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Published in: Natural Computing 4/2019

04-10-2019

Lattice-based versus lattice-free individual-based models: impact on coexistence in competitive communities

Authors: Aisling J. Daly, Ward Quaghebeur, Tim M. A. Depraetere, Jan M. Baetens, Bernard De Baets

Published in: Natural Computing | Issue 4/2019

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Abstract

Individual-based modelling is an increasingly popular framework for modelling biological systems. Many of these models represent space as a lattice, thus imposing unrealistic limitations on the movement of the modelled individuals. We adapt an existing model of three competing species by using a lattice-free approach, thereby improving the realism of the spatial dynamics. We retrieve the same qualitative dynamics as the lattice-based approach. However, by facilitating a higher spatial heterogeneity and allowing for small spatial refuges to form and persist, the maintenance of coexistence is promoted, in correspondence with experimental results. We also implement a directed movement mechanism allowing individuals of different species to pursue or flee from each other. Simulations show that the effects on coexistence depend on the level of aggregation in the community: a high level of aggregation is advantageous for maintaining coexistence, whereas a low level of aggregation is disadvantageous. This agrees with experimental results, where pursuing and escaping behaviour has been observed to be advantageous only in certain circumstances.

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Literature
go back to reference Adamson MW, Morozov AY (2012) Revising the role of species mobility in maintaining biodiversity in communities with cyclic competition. Bull Math Biol 74(9):2004–2031MathSciNetCrossRefMATH Adamson MW, Morozov AY (2012) Revising the role of species mobility in maintaining biodiversity in communities with cyclic competition. Bull Math Biol 74(9):2004–2031MathSciNetCrossRefMATH
go back to reference Arsenault DJ, Himmelman JH (1996) Size-related changes in vulnerability to predators and spatial refuge use by juvenile Iceland scallops Chlamys islandica. Mar Ecol Prog Ser 140(1–3):115–122CrossRef Arsenault DJ, Himmelman JH (1996) Size-related changes in vulnerability to predators and spatial refuge use by juvenile Iceland scallops Chlamys islandica. Mar Ecol Prog Ser 140(1–3):115–122CrossRef
go back to reference Ashby MN, Rine J, Mongodin EF, Nelson KE, Dimster-Denk D (2007) Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities. Appl Environ Microbiol 73(14):4532–4542CrossRef Ashby MN, Rine J, Mongodin EF, Nelson KE, Dimster-Denk D (2007) Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities. Appl Environ Microbiol 73(14):4532–4542CrossRef
go back to reference Auchincloss AH, Riolo RL, Brown DG, Cook J, Diez Roux AV (2011) An agent-based model of income inequalities in diet in the context of residential segregation. Am J Prev Med 40(3):303–311CrossRef Auchincloss AH, Riolo RL, Brown DG, Cook J, Diez Roux AV (2011) An agent-based model of income inequalities in diet in the context of residential segregation. Am J Prev Med 40(3):303–311CrossRef
go back to reference Avelino PP, Bazeia D, Losano L, Menezes J, de Oliveira BF (2017) Spiral patterns and biodiversity in lattice-free Lotka–Volterra models. arXiv preprint. pp. 1–5. arXiv:1710.05066 Avelino PP, Bazeia D, Losano L, Menezes J, de Oliveira BF (2017) Spiral patterns and biodiversity in lattice-free Lotka–Volterra models. arXiv preprint. pp. 1–5. arXiv:​1710.​05066
go back to reference Avelino PP, Bazeia D, Losano L, Menezes J, de Oliveira BF, Santos MA (2018) How directional mobility affects biodiversity in rock-paper-scissors models. Phys Rev E 97(1–3):032415CrossRef Avelino PP, Bazeia D, Losano L, Menezes J, de Oliveira BF, Santos MA (2018) How directional mobility affects biodiversity in rock-paper-scissors models. Phys Rev E 97(1–3):032415CrossRef
go back to reference Baetens J, De Loof K, De Baets B (2013) Influence of the topology of a cellular automation on its dynamical properties. Commun Nonlinear Sci Numer Simul 11:651–688CrossRefMATH Baetens J, De Loof K, De Baets B (2013) Influence of the topology of a cellular automation on its dynamical properties. Commun Nonlinear Sci Numer Simul 11:651–688CrossRefMATH
go back to reference Beppu K, Izri Z, Gohya J, Eto K, Ichikawa M, Maeda YT (2017) Geometry-driven collective ordering of bacterial vortices. Soft Matter 13(29):5038–5043CrossRef Beppu K, Izri Z, Gohya J, Eto K, Ichikawa M, Maeda YT (2017) Geometry-driven collective ordering of bacterial vortices. Soft Matter 13(29):5038–5043CrossRef
go back to reference Bernard EP, Krauth W (2011) Two-step melting in two dimensions: first-order liquid-hexatic transition. Phys Rev Lett 107(15):155704CrossRef Bernard EP, Krauth W (2011) Two-step melting in two dimensions: first-order liquid-hexatic transition. Phys Rev Lett 107(15):155704CrossRef
go back to reference Birch C, Oom S, Beecham J (2006) Rectangular and hexagonal grids used for observation, experiment and simulation in ecology. Ecol Model 206(3):347–359 Birch C, Oom S, Beecham J (2006) Rectangular and hexagonal grids used for observation, experiment and simulation in ecology. Ecol Model 206(3):347–359
go back to reference Buss LW (1979) Competitive networks: nontransitive competitive relationships in cryptic coral reef environments. Am Nat 113(2):223–234CrossRef Buss LW (1979) Competitive networks: nontransitive competitive relationships in cryptic coral reef environments. Am Nat 113(2):223–234CrossRef
go back to reference Finke DL, Denno RF (2006) Spatial refuge from intraguild predation: implications for prey suppression and trophic cascades. Oecologia 149(2):265–275CrossRef Finke DL, Denno RF (2006) Spatial refuge from intraguild predation: implications for prey suppression and trophic cascades. Oecologia 149(2):265–275CrossRef
go back to reference Ginovart M (2002) INDISIM, an individual-based discrete simulation model to study bacterial cultures. J Theor Biol 214(2):305–319CrossRef Ginovart M (2002) INDISIM, an individual-based discrete simulation model to study bacterial cultures. J Theor Biol 214(2):305–319CrossRef
go back to reference Gonnella G, Lamura A, Suma A (2014) Phase segregation in a system of active dumbbells. Int J Mod Phys C 25(12):1441004CrossRef Gonnella G, Lamura A, Suma A (2014) Phase segregation in a system of active dumbbells. Int J Mod Phys C 25(12):1441004CrossRef
go back to reference Grimm V, Berger U, DeAngelis DL, Polhill JG, Giske J, Railsback SF (2010) The ODD protocol: a review and first update. Ecol Model 221(23):2760–2768CrossRef Grimm V, Berger U, DeAngelis DL, Polhill JG, Giske J, Railsback SF (2010) The ODD protocol: a review and first update. Ecol Model 221(23):2760–2768CrossRef
go back to reference Hurlbert SH (1978) The measurement of niche overlap and some relatives. Ecology 59(1):67–77CrossRef Hurlbert SH (1978) The measurement of niche overlap and some relatives. Ecology 59(1):67–77CrossRef
go back to reference Kennedy J, Eberhart R (1995) Particle swarm optimization. In: Proceedings of the IEEE conference on neural networks, vol 4, pp 1942–1948 Kennedy J, Eberhart R (1995) Particle swarm optimization. In: Proceedings of the IEEE conference on neural networks, vol 4, pp 1942–1948
go back to reference Kerr B, Riley MA, Feldman MW, Bohannan BJM (2002) Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors. Nature 418(6894):171–174CrossRef Kerr B, Riley MA, Feldman MW, Bohannan BJM (2002) Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors. Nature 418(6894):171–174CrossRef
go back to reference Kirkup BC, Riley MA (2004) Antibiotic-mediated antagonism leads to a bacterial game of rock-paper-scissors in vivo. Nature 428(6981):412–414CrossRef Kirkup BC, Riley MA (2004) Antibiotic-mediated antagonism leads to a bacterial game of rock-paper-scissors in vivo. Nature 428(6981):412–414CrossRef
go back to reference Kreft JU, Booth G, Wimpenny JWT (1998) BacSim, a simulator for individual-based modelling of bacterial colony growth. Microbiology 144(12):3275–3287CrossRef Kreft JU, Booth G, Wimpenny JWT (1998) BacSim, a simulator for individual-based modelling of bacterial colony growth. Microbiology 144(12):3275–3287CrossRef
go back to reference Kreft JU, Picioreanu C, Wimpenny JWT, van Loosdrecht MCM (2001) Individual-based modelling of biofilms. Microbiology 147(Pt 11):2897–2912CrossRef Kreft JU, Picioreanu C, Wimpenny JWT, van Loosdrecht MCM (2001) Individual-based modelling of biofilms. Microbiology 147(Pt 11):2897–2912CrossRef
go back to reference Laird RA, Schamp BS (2008) Does local competition increase the coexistence of species in intransitive networks? Ecology 89(1):237–247CrossRef Laird RA, Schamp BS (2008) Does local competition increase the coexistence of species in intransitive networks? Ecology 89(1):237–247CrossRef
go back to reference Laird RA, Schamp BS (2009) Species coexistence, intransitivity, and topological variation in competitive tournaments. J Theor Biol 256(1):90–95MathSciNetCrossRefMATH Laird RA, Schamp BS (2009) Species coexistence, intransitivity, and topological variation in competitive tournaments. J Theor Biol 256(1):90–95MathSciNetCrossRefMATH
go back to reference Landau L, Lifshitz E (1986) EM Lifshitz theory of elasticity, 3rd edn. Pergamon Press, New York Landau L, Lifshitz E (1986) EM Lifshitz theory of elasticity, 3rd edn. Pergamon Press, New York
go back to reference Luisa M, Merler S, Rizzo C, Ajelli M, Massari M, Furlanello C, Tomba GS, Iannelli M (2008) Mitigation measures for pandemic influenza in Italy: an individual-based model considering different scenarios. PLoS ONE 3(3):e1790CrossRef Luisa M, Merler S, Rizzo C, Ajelli M, Massari M, Furlanello C, Tomba GS, Iannelli M (2008) Mitigation measures for pandemic influenza in Italy: an individual-based model considering different scenarios. PLoS ONE 3(3):e1790CrossRef
go back to reference Mattson W, Rice BM (1999) Near-neighbor calculations using a modified cell-linked list method. Comput Phys Commun 119(2):135–148CrossRef Mattson W, Rice BM (1999) Near-neighbor calculations using a modified cell-linked list method. Comput Phys Commun 119(2):135–148CrossRef
go back to reference Osborne JM, Fletcher AG, Pitt-Francis JM, Maini PK, Gavaghan DJ (2017) Comparing individual-based approaches to modelling the self-organization of multicellular tissues. PLoS Comput Biol 13(2):1–34CrossRef Osborne JM, Fletcher AG, Pitt-Francis JM, Maini PK, Gavaghan DJ (2017) Comparing individual-based approaches to modelling the self-organization of multicellular tissues. PLoS Comput Biol 13(2):1–34CrossRef
go back to reference Railsback SF, Grimm V (2011) Agent-based and individual-based modeling: a practical introduction. Princeton University Press, PrincetonMATH Railsback SF, Grimm V (2011) Agent-based and individual-based modeling: a practical introduction. Princeton University Press, PrincetonMATH
go back to reference Railsback SF, Lytinen SL, Jackson SK (2006) Agent-based simulation platforms: review and development recommendations. Simulation 82(9):609–623CrossRef Railsback SF, Lytinen SL, Jackson SK (2006) Agent-based simulation platforms: review and development recommendations. Simulation 82(9):609–623CrossRef
go back to reference Reichenbach T, Mobilia M, Frey E (2007) Mobility promotes and jeopardizes biodiversity in rock-paper-scissors games. Nature 448(7157):1046–1049CrossRef Reichenbach T, Mobilia M, Frey E (2007) Mobility promotes and jeopardizes biodiversity in rock-paper-scissors games. Nature 448(7157):1046–1049CrossRef
go back to reference Reynolds C (1987) Flocks, herds, and schools: a distributed behavioral model. Comput Graph 21(4):25–34CrossRef Reynolds C (1987) Flocks, herds, and schools: a distributed behavioral model. Comput Graph 21(4):25–34CrossRef
go back to reference Schreiber SJ, Lipcius RN, Seitz RD, Long WC (2006) Dancing between the devil and deep blue sea: The stabilizing effect of enemy-free and victimless sinks. Oikos 113(1):67–81CrossRef Schreiber SJ, Lipcius RN, Seitz RD, Long WC (2006) Dancing between the devil and deep blue sea: The stabilizing effect of enemy-free and victimless sinks. Oikos 113(1):67–81CrossRef
go back to reference Taylor DR, Aarssen LW (1990) Complex competitive relationships among genotypes of three perennial grasses: implications for species coexistence. Am Nat 136(3):305–327CrossRef Taylor DR, Aarssen LW (1990) Complex competitive relationships among genotypes of three perennial grasses: implications for species coexistence. Am Nat 136(3):305–327CrossRef
go back to reference Touhami A, Nysten B, Dufrêne Y (2003) Nanoscale mapping of the elasticity of microbial cells by atomic force microscopy. Microbiology 19(11):4539–4543 Touhami A, Nysten B, Dufrêne Y (2003) Nanoscale mapping of the elasticity of microbial cells by atomic force microscopy. Microbiology 19(11):4539–4543
go back to reference Verlet L (1967) Computer “experiments” on classical fluids. Phys Rev 159(1):98–103CrossRef Verlet L (1967) Computer “experiments” on classical fluids. Phys Rev 159(1):98–103CrossRef
go back to reference Vukov J, Szolnoki A, Szabó G (2013) Diverging fluctuations in a spatial five-species cyclic dominance game. Phys Rev E Stat Nonlinear Soft Matter Phys 88(2):1–8CrossRef Vukov J, Szolnoki A, Szabó G (2013) Diverging fluctuations in a spatial five-species cyclic dominance game. Phys Rev E Stat Nonlinear Soft Matter Phys 88(2):1–8CrossRef
go back to reference Wilsey BJ (2004) Realistically low species evenness does not alter grassland species-richness: productivity relationships. Ecology 85(10):2693–2700CrossRef Wilsey BJ (2004) Realistically low species evenness does not alter grassland species-richness: productivity relationships. Ecology 85(10):2693–2700CrossRef
Metadata
Title
Lattice-based versus lattice-free individual-based models: impact on coexistence in competitive communities
Authors
Aisling J. Daly
Ward Quaghebeur
Tim M. A. Depraetere
Jan M. Baetens
Bernard De Baets
Publication date
04-10-2019
Publisher
Springer Netherlands
Published in
Natural Computing / Issue 4/2019
Print ISSN: 1567-7818
Electronic ISSN: 1572-9796
DOI
https://doi.org/10.1007/s11047-019-09767-1

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