Individual-based models in ecology after four decades

Jiang, Jiang; Grimm, Volker

doi:10.12703/p6-39

Cited by 250 publications

(203 citation statements)

References 62 publications

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“…Depending on the experimental platform used, especially if diffusion plays an important role, combining FBA and individual based modeling (IBM) would encompass the spatial information necessary to accurately simulate such processes (DeAngelis and Gross, 1992; Kreft et al, 1998, 2001; Grimm and Railsback, 2005; Lardon et al, 2011; DeAngelis and Grimm, 2014). …”

Section: Discussion and Outlookmentioning

confidence: 99%

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia

Said

2017

Front. Microbiol.

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The metabolic diversity present in microbial communities enables cooperation toward accomplishing more complex tasks than possible by a single organism. Members of a consortium communicate by exchanging metabolites or signals that allow them to coordinate their activity through division of labor. In contrast with monocultures, evidence suggests that microbial consortia self-organize to form spatial patterns, such as observed in biofilms or in soil aggregates, that enable them to respond to gradient, to improve resource interception and to exchange metabolites more effectively. Current biotechnological applications of microorganisms remain rudimentary, often relying on genetically engineered monocultures (e.g., pharmaceuticals) or mixed-cultures of partially known composition (e.g., wastewater treatment), yet the vast potential of “microbial ecological power” observed in most natural environments, remains largely underused. In line with the Unified Microbiome Initiative (UMI) which aims to “discover and advance tools to understand and harness the capabilities of Earth's microbial ecosystems,” we propose in this concept paper to capitalize on ecological insights into the spatial and modular design of interlinked microbial consortia that would overcome limitations of natural systems and attempt to optimize the functionality of the members and the performance of the engineered consortium. The topology of the spatial connections linking the various members and the regulated fluxes of media between those modules, while representing a major engineering challenge, would allow the microbial species to interact. The modularity of such spatially linked microbial consortia (SLMC) could facilitate the design of scalable bioprocesses that can be incorporated as parts of a larger biochemical network. By reducing the need for a compatible growth environment for all species simultaneously, SLMC will dramatically expand the range of possible combinations of microorganisms and their potential applications. We briefly review existing tools to engineer such assemblies and optimize potential benefits resulting from the collective activity of their members. Prospective microbial consortia and proposed spatial configurations will be illustrated and preliminary calculations highlighting the advantages of SLMC over co-cultures will be presented, followed by a discussion of challenges and opportunities for moving forward with some designs.

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Section: Discussion and Outlookmentioning

confidence: 99%

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia

Said

2017

Front. Microbiol.

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“…Implementing models that take into account the growth trajectory of individuals in a population has provided a better understanding of the source variation in the growth parameters, as the pattern that emerges at the population level is derived from processes generated at the individual level (Alós et al, 2010;Vincenzi et al, 2014;DeAngelis, Grimm, 2014). Furthermore, the use of an approach at the individual level is more appropriate since individual variation is controlled by considering the growth trajectory of each specimen.…”

Section: Discussionmentioning

confidence: 99%

“…However, these factors do not act alone, as there is a complex interaction between them (Dieterman et al, 2012). Growth is simultaneously due to individual response to variability (the individual genotype), and behavioural differences in reproduction, habitat selection and foraging-based migration between sexes (DeAngelis, Grimm, 2014). Additionally, the environment in which an individual occurs can generate variations in growth parameters due to the nature and extent of available resources (Siangas et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Individual, spatial and inter-sex variation in somatic growth: a study of Piaractus mesopotamicus (Characiformes: Serrasalmidae), a long-distance freshwater Neotropical migratory fish

et al. 2017

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Growth is a fundamental biological process, driven by multiple endogenous (intra-individual) and exogenous (environmental) factors that maintain individual fitness and population stability. The current study aims to assess whether individual, spatial (headwaters and floodplains) and inter-sex variation occurs in the growth of Piaractus mesopotamicus in the Cuiabá River basin. Samples were collected monthly from July 2006 to July 2007, at two areas in the Cuiabá River basin (headwaters and floodplain). Three growth models (individuals; individuals and sex factors; individuals and areas factors) were developed and compared the fish growth parameters using Akaike information criterion (AIC). The best fit to the length-at-age data was obtained by a model that considered individual variation and sex. The theoretical maximum average length (L ∞ ) was 64.99 cm for females, and 63.23 cm for males. Females showed a growth rate (k) of 0.230 yr -1 and males of 0.196 yr -1 . Thus, could be concluded that individual variability and sex were the main sources of variation in P. mesopotamicus somatic growth parameters.Keywords: Age, Growth models, Inter-sex variation, Otoliths, Von Bertalanffy O crescimento é um processo biológico fundamental, impulsionado por múltiplos fatores endógenos (intra-individual) e exógenos (ambientais) que mantém o fitness individual e a estabilidade populacional. Este trabalho tem como objetivo avaliar se ocorre variação individual, espacial (região de cabeceira e planície de inundação) e entre sexo no crescimento de Piaractus mesopotamicus na bacia do rio Cuiabá. Amostragens foram realizadas mensalmente entre julho de 2006 a julho de 2007, em duas áreas da bacia do rio Cuiabá (região de cabeceira e planície de inundação). Três modelos de crescimento (indivíduos, indivíduos e sexo como fator, indivíduos e área como fator) foram elaborados e comparados os parâmetros de crescimentos dos peixes com base no critério de Informação de Akaike (AIC). O melhor ajuste aos dados de comprimento na idade data foi obtido pelo modelo que considerou a variação individual e o sexo. O comprimento médio máximo teórico (L ∞ ) das fêmeas foi 64,99 cm e para os machos 63,23 cm. O coeficiente de crescimento (k) médio foi de 0,230 yr -1 e 0,196 yr -1 , respectivamente para fêmeas e machos. Portanto, pode-se concluir que variabilidade individual e sexo foram as principais origem de variação dos parâmetros de crescimento somático de P. mesopotamicus. Palavras-chave:Dimorfismo sexual, Idade, Modelos de crescimento, Otólitos,

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“…In the 1970s a different tradition, based on Individual Based Modelling (IBM; DeAngelis and Grimm, 2014;Huston et al, 1988) arose. This paradigm merged perspectives from artificial life (Langton, 1986;von Neumann, 1966) and artificial intelligence (Newell and Simon, 1956) with another major tradition in mathematical ecology, community ecology.…”

Section: Behaviour In the Individual-based Paradigmmentioning

confidence: 99%

From sensing to emergent adaptations: Modelling the proximate architecture for decision-making

Eliassen

Andersen

Jørgensen

et al. 2016

Ecological Modelling

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a b s t r a c tDuring the past 50 years, evolutionary theory for animal behaviour has branched into different methodological frameworks focussing on age-, state-, density-, and frequency-dependent processes. These approaches have led to valuable insights in optimal responses, state dependent choices, and behavioural strategies in social contexts. We argue that time is ripe for an integration of these methodologies based on a rigorous implementation of proximate mechanisms. We describe such a modelling framework that is based on the architectural structures of sensing and information processing, physiological and neurological states, and behavioural control in animals. An individual-based model of this decision architecture is embedded in a genetic algorithm that finds evolutionary adaptations. This proximate architecture framework can be utilized for modelling behavioural challenges in complex environments, for example how animals make behavioural decisions based on multiple sources of information, or adapt to changing environments. The framework represents the evolution of the proximate mechanisms that underlie animal decision making, and it aligns with individual-based ecology by emphasizing the role of local information, perception, and individual behaviour.

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Individual-based models in ecology after four decades

Cited by 250 publications

References 62 publications

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia

Individual, spatial and inter-sex variation in somatic growth: a study of Piaractus mesopotamicus (Characiformes: Serrasalmidae), a long-distance freshwater Neotropical migratory fish

From sensing to emergent adaptations: Modelling the proximate architecture for decision-making

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