/and Lamarckian? Biol Direct 4, 42.
39. Van Melderen, L., and Saavedra De Bast, M. (2009) Bacterial toxin-antitoxin systems: more than selfish entities? PLoS Genet 5, e1000437.
40. DeLong, E.F. (2007) Microbiology. Life on the thermodynamic edge. Science 317, 327-328.
41. Bapteste, E., and Burian, R.M. (2010) On the Need for Integrative Phylogenomics, and Some Steps Toward its Creation. Biology and Philosophy 25, 711-736.
42. Valas, R.E., and Bourne, P.E. (2010) Save the tree of life or get lost in the woods. Biol Direct 5, 44.
43. Dagan, T., and Martin, W. (2009) Microbiology. Seeing green and red in diatom genomes. Science 324, 1651-1652.
44. Dagan, T., Roettger, M., Bryant, D., and Martin, W. (2010) Genome networks root the tree of life between prokaryotic domains. Genome Biol Evol 2, 379-392.
45. Cotton, J.A., and McInerney, J.O. (2010) Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. Proc Natl Acad Sci USA.
46. Lapointe, F.J., Lopez, P., Boucher, Y., Koenig, J., and Bapteste, E. (2010) Clanistics: A multi-level perspective for harvesting unrooted gene trees. Trends Microbiol 18, 341-347.
47. Schliep, K., Lopez, P., Lapointe, F.J., and Bapteste, E. (2010) Harvesting Evolutionary Signals in a Forest of Prokaryotic Gene Trees. Mol Biol Evol, ahead of print 48. Franklin, L.R. (2005) Exploratory experiments. Philosophy of Science 72, 888-899.
48. Burian, R.M. (2007) On microRNA and the need for exploratory experimentation in postgenomic molecular biology. History and Philosophy of the Life Sciences 29(3), 285-312.
49. Elliott, K.C. (2007) Varieties of exploratory experimentation in nanotoxicology. History and Philosophy of the Life Sciences 29(3), 313-336.
50. O'Malley,M.A. (2007)Exploratory experimentation and scientific practice:Metagenomics and the proteorhodopsin case.History and Philosophy of the Life Sciences 29(3), 337-360.
51. Strasser, B.J. (2008) GenBank-Natural History in the 21st Century? Science 322, 537-538.
52. Strasser B.J. (2010) Laboratories, Museums, and the Comparative Perspective: Alan A. Boyden's Serological Taxonomy, 1925-1962. Historical Studies in the Natural Sciences 40 (2), 149-182.
53. Bapteste, E., and Boucher, Y. (2008) Lateral gene transfer challenges principles of microbial systematics. Trends Microbiol 16, 200-207.
54. Walsby, A.E. (1994) Gas vesicles. Microbiol Rev 58, 94-144.
55. Lo, I., Denef, V.J., Verberkmoes, N.C., Shah, M.B., Goltsman, D., DiBartolo, G., Tyson, G. W., Allen, E.E., Ram, R.J., Detter, J.C., Richardson, P., Thelen, M.P., Hettich, R.L., and Banfield, J.F. (2007) Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446, 537-541.
56. Nesbo, C.L., Bapteste, E., Curtis, B., Dahle, H., Lopez, P., Macleod, D., Dlutek, M., Bowman, S., Zhaxybayeva, O., Birkeland, N.K., and Doolittle, W.F. (2009) The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea. J Bacteriol 191, 1974-1978.
57. Wilmes, P., Simmons, S.L., Denef, V.J., and Banfield, J.F. (2009) The dynamic genetic repertoire of microbial communities. FEMS Microbiol Rev 33, 109-132.
58. Vogl, K., Wenter, R., Dressen, M., Schlickenrieder, M., Ploscher, M., Eichacker, L., and Overmann, J. (2008) Identification and analysis of four candidate symbiosis genes from 'Chlorochromatium aggregatum', a highly developed bacterial symbiosis. Environ Microbiol 10, 2842-2856.
59. Wanner,G.,Vogl,K., andOvermann, J. (2008) Ultrastructural characterization of the prokaryotic symbiosis in " Chlorochromatiumaggregatum". J Bacteriol 190, 3721-3730.
60. Lindell, D., Jaffe, J.D., Coleman, M.L., Futschik, M.E., Axmann, I.M., Rector, T., Kettler, G., SulliVan, M.B., Steen, R., Hess, W.R., Church, G.M., and Chisholm, S.W. (2007) Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature 449, 83-86.
61. Lindell, D., SulliVan, M.B., Johnson, Z.I., Tolonen, A.C., Rohwer, F., and Chisholm, S.W. (2004) Transfer of photosynthesis genes to and from Prochlorococcus viruses. Proc Natl Acad Sci USA 101, 11013-11018.
62. Palenik, B., Ren, Q., Tai, V., and Paulsen, I.T. (2009) Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity. Environ Microbiol 11, 349-359.
63. Zeidner, G., Bielawski, J.P., Shmoish, M., Scanlan, D.J., Sabehi, G., and Beja, O. (2005) Potential photosynthesis gene recombination between Prochlorococcus and Synechococcus via viral intermediates. Environ Microbiol 7, 1505-1513.
64. Gill, S.R., Pop, M., Deboy, R.T., Eckburg, P. B., Turnbaugh, P.J., Samuel, B.S., Gordon, J. I., Relman, D.A., Fraser-Liggett, C.M., and Nelson, K.E. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312, 1355-1359.
65. Qu, A., Brulc, J.M., Wilson, M.K., Law, B.F., Theoret, J.R., Joens, L.A., Konkel, M.E., Angly, F., Dinsdale, E.A., Edwards, R.A., Nelson, K.E., and White, B.A. (2008) Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS One 3, e2945.
66. Simpson, G.G. (1961) Principles of Animal Taxonomy. New York: Columbia Univ Press.
67. Lane, C.E., and Archibald, J.M. (2008) The eukaryotic tree of life: endosymbiosis takes its TOL. Trends Ecol Evol 23, 268-275.
68. Alperovitch-Lavy, A., Sharon, I., Rohwer, F., Aro, E.M., Glaser, F., Milo, R., Nelson, N., and Beja, O. (2010) Reconstructing a puzzle: existence of cyanophages containing both photosystem-I and photosystem-II gene suites inferred from oceanic metagenomic datasets. Environ Microbiol.
69. Lozupone, C.A., Hamady, M., Cantarel, B.L., Coutinho, P.M., Henrissat, B., Gordon, J.I., and Knight, R. (2008) The convergence of carbohydrate active gene repertoires in human gut microbes. Proc Natl Acad Sci USA 105, 15076-15081.
70. Moustafa, A., Beszteri, B., Maier, U.G., Bowler, C., Valentin, K., and Bhattacharya, D. (2009) Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science 324, 1724-1726.
71. Lane, C.E., and Durnford, D. (2010) Endosymbiosis and the evolution of plastids. In: Molecular Phylogeny of Microorganisms. Oren, A., and Papke, R.T. eds. Norwich: Horizon Press.
72. Bouchard, F. (2010) Symbiosis, Lateral Function Transfer and the (many) saplings of life. Biology and Philosophy 25, 623-641.
73. Janzen, D.H. (1980) When is it coevolution? Evolution 34, 611-612.
74. Pernthaler, A., Dekas, A.E., Brown, C.T., Goffredi, S.K., Embaye, T., and Orphan, V.J. (2008) Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics. Proc Natl Acad Sci USA 105, 7052-7057.
75. Overmann, J. (2010) The phototrophic consortium "Chlorochromatium aggregatum"-a model for bacterial heterologous multicellularity. Adv Exp Med Biol 675, 15-29.
76. Wenter, R., Hutz, K., Dibbern, D., Li, T., Reisinger, V., Ploscher, M., Eichacker, L., Eddie, B., Hanson, T., Bryant, D.A., and Overmann, J. (2010) Expression-based identification of genetic determinants of the bacterial symbiosis 'Chlorochromatium aggregatum'. Environ Microbiol.
77. Ehinger, M., Koch, A.M., and Sanders, I.R. (2009) Changes in arbuscular mycorrhizal fungal phenotypes and genotypes in response to plant species identity and phosphorus concentration. New Phytol. 184, 412-423.
78. Scheublin, T.R., Sanders, I.R., Keel, C., and Van der Meer, J.R. (2010) Characterisation of microbial communities colonising the hyphal surfaces of arbuscular mycorrhizal fungi. ISME J 4, 752-763.
79. Hijri, I., Sykorova, Z., Oehl, F., Ineichen, K., Mader, P., Wiemken, A., and Redecker, D. (2006) Communities of arbuscular mycorrhizal fungi in arable soils are not necessarily low in diversity. Mol Ecol 15, 2277-2289.
80. Kuhn, G., Hijri, M., and Sanders, I.R. (2001) Evidence for the evolution of multiple genomes in arbuscular mycorrhizal fungi. Nature 414, 745-748.
81. Odenbaugh, J. (2007) Seeing the Forest and the Trees: Realism about Communities and Ecosystems. Philosophy of Science 74, 628-641.
82. Hutchinson, G.E. (1948) Circular Causal Systems in Ecology. Annals of the New York Academy of Sciences 50, 221-246.
83. Tansley, A.G. (1935) The Use and Abuse of Vegetational Terms and Concepts. Ecology 16, 284-307.
84. Swenson, W., Wilson, D.S., and Elias, R. (2000) Artificial Ecosystem Selection. Proceedings of the National Academy of Science 97, 9110-9114.
85. Bouchard, F. (2011) How ecosystem evolution strengthens the case for functional pluralism. In: Functions: selection and mechanisms. Huneman, P. ed.: Synthese Library, Springer.
86. Konstantinidis, K.T., and Tiedje, J.M. (2005) Genomic insights that adVance the species definition for prokaryotes. Proc Natl Acad Sci USA 102, 2567-2572.
87. Doolittle, W.F. (2009) Eradicating Typological Thinking in Prokaryotic Systematics and Evolution. Cold Spring Harb Symp Quant Biol.
88. Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T. (2011) Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res 21(4), 599-609. Epub 2011 Jan 26.
89. Broogard, B. (2004) Species as Individuals". Biology and Philosophy 19, 223-242.
90. Ereshefsky, M. (2010) Mystery of mysteries: Darwin and the species problem. Cladistics 26, 1-13.
91. Falkowski, P.G., Fenchel, T., and Delong, E. F. (2008) The microbial engines that drive Earth's biogeochemical cycles. Science 320, 1034-1039.
92. Doolittle, W.F., and Zhaxybayeva, O. (2010) Metagenomics and the Units of Biological Organization. Bioscience 60, 102-112.
93. Lerat, E., Daubin, V., and Moran, N.A. (2003) From gene trees to organismal phylogeny in prokaryotes: The case of the gamma-Proteobacteria. PLoS Biol 1, E19.
94. 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, M.E., Frapy, E., Garry, L., Ghigo, J.M., Gilles, A.M., Johnson, J., Le Bouguenec, C., Lescat, M., Mangenot, S., Martinez-Jehanne, V., Matic, I., Nassif, X., Oztas, S., Petit, M.A., Pichon, C., Rouy, Z., Ruf, C.S., Schneider, D., Tourret, J., Vacherie, B., Vallenet, D., Medigue, C., Rocha, E. P., and Denamur, E. (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 5, e1000344.
95. Dinsdale, E.A., Edwards, R.A.,Hall, D., Angly, F., Breitbart,M., Brulc, J.M., Furlan, M., Desnues, C., Haynes, M., Li, L., McDaniel, L., Moran, M.A., Nelson, K.E., Nilsson, C., Olson, R., Paul, J., Brito, B.R., Ruan, Y., Swan, B.K., Stevens, R., Valentine, D.L., Thurber, R.V., Wegley, L., White, B.A., and Rohwer, F. (2008) Functional metagenomic profilingof nine biomes.Nature 452,629-632.
96. Bouchard, F. (2008) Causal Processes, Fitness and the Differential Persistence of Lineages. Philosophy of Science 75, 560-570.
97. Csardi, G., and Nepusz, T. (2006) The igraph software package for complex network research. InterJournal Complex Systems, 1695.
98. Newman, M.E. (2006) Finding community structure in networks using the eigenvectors of matrices. Phys Rev E Stat Nonlin Soft Matter Phys 74, 36104.
99. Tatusov, R.L., Koonin, E.V., and Lipman, D. J. (1997) A genomic perspective on protein families. Science 278, 631-637.
100. Li,W. (2009) Analysis and comparison of very large metagenomes with fast clustering and functional annotation. BMC Bioinformatics 10, 359.
101. Killcoyne, S., Carter, G.W., Smith, J., and Boyle, J. (2009) Cytoscape: A communitybased framework for network modeling. Methods Mol Biol 563, 219-239.
102. Boucher, Y., Cordero, O.X., Takemura, A., Hunt, D.E., Schliep, K., Bapteste, E., Lopez, P., Tarr, C.L., and Polz, M.F. (2011) Local mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populations. MBio 2(2). pii: e00335-10. doi:10.1128/mBio.00335-10.
103. Lawrence, J. (1999) Selfish operons: The evolutionary impact of gene clustering in prokaryotes and eukaryotes. Curr Opin Genet Dev 9 (6), 642-8. Review.