Productivity and diversity in a cross-feeding population of artificial organisms

Evolution

Volumn 64, Issue 9, 2010, Pages 2716-2730

  Gerlee, Philip ^a   Lundh, Torbjörn ^b  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

Author keywords

Artificial life; Cross feeding; Productivity; Species diversity

Indexed keywords

BIOLOGICAL PRODUCTION; COLIFORM BACTERIUM; ENTROPY; EXPERIMENTAL STUDY; FREQUENCY DEPENDENCE; NUTRIENT USE EFFICIENCY; SPECIES DIVERSITY;

ARTICLE; BIODIVERSITY; BIOLOGICAL MODEL; COMPUTER SIMULATION; EVOLUTION; POPULATION DYNAMICS;

BIODIVERSITY; BIOLOGICAL EVOLUTION; COMPUTER SIMULATION; MODELS, BIOLOGICAL; POPULATION DYNAMICS;

ESCHERICHIA COLI;

EID: 77956451212     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2010.01020.x     Document Type: Article

References (51)

1. Adami C. Introduction to Artificial Life 1998, Springer, New York
2. Adami C. Digital genetics: unravelling the genetic basis of evolution. Nat. Rev. Genet. 2006, 7:109-118.
3. Bronstein J. Our current understanding of mutualism. Q. Rev. Biol. 1994, 69:31-51.
4. Chow S S, Wilke C O, Ofria C, Lenski R E, Adami C. Adaptive radiation from resource competition in digital organisms. Science 2004, 305:84-86.
5. Costa E, Perez J, Kreft J-U. Why is metabolic labour divided in nitrification. Trends Microbiol. 2006, 14:213-219.
6. Czaran T, Hoekstra R, Page L. Chemical warfare between microbes promotes biodiversity. Proc. Natl. Acad. Sci. USA 2002, 99:786-790.
7. Dejonghe W, Berteloot E, Goris J, Boon N, Crul K, Maertens S, Höfte M, Vos P D, Verstraete W, Top E. Synergistic degradation of linuron by a bacterial consortium and isolation of a single linuron-degrading variovorax strain. Appl Environ Microbiol 2003, 69:1532-1541.
8. Deutsch A, Dormann S. Cellular automaton modeling of biological pattern formation 2005, Birkhäuser, Boston
9. Doebeli M. A model for the evolutionary dynamics of cross-feeding polymorphisms in microorganisms. Pop. Ecol. 2002, 44:59-70.
10. Fryer G, Iles T. Alternative routes to evolutionary success as exhibited by african cichlid fishes of the genus tilapia and the species flocks of the great lakes. Evolution 1969, 23:359-369.
11. Gardner M. Mathematical games: the fantastic combinations of john conway's new solitaire game " life" Scientific Am. 1970, 223:120-123.
12. Gerlee P, Lundh T. The emergence of overlapping scale-free genetic architecture in digital organisms. Artificial Life 2008, 14:265-275.
13. Gerlee P, Lundh T, Zhang B, Anderson A R A. Gene divergence and pathway duplication in the metabolic network of yeast and digital organisms. J R Soc Interface 2009, 6:1233-1245.
14. Grime J P. Competitive exclusion in herbaceous vegetation. Nature 1973, 242:344-347.
15. Hardin G. The competitive exclusion principle. Science 1960, 131:1292-1297.
16. Helling R B, Vargas C N, Adams J. Evolution of escherichia coli during growth in a constant environment. Genetics 1987, 116:349-358.
17. Hessler R, Sanders H. Faunal diversity in the deep-sea. Deep-Sea Research 1967, 14:65-79.
18. Huisman J, Weissing F J. Biodiversity of plankton by species oscillations and chaos. Nature 1999, 402:407-410.
19. Hutchinson G. Homage to santa rosalia or why are there so many kinds of animals?. Am. Nat. 1959, 93:145-159.
20. Kassen R, Buckling A, Bell G, Rainey P B. Diversity peaks at intermediate productivity in a laboratory microcosm. Nature 2000, 406:508-512.
21. Katsuyama C, Nakaoka S, Takeuchi Y, Tago K, Hayatsu M, Kato K. Complementary cooperation between two syntrophic bacteria in pesticide degradation. J. Theor. Biol. 2009, 256:644-654.
22. Kerr B, Riley M A, Feldman M W, Bohannan B J M. Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors. Nature 2002, 418:171-174.
23. Laird R A, Schamp B S. Species coexistence, intransitivity, and topological variation in competitive tournaments. J. Theor. Biol. 2009, 256:90-95.
24. Lenski R, Ofria C, Collier T, Adami C. Genome complexity, robustness and genetic interactions in digital organisms. Nature 1999, 400:661-664.
25. Lenski R, Ofria C, Pennock R, Adami C. The evolutionary origin of complex features. Nature 2003, 423:139-144.
26. Lestienne R. The creative power of chance 1998, Univ. of Illinois Press, Illinois
27. Lindgren K. Information theory for complex systems (lecture notes). Chalmers 2003
28. Odum E. Fundamentals of Ecology 1959, Saunders, Philadelphia
29. Ornstein D S, Weiss B. Entropy and data compression schemes. IEEE Tran. Inform. Theory 1993, 39:78-83.
30. Ostrowski E A, Ofria C, Lenski R E. Ecological specialization and adaptive decay in digital organisms. Am Nat 2007, 169:E1-E20.
31. Pelz O, Tesar M, Wittich R, Moore E R B, Timmis K N, Abraham W R. Towards elucidation of microbial community metabolic pathways: unravelling the network of carbon sharing in a pollutant-degrading bacterial consortium by immunocapture and isotopic ratio mass spectrometry. Environ. Microbiol. 1999, 1:167-174.
32. Pfeiffer T, Bonhoeffer S. Evolution of cross-feeding in microbial populations. Am Nat 2004, 163:E126-E135.
33. Rainey P, Travisano M. Adaptive radiation in a heterogeneous environment. Nature 1998, 394:69-72.
34. Rainey P B, Buckling A, Kassen R, Travisano M. The emergence and maintenance of diversity: insights from experimental bacterial populations. Trends Ecol. Evol. 2000, 15:243-247.
35. Ray T. An approach to the synthesis of life. Artificial Life II 1992, 371-408. Langton CTaylor CFarmer JRasmussen S. eds, Addison-Wesley, Redwood City, CA
36. Rozen D, Lenski R. Long-term experimental evolution in escherichia coli. viii. dynamics of a balanced polymorphism. Am. Nat. 2000, 155:24-35.
37. Saxer G, Doebeli M, Travisano M. Spatial structure leads to ecological breakdown and loss of diversity. Proc. Biol. Sci. Lond. B 2009, 276:2065-2070.
38. Schluter D. The ecology of adaptive radiation 2000, Oxford Press, Oxford
39. Schrödinger E. What is Life? 1944, Cambridge Univ. Press, Cambridge
40. Shannon C E. A mathematical theory of communication. The Bell System Technical Journal 1948, 27.
41. Stams A J. Metabolic interactions between anaerobic bacteria in methanogenic environments. Antonie Van Leeuwenhoek 1994, 66:271-294.
42. Tilman D. Resource competition and community structure 1982, Princeton Univ. Press, Princeton
43. Travisano M, Rainey P B. Studies of adaptive radiation using model microbial systems. Am. Nat. 2000, 156:S35-S44.
44. Ulam S. On some mathematical problems connected with patterns of growth of figures 1962, Essays on Cellular Automata, Univ. of Illinois
45. Valentine J. Resource supply and species diversity patterns. Lethaia 1971, 4:51-61.
46. von Neumann J, Burks A. Theory of self-reproducing automata 1966, Univ. of Illinois Press, Champaign
47. Waide R, Willig M, Steiner C, M G, Gough L, Dodson S, Juday G, Parmenter R. The relationship between productivity and species richness. Annu. Rev. Ecol. Syst. 1999, 30:257-300.
48. White A, Handler P, S E L. Principles of biochemistry 1973, 5th ed., New York, McGraw-Hill
49. Wilke C, Adami C. The biology of digital organisms. Trends Ecol. Evol. 2002, 17:528-532.
50. Wolfram S. Statistical mechanics of cellular automata. Rev. Modern Phys. 1983, 55:601-644.
51. Yedid G, Ofria C, Lenski R. Selective press extinctions, but not random pulse extinctions, cause delayed ecological recovery in communities of digital organisms. Am Nat 2009, 173:E139-E154.