Evolutionary analyses of non-genealogical bonds produced by introgressive descent

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 45, 2012, Pages 18266-18272

  Bapteste, Eric ^a   Lopez, Philippe ^a   Bouchard, Frédéric ^b   Baquero, Fernando ^c   McInerney, James O ^d   Buriane, Richard M ^e  

^a Université Pierre et Marie Curie ^*  (France)

^b UNIVERSITÉ DE MONTRÉAL   (Canada)

^c HOSPITAL RAMÓN Y CAJAL   (Spain)

^d NATIONAL UNIVERSITY OF IRELAND   (Ireland)

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

Author keywords

Biodiversity structure; Evolutionary transitions; Lateral gene transfer; Network of life; Symbiosis

Indexed keywords

ARTICLE; BIODIVERSITY; CONVERGENT EVOLUTION; EVOLUTIONARY HOMOLOGY; EVOLUTIONARY RATE; GENE REGULATORY NETWORK; GENE TRANSFER; GENEALOGY; GENETIC REASSORTMENT; GENETIC SIMILARITY; MICROBIAL CONSORTIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; POPULATION GENETICS; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

BASE SEQUENCE; DATABASES, GENETIC; EVOLUTION, MOLECULAR; GENE REGULATORY NETWORKS; GENEALOGY AND HERALDRY; INBREEDING; PHYLOGENY;

EID: 84868599126     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1206541109     Document Type: Article

References (86)

1. Lewontin RC (1970) The units of selection. Annu Rev Ecol Syst 1:1-18.
2. Dawkins R (1976) The Selfish Gene (Oxford Univ Press, Oxford).
3. Dawkins R (1982) The Extended Phenotype: The Gene as the Unit of Selection (Oxford Univ Press, Oxford).
4. Hull DL (1980) Individuality and selection. Annu Rev Ecol Syst 11:311-332.
5. Lloyd EA (2012) The Stanford Encyclopedia of Philosophy, ed Zalta EN (Metaphysics Research Lab, Stanford, CA), pp 1-40.
6. Brandon RN (1982) The levels of selection. PSA 1982, eds Asquith P, Nickles T (Philosophy of Science Association, East Lansing, MI), vol. 1, pp 315-323.
7. Gould SJ, Lloyd EA (1999) Individuality and adaptation across levels of selection: How shall we name and generalize the unit of Darwinism? Proc Natl Acad Sci USA 96(21):11904-11909. (Pubitemid 29502831)
8. Keller L (1999) Levels of Selection in Evolution (Princeton Univ Press, Princeton).
9. Okasha S (2006) Evolution and the Levels of Selection (Oxford Univ Press, Oxford).
10. Wilson DS (1997) Altruism and organism: Disentangling the themes of multilevel selection theory. Am Nat 150(Suppl 1):S122-S134.
11. Hamilton WD (1964) The genetical evolution of social behaviour. I. J Theor Biol 7(1):1-16.
12. Hamilton WD (1964) The genetical evolution of social behaviour. II. J Theor Biol 7(1):17-52.
13. Williams GC (1966) Adaptation and Natural Selection (Princeton Univ Press, Princeton).
14. Nowak MA, Tarnita CE, Wilson EO (2010) The evolution of eusociality. Nature 466(7310):1057-1062.
15. Strassmann JE, Queller DC (2007) Insect societies as divided organisms: The complexities of purpose and cross-purpose. Proc Natl Acad Sci USA 104(Suppl 1):8619-8626. (Pubitemid 47175455)
16. Turner JS (2000) The Extended Organism: The Physiology of Animal-Built Structures (Harvard Univ Press, Cambridge, MA).
17. Wilson DS, Sober E (1989) Reviving the superorganism. J Theor Biol 136(3):337-356.
18. Godfrey-Smith P (2009) Darwinian Populations and Natural Selection (Oxford Univ Press, Oxford).
19. Maynard Smith J, Szathmáry E (1995) The Major Transitions in Evolution (Freeman, New York).
20. Michod RE (1999) Darwinian Dynamics: Evolutionary Transitions in Fitness and Individuality (Princeton Univ Press, Princeton).
21. Okasha S (2008) A Companion to the Philosophy of Biology, eds Sarkar S, Plutynski A (Wiley-Blackwell, Oxford), pp 138-157.
22. Buss LW (1987) The Evolution of Individuality (Princeton Univ Press, Princeton).
23. Queller DC (1997) Cooperators since life began. Q Rev Biol 72:184-188.
24. Margulis L (1981) Symbiosis in Cell Evolution (Freeman, San Francisco).
25. Bapteste E, et al. (2009) Prokaryotic evolution and the tree of life are two different things. Biol Direct 4:34.
26. Baquero F (2004) From pieces to patterns: Evolutionary engineering in bacterial pathogens. Nat Rev Microbiol 2(6):510-518.
27. Levitt M (2009) Nature of the protein universe. Proc Natl Acad Sci USA 106(27):11079-11084.
28. Alperovitch-Lavy A, et al. (2011) Reconstructing a puzzle: Existence of cyanophages containing both photo-system-I and photosystem-II gene suites inferred from oceanic metagenomic datasets. Environ Microbiol 13(1):24-32.
29. Boucher Y, et al. (2011) Local mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populations. MBio 2(2): pii: e00335-10.
30. Brazelton WJ, Baross JA (2010) Metagenomic comparison of two Thiomicrospira lineages inhabiting contrasting deep-sea hydrothermal environments. PLoS One 5(10):e13530.
31. Lozupone CA, et al. (2008) The convergence of carbohydrate active gene repertoires in human gut microbes. Proc Natl Acad Sci USA 105(39):15076-15081.
32. Smillie CS, et al. (2011) Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480(7376):241-244.
33. Lukjancenko O, Wassenaar TM, Ussery DW (2010) Comparison of 61 sequenced Escherichia coli genomes. Microb Ecol 60(4):708-720.
34. Xie W, et al. (2011) Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries. ISME J 5(3):414-426.
35. Zhang T, Zhang XX, Ye L (2011) Plasmid metagenome reveals high levels of antibiotic resistance genes and mobile genetic elements in activated sludge. PLoS One 6(10):e26041.
36. Skippington E, Ragan MA (2011) Lateral genetic transfer and the construction of genetic exchange communities. FEMS Microbiol Rev 35(5):707-735.
37. Overmann J (2010) The phototrophic consortium "Chlorochromatium aggregatum"-a model for bacterialheterologous multicellularity. Adv Exp Med Biol 675:15-29.
38. Marin B, Nowack EC, Melkonian M (2005) A plastid in the making: Evidence for a second primary endosymbiosis. Protist 156(4):425-432. (Pubitemid 41682020)
39. Moustafa A, et al. (2009) Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science 324 (5935):1724-1726.
40. Kirk DL (1998) Volvox: Molecular-Genetic Origins of Multicellularity and Cellular Differentiation (Cambridge Univ Press, Cambridge, UK).
41. Kessin RH (2001) Dictyostelium: Evolution, Cell Biology, and the Development of Multicellularity (Cambridge Univ Press, Cambridge, UK).
42. Gilbert SF, Epel D (2009) Ecological Developmental Biology: Integrating Epigenetics, Medicine, and Evolution (Sinauer, Sunderland, MA).
43. Werren JH, Baldo L, Clark ME (2008) Wolbachia: Master manipulators of invertebrate biology. Nat Rev Microbiol 6(10):741-751.
44. Büdel B, Scheidegger C (2008) Lichen Biology, ed Nash TH (Cambridge Univ Press, Cambridge, UK), 3rd Ed, pp 40-68.
45. Honegger R, Scherrer S (2008) Lichen Biology, ed Nash TH (Cambridge Univ Press, Cambridge, UK), 3rd Ed, pp 94-103.
46. Bouchard F (2010) Symbiosis, lateral function transfer and the (many) saplings of life. Biol Philos 25:623-641.
47. Dagan T, Artzy-Randrup Y, Martin W (2008) Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci USA 105(29):10039-10044.
48. Halary S, Leigh JW, Cheaib B, Lopez P, Bapteste E (2010) Network analyses structure genetic diversity in independent genetic worlds. Proc Natl Acad Sci USA 107(1):127-132.
49. Lima-Mendez G, Van Helden J, Toussaint A, Leplae R (2008) Reticulate representation of evolutionary and functional relationships between phage genomes. Mol Biol Evol 25(4):762-777. (Pubitemid 351398332)
50. Lawrey JD (1984) Biology of Lichenized Fungi (Praeger, New York).
51. Zhang W, Fisher JF, Mobashery S (2009) The bifunctional enzymes of antibiotic resistance. Curr Opin Microbiol 12(5):505-511.
52. Böltner D, MacMahon C, Pembroke JT, Strike P, Osborn AM (2002) R391: A conjugative integrating mosaic comprised of phage, plasmid, and transposon elements. J Bacteriol 184(18):5158-5169. (Pubitemid 34971042)
53. Canchaya C, Giubellini V, Ventura M, de los Reyes-Gavilán CG, Margolles A (2010) Mosaic-like sequences containing transposon, phage, and plasmid elements among Listeria monocytogenes plasmids. Appl Environ Microbiol 76(14):4851-4857.
54. Zhaxybayeva O, et al. (2009) On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proc Natl Acad Sci USA 106(14): 5865-5870.
55. Cotton JA, McInerney JO (2010) Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. Proc Natl Acad Sci USA 107(40):17252-17255.
56. Embley TM, Martin W (2006) Eukaryotic evolution, changes and challenges. Nature 430:623-630.
57. Andam CP, Fournier GP, Gogarten JP (2011) Multilevel populations and the evolution of antibiotic resistance through horizontal gene transfer. FEMS Microbiol Rev 35(5):756-767.
58. Colson P, Raoult D (2010) Gene repertoire of amoeba-associated giant viruses. Intervirology 53(5):330-343.
59. Antonova ES, Hammer BK (2011) Quorum-sensing autoinducer molecules produced by members of a multispecies biofilm promote horizontal gene transfer to Vibrio cholerae. FEMS Microbiol Lett 322(1):68-76.
60. Jones BV (2010) The human gut mobile metagenome: A metazoan perspective. Gut Microbes 1(6):415-431.
61. Qu A, et al. (2008) Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS One 3(8):e2945.
62. Walser J-C (2004) Molecular evidence for limited dispersal of vegetative propagules in the epiphytic lichen Lobaria pulmonaria. Am J Bot 91(8):1273-1276.
63. Beauregard-Racine J, et al. (2011) Of woods and webs: Possible alternatives to the tree of life for studying genomic fluidity in E. coli. Biol Direct 6(1):39.
64. Brandstädt A, Le VB, Spinrad JP (1999) Graph Classes: A Survey (SIAM, Philadelphia).
65. Berry A, Pogorelcnik R, Simonet G (2010) An introduction to clique minimal separator decomposition. Algorithms 3:197-215.
66. Baquero F (2011) The 2010 Garrod Lecture: The dimensions of evolution in antibiotic resistance: Ex unibus plurum et ex pluribus unum. J Antimicrob Chemother 66(8):1659-1672.
67. Koonin EV (2011) The Logic of Chance: The Nature and Origin of Biological Evolution (FT Press, Upper Saddle River, NJ).
68. Makino K, Uno T (2004) New algorithms for enumerating all maximal cliques. LNCS 3111 260-272.
69. Feder ME (2007) Evolvability of physiological and biochemical traits: Evolutionary mechanisms including and beyond single-nucleotide mutation. J Exp Biol 210(Pt 9):1653-1660.
70. Paauw A, Leverstein-van Hall MA, Verhoef J, Fluit AC (2010) Evolution in quantum leaps: Multiple combinatorial transfers of HPI and other genetic modules in Enterobacteriaceae. PLoS One 5(1):e8662.
71. Sterelny K (2004) Modularity in Evolution and Development, eds Schlosser G, Wagner GP (Univ of Chicago Press, Chicago), pp 490-518.
72. Bezuidt O, Pierneef R, Mncube K, Lima-Mendez G, Reva ON (2011) Mainstreams of horizontal gene exchange in enterobacteria: Consideration of the outbreak of enterohemorrhagic E. coli O104:H4 in Germany in 2011. PLoS One 6(10):e25702.
73. Bielaszewska M, et al. (2011) Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: A microbiological study. Lancet Infect Dis 11(9):671-676.
74. Rogers BA, Sidjabat HE, Paterson DL (2011) Escherichia coli O25b-ST131: A pandemic, multiresistant, community-associated strain. J Antimicrob Chemother 66(1):1-14.
75. Woese CR (2002) On the evolution of cells. Proc Natl Acad Sci USA 99(13):8742-8747.
76. Gogarten JP, Townsend JP (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 3(9):679-687. (Pubitemid 41195085)
77. Zhaxybayeva O, Gogarten JP (2004) Cladogenesis, coalescence and the evolution of the three domains of life. Trends Genet 20(4):182-187. (Pubitemid 38369189)
78. Forterre P (2002) The origin of DNA genomes and DNA replication proteins. Curr Opin Microbiol 5(5):525-532.
79. Gribaldo S, Poole AM, Daubin V, Forterre P, Brochier-Armanet C (2010) The origin of eukaryotes and their relationship with the Archaea: Are we at a phylogenomic impasse? Nat Rev Microbiol 8(10):743-752.
80. Levin BR (2010) Nasty viruses, costly plasmids, population dynamics, and the conditions for establishing and maintaining CRISPR-mediated adaptive immunity in bacteria. PLoS Genet 6(10):e1001171.
81. Vale PF, Little TJ (2010) CRISPR-mediated phage resistance and the ghost of coevolution past. Proc Biol Sci 277(1691):2097-2103.
82. Cohan FM, Perry EB (2007) A systematics for discovering the fundamental units of bacterial diversity. Curr Biol 17(10):R373-R386. (Pubitemid 46702658)
83. Wiedenbeck J, Cohan FM (2011) Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol Rev 35(5):957-976.
84. Martin A, Dunnington EA, Briles WE, Briles RW, Siegel PB (1989) Marek's disease and major histocompatibility complex haplotypes in chickens selected for high or low antibody response. Anim Genet 20(4):407-414.
85. Bodnar JW, Killian J, Nagle M, Ramchandani S (1997) Deciphering the language of the genome. J Theor Biol 189(2):183-193. (Pubitemid 27523542)
86. Searls DB (2002) The language of genes. Nature 420(6912):211-217.