The impact of initial evenness on biodiversity maintenance for a four-species in silico bacterial community

Journal of Theoretical Biology

Volumn 387, Issue , 2015, Pages 189-205

  Daly, Aisling J ^a   Baetens, Jan M ^a   De Baets, Bernard ^a  

^a GHENT UNIVERSITY   (Belgium)

Author keywords

Cyclic competition; Evenness; Individual based model; Rock paper scissors

Indexed keywords

BACTERIUM; BIODIVERSITY; COMPETITION (ECOLOGY); ECOSYSTEM DYNAMICS; INDIVIDUAL-BASED MODEL; MICROBIAL COMMUNITY; SPECIES EVENNESS;

BACTERIA (MICROORGANISMS);

BACTERIUM; BIODIVERSITY; COMPUTER SIMULATION; EVOLUTION; METABOLISM; PROBABILITY; SPECIES DIFFERENCE; TIME FACTOR;

BACTERIA; BIODIVERSITY; BIOLOGICAL EVOLUTION; COMPUTER SIMULATION; PROBABILITY; SPECIES SPECIFICITY; TIME FACTORS;

EID: 84944909787     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2015.09.036     Document Type: Article

References (75)

1. Adamson M., Morozov A. Revising the role of species mobility in maintaining biodiversity in communities with cyclic competition. Bull. Math. Biol. 2012, 74(9):2004-2031.
2. Beisel J.-N., Usseglio-Polatera P., Bachmann V., Moreteau J.-C. A comparative analysis of evenness index sensitivity. Int. Rev. Hydrobiol. 2003, 88(1):3-15.
3. Berec L. Techniques of spatially explicit individual-based models: construction, simulation, and mean-field analysis. Ecol. Model. 2002, 150(1):55-81.
4. Berr M., Reichenbach T., Schottenloher M., Frey E. Zero-one survival behavior of cyclically competing species. Phys. Rev. Lett. 2009, 102(4):048102.
5. Cases S.O., Durney C.H., Pleimling M., Zia R. Cyclic competition of four species. mean-field theory and stochastic evolution. EPL (Europhys. Lett.) 2010, 92(5):58003.
6. Cheng, H., Yao, N., Huang, Z.G., Park, J., Do, Y., Lai, Y.C., 2014. Mesoscopic interactions and species coexistence in evolutionary game dynamics of cyclic competitions. Sci. Rep. 4, 7486.
7. Crowder D., Northfield T., Strand M., Snyder W. Organic agriculture promotes evenness and natural pest control. Nature 2010, 466(7302):109-112.
8. Davidson R. Reliable inference for the Gini index. J. Econom. 2009, 150(1):30-40.
9. De Deyn G., Raaijmakers C., Zoomer H., Berg M., de Ruiter P., Verhoef H., Bezemer T., van der Putten W. Soil invertebrate fauna enhances grassland succession and diversity. Nature 2003, 422(6933):711-713.
10. De Roy K., Marzorati M., Negroni A., Thas O., Balloi A., Fava F., Verstraete W., Daffonchio D., Boon N. Environmental conditions and community evenness determine the outcome of biological invasion. Nat. Commun. 2013, 4:1383.
11. Derry A., Staddon W., Trevors J. Functional diversity and community structure of microorganisms in uncontaminated and creosote-contaminated soils as determined by sole-carbon-source-utilization. World J. Microbiol. Biotechnol. 1998, 14(4):571-578.
12. Dobrinevski A., Frey E. Extinction in neutrally stable stochastic Lotka-Volterra models. Phys. Rev. E 2012, 85(5):051903.
13. Doering C., Sargsyan K., Sander L. Extinction times for birth-death processes: exact results, continuum asymptotics, and the failure of the Fokker-Planck approximation. Multiscale Model. Simul. 2005, 3(2):283-299.
14. Durney C., Case S., Pleimling M., Zia R. Saddles, arrows, and spirals. deterministic trajectories in cyclic competition of four species. Phys. Rev. E 2011, 83(5):051108.
15. Durney C., Case S., Pleimling M., Zia R. Stochastic evolution of four species in cyclic competition. J. Stat. Mech.: Theory Exp. 2012, 2012(06):P06014.
16. Dutton R., Brigham R. A characterization of competition graphs. Discret. Appl. Math. 1983, 6(3):315-317.
17. Ebenman B., Jonsson T. Using community viability analysis to identify fragile systems and keystone species. Trends Ecol. Evol. 2005, 20(10):568-575.
18. Eliazar I. Randomness, evenness, and Rényi's index. Phys. A: Stat. Mech. Appl. 2011, 390(11):1982-1990.
19. Eliazar I., Sokolov I. Maximization of statistical heterogeneity: from Shannon's entropy to Gini's index. Phys. A: Stat. Mech. Appl. 2010, 389(16):3023-3038.
20. Eliazar I., Sokolov I. Measuring statistical evenness. a panoramic overview. Phys. A: Stat.l Mech. Appl. 2012, 391(4):1323-1353.
21. Ferrer J., Prats C., López D. Individual-based modelling. an essential tool for microbiology. J. Biol. Phys. 2008, 34(1-2):19-37.
22. Frachebourg L., Krapivsky P., Ben-Naim E. Spatial organization in cyclic Lotka-Volterra systems. Phys. Rev. E 1996, 54(6):6186.
23. Frey E., Reichenbach T. Principles of Evolution 2011.
24. Gibson D. The relationship of sheep grazing and soil heterogeneity to plant spatial patterns in dune grassland. J. Ecol. 1988, 76:233-252.
25. Gilg O., Hanski I., Sittler B. Cyclic dynamics in a simple vertebrate predator-prey community. Science 2003, 302(5646):866-868.
26. Gillespie D. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comput. Phys. 1976, 22(4):403-434.
27. Ginot V., Gaba S., Beaudouin R., Aries F., Monod H. Combined use of local and ANOVA-based global sensitivity analyses for the investigation of a stochastic dynamic model. application to the case study of an individual-based model of a fish population. Ecol. Model. 2006, 193(3):479-491.
28. Glendinning P. Stability, Instability and Chaos. An Introduction to the Theory of Nonlinear Differential Equations 1994, Cambridge University Press.
29. Grime J. Benefits of plant diversity to ecosystems. immediate filter and founder effects. J. Ecol. 1998, 86(6):902-910.
30. Guill C., Drossel B., Just W., Carmack E. A three-species model explaining cyclic dominance of Pacific salmon. J. Theor. Biol. 2011, 276(1):16-21.
31. Harch B., Correll R., Meech W., Kirkby C., Pankhurst C. Using the Gini coefficient with BIOLOG substrate utilisation data to provide an alternative quantitative measure for comparing bacterial soil communities. J. Microbiol. Methods 1997, 30(1):91-101.
32. Harpole W., Suding K. Frequency-dependence stabilizes competitive interactions among four annual plants. Ecol. Lett. 2007, 10(12):1164-1169.
33. Heip C. A new index measuring evenness. J. Mar. Biol. Assoc. U.K. 1974, 54(03):555-557.
34. Hellweger F., Bucci V. A bunch of tiny individuals-individual-based modelling for microbes. Ecol. Model. 2009, 220(1):8-22.
35. Hill M. Diversity and evenness. a unifying notation and its consequences. Ecology 1973, 54(2):427-432.
36. Hillebrand H., Bennett D., Cadotte M. Consequences of dominance. a review of evenness effects on local and regional ecosystem processes. Ecology 2008, 89(6):1510-1520.
37. Hooper D., Chapin F., Ewel J., Hector A., Inchausti P., Lavorel S., Lawton J., Lodge D., Loreau M., Naeem S., Schmid B., Setala H., Symstad A., Vandermeer J., Wardle D. Effects of biodiversity on ecosystem functioning. a consensus of current knowledge. Ecol. Monogr. 2005, 75(1):3-35.
38. Huston M. Hidden treatments in ecological experiments. re-evaluating the ecosystem function of biodiversity. Oecologia 1997, 110(4):449-460.
39. Intoy B., Pleimling M. Extinction in four species cyclic competition. J. Stat. Mech.: Theory Exp. 2013, 2013(08):P08011.
40. Isbell F., Polley H., Wilsey B. Biodiversity, productivity and the temporal stability of productivity. patterns and processes. Ecol. Lett. 2009, 12(5):443-451.
41. Isbell F., Polley H., Wilsey B. Species interaction mechanisms maintain grassland plant species diversity. Ecology 2009, 90(7):1821-1830.
42. Jackson J., Buss L. Alleopathy and spatial competition among coral reef invertebrates. Proc. Natl. Acad. Sci. U.S.A. 1975, 72(12):5160-5163.
43. Kerr B., Riley M., Feldman M., Bohannan B. Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors. Nature 2002, 418(6894):171-174.
44. Kirkpatrick S., Gelatt C., Vecchi M. Optimization using simulated annealing. Science 1983, 220(4598):671-680.
45. Laird R., Schamp B. Competitive intransitivity promotes species coexistence. Am. Nat. 2006, 168(2):182-193.
46. Laird R., Schamp B. Competitive intransitivity, population interaction structure, and strategy coexistence. J. Theor. Biol. 2015, 365:149-158.
47. Lambert P., Aronson J. Inequality decomposition analysis and the Gini coefficient revisited. Econ. J. 1993, 1221-1227.
48. Lemieux J., Cusson M. Effects of habitat-forming species richness, evenness, identity, and abundance on benthic intertidal community establishment and productivity. PLoS ONE 2014, 9(10):e109261.
49. Lilburne L., Tarantola S. Sensitivity analysis of spatial models. Int. J. Geogr. Inf. Sci. 2009, 23(2):151-168.
50. Lütz A., Risau-Gusman S., Arenzon J. Intransitivity and coexistence in four species cyclic games. J. Theor. Biol. 2013, 317:286-292.
51. Magurran A. Measuring Biological Diversity 2004, Blackwell Science Ltd, Oxford, UK.
52. Mendes R., Evangelista L., Thomaz S., Agostinho A., Gomes L. A unified index to measure ecological diversity and species rarity. Ecography 2008, 31(4):450-456.
53. Mouritsen K., Poulin R. Parasites boosts biodiversity and changes animal community structure by trait-mediated indirect effects. Oikos 2005, 108(2):344-350.
54. Nadell C., Foster K., Xavier J. Emergence of spatial structure in cell groups and the evolution of cooperation. PLoS Comput. Biol. 2010, 6(3):e1000716.
55. Parker M., Kamenev A. Mean extinction time in predator-prey model. J. Stat. Phys. 2010, 141(2):201-216.
56. Polley H., Wilsey B., Derner J. Do species evenness and plant density influence the magnitude of selection and complementarity effects in annual plant species mixtures?. Ecol. Lett. 2003, 6(3):248-256.
57. Reardon S., Firebaugh G. Measures of multigroup segregation. Sociol. Methodol. 2002, 32(1):33-67.
58. Reichenbach T., Mobilia M., Frey E. Mobility promotes and jeopardizes biodiversity in rock-paper-scissors games. Nature 2007, 448(7157):1046-1049.
59. Reichenbach T., Mobilia M., Frey E. Self-organization of mobile populations in cyclic competition. J. Theor. Biol. 2008, 254(2):368-383.
60. Rousseau R., van Hecke P. Measuring biodiversity. Acta Biotheor. 1999, 47(1):1-5.
61. Sinervo B., Lively C. The rock-paper-scissors game and the evolution of alternative male strategies. Nature 1996, 380(6571):240-243.
62. Smith B., Wilson J. A consumer's guide to evenness indices. Oikos 1996, 70-82.
63. Smith M., Knapp A. Dominant species maintain ecosystem function with non-random species loss. Ecol. Lett. 2003, 6(6):509-517.
64. Sobol I. Global sensitivity indices for nonlinear mathematical models and their Monte Carlo estimates. Math. Comput. Simul. 2001, 55(1):271-280.
65. Szabó, G., Fath, G., 2007. Evolutionary games on graphs. Phys. Rep. 446 (4), 97-216.
66. Szabó G., Sznaider G. Phase transition and selection in a four-species cyclic predator-prey model. Phys. Rev. E 2004, 69(3):031911.
67. Tuomisto H. An updated consumer's guide to evenness and related indices. Oikos 2012, 121(8):1203-1218.
68. Vincke S., Van de Vijver B., Gremmen N., Beyens L. The moss dwelling testacean fauna of the Stromness Bay (South Georgia). Acta Protozool. 2006, 45(1):65.
69. Wilcove D., Rothstein D., Dubow J., Phillips A., Losos E. Quantifying threats to imperiled species in the United States. BioScience 1998, 48(8):607-615.
70. Wills C., Harms K., Condit R., King D., Thompson J., He F., Muller-Landau H., Ashton P., Losos E., Comita L., et al. Nonrandom processes maintain diversity in tropical forests. Science 2006, 311(5760):527-531.
71. Wilsey B., Polley H. Realistically low species evenness does not alter grassland species-richness-productivity relationships. Ecology 2004, 85(10):2693-2700.
72. Wilsey B., Potvin C. Biodiversity and ecosystem functioning. importance of species evenness in an old field. Ecology 2000, 81(4):887-892.
73. Wilsey B., Teaschner T., Daneshgar P., Isbell F., Polley H. Biodiversity maintenance mechanisms differ between native and novel exotic-dominated communities. Ecol. Lett. 2009, 12(5):432-442.
74. Wittebolle L., Marzorati M., Clement L., Balloi A., Daffonchio D., Heylen K., De Vos P., Verstraete W., Boon N. Initial community evenness favours functionality under selective stress. Nature 2009, 458(7238):623-626.
75. Zhang Y., Chen H., Reich P. Forest productivity increases with evenness, species richness and trait variation. a global meta-analysis. J. Ecol. 2012, 100(3):742-749.