Ecological Networks: From Structural Analysis to Synchronization
Ecological systems are exposed and are influenced by
various natural and anthropogenic disturbances. They produce
various effects and states seeking response symmetry to a state of
global phase coherence or stability and balance of their food webs.
This research project addresses the development of a computational
methodology for modeling plankton food webs. The use of
algorithms to establish connections, the generation of representative
fuzzy multigraphs and application of technical analysis of complex
networks provide a set of tools for defining, analyzing and evaluating
community structure of coastal aquatic ecosystems, beyond the
estimate of possible external impacts to the networks. Thus, this
study aims to develop computational systems and data models to
assess how these ecological networks are structurally and
functionally organized, to analyze the types and degree of
compartmentalization and synchronization between oscillatory and
interconnected elements network and the influence of disturbances on
the overall pattern of rhythmicity of the system.
[1] M. Cody, Diamond (Ed) Ecology and Evolution of Communities.
Belknap Press, 1975, New York.
[2] S.L. Pimm, Food Webs, 2nd ed, Chicago University Press New York,
2002.
[3] R.V. Solé, J.M., Montoya, “Complexity and fragility in ecological
networks.” Proc. R. Soc. Lond no. 268, 2001 pp. 2930-2945.
[4] J. Bascompte, P. Jordano, C.J. Melian, J.M. Olesen, “The nested
assembly of plant animal mutualistic networks” Proc. Natl. Acad. Sci.
USA no. 100, 2003, pp. 9383-9387.
[5] P.R. Guimarães, G., Machado de Aguiar, M. A.M, Jordano, J.
Bascompte., Pinheiro. J, S. F. A. dos Reis. “Build-up mechanisms
determining the topology of mutualistic networks, Journal of Theoretical
Biology” no. 249, 2007, pp. 181-189.
[6] E. Thebault, C. Fontaine. “Does asymmetric specialization differ
between mutualistic and trophic networks?” Oikos, no 117, 2008, pp.
555-563.
[7] DP. Vazquez, R., Poulin, B.R. Krasnov, G., I. Shenbrot. “Species
abundance and the distribution of specialization in host-parasite
interaction networks, Journal of Animal Ecology” no. 74, 2005, pp. 946-
955.
[8] A.R.E. Sinclair, S. M. Duma, J.S. Brashares. “Patterns of predation in a
diverse predator-prey system, Nature no.425, 2003, pp. 288-290.
[9] B. J.M. Bohannan. “Linking genetic change to community evolution:
insights studies of bacteria and bacteriophage”. Ecology Letters no. 3,
2000, pp. 464-464.
[10] G. Caldarelli, D. Garlaschelli, L. Pietronero. “Food Web Structure and
the Evolution of Complex network”. Pastor-Satorras., R. Diaz-Guilera.
A. (Eds) no. 625, 2003, pp. 148-166.
[11] G. Bell, “The evolution of trophic structure.” Heredity no.99, 2007, pp.
494-505.
[12] J.L. Garcia-Domingo, J. Saldaña, “Food-web complexity emerging from
ecological dynamics on adaptive networks”. Journal of Theoretical
Biology no.247 (4), 2007, pp. 819-826.
[13] J.O. Riede, C.B. Banasek-Richter, S.A. Navarrete, M.C. Wieters,
Emmerson, U. Jacob, U. Brose, “Scalingof Food-Web Properties with
Diversity and Complexity across Ecosystems”. Advances in Ecological
Research no.42, 2010, pp. 139-166.
[14] R. Linderman “The tropic-dynamic aspect of ecology”. Ecology no.23,
1942, pp. 399-418.
[15] S.H. Strogatz “From Kuramoto to Crawford: exploring the onset of
synchronization in populations of coupled oscillators. Physica D:
Nonlinear Phenomena”., vol. 43, no. 1, 2008, pp. 1-20.
[16] H. Fujisaka, T.Yamada, “Stability theory of synchronized motion in
coupled-oscillator systems. Progress of Theoretical Physics” 69, no.1,
1983, pp. 32-47.
[17] L.M. Pecora, T.L. Carrol , “Synchronization in chaotic systems. Physical
Review Letters” 64, no. 8, 1990, pp. 821-824.
[18] M.Schatz Bennett, F. Rockwood, K.Wiesenfeld. “Huygens’s clocks,
Proceedings of the Royal Society”, A 458, 2009 pp. 563-579.
[19] T. Danino, O. Mondragón-Palomino, L. Tsimring, J. Hasty. “A
synchronized quorum of genetic clocks.” Nature no. 463 (7279), 2010,
pp. 326-330.
[20] A. Arenas, A. Dias-Guilera, J. Kurths, Y. Zhou. “Synchronization in
complex networks. Physics Reports no. 469 (3), 2008, pp. 93-153.
[21] A. Vladimirov, G. Kozyreff, P. Mandel. “Synchronization of weakly
stable oscillators and semiconductor laser arrays”. Europhysics Letters,
no. 61, 2003, pp. 613-619.
[22] K. Wiesenfeld, P. Colet, S. Strogatz. “Synchronization transitions in a
disordered Josephson series array. Physical Review Letters”. No. 76,
1996, pp. 404-407.
[23] W. Lewandowski, J. Azoubib, W. Klepczynski “W.GPS: primary tool
for time transfer.Proceedings of the IEEE” no. (87), 1999, pp. 163-172.
[24] D. Li, K. Wong, Y. Hu, A. Sayeed. “Detection, classification and
tracking of targets in distributed sensor networks. IEEE Signal
Processing Magazine”. no. 19, 2002, pp. 17-19.
[25] Y. Jian, et al. “Notch signalling and the synchronization of the somite
segmentation clock”. Nature no.408, 2000, pp. 475-478.
[26] L. Glass. “Synchronization and rhythmic processes in physiology”.
Nature, no. 410, 2001, pp. 277-284.
[27] J. Chabot, J. Pedraza, P. Luitel, A.A. van Oudenaarden. “Stochastic gene
expression out-of-steady-state in thecyanobacterial circadian clock”.
Nature no. 450, 2007, pp. 1249-1252.
[28] L. Schimansky-Geier. “Analysis and Control of Complex Nonlinear
Processes in Physics Chemistry and Biology” World Scientific Jan.
2007.
[29] F. Grenier, I. Timofeev, M. Steriade. “Neocortical very fast oscillations
(ripples, 80-200 Hz) during seizures: intracellular correlates”. Journal of
Neurophysiology no. 89, 2003, pp 841.
[30] C. Rulquin, J.J, Arenson. “Globally synchronized oscillations in
complex cyclic games”. Phys. Rev. No. 89, 2014, pp. 032-133.
[31] L. Stone, R. Olinky, B. Blasius, A. Huppert, B. Cazelles. “Complex
Synchronization Phenomenon in Ecological Systems”. CP 622
Experimental Chaoses: 6th Experimental Chaos Conference. Edited by
S. Boccaletiet al. 2002.
[32] C.J. Krebs, R. Boonstra, S. Boutin, A.R.E, Sinclair. “What drives the 10-
year Cycle of Snowshoe Hares?” BioScience no.51 (1), 2001, pp. 25-35.
[33] C.A. Charles A. Boch, B. Ananthasu, A.M. Sweeney, F.J. Doyle III,
D.E. Morse. “Effects of Light Dynamics on Coral Spawning Synchrony.
Biol Bul1”.no. 220 (3), 2013, pp. 161-173.
[34] T.C. Gouhier, F. Guichard, B.A. Menge. “Ecological processes can
synchronize marine population dynamics over continental scales”,
PNAS. 1-6. Doi/10.1073/pnas. 0914588107, 2010.
[35] T.C. Gouhier, F. Guichard, A. Gonzalez. “Synchrony and Stability of
Food Webs in Metacommunities. American Naturalist” no. 175 (2)
2010, pp. 16-34.
[36] G.C. Pereira, L.P. Andrade, R.P. Espínola, N.F.F. Ebecken. “Structural
Analysis and Static Simulation of Coastal Planktonic Network”, Journal
of Intelligent Learning Systems and Applications (6), 2014b, pp 113-
124.
[37] J. Timothy Ross. “Fuzzy Logic with Engeneering Applications”, 2nd ed.
WestSussex, England, John Wiley & Sons, Ltd, 2004.
[38] L.P. Andrade. “Fuzzy Modeling of Plankton Networks”, PhD Thesis,
Federal University of Rio de Janeiro. 2014.
[39] M. Dorigo, T. Stützle. “Ant Colony Optimization Massachusetts, MIT
Press, Massachusetts” 2004.
[40] D. Jin “Ant Colony Optimization with Markov Random Walk for
Community Detection in Graphs”. J.Z., In Huang.
[41] Y. Liu, Lian L., Junyong L. “Adaptive Ant Colony Clustering Method
Applied to Finding Closely Communicating Community” Journal of
Networks, vol. 7 no. 2, 2012, pp. 249-258.
[42] L.B. Romdhane, Y. Chaabani, H. Zardi. “A robust ant colony
optimization-based algorithm for community mining in large scale
oriented social graphs”, Expert Systems with Applications, no. 40 (14),
2013, pp. 5709-5718.
[43] B. Cazelles and Boudjema. “The Moran effect and phase
synchronization in complex spatial community dynamics”. Amer Nat.,
no. 157, 2001, pp. 670-676.
[44] A. L. Lloyd and R.M. May. “Synchronicity, chaos and population
cycles: Spatial coherence in an uncertain world”. Trends Ecol. Evol. No.
14, 1999, pp. 417-418.
[45] Y.A. Kuznetsov, O. De Feo and Rinaldi. “Belyakov homoclinic
bifurcations in a tritrophic fod chain model”. SIAM J. Appl. Math., no.
62, 2001, pp. 462-487.
[46] B. Cazelles, S. Bottani, L. Stone. “Unexpected coherence and
conservation”. Proc. Roy. Soc. Lond. No 268, 2001, pp. 2595-2602.
[47] I. Belykh, C., Piccardi, S. Rinaldi. “Synchrony in tritrophic food chain
metacommunities”. Journal of Biological Dynamics no.3 (5), 2009, pp.
497-514.
[48] Y. Kuramoto. “Self-entrainment of a population of coupled nonlinear
oscillators. In: Symposium on Mathematical Problems in Theoretical
Physics”. Lecture Notes in Physics, 1975, pp. 420-422.
[49] J.W. Duncan. “Small Worlds: The Dynamics of Networks between
Order and Randomness.” Princeton University Press, 1999, 262 pages.
[50] H. Hong, M.Y. Choi, B.J. Kim. “Synchronization on small world
networks.” Physical Review E, vol. 65 no. 2, 2002, pp. 026-139.
[51] J. Gomez-Gardenes, Y. Moreno, A. Arenas. “Paths to synchronization
on complex networks”. Phys Rev Lett, vol. 98 no. 3, 2007, pp. 034-101.
[1] M. Cody, Diamond (Ed) Ecology and Evolution of Communities.
Belknap Press, 1975, New York.
[2] S.L. Pimm, Food Webs, 2nd ed, Chicago University Press New York,
2002.
[3] R.V. Solé, J.M., Montoya, “Complexity and fragility in ecological
networks.” Proc. R. Soc. Lond no. 268, 2001 pp. 2930-2945.
[4] J. Bascompte, P. Jordano, C.J. Melian, J.M. Olesen, “The nested
assembly of plant animal mutualistic networks” Proc. Natl. Acad. Sci.
USA no. 100, 2003, pp. 9383-9387.
[5] P.R. Guimarães, G., Machado de Aguiar, M. A.M, Jordano, J.
Bascompte., Pinheiro. J, S. F. A. dos Reis. “Build-up mechanisms
determining the topology of mutualistic networks, Journal of Theoretical
Biology” no. 249, 2007, pp. 181-189.
[6] E. Thebault, C. Fontaine. “Does asymmetric specialization differ
between mutualistic and trophic networks?” Oikos, no 117, 2008, pp.
555-563.
[7] DP. Vazquez, R., Poulin, B.R. Krasnov, G., I. Shenbrot. “Species
abundance and the distribution of specialization in host-parasite
interaction networks, Journal of Animal Ecology” no. 74, 2005, pp. 946-
955.
[8] A.R.E. Sinclair, S. M. Duma, J.S. Brashares. “Patterns of predation in a
diverse predator-prey system, Nature no.425, 2003, pp. 288-290.
[9] B. J.M. Bohannan. “Linking genetic change to community evolution:
insights studies of bacteria and bacteriophage”. Ecology Letters no. 3,
2000, pp. 464-464.
[10] G. Caldarelli, D. Garlaschelli, L. Pietronero. “Food Web Structure and
the Evolution of Complex network”. Pastor-Satorras., R. Diaz-Guilera.
A. (Eds) no. 625, 2003, pp. 148-166.
[11] G. Bell, “The evolution of trophic structure.” Heredity no.99, 2007, pp.
494-505.
[12] J.L. Garcia-Domingo, J. Saldaña, “Food-web complexity emerging from
ecological dynamics on adaptive networks”. Journal of Theoretical
Biology no.247 (4), 2007, pp. 819-826.
[13] J.O. Riede, C.B. Banasek-Richter, S.A. Navarrete, M.C. Wieters,
Emmerson, U. Jacob, U. Brose, “Scalingof Food-Web Properties with
Diversity and Complexity across Ecosystems”. Advances in Ecological
Research no.42, 2010, pp. 139-166.
[14] R. Linderman “The tropic-dynamic aspect of ecology”. Ecology no.23,
1942, pp. 399-418.
[15] S.H. Strogatz “From Kuramoto to Crawford: exploring the onset of
synchronization in populations of coupled oscillators. Physica D:
Nonlinear Phenomena”., vol. 43, no. 1, 2008, pp. 1-20.
[16] H. Fujisaka, T.Yamada, “Stability theory of synchronized motion in
coupled-oscillator systems. Progress of Theoretical Physics” 69, no.1,
1983, pp. 32-47.
[17] L.M. Pecora, T.L. Carrol , “Synchronization in chaotic systems. Physical
Review Letters” 64, no. 8, 1990, pp. 821-824.
[18] M.Schatz Bennett, F. Rockwood, K.Wiesenfeld. “Huygens’s clocks,
Proceedings of the Royal Society”, A 458, 2009 pp. 563-579.
[19] T. Danino, O. Mondragón-Palomino, L. Tsimring, J. Hasty. “A
synchronized quorum of genetic clocks.” Nature no. 463 (7279), 2010,
pp. 326-330.
[20] A. Arenas, A. Dias-Guilera, J. Kurths, Y. Zhou. “Synchronization in
complex networks. Physics Reports no. 469 (3), 2008, pp. 93-153.
[21] A. Vladimirov, G. Kozyreff, P. Mandel. “Synchronization of weakly
stable oscillators and semiconductor laser arrays”. Europhysics Letters,
no. 61, 2003, pp. 613-619.
[22] K. Wiesenfeld, P. Colet, S. Strogatz. “Synchronization transitions in a
disordered Josephson series array. Physical Review Letters”. No. 76,
1996, pp. 404-407.
[23] W. Lewandowski, J. Azoubib, W. Klepczynski “W.GPS: primary tool
for time transfer.Proceedings of the IEEE” no. (87), 1999, pp. 163-172.
[24] D. Li, K. Wong, Y. Hu, A. Sayeed. “Detection, classification and
tracking of targets in distributed sensor networks. IEEE Signal
Processing Magazine”. no. 19, 2002, pp. 17-19.
[25] Y. Jian, et al. “Notch signalling and the synchronization of the somite
segmentation clock”. Nature no.408, 2000, pp. 475-478.
[26] L. Glass. “Synchronization and rhythmic processes in physiology”.
Nature, no. 410, 2001, pp. 277-284.
[27] J. Chabot, J. Pedraza, P. Luitel, A.A. van Oudenaarden. “Stochastic gene
expression out-of-steady-state in thecyanobacterial circadian clock”.
Nature no. 450, 2007, pp. 1249-1252.
[28] L. Schimansky-Geier. “Analysis and Control of Complex Nonlinear
Processes in Physics Chemistry and Biology” World Scientific Jan.
2007.
[29] F. Grenier, I. Timofeev, M. Steriade. “Neocortical very fast oscillations
(ripples, 80-200 Hz) during seizures: intracellular correlates”. Journal of
Neurophysiology no. 89, 2003, pp 841.
[30] C. Rulquin, J.J, Arenson. “Globally synchronized oscillations in
complex cyclic games”. Phys. Rev. No. 89, 2014, pp. 032-133.
[31] L. Stone, R. Olinky, B. Blasius, A. Huppert, B. Cazelles. “Complex
Synchronization Phenomenon in Ecological Systems”. CP 622
Experimental Chaoses: 6th Experimental Chaos Conference. Edited by
S. Boccaletiet al. 2002.
[32] C.J. Krebs, R. Boonstra, S. Boutin, A.R.E, Sinclair. “What drives the 10-
year Cycle of Snowshoe Hares?” BioScience no.51 (1), 2001, pp. 25-35.
[33] C.A. Charles A. Boch, B. Ananthasu, A.M. Sweeney, F.J. Doyle III,
D.E. Morse. “Effects of Light Dynamics on Coral Spawning Synchrony.
Biol Bul1”.no. 220 (3), 2013, pp. 161-173.
[34] T.C. Gouhier, F. Guichard, B.A. Menge. “Ecological processes can
synchronize marine population dynamics over continental scales”,
PNAS. 1-6. Doi/10.1073/pnas. 0914588107, 2010.
[35] T.C. Gouhier, F. Guichard, A. Gonzalez. “Synchrony and Stability of
Food Webs in Metacommunities. American Naturalist” no. 175 (2)
2010, pp. 16-34.
[36] G.C. Pereira, L.P. Andrade, R.P. Espínola, N.F.F. Ebecken. “Structural
Analysis and Static Simulation of Coastal Planktonic Network”, Journal
of Intelligent Learning Systems and Applications (6), 2014b, pp 113-
124.
[37] J. Timothy Ross. “Fuzzy Logic with Engeneering Applications”, 2nd ed.
WestSussex, England, John Wiley & Sons, Ltd, 2004.
[38] L.P. Andrade. “Fuzzy Modeling of Plankton Networks”, PhD Thesis,
Federal University of Rio de Janeiro. 2014.
[39] M. Dorigo, T. Stützle. “Ant Colony Optimization Massachusetts, MIT
Press, Massachusetts” 2004.
[40] D. Jin “Ant Colony Optimization with Markov Random Walk for
Community Detection in Graphs”. J.Z., In Huang.
[41] Y. Liu, Lian L., Junyong L. “Adaptive Ant Colony Clustering Method
Applied to Finding Closely Communicating Community” Journal of
Networks, vol. 7 no. 2, 2012, pp. 249-258.
[42] L.B. Romdhane, Y. Chaabani, H. Zardi. “A robust ant colony
optimization-based algorithm for community mining in large scale
oriented social graphs”, Expert Systems with Applications, no. 40 (14),
2013, pp. 5709-5718.
[43] B. Cazelles and Boudjema. “The Moran effect and phase
synchronization in complex spatial community dynamics”. Amer Nat.,
no. 157, 2001, pp. 670-676.
[44] A. L. Lloyd and R.M. May. “Synchronicity, chaos and population
cycles: Spatial coherence in an uncertain world”. Trends Ecol. Evol. No.
14, 1999, pp. 417-418.
[45] Y.A. Kuznetsov, O. De Feo and Rinaldi. “Belyakov homoclinic
bifurcations in a tritrophic fod chain model”. SIAM J. Appl. Math., no.
62, 2001, pp. 462-487.
[46] B. Cazelles, S. Bottani, L. Stone. “Unexpected coherence and
conservation”. Proc. Roy. Soc. Lond. No 268, 2001, pp. 2595-2602.
[47] I. Belykh, C., Piccardi, S. Rinaldi. “Synchrony in tritrophic food chain
metacommunities”. Journal of Biological Dynamics no.3 (5), 2009, pp.
497-514.
[48] Y. Kuramoto. “Self-entrainment of a population of coupled nonlinear
oscillators. In: Symposium on Mathematical Problems in Theoretical
Physics”. Lecture Notes in Physics, 1975, pp. 420-422.
[49] J.W. Duncan. “Small Worlds: The Dynamics of Networks between
Order and Randomness.” Princeton University Press, 1999, 262 pages.
[50] H. Hong, M.Y. Choi, B.J. Kim. “Synchronization on small world
networks.” Physical Review E, vol. 65 no. 2, 2002, pp. 026-139.
[51] J. Gomez-Gardenes, Y. Moreno, A. Arenas. “Paths to synchronization
on complex networks”. Phys Rev Lett, vol. 98 no. 3, 2007, pp. 034-101.
@article{"International Journal of Earth, Energy and Environmental Sciences:70864", author = "N. F. F. Ebecken and G. C. Pereira", title = "Ecological Networks: From Structural Analysis to Synchronization", abstract = "Ecological systems are exposed and are influenced by
various natural and anthropogenic disturbances. They produce
various effects and states seeking response symmetry to a state of
global phase coherence or stability and balance of their food webs.
This research project addresses the development of a computational
methodology for modeling plankton food webs. The use of
algorithms to establish connections, the generation of representative
fuzzy multigraphs and application of technical analysis of complex
networks provide a set of tools for defining, analyzing and evaluating
community structure of coastal aquatic ecosystems, beyond the
estimate of possible external impacts to the networks. Thus, this
study aims to develop computational systems and data models to
assess how these ecological networks are structurally and
functionally organized, to analyze the types and degree of
compartmentalization and synchronization between oscillatory and
interconnected elements network and the influence of disturbances on
the overall pattern of rhythmicity of the system.", keywords = "Ecological networks, plankton food webs, fuzzy
multigraphs, dynamic of networks.", volume = "9", number = "9", pages = "1078-5", }
