Biodiv Sci ›› 2020, Vol. 28 ›› Issue (11): 1431-1443. DOI: 10.17520/biods.2020225
• Reviews • Previous Articles
Received:
2020-06-01
Accepted:
2020-07-16
Online:
2020-11-20
Published:
2020-07-30
Contact:
Quanxing Liu
Zhenpeng Ge, Quanxing Liu. More than the sum of its parts: Self-organized patterns and emergent properties of ecosystems[J]. Biodiv Sci, 2020, 28(11): 1431-1443.
Fig. 1 The regular patterns of mussel and “cell”, and the scale-dependent feedback and density-dependent feedback. (a) Mussel bed in the intertidal zone of Wadden Sea, the Netherlands, the image come from the corresponding author of this paper; (b) The recurrence of a cell based on liquid light technology, the image is modified from https://liquidlightlab.com/home.html Copyright Oil art: Steve Pavlovsky/Liquid Light Lab.; (c) Schematic representation of scale-dependent feedback; (d) Schematic representation of density-dependent movement, (c) and (d) are modified from Liu et al (2016).
Fig. 2 Phase diagram and numerical simulations of the equations (7) and (8). In the upper figure, the red solid line is the boundary between homogeneous zone and binodal zone, and the solid blue line is the boundary between binodal zone and spinodal decomposition zone. ‘1’ to ‘5’ in the upper figure correspond to the below five figures which are the numerical simulation results, ‘1’ and ‘5’ are located in homogeneous zone where the system doesn’t have pattern; ‘2’ and ‘4’ are located in binodal zone where the system has spot pattern, ‘3’ is located in the spinodal decomposition zone where the system has labyrinth pattern. The numerical simulation adopts periodic boundary condition, and the corresponding matlab code can be downloaded at https://github.com/liufengyinxue/Liu_Mussel_ PNAS.
Fig. 4 The predominant research ideas of self-organization ecology in the future (The English version see appendix 1). After years of development, Turing's principle was found to be unable to fully explain the multi-scale patterns of various ecosystems, as well as the phase separation principle. Therefore, a new theoretical framework needs to be developed in the future to understand the multi-scale patterns of ecosystems. Transient pattern will be paid more attention in the future due to its unique ecological functioning. The response of organisms to environmental change leads to changes in biological behavior, and how this response emerges to the ecosystem level is critical to understanding the self-organization of ecosystems across scales.
[1] | Alberti S (2017) Phase separation in biology. Current Biology, 27, R1097-R1102. |
[2] |
Alberti S, Dormann D (2019) Liquid-liquid phase separation in disease. Annual Review of Genetics, 53, 171-194.
URL PMID |
[3] |
Alberti S, Gladfelter A, Mittag T (2019) Considerations and challenges in studying liquid-liquid phase separation and biomolecular condensates. Cell, 176, 419-434.
DOI URL PMID |
[4] |
Anderson PW (1972) More is different. Science, 177, 393-396.
DOI URL PMID |
[5] |
Battle C, Broedersz CP, Fakhri N, Geyer VF, Howard J, Schmidt CF, MacKintosh FC (2016) Broken detailed balance at mesoscopic scales in active biological systems. Science, 352, 604-607.
DOI URL PMID |
[6] |
Ben-Hur E, Kadmon R (2020) Heterogeneity-diversity relationships in sessile organisms: A unified framework. Ecology Letters, 23, 193-207.
DOI URL PMID |
[7] |
Bergmann F, Rapp L, Zimmermann W (2018) Active phase separation: A universal approach. Physical Review E, 98, 020603.
DOI URL PMID |
[8] | Bertalanffy L (1969) General System Theory: Foundations, Development, Applications. Georges Braziller, Inc., New York. |
[9] |
Boeynaems S, Alberti S, Fawzi NL, Mittag T, Polymenidou M, Rousseau F, Schymkowitz J, Shorter J, Wolozin B, van den Bosch L, Tompa P, Fuxreiter M (2018) Protein phase separation: A new phase in cell biology. Trends in Cell Biology, 28, 420-435.
URL PMID |
[10] |
Boija A, Klein IA, Sabari BR, Dall’Agnese A, Coffey EL, Zamudio AV, Li CH, Shrinivas K, Manteiga JC, Hannett NM, Abraham BJ, Afeyan LK, Guo YE, Rimel JK, Fant CB, Schuijers J, Lee TI, Taatjes DJ, Young RA (2018) Transcription factors activate genes through the phase-separation capacity of their activation domains. Cell, 175, 1842-1855.
DOI URL PMID |
[11] |
Brangwynne CP, Eckmann CR, Courson DS, Rybarska A, Hoege C, Gharakhani J, Julicher F, Hyman AA (2009) Germline P granules are liquid droplets that localize by controlled dissolution/condensation. Science, 324, 1729-1732.
URL PMID |
[12] | Burke J, Knobloch E (2006) Localized states in the generalized Swift-Hohenberg equation. Physical Review E, 73, 056211. |
[13] | Cahn JW, Hilliard JE (1958) Free energy of a nonuniform system. I. Interfacial free energy. The Journal of Chemical Physics, 28, 258-267. |
[14] | Camazine S (2001) Self-organization in Biological Systems. Princeton University Press, Princeton. |
[15] | Cates ME, Marenduzzo D, Pagonabarraga I, Tailleur J (2010) Arrested phase separation in reproducing bacteria creates a generic route to pattern formation. Proceedings of the National Academy of Sciences, USA, 107, 11715-11720. |
[16] | Cates ME, Tailleur J (2015) Motility-induced phase separation. Annual Review of Condensed Matter Physics, 6, 219-244. |
[17] | Cohen DS, Murray JD (1981) A generalized diffusion model for growth and dispersal in a population. Journal of Mathematical Biology, 12, 237-249. |
[18] | Coveney S (2015) Fundamentals of Phase Separation in Polymer Blend Thin Films. Springer International Publishing, Cham. |
[19] | Cuddington K (2007) Ecosystem Engineers: Plants to Protists. Academic Press, Boston. |
[20] | D’Odorico P, Laio F, Ridolfi L (2006) Patterns as indicators of productivity enhancement by facilitation and competition in dryland vegetation. Journal of Geophysical Research: Biogeosciences, 111, G03010. |
[21] |
de Jager M, Weissing FJ, Herman PMJ, Nolet BA, van de Koppel J (2011) Levy walks evolve through interaction between movement and environmental complexity. Science, 332, 1551-1553.
DOI URL PMID |
[22] | de Paoli H, van der Heide T, van den Berg A, Silliman BR, Herman PMJ, van de Koppel J (2017) Behavioral self-organization underlies the resilience of a coastal ecosystem. Proceedings of the National Academy of Sciences, USA, 114, 8035-8040. |
[23] |
Engelhardt KAM, Ritchie ME (2001) Effects of macrophyte species richness on wetland ecosystem functioning and services. Nature, 411, 687-689.
DOI URL PMID |
[24] |
Franklin O, Harrison SP, Dewar R, Farrior CE, Brännström Å, Dieckmann U, Pietsch S, Falster D, Cramer W, Loreau M, Wang H, Mäkelä A, Rebel KT, Meron E, Schymanski SJ, Rovenskaya E, Stocker BD, Zaehle S, Manzoni S, van Oijen M, Wright IJ, Ciais P, van Bodegom PM, Peñuelas J, Hofhansl F, Terrer C, Soudzilovskaia NA, Midgley G, Prentice IC (2020) Organizing principles for vegetation dynamics. Nature Plants, 6, 444-453.
URL PMID |
[25] |
Gilad E, von Hardenberg J, Provenzale A, Shachak M, Meron E (2004) Ecosystem engineers: From pattern formation to habitat creation. Physical Review Letters, 93, 098105.
URL PMID |
[26] | Guttal V, Jayaprakash C (2007) Self-organization and productivity in semi-arid ecosystems: Implications of seasonality in rainfall. Journal of Theoretical Biology, 248, 490-500. |
[27] | Haken H (1988) Information and Self-organization: A Macroscopic Approach to Complex Systems. Springer-Verlag, New York. |
[28] | Halatek J, Frey E (2018) Rethinking pattern formation in reaction-diffusion systems. Nature Physics, 14, 507-514. |
[29] | Hastings A, Abbott KC, Cuddington K, Francis T, Gellner G, Lai YC, Morozov A, Petrovskii S, Scranton K, Zeeman ML (2018) Transient phenomena in ecology. Science, 361, eaat6412. |
[30] | Hiemstra CA, Liston GE, Reiners WA (2006) Observing, modelling, and validating snow redistribution by wind in a Wyoming upper treeline landscape. Ecological Modelling, 197, 35-51. |
[31] | Juergens N (2015) Exploring common ground for different hypotheses on Namib fairy circles. Ecography, 38, 12-14. |
[32] |
Kerr B, Riley MA, Feldman MW, Bohannan BJM (2002) Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors. Nature, 418, 171-174.
DOI URL PMID |
[33] |
Klausmeier CA (1999) Regular and irregular patterns in semiarid vegetation. Science, 284, 1826-1828.
DOI URL PMID |
[34] |
Kondo S, Miura T (2010) Reaction-diffusion model as a framework for understanding biological pattern formation. Science, 329, 1616-1620.
DOI URL PMID |
[35] | Levin SA (1992) The problem of pattern and scale in ecology. Ecology, 73, 1943-1967. |
[36] | Levin SA (2005) Self-organization and the emergence of complexity in ecological systems. BioScience, 55, 1075-1079. |
[37] | Liu QX, Doelman A, Rottschafer V, de Jager M, Herman PMJ, Rietkerk M, van de Koppel J (2013) Phase separation explains a new class of self-organized spatial patterns in ecological systems. Proceedings of the National Academy of Sciences, USA, 110, 11905-11910. |
[38] | Liu QX, Herman PMJ, Mooij WM, Huisman J, Scheffer M, Olff H, van de Koppel J (2014) Pattern formation at multiple spatial scales drives the resilience of mussel bed ecosystems. Nature Communications, 5, 6234. |
[39] |
Liu QX, Rietkerk M, Herman PMJ, Piersma T, Fryxell JM, van de Koppel J (2016) Phase separation driven by density-dependent movement: A novel mechanism for ecological patterns. Physics of Life Reviews, 19, 107-121.
DOI URL PMID |
[40] | Loreau M, Mouquet N, Gonzalez A (2003) Biodiversity as spatial insurance in heterogeneous landscapes. Proceedings of the National Academy of Sciences, USA, 100, 12765-12770. |
[41] | Meinhardt H (2003) The Algorithmic Beauty of Sea Shells. Springer, Berlin. |
[42] | Meron E (2015) Nonlinear Physics of Ecosystems. CRC Press, Taylor & Francis Group, Boca Raton. |
[43] |
Meron E (2016) Pattern formation—A missing link in the study of ecosystem response to environmental changes. Mathematical Biosciences, 271, 1-18.
DOI URL PMID |
[44] | Mistr S, Bercovici D (2003) A theoretical model of pattern formation in coral reefs. Ecosystems, 6, 61-74. |
[45] | Nathan J, Osem Y, Shachak M, Meron E (2016) Linking functional diversity to resource availability and disturbance: A mechanistic approach for water-limited plant communities. Journal of Ecology, 104, 419-429. |
[46] |
Nathan J, von Hardenberg J, Meron E (2013) Spatial instabilities untie the exclusion-principle constraint on species coexistence. Journal of Theoretical Biology, 335, 198-204.
DOI URL PMID |
[47] | Nicolis G, Prigogine I (1977) Self-organization in Nonequilibrium Systems: From Dissipative Structures to Order Through Fluctuations. Wiley, New York. |
[48] | Ouyang Q, Swinney HL (1991) Transition from a uniform state to hexagonal and striped Turing patterns. Nature, 352, 610-612. |
[49] | Paine RT (1966) Food web complexity and species diversity. The American Naturalist, 100, 65-75. |
[50] | Pereira ML, Sadras VO, Batista W, Casal JJ, Hall AJ (2017) Light-mediated self-organization of sunflower stands increases oil yield in the field. Proceedings of the National Academy of Sciences, USA, 114, 7975-7980. |
[51] | Prigogine I (1967) On symmetry-breaking instabilities in dissipative systems. Journal of Chemical Physics, 46, 3542. |
[52] |
Pringle RM, Doak DF, Brody AK, Jocque R, Palmer TM (2010) Spatial pattern enhances ecosystem functioning in an African savanna. PLoS Biology, 8, e1000377.
DOI URL PMID |
[53] | Rietkerk M, Dekker SC, de Ruiter PC, van de Koppel J (2004) Self-organized patchiness and catastrophic shifts in ecosystems. Science, 305, 1926-1929. |
[54] |
Rietkerk M, van de Koppel J (2008) Regular pattern formation in real ecosystems. Trends in Ecology & Evolution, 23, 169-175.
DOI URL PMID |
[55] |
Sabari BR, Dall’Agnese A, Boija A, Klein IA, Coffey EL, Shrinivas K, Abraham BJ, Hannett NM, Zamudio AV, Manteiga JC, Li CH, Guo YE, Day DS, Schuijers J, Vasile E, Malik S, Hnisz D, Lee TI, Cisse II, Roeder RG, Sharp PA, Chakraborty AK, Young RA (2018) Coactivator condensation at super-enhancers links phase separation and gene control. Science, 361, eaar3958.
URL PMID |
[56] | Scheffer M, van Nes EH (2006) Self-organized similarity, the evolutionary emergence of groups of similar species. Proceedings of the National Academy of Sciences, USA, 103, 6230-6235. |
[57] | Schnitzer MJ (1993) Theory of continuum random walks and application to chemotaxis. Physical Review E, 48, 2553-2568. |
[58] | Schrödinger E (1962) What is Life: The Physical Aspect of the Living Cell. University Press Macmillan Co., New York. |
[59] |
Shin Y, Brangwynne CP (2017) Liquid phase condensation in cell physiology and disease. Science, 357, eaaf4382.
DOI URL PMID |
[60] | Speck T, Bialké J, Menzel AM, Löwen H (2014) Effective Cahn-Hilliard equation for the phase separation of active brownian particles. Physical Review Letters, 112, 218304. |
[61] | Stavi I, Rachmilevitch S, Hjazin A, Yizhaq H (2018) Geodiversity decreases shrub mortality and increases ecosystem tolerance to droughts and climate change. Earth Surface Processes & Landforms, 43, 2808-2817. |
[62] | Tarnita CE, Bonachela JA, Sheffer E, Guyton JA, Coverdale TC, Long RA, Pringle RM (2017) A theoretical foundation for multi-scale regular vegetation patterns. Nature, 541, 398-401. |
[63] | Tejedor A, Longjas A, Edmonds DA, Zaliapin I, Georgiou TT, Rinaldo A, Foufoula-Georgiou E (2017) Entropy and optimality in river deltas. Proceedings of the National Academy of Sciences, USA, 114, 11651-11656. |
[64] | Tsimring L, Levine H, Aranson I, Ben-Jacob E, Cohen I, Shochet O, Reynolds WN (1995) Aggregation patterns in stressed bacteria. Physical Review Letters, 75, 1859-1862. |
[65] | Turing A (1952) The chemical basis of morphogenesis. Philosophical Transactions of the Royal Society of London Series B: Biological Sciences, 237, 37-72. |
[66] | van de Koppel J, Gascoigne JC, Theraulaz G, Rietkerk M, Mooij WM, Herman PMJ (2008) Experimental evidence for spatial self-organization and its emergent effects in mussel bed ecosystems. Science, 322, 739-742. |
[67] |
van de Koppel J, Rietkerk M, Dankers N, Herman PMJ (2005) Scale-dependent feedback and regular spatial patterns in young mussel beds. The American Naturalist, 165, E66-E77.
DOI URL PMID |
[68] |
van de Koppel J, Crain CM (2006) Scale‐dependent inhibition drives regular tussock spacing in a freshwater marsh. The American Naturalist, 168, E136-E147.
DOI URL PMID |
[69] |
van der Heide T, Bouma TJ, van Nes EH, van de Koppel J, Scheffer M, Roelofs JGM, van Katwijk MM, Smolders AJP (2010) Spatial self-organized patterning in seagrasses along a depth gradient of an intertidal ecosystem. Ecology, 91, 362-369.
DOI URL PMID |
[70] |
Vicsek T, Czirók A, Ben-Jacob E, Cohen II, Shochet O (1995) Novel type of phase transition in a system of self-driven particles. Physical Review Letters, 75, 1226-1229.
DOI URL PMID |
[71] |
von Hardenberg J, Meron E, Shachak M, Zarmi Y (2001) Diversity of vegetation patterns and desertification. Physical Review Letters, 87, 198101.
DOI URL PMID |
[72] |
Weerman EJ, van de Koppel J, Eppinga MB, Montserrat F, Liu QX, Herman PMJ (2010) Spatial self-organization on intertidal mudflats through biophysical stress divergence. The American Naturalist, 176, E15-E32.
DOI URL PMID |
[73] | Werdelin L, Olsson L (1997) How the leopard got its spots: A phylogenetic view of the evolution of felid coat patterns. Biological Journal of the Linnean Society, 62, 383-400. |
[74] | Yizhaq H, Gilad E, Meron E (2005) Banded vegetation: Biological productivity and resilience. Physica A: -Statistical Mechanics and Its Applications, 356, 139-144. |
[75] | Zelnik YR, Meron E, Bel G (2015) Gradual regime shifts in fairy circles. Proceedings of the National Academy of Sciences, USA, 112, 12327-12331. |
[76] |
Zhabotinskii AM (1964) Periodic course of the oxidation of malonic acid in a solution (studies on the kenetics of beolusov’s reaction). Biofizika, 9, 306-311.
URL PMID |
[77] | Zhao L, Zhang K, Koen S, Li XZ, Liu QX, van de Koppel J (2021) Fairy circles reveal the resilience of self-organized salt marshes. Science Advances, 7, abe1100. |
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