Random walk in genome space: A key ingredient of intermittent dynamics of community assembly on evolutionary time scales

Journal of Theoretical Biology

Volumn 264, Issue 3, 2010, Pages 663-672

  Murase, Yohsuke ^a   Shimada, Takashi ^a   Ito, Nobuyasu ^a   Rikvold, Per Arne ^b  

^a UNIVERSITY OF TOKYO   (Japan)

^b Florida State University   (United States)

Author keywords

Community assembly; Coordinated stasis; Density dependent selection; Migration; Species lifetime distribution

Indexed keywords

EXTINCTION; GENOME; MIGRATION; MODELING; MUTATION; POPULATION DYNAMICS; RANDOM WALK METHOD;

AGE; ARTICLE; COMMUNITY DYNAMICS; CONTROLLED STUDY; EVOLUTION; GENOME; MATHEMATICAL MODEL; MIGRATION; MORTALITY; MUTATION; POPULATION DYNAMICS; PRIORITY JOURNAL; RANDOM WALK; SPECIES DISTRIBUTION; STATISTICS;

ANIMALS; BIODIVERSITY; EVOLUTION, MOLECULAR; EXTINCTION, BIOLOGICAL; GENOME; MODELS, GENETIC; MONTE CARLO METHOD; MUTATION; POPULATION DYNAMICS; TIME FACTORS;

EID: 77952600327     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2010.03.043     Document Type: Article

References (54)

1. Alroy J., Marshall C.R., Bambach R.K., Bezusko K., Foote M., Fürsich F.T., Hansen T.A., Holland S.M., Ivany L.C., Jablonski D., Jacobs D.K., Jones D.C., Kosnik M.A., Lidgard S., Low S., Miller A.I., Novack-Gottshall P.M., Olszewski T.D., Patzkowsky M.E., Raup D.M., Roy K., Sepkoski J.J., Sommers M.G., Wagner P.J., Webber A. Effects of sampling standardization on estimates of phanerozoic marine diversification. Proc. Natl. Acad. Sci. USA 2001, 98(11):6261-6266.
2. Bak P., Sneppen K. Punctuated equilibrium and criticality in a simple model of evolution. Phys. Rev. Lett. 1993, 71(24):4083-4086.
3. Benton M.J. The red queen and the court jester: species diversity and the role of biotic and abiotic factors through time. Science 2009, 323(5915):728-732.
4. Brett C., Ivany L., Schopf K. Coordinated stasis: an overview. Palaeogeogr. Palaeoclimatol. Palaeoecol. 1997, 127(1):1-20.
5. Brett, C.E., Baird, G.C., 1995. Coordinated stasis and evolutionary ecology of silurian to middle devonian faunas in the Appalachian basin. In: Erwin, D.H., Anstey, R.L. (Eds.), New Approaches to Speciation in the Fossil Record Columbia University Press, New York, pp. 285-315.
6. Caldarelli G., Higgs P.G., McKane A.J. Modelling coevolution in multispecies communities. J. Theor. Biol. 1998, 193(2):345-358.
7. Carlton J., Geller J. Ecological roulette: the global transport of nonindigenous marine organisms. Science 1993, 261(5117):78.
8. Carlton J.T. Biological invasions and cryptogenic species. Ecology 1996, 77(6):1653-1655.
9. Chowdhury D., Stauffer D., Kunwar A. Unification of small and large time scales for biological evolution: deviations from power law. Phys. Rev. Lett. 2003, 90(6):068101.
10. Christensen K., di Collobiano S.A., Hall M., Jensen H.J. Tangled nature: a model of evolutionary ecology. J. Theor. Biol. 2002, 216(1):73-84.
11. Cox D., Miller H. The Theory of Stochastic Processes 1965, Methuen & Co., London.
12. di Collobiano S.A., Christensen K., Jensen H.J. The tangled nature model as an evolving quasi-species model. J. Phys. A Math. Gen. 2003, 36(4):883-891.
13. DiMichele W.A., Behrensmeyer A.K., Olszewski T.D., Labandeira C.C., Pandolfi J.M., Wing S.L., Bobe R. Long-term stasis in ecological assemblages: evidence from the fossil record. Ann. Rev. Ecol. Evol. Syst. 2004, 35(1):285-322.
14. Doran N.A., Arnold A.J., Parker W.C., Huffer F.W. Is extinction age dependent?. Palaios 2006, 21(6):571-579.
15. Drossel B., Higgs P.G., McKane A.J. The influence of predator-prey population dynamics on the long-term evolution of food web structure. J. Theor. Biol. 2001, 208:91-107.
16. Drossel B., McKane A.J., Quince C. The impact of nonlinear functional responses on the long-term evolution of food web structure. J. Theor. Biol. 2004, 229(4):539-548.
17. Dunne J.A., Williams R.J., Martinez N.D. Food-web structure and network theory: the role of connectance and size. Proc. Natl. Acad. Sci. USA 2002, 99(20):12917-12922.
18. Dunne J.A., Williams R.J., Martinez N.D. Network structure and biodiversity loss in food webs: robustness increases with connectance. Ecol. Lett. 2002, 5(4):558-567.
19. Eigen M. A principle of natural self-organization. Naturwissenschaften 1977, 64(11):541-565.
20. Ferriere R., Cazelles B. Universal power laws govern intermittent rarity in communities of interacting species. Ecology 1999, 80(5):1505-1521.
21. Filotas E., Grant M., Parrott L., Rikvold P.A. The effect of positive interactions on community structure in a multi-species metacommunity model along an environmental gradient. Ecol. Modell. 2010, 221:885-894.
22. Filotas, E., Grant, M., Parrott, L., Rikvold, P.A., 2010. Positive interactions and the emergence of community structure in evolving metacommunities. E-print arXiv:1001:1111, submitted for publication.
23. Finnegan S., Payne J.L., Wang S.C. The red queen revisited: reevaluating the age selectivity of phanerozoic marine genus extinctions. Paleobiology 2008, 34(3):318-341.
24. Gavrilets S. Fitness Landscapes and the Origin of Species 2004, Princeton University Press, Princeton, New Jersey, USA.
25. Gavrilets S., Gravner J. Percolation on the fitness hypercube and the evolution of reproductive isolation. J. Theor. Biol. 1997, 184(1):51-64.
26. Gavrilets S., Hastings A. Intermittency and transient chaos from simple frequency-dependent selection. Proc. R. Soc. London B 1995, 261(1361):233-238.
27. Hall M., Christensen K., di Collobiano S.A., Jensen H.J. Time-dependent extinction rate and species abundance in a tangled-nature model of biological evolution. Phys. Rev. E 2002, 66(1):011904.
28. Hubbell S.P. The Unified Neutral Theory of Biodiversity and Biogeography 2001, Princeton University Press, Princeton, New Jersey, USA.
29. Huisman J., Weissing F.J. Biological conditions for oscillations and chaos generated by multispecies competition. Ecology 2001, 82(10):2682-2695.
30. Ives A.R., Jansen V.A.A. Complex dynamics in stochastic tritrophic models. Ecology 1998, 79(3):1039-1052.
31. Kolar C.S., Lodge D.M. Progress in invasion biology: predicting invaders. Trends Ecol. Evol. 2001, 16(4):199-204.
32. Krebs C.J. Ecological Methodology 1989, Harper and Row Publishers, New York.
33. Laird S., Jensen H.J. The tangled nature model with inheritance and constraint: evolutionary ecology restricted by a conserved resource. Ecol. Complex 2006, 3(3):253-262.
34. Lodge D.M. Biological invasions: lessons for ecology. Trends Ecol. Evol. 1993, 8(4):133-137.
35. McKane A.J. Evolving complex food webs. Eur. Phys. J. B 2004, 38(2):287-295.
36. Murase, Y., Shimada, T., Ito, N., Rikvold, P.A., 2010. Effects of demographic stochasticity on biological community assembly on evolutionary time scales, Phys. Rev. E, to be published.
37. Newman M. A new picture of life's history on earth. Proc. Natl. Acad. Sci. USA 2001, 98(11):5955-5956.
38. Newman M., Palmer R. Modeling Extinction 2003, Oxford University Press, USA.
39. Pigolotti S., Flammini A., Marsili M., Maritan A. Species lifetime distribution for simple models of ecologies. Proc. Natl. Acad. Sci. USA 2005, 102(44):15747-15751.
40. Raup D.M. Taxonomic survivorship curves and van Valen's law. Paleobiology 1975, 1(1):82-96.
41. Rikvold P.A. Self-optimization, community stability, and fluctuations in two individual-based models of biological coevolution. J. Math. Biol. 2007, 55:653.
42. Rikvold P.A. Complex dynamics in coevolution models with ratio-dependent functional response. Ecol. Complex 2009, 6(4):443-452.
43. Rikvold P.A., Sevim V. An individual-based predator-prey model for biological coevolution: fluctuations, stability, and community structure. Phys. Rev. E 2007, 75(5):051920.
44. Rikvold P.A., Zia R.K.P. Punctuated equilibria and 1/f noise in a biological coevolution model with individual-based dynamics. Phys. Rev. E 2003, 68(3):031913.
45. Sevim V., Rikvold P.A. Effects of correlated interactions in a biological coevolution model with individual-based dynamics. J. Phys. A Math. Gen. 2005, 38(43):9475-9489.
46. Shimada T., Yukawa S., Ito N. Self-organization in an ecosystem. Artif. Life Robotics 2002, 6:78.
47. Shimada T., Yukawa S., Ito N. Life-span of families in fossil data forms q-exponential distribution. Int. J. Mod. Phys. C 2003, 14(9):1267-1271.
48. Thompson J.N. Rapid evolution as an ecological process. Trends Ecol. Evol. 1998, 13(8):329-332.
49. Thompson J.N. The evolution of species interactions. Science 1999, 284(5423):2116-2118.
50. Tokita K., Yasutomi A. Emergence of complex and stable network in a model ecosystem with extinction and mutation. Theor. Pop. Biol. 2003, 63:131-146.
51. van Valen L. A new evolutionary law. Evol. Theor. 1973, 1(1):1-30.
52. Vitousek P.M., Mooney H.A., Lubchenco J., Melillo J.M. Human domination of Earth's ecosystem. Science 1997, 277(25):494-499.
53. Yoshida T., Jones L., Ellner S., Fussmann G., Hairston N. Rapid evolution drives ecological dynamics in a predator-prey system. Nature (London) 2003, 424(6946):303-306.
54. Zia R.K.P., Rikvold P.A. Fluctuations and correlations in an individual-based model of biological coevolution. J. Phys. A Math. Gen. 2004, 37(19):5135-5155.