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      Individual-based models in ecology after four decades

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          Abstract

          Individual-based models simulate populations and communities by following individuals and their properties. They have been used in ecology for more than four decades, with their use and ubiquity in ecology growing rapidly in the last two decades. Individual-based models have been used for many applied or “pragmatic” issues, such as informing the protection and management of particular populations in specific locations, but their use in addressing theoretical questions has also grown rapidly, recently helping us to understand how the sets of traits of individual organisms influence the assembly of communities and food webs. Individual-based models will play an increasingly important role in questions posed by complex ecological systems.

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          Rebuilding community ecology from functional traits.

          There is considerable debate about whether community ecology will ever produce general principles. We suggest here that this can be achieved but that community ecology has lost its way by focusing on pairwise species interactions independent of the environment. We assert that community ecology should return to an emphasis on four themes that are tied together by a two-step process: how the fundamental niche is governed by functional traits within the context of abiotic environmental gradients; and how the interaction between traits and fundamental niches maps onto the realized niche in the context of a biotic interaction milieu. We suggest this approach can create a more quantitative and predictive science that can more readily address issues of global change.
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            Modelling disease outbreaks in realistic urban social networks.

            Most mathematical models for the spread of disease use differential equations based on uniform mixing assumptions or ad hoc models for the contact process. Here we explore the use of dynamic bipartite graphs to model the physical contact patterns that result from movements of individuals between specific locations. The graphs are generated by large-scale individual-based urban traffic simulations built on actual census, land-use and population-mobility data. We find that the contact network among people is a strongly connected small-world-like graph with a well-defined scale for the degree distribution. However, the locations graph is scale-free, which allows highly efficient outbreak detection by placing sensors in the hubs of the locations network. Within this large-scale simulation framework, we then analyse the relative merits of several proposed mitigation strategies for smallpox spread. Our results suggest that outbreaks can be contained by a strategy of targeted vaccination combined with early detection without resorting to mass vaccination of a population.
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              Nothing in Biology Makes Sense except in the Light of Evolution

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                Author and article information

                Contributors
                Journal
                F1000Prime Rep
                F1000Prime Rep
                F1000Prime Reports
                Faculty of 1000 Ltd
                2051-7599
                02 June 2014
                2014
                : 6
                : 39
                Affiliations
                [1 ]Department of Biology, University of Miami Box 249118, Coral Gables, Florida 33143USA
                [2 ]Department of Ecological Modelling, Helmholtz Centre for Environmental Research–UFZ, Permoserstr. 15, 04318 LeipzigGermany
                [3 ]Institute for Biochemistry and Biology, University of Potsdam, Maulbeerallee 214469 PotsdamGermany
                [4 ]German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Deutscher Platz 5e, 04103 LeipzigGermany
                Article
                39
                10.12703/P6-39
                4047944
                24991416
                faa62392-314e-4095-9c8b-2a3e4bbaaead
                © 2014 Faculty of 1000 Ltd

                All F1000Prime Reports articles are distributed under the terms of the Creative Commons Attribution-Non Commercial License, which permits non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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