1
|
Massing JC, Gross T. Generalized Structural Kinetic Modeling: A Survey and Guide. Front Mol Biosci 2022; 9:825052. [PMID: 35573734 PMCID: PMC9098827 DOI: 10.3389/fmolb.2022.825052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
Many current challenges involve understanding the complex dynamical interplay between the constituents of systems. Typically, the number of such constituents is high, but only limited data sources on them are available. Conventional dynamical models of complex systems are rarely mathematically tractable and their numerical exploration suffers both from computational and data limitations. Here we review generalized modeling, an alternative approach for formulating dynamical models to gain insights into dynamics and bifurcations of uncertain systems. We argue that this approach deals elegantly with the uncertainties that exist in real world data and enables analytical insight or highly efficient numerical investigation. We provide a survey of recent successes of generalized modeling and a guide to the application of this modeling approach in future studies such as complex integrative ecological models.
Collapse
Affiliation(s)
- Jana C. Massing
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany
- Helmholtz Centre for Marine and Polar Research, Alfred-Wegener-Institute, Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky University, Oldenburg, Germany
- *Correspondence: Jana C. Massing,
| | - Thilo Gross
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany
- Helmholtz Centre for Marine and Polar Research, Alfred-Wegener-Institute, Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky University, Oldenburg, Germany
| |
Collapse
|
2
|
Medeiros ES, Feudel U, Zakharova A. Asymmetry-induced order in multilayer networks. Phys Rev E 2021; 104:024302. [PMID: 34525566 DOI: 10.1103/physreve.104.024302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 07/17/2021] [Indexed: 11/07/2022]
Abstract
Symmetries naturally occur in real-world networks and can significantly influence the observed dynamics. For instance, many synchronization patterns result from the underlying network symmetries, and high symmetries are known to increase the stability of synchronization. Yet here we find that general macroscopic features of network solutions such as regularity can be induced by breaking their symmetry of interactions. We demonstrate this effect in an ecological multilayer network where the topological asymmetries occur naturally. These asymmetries rescue the system from chaotic oscillations by establishing stable periodic orbits and equilibria. We call this phenomenon asymmetry-induced order and uncover its mechanism by analyzing both analytically and numerically the absence of dynamics on the system's synchronization manifold. Moreover, the bifurcation scenario describing the route from chaos to order is also disclosed. We demonstrate that this result also holds for generic node dynamics by analyzing coupled paradigmatic Rössler and Lorenz systems.
Collapse
Affiliation(s)
- Everton S Medeiros
- Institut für Theoretische Physik, Technische Universität Berlin, 10623 Berlin, Germany
| | - Ulrike Feudel
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University Oldenburg, 26111 Oldenburg, Germany
| | - Anna Zakharova
- Institut für Theoretische Physik, Technische Universität Berlin, 10623 Berlin, Germany
| |
Collapse
|
3
|
Stability aware spatial cut of metapopulations ecological networks. ECOLOGICAL COMPLEXITY 2021. [DOI: 10.1016/j.ecocom.2021.100948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
4
|
Gross T, Allhoff KT, Blasius B, Brose U, Drossel B, Fahimipour AK, Guill C, Yeakel JD, Zeng F. Modern models of trophic meta-communities. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190455. [PMID: 33131442 PMCID: PMC7662193 DOI: 10.1098/rstb.2019.0455] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2020] [Indexed: 02/06/2023] Open
Abstract
Dispersal and foodweb dynamics have long been studied in separate models. However, over the past decades, it has become abundantly clear that there are intricate interactions between local dynamics and spatial patterns. Trophic meta-communities, i.e. meta-foodwebs, are very complex systems that exhibit complex and often counterintuitive dynamics. Over the past decade, a broad range of modelling approaches have been used to study these systems. In this paper, we review these approaches and the insights that they have revealed. We focus particularly on recent papers that study trophic interactions in spatially extensive settings and highlight the common themes that emerged in different models. There is overwhelming evidence that dispersal (and particularly intermediate levels of dispersal) benefits the maintenance of biodiversity in several different ways. Moreover, some insights have been gained into the effect of different habitat topologies, but these results also show that the exact relationships are much more complex than previously thought, highlighting the need for further research in this area. This article is part of the theme issue 'Integrative research perspectives on marine conservation'.
Collapse
Affiliation(s)
- Thilo Gross
- University of California Davis, Department of Computer Science, 1 Shields Avenue, Davis, CA 95616, USA
- Alfred Wegener Institut. Helmholtz Zentrum für Polar und Meeresforschung, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Univeristät Oldenburg, Institut für Chemie und Biologie des Meeres, Carl-von-Ossietzky-Strasse 9-11, 26111 Oldenburg, Germany
- Helmholtz Institute for Functional Marine Bidiversity, Ammerländer Heerstrasse 231, Oldenburg, Germany
| | - Korinna T. Allhoff
- Universität Tübingen, Department of Biology, Auf der Morgenstelle 5, 72076 Tübingen, Germany
| | - Bernd Blasius
- Alfred Wegener Institut. Helmholtz Zentrum für Polar und Meeresforschung, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Univeristät Oldenburg, Institut für Chemie und Biologie des Meeres, Carl-von-Ossietzky-Strasse 9-11, 26111 Oldenburg, Germany
| | - Ulrich Brose
- German Centre for Integrative Biodiversity Research, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute for Biodiversity, Friedrich Schiller University Jena, Dornburger-Strasse 159, 07743 Jena, Germany
| | - Barbara Drossel
- TU Darmstadt, Institut für Festkörperphysik, Hochschulstrasse 6, 64289 Darmstadt, Germany
| | - Ashkaan K. Fahimipour
- National Oceanic and Atmospheric Administration, Southwest Fisheries Science Center, 110 McAllister Way, Santa Cruz, CA 95060, USA
| | - Christian Guill
- Universität Potsdam, Institut für Biochemie und Biologie, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Justin D. Yeakel
- University of California, Merced, School of Natural Sciences, 5200 North Lake Road, Merced, CA 95343, USA
| | - Fanqi Zeng
- University of Bristol, Department of Engineering Mathematics, Merchant Venturers Building, Bristol BS8 1UB, UK
| |
Collapse
|
5
|
Peterson JM, Earl JE, Fuhlendorf SD, Elmore RD, Haukos DA, Tanner AM, Carleton SA. Estimating response distances of lesser prairie‐chickens to anthropogenic features during long‐distance movements. Ecosphere 2020. [DOI: 10.1002/ecs2.3202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Jacob M. Peterson
- Department of Natural Resource Ecology and Management Oklahoma State University Stillwater Oklahoma74078USA
| | - Julia E. Earl
- School of Biological Sciences Louisiana Tech University Ruston Louisiana71272USA
| | - Samuel D. Fuhlendorf
- Department of Natural Resource Ecology and Management Oklahoma State University Stillwater Oklahoma74078USA
| | - R. Dwayne Elmore
- Department of Natural Resource Ecology and Management Oklahoma State University Stillwater Oklahoma74078USA
| | - David A. Haukos
- U.S. Geological Survey Kansas Cooperative Fish and Wildlife Research Unit Kansas State University Manhattan Kansas66506USA
| | - Ashley M. Tanner
- Department of Natural Resource Ecology and Management Oklahoma State University Stillwater Oklahoma74078USA
| | - Scott A. Carleton
- U.S. Geological Survey New Mexico Cooperative Fish and Wildlife Research Unit New Mexico State University Las Cruces New Mexico87103USA
| |
Collapse
|
6
|
|
7
|
D'Agata A. Dynamics of spatially dispersed population under ideal free distribution. J Theor Biol 2020; 486:110071. [PMID: 31704312 DOI: 10.1016/j.jtbi.2019.110071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/27/2019] [Accepted: 11/02/2019] [Indexed: 10/25/2022]
Affiliation(s)
- Antonio D'Agata
- Department of Political and Social Science, University of Catania, Via Vittorio Emanuele 8, 95131 Catania, Italy.
| |
Collapse
|
8
|
Postiglioni R, Bidegaray-Batista L, Simó M, Arnedo MA. Move to stay: genetic structure and demographic history of a wolf spider inhabiting coastal sand dunes of southern South America. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1689197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Rodrigo Postiglioni
- Departamento de Ecología y Biología Evolutiva, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, Montevideo, CP 11600, Uruguay
- Sección Entomología. Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, CP 11400, Uruguay
| | - Leticia Bidegaray-Batista
- Departamento de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, Montevideo, CP 11600, Uruguay
| | - Miguel Simó
- Departamento de Ecología y Biología Evolutiva, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, Montevideo, CP 11600, Uruguay
- Sección Entomología. Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, CP 11400, Uruguay
| | - Miquel A. Arnedo
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 643, Barcelona, CP 08028, Spain
| |
Collapse
|
9
|
Arino J, Bajeux N, Kirkland S. Number of Source Patches Required for Population Persistence in a Source-Sink Metapopulation with Explicit Movement. Bull Math Biol 2019; 81:1916-1942. [PMID: 30847643 DOI: 10.1007/s11538-019-00593-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/26/2019] [Indexed: 11/27/2022]
Abstract
We consider a simple metapopulation model with explicit movement of individuals between patches, in which each patch is either a source or a sink. We prove that similarly to the case of patch occupancy metapopulations with implicit movement, there exists a threshold number of source patches such that the population potentially becomes extinct below the threshold and established above the threshold. In the case where the matrix describing the movement of populations between spatial locations is irreducible, the result is global; further, assuming a complete mobility graph with equal movement rates, we use the principle of equitable partitions to obtain an explicit expression for the threshold. Brief numerical considerations follow.
Collapse
Affiliation(s)
- Julien Arino
- Department of Mathematics, University of Manitoba, Winnipeg, MB, Canada.
| | - Nicolas Bajeux
- Department of Mathematics, University of Manitoba, Winnipeg, MB, Canada
- Université Côte d'Azur, Inria BIOCORE Team, INRA, Sophia Antipolis, France
| | - Steve Kirkland
- Department of Mathematics, University of Manitoba, Winnipeg, MB, Canada
| |
Collapse
|
10
|
Brechtel A, Gramlich P, Ritterskamp D, Drossel B, Gross T. Master stability functions reveal diffusion-driven pattern formation in networks. Phys Rev E 2018; 97:032307. [PMID: 29776185 DOI: 10.1103/physreve.97.032307] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Indexed: 11/07/2022]
Abstract
We study diffusion-driven pattern formation in networks of networks, a class of multilayer systems, where different layers have the same topology, but different internal dynamics. Agents are assumed to disperse within a layer by undergoing random walks, while they can be created or destroyed by reactions between or within a layer. We show that the stability of homogeneous steady states can be analyzed with a master stability function approach that reveals a deep analogy between pattern formation in networks and pattern formation in continuous space. For illustration, we consider a generalized model of ecological meta-food webs. This fairly complex model describes the dispersal of many different species across a region consisting of a network of individual habitats while subject to realistic, nonlinear predator-prey interactions. In this example, the method reveals the intricate dependence of the dynamics on the spatial structure. The ability of the proposed approach to deal with this fairly complex system highlights it as a promising tool for ecology and other applications.
Collapse
Affiliation(s)
- Andreas Brechtel
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - Philipp Gramlich
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - Daniel Ritterskamp
- Department of Engineering Mathematics, Merchant Venturers School of Engineering, University of Bristol, Woodland Road, Bristol BS8 1UB, United Kingdom
| | - Barbara Drossel
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - Thilo Gross
- Department of Engineering Mathematics, Merchant Venturers School of Engineering, University of Bristol, Woodland Road, Bristol BS8 1UB, United Kingdom
| |
Collapse
|
11
|
Gilpin W, Feldman MW. A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape. PLoS Comput Biol 2017; 13:e1005644. [PMID: 28678792 PMCID: PMC5517034 DOI: 10.1371/journal.pcbi.1005644] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 07/19/2017] [Accepted: 06/23/2017] [Indexed: 11/19/2022] Open
Abstract
In many ecosystems, natural selection can occur quickly enough to influence the population dynamics and thus future selection. This suggests the importance of extending classical population dynamics models to include such eco-evolutionary processes. Here, we describe a predator-prey model in which the prey population growth depends on a prey density-dependent fitness landscape. We show that this two-species ecosystem is capable of exhibiting chaos even in the absence of external environmental variation or noise, and that the onset of chaotic dynamics is the result of the fitness landscape reversibly alternating between epochs of stabilizing and disruptive selection. We draw an analogy between the fitness function and the free energy in statistical mechanics, allowing us to use the physical theory of first-order phase transitions to understand the onset of rapid cycling in the chaotic predator-prey dynamics. We use quantitative techniques to study the relevance of our model to observational studies of complex ecosystems, finding that the evolution-driven chaotic dynamics confer community stability at the "edge of chaos" while creating a wide distribution of opportunities for speciation during epochs of disruptive selection-a potential observable signature of chaotic eco-evolutionary dynamics in experimental studies.
Collapse
Affiliation(s)
- William Gilpin
- Department of Applied Physics, Stanford University, Stanford, California, United States of America
| | - Marcus W. Feldman
- Department of Biology, Stanford University, Stanford, California, United States of America
| |
Collapse
|
12
|
Ristl K, Plitzko SJ, Drossel B. Complex response of a food-web module to symmetric and asymmetric migration between several patches. J Theor Biol 2014; 354:54-9. [PMID: 24641820 DOI: 10.1016/j.jtbi.2014.03.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 03/04/2014] [Accepted: 03/07/2014] [Indexed: 11/16/2022]
Abstract
We investigate the stability of a diamond food-web module on two patches coupled by migration in terms of robustness, which is the proportion of surviving species in the system. The parameters are chosen such that the dynamics on an isolated patch have a periodic attractor with all four species present as well as an attractor where the prey that is preferred by the top predator dies out. The migration rate and the migration bias between the two patches are varied, resulting in a surprisingly complex relation between migration rate and robustness. In particular, while the degree of synchronization usually increases with increasing migration rate, robustness can increase as well as decrease. We find that the main results also hold when the number of patches is larger. Different types of connectivity patterns between patches can lead to different extent of migration bias if the migration rate out of each patch is the same.
Collapse
Affiliation(s)
- Konstantin Ristl
- Institut für Festkörperphysik, TU Darmstadt, Hochschulstraße 6, D-64289 Darmstadt, Germany.
| | - Sebastian J Plitzko
- Institut für Festkörperphysik, TU Darmstadt, Hochschulstraße 6, D-64289 Darmstadt, Germany.
| | - Barbara Drossel
- Institut für Festkörperphysik, TU Darmstadt, Hochschulstraße 6, D-64289 Darmstadt, Germany.
| |
Collapse
|