Before the Endless Forms: Embodied Model of Transition from Single Cells to Aggregates to Ecosystem Engineering

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Solé, Ricard V ^a,b,c,d   Valverde, Sergi ^a,c,d  

^a UNIVERSITAT POMPEU FABRA   (Spain)

^b SANTA FE INSTITUTE   (United States)

^c INSTITUTE OF EVOLUTIONARY BIOLOGY CSIC UNIVERSITAT POMPEU FABRA   (Spain)

^d CA' FOSCARI UNIVERSITY OF VENICE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL ACTIVITY; CELL AGGREGATION; CELL MATURATION; CELL TRANSFORMATION; EVOLUTIONARY DEVELOPMENTAL BIOLOGY; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MORPHOGENESIS;

ALGORITHMS; BIOLOGICAL EVOLUTION; CELL COMMUNICATION; CELL PHYSIOLOGICAL PHENOMENA; COMPUTER SIMULATION; ENVIRONMENT; MODELS, THEORETICAL; MORPHOGENESIS;

EID: 84876170005     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0059664     Document Type: Article

References (59)

1. Carroll SB (2005) Endless forms most beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom. W. W. Norton and Co.
2. Grossberg RK, Strahmann RR, (2007) The Evolution of Multicellularity: A Minor Major Transition? Annual Reviews of Ecology and Evolution and Systematics 38: 621654.
3. Knoll AH, (2011) The Multiple Origins of Complex Multicellularity Annual Reviews in Earth and Planetary Science. 39: 217-239.
4. Lipps JH, Signor PH (1992) Origin and early evolution of the Metazoa. Plenum Press, New York.
5. Rokas A, (2008) The molecular origins of multicellular transitions. Current Opinion Genetics and Development 18: 472-478.
6. King N, (2004) The unicellular ancestry of animal development. Developmental Cell. 7: 313325.
7. Maynard Smith J, Szathmary E (1995) The major transitions in evolution. Oxford U. Press.
8. Niklas K (1997) The Evolutionary Biology of Plants. University of Chicago Press. Chicago.
9. Bonner JT (2001) First signals: the evolution of multicellular development. Princeton U. Press.
10. Fedonkin MA (2007) The Rise of Animals: Evolution and Diversification of the Kingdom Animalia. JHU Press.
11. Newman SA, Forgacs, G Muller GB (2006) Before programs: the physical origination of multicellular forms. International Journal of Developmental Biology 50: 289-299.
12. Eldredge N (1985) Unfinished Synthesis: Biological Hierarchies and Modern Evolutionary Thought. Oxford University Press.
13. McShea DW, (2001) The hierarchical structure of organisms: a scale and documentation of a trend in the maximum. Paleobiology 27: 405-423.
14. Sebe-Pedros A, Roger AJ, Lang FB, King N, Ruiz-Trillo I, (2010) Ancient origin of the integrinmediated adhesion and signaling machinery. Proceedings of the National Academy of Sciences USA. 107: 10142-10147.
15. Solé RV, Fernandez P, Kauffman SA, (2003) Adaptive walks in a gene network model of morphogenesis: insights into the Cambrian explosion. International Journal of Developmental Biology 47: 685-693.
16. Fujimoto K, Ishihara S, Kaneko K, (2008) Network evolution of body plans. PLoS ONE 3: e2772.
17. Tusscher KH, Hogeweg P, (2011) Evolution of networks for body plan patterning; interplay of modularity, robustness and evolvability. PLoS Computational Biology 7: e1002208.
18. Newman SA, Baht R, (2008) Dynamical patterning modules: physico-genetic determinants of morphological development and evolution. Physical Biology 5: 015008.
19. Graner F, Glazier JA, (1992) Simulation of biological cell sorting using a two-dimensional extended Potts model. Physical Review Letters 69: 2013-2016.
20. Glazier JA, Graner F, (1993) Simulation of the differential adhesion driven rearrangement of biological cells. Physical Review E 47: 21282154.
21. Hogeweg P, (2000) Evolving Mechanisms of Morphogenesis: on the Interplay between Differential Adhesion and Cell Differentiation. Journal of Theoretical Biology 203: 317333.
22. Hogeweg P, (2000) Shapes in the shadow: Evolutionary dynamics of morphogenesis. Artificial Life 6: 85-101.
23. Savill NJ, Hogeweg P, (1997) Modeling morphogenesis: from single cells to crawling slugs. Journal of Theoretical Biology 184: 229-235.
24. Sims K, (1994) Evolving 3D morphology and behavior by competition. Artificial Life 1: 353-372.
25. Pfeifer R, Lungarella M, Lida F, (2007) Self-Organization, Embodiment, and Biologically Inspired Robotics. Science 318: 1088-1093.
26. Eggenberger P (1997) Evolving morphologies of simulated 3d organisms based on differential gene expression. In. Fourth Europ. Conf. Artificial Life, P. Husbands and I. Harvey, editors. 205-213. MIT Press.
27. Doursat R (2008) Organically grown architectures: creating decentralized, autonomous systems by embryomorphic engineering. In: Organic Computing, R. P. Würtz, ed: 167-200. Springer-Verlag.
28. Cummings F, (2006) On the origin of pattern and form in early metazoans. International Journal of Developmental Biology 50: 193-208.
29. Kaandorp JA, Blom JG, Verhoef J, Filatov M, Postma M, et al. (2008) Modelling genetic regulation of growth and form in a branching sponge. Proceedings of the Royal Society B 275: 2569-2575.
30. Coen E, Rolland-Lagan AG, Matthews M, Bangham JA, Prusinkiewicz P, (2004) The genetics of geometry.Proceedings of the National Academy of Sciences USA. 101: 4728-4735.
31. Müller GB, (2007) Evo-devo: extending the evolutionary synthesis. Nature Reviews Genetics 8: 943-949.
32. Forgacs G, Newman SA (2005) Biological physics of the developing embryo. Cambridge Univ. Press, Cambridge.
33. Erwin DH, (2008) Macroevolution of ecosystem engineering, niche construction and diversity. Trends Ecol Evol. 23: 304-310.
34. Jones CG, Lawton JM, Shachak M, (1994) Organisms as ecosystem engineers. OIKOS 69: 373-370.
35. Jones CG, Lawton JM, Shachak M, (1997) Positive and negative effects of organisms as physical ecosystem engineers. Ecology 78: 1946-1957.
36. Erwin DH, Tweedt S, (2012) Ecological drivers of the Ediacaran-Cambrian diversification of Metazoa. Evolutionary Ecology 26: 417-433.
37. Hastings A, (2006) Ecosystem engineering in space and time. Ecology Letters 10: 153-164.
38. Palsson E, (2001) A Three-dimensional model of cell movement in multicellular systems. Future Generation Computer Systems17: 835-852.
39. Palsson E, Othmer HG, (2000) A model for individual and collective cell movement in Distyostlium discoideum. Proceedings of the National Academy of Sciences USA 97: 10448-10453.
40. Newman TJ, (2005) Modeling Multi-cellular Systems using Sub-cellular Elements. Mathematical biosciences and engineering 2: 611-622.
41. Sandersius SA, Newman TJ, (2008) Modelling cell rheology with the subcellular element model. Physical Biology 5: 015002.
42. Bell N, Yu Y, Muchs PJ (2005) Particle-Based Simulation of Granular Materials. In: SCA '05 Proceedings of the 2005 ACM SIGGRAPH Eurographics symposium on Computer animation. 77-86.
43. Ericson C (2005) Real-Time Collision Detection. Morgan Kaufmann.
44. Solé RV (2011) Phase Transitions. Princeton U. Press. Princeton.
45. Greig D, Louis EJ, Borts RH, Travisano M, (2002) Hybrid speciation in experimental populations of yeast. Science 298: 1773-1775.
46. Rainey PB, Travisano M, (1998) Adaptive radiation in a heterogeneous environment. Nature 394: 69-72.
47. Travisano M, Mongold JA, Bennett AF, Lenski RE, (1995) Experimental tests of the roles of adaptation, chance, and history in evolution. Science 267: 87-90.
48. Lenski RE, Travisano M, (1994) Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Proceedings of the National Academy of Sciences USA 91: 6808-6814.
49. Ratcliff WC, Denison RF, Borrello M, Travisano M, (2012) Experimental evolution of multicellularity. Proceedings of the National Academy of Sciences USA 109: 1595-1600.
50. Erwin DH, (1998) The end and the beginning: recoveries from mass extinctions. Trends in Ecology and Evolution 13: 344349.
51. Erwin DH, (2001) Lessons from the past: biotic recoveries from mass extinction. Proceedings of the National Academy of Sciences USA 98: 53995403.
52. Erwin DH, (1994) The PermoTriassic extinction. Nature 367: 231236.
53. Benton MJ, Twitchett RJ, (2003) How to kill (almost) all life: the end-Permian extinction event. Trends in Ecology and Evolution 18: 358365.
54. Chen ZQ, Benton MJ, (2012) The timing and pattern of biotic recovery following the end-Permian mass extinction. Nature Geoscience 5: 375383.
55. Solé RV, Montoya JM, Erwin DH, (2002) Recovery after mass extinction: evolutionary assembly in large-scale biosphere dynamics. Philosophical Transactions of the Royal Society B 357: 697707.
56. Roopnarine PD, (2006) Extinction cascades and catastrophe in ancient food webs. Paleobiology 32: 1-19.
57. Yedid G, Stredwick J, Ofria CA, Agapow PM, (2012) A comparison of the e_ects of random and selective mass extinctions on erosion of evolutionary history in communities of digital organisms. PLoS ONE 7: e37233.
58. Queller DC, (1997) Cooperation since life began. Quarterly Review of Biology 72: 184-188.
59. Queller DC, (2000) Relatedness and the fraternal major transitions. Philosophical Transactions of the Royal Society B 355: 1647-1655.