This article possibly contains original research .(July 2012) |
EcoSim is an individual-based predator-prey ecosystem simulation in which agents can evolve. It has been designed to investigate several broad ecological questions, as well as long-term evolutionary patterns and processes such as speciation and macroevolution. [1] [2] [3] [4] EcoSim has been designed by Robin Gras at the University of Windsor in 2009 and it is still currently [ when? ] used for research in his Bioinformatics and Ecosystem Simulation Lab.
The agents have a behavior model which allows the evolutionary process to modify the behaviors of the predators and prey. Furthermore, there is a speciation mechanism which allows to study global patterns as well as species-specific patterns. In EcoSim, an individual's genomic data codes for its behavioral model and is represented by a fuzzy cognitive map (FCM). The FCM contains sensory concepts such as foodClose or predatorClose, internal states such as fear or hunger, and motor concepts such as escape or reproduce. The FCM is represented as an array of floating-point values which represent the extent to which one concept influences another. For example, it would be expected that the sensory concept predatorClose would positively affect the internal concept fear, which would then positively affect the escape motor concept. These relationships among concepts evolve over time, sometimes giving a new meaning to a concept. Furthermore, the FCM is heritable, meaning that a new agent is given an FCM which is a combination of that of its parents with possible mutations.
EcoSim subscribes to the “genotypic cluster” definition of a species. [5] Speciation has been implemented using a 2-means clustering algorithm technique designed to allow the splitting of an existing species into two species, by clustering the individuals that initially belonged to the first species into one of the new two species, each one of them containing the agents that are mutually the most similar. Since EcoSim has the capacity to allow speciation events to occur, it is possible to track speciation events throughout a run of the simulation and construct the actual phylogenetic tree. [6]
Each agent also possesses several physical characteristics such as: maximum and current ages, minimum age for mating, maximum and current speeds, vision distance, maximum and current levels of energy, and the amount of energy transmitted to the offspring. Energy is provided to individuals by the resources (grass or meat) they find in their environment. An agent consumes some energy each time it performs an action and proportionally to the complexity (number of edges) of its FCM. If an individual uses all its energy, it dies.
A typical run lasts several tens of thousands of time steps. Each time step involves the time needed for each agent to perceive its environment, use its behavioral model to make a decision, perform its action as well as the time to update the species membership, including speciation events and all the world parameters. In a typical run, more than one billion of agents can be born and several thousands of species can be generated, which allows new behaviors to emerge and agents to adapt to a constantly changing environment. In addition, a food chain consisting of three levels, primary producers, predators and preys, has been implemented allowing complex interactions between agents and co-evolution to occur. All events, the mental state and action of every agent, are saved for every time step of every run. This allows a deep statistical analysis of the whole system using several dedicated tools that we have conceived to extract, measure and correlate any possible facts that could be useful to understand the underlying and emerging properties of the system. [7]
Several studies have already been done using EcoSim. For example, Devaurs and Gras [8] have analyzed the species abundance patterns observed in the communities generated by EcoSim, based on Fisher's log series. This study shows that the communities of species generated by the simulation follow the same lognormal law as natural communities and that EcoSim can help to evaluate the overall level of diversity of a given community. In other studies, the chaotic behavior of the system with multi-fractal properties has been proven in [9] as it also has been observed for real ecosystems. Mashayekhi and Gras [10] investigated the effect of spatial distribution and spatiotemporal information on speciation. In more recent research, Golestani et al. [11] investigated how small, randomly distributed physical obstacles influence the distribution of populations and species, the level of population connectivity (e.g., gene flow), as well as the mode and tempo of speciation.
Theoretical ecology is the scientific discipline devoted to the study of ecological systems using theoretical methods such as simple conceptual models, mathematical models, computational simulations, and advanced data analysis. Effective models improve understanding of the natural world by revealing how the dynamics of species populations are often based on fundamental biological conditions and processes. Further, the field aims to unify a diverse range of empirical observations by assuming that common, mechanistic processes generate observable phenomena across species and ecological environments. Based on biologically realistic assumptions, theoretical ecologists are able to uncover novel, non-intuitive insights about natural processes. Theoretical results are often verified by empirical and observational studies, revealing the power of theoretical methods in both predicting and understanding the noisy, diverse biological world.
A herbivore is an animal anatomically and physiologically adapted to eating plant material, for example foliage or marine algae, for the main component of its diet. As a result of their plant diet, herbivorous animals typically have mouthparts adapted to rasping or grinding. Horses and other herbivores have wide flat teeth that are adapted to grinding grass, tree bark, and other tough plant material.
Predation is a biological interaction where one organism, the predator, kills and eats another organism, its prey. It is one of a family of common feeding behaviours that includes parasitism and micropredation and parasitoidism. It is distinct from scavenging on dead prey, though many predators also scavenge; it overlaps with herbivory, as seed predators and destructive frugivores are predators.
A food web is the natural interconnection of food chains and a graphical representation of what-eats-what in an ecological community. Ecologists can broadly define all life forms as either autotrophs or heterotrophs, based on their trophic levels, the position that they occupy in the food web. To maintain their bodies, grow, develop, and to reproduce, autotrophs produce organic matter from inorganic substances, including both minerals and gases such as carbon dioxide. These chemical reactions require energy, which mainly comes from the Sun and largely by photosynthesis, although a very small amount comes from bioelectrogenesis in wetlands, and mineral electron donors in hydrothermal vents and hot springs. These trophic levels are not binary, but form a gradient that includes complete autotrophs, which obtain their sole source of carbon from the atmosphere, mixotrophs, which are autotrophic organisms that partially obtain organic matter from sources other than the atmosphere, and complete heterotrophs that must feed to obtain organic matter.
Swarm behaviour, or swarming, is a collective behaviour exhibited by entities, particularly animals, of similar size which aggregate together, perhaps milling about the same spot or perhaps moving en masse or migrating in some direction. It is a highly interdisciplinary topic.
A keystone species is a species that has a disproportionately large effect on its natural environment relative to its abundance, a concept introduced in 1969 by the zoologist Robert T. Paine. Keystone species play a critical role in maintaining the structure of an ecological community, affecting many other organisms in an ecosystem and helping to determine the types and numbers of various other species in the community. Without keystone species, the ecosystem would be dramatically different or cease to exist altogether. Some keystone species, such as the wolf, are also apex predators.
Foraging is searching for wild food resources. It affects an animal's fitness because it plays an important role in an animal's ability to survive and reproduce. Foraging theory is a branch of behavioral ecology that studies the foraging behavior of animals in response to the environment where the animal lives.
The three-spined stickleback is a fish native to most inland and coastal waters north of 30°N. It has long been a subject of scientific study for many reasons. It shows great morphological variation throughout its range, ideal for questions about evolution and population genetics. Many populations are anadromous and very tolerant of changes in salinity, a subject of interest to physiologists. It displays elaborate breeding behavior and it can be social making it a popular subject of inquiry in fish ethology and behavioral ecology. Its antipredator adaptations, host-parasite interactions, sensory physiology, reproductive physiology, and endocrinology have also been much studied. Facilitating these studies is the fact that the three-spined stickleback is easy to find in nature and easy to keep in aquaria.
An agent-based model (ABM) is a computational model for simulating the actions and interactions of autonomous agents in order to understand the behavior of a system and what governs its outcomes. It combines elements of game theory, complex systems, emergence, computational sociology, multi-agent systems, and evolutionary programming. Monte Carlo methods are used to understand the stochasticity of these models. Particularly within ecology, ABMs are also called individual-based models (IBMs). A review of recent literature on individual-based models, agent-based models, and multiagent systems shows that ABMs are used in many scientific domains including biology, ecology and social science. Agent-based modeling is related to, but distinct from, the concept of multi-agent systems or multi-agent simulation in that the goal of ABM is to search for explanatory insight into the collective behavior of agents obeying simple rules, typically in natural systems, rather than in designing agents or solving specific practical or engineering problems.
An apex predator, also known as a top predator, is a predator at the top of a food chain, without natural predators of its own.
Aposematism is the advertising by an animal to potential predators that it is not worth attacking or eating. This unprofitability may consist of any defenses which make the prey difficult to kill and eat, such as toxicity, venom, foul taste or smell, sharp spines, or aggressive nature. These advertising signals may take the form of conspicuous coloration, sounds, odours, or other perceivable characteristics. Aposematic signals are beneficial for both predator and prey, since both avoid potential harm.
Optimal foraging theory (OFT) is a behavioral ecology model that helps predict how an animal behaves when searching for food. Although obtaining food provides the animal with energy, searching for and capturing the food require both energy and time. To maximize fitness, an animal adopts a foraging strategy that provides the most benefit (energy) for the lowest cost, maximizing the net energy gained. OFT helps predict the best strategy that an animal can use to achieve this goal.
AgentSheets was one of the first modern block-based programming languages designed for children. The idea of AgentSheets was to overcome syntactic challenges found in common text-based programming languages by using drag-and-drop mechanisms conceptualizing commands such as conditions and actions as editable blocks that could be composed into programs. Ideas such as this would go on to be used in various other programming languages, such as Scratch. AgentSheets is used to create media-rich projects such as games and interactive simulations. The main building blocks of AgentSheets are interactive objects, or "agents," that are programmed through rules. Using conditions, agents can sense the user input including mouse, keyboard, and even speech recognition and web page content in more advanced versions. Using actions agents can move, produce sounds, open web pages, and compute formulas.
An ecosystem model is an abstract, usually mathematical, representation of an ecological system, which is studied to better understand the real system.
Continuous Simulation refers to simulation approaches where a system is modeled with the help of variables that change continuously according to a set of differential equations.
Pursuit predation is a form of predation in which predators actively give chase to their prey, either solitarily or as a group. It is an alternate predation strategy to ambush predation — pursuit predators rely on superior speed, endurance and/or teamwork to seize the prey, while ambush predators use concealment, luring, exploiting of surroundings and the element of surprise to capture the prey. While the two patterns of predation are not mutually exclusive, morphological differences in an organism's body plan can create an evolutionary bias favoring either type of predation.
Reinforcement is a process of speciation where natural selection increases the reproductive isolation between two populations of species. This occurs as a result of selection acting against the production of hybrid individuals of low fitness. The idea was originally developed by Alfred Russel Wallace and is sometimes referred to as the Wallace effect. The modern concept of reinforcement originates from Theodosius Dobzhansky. He envisioned a species separated allopatrically, where during secondary contact the two populations mate, producing hybrids with lower fitness. Natural selection results from the hybrid's inability to produce viable offspring; thus members of one species who do not mate with members of the other have greater reproductive success. This favors the evolution of greater prezygotic isolation. Reinforcement is one of the few cases in which selection can favor an increase in prezygotic isolation, influencing the process of speciation directly. This aspect has been particularly appealing among evolutionary biologists.
Compared to terrestrial environments, marine environments have biomass pyramids which are inverted at the base. In particular, the biomass of consumers is larger than the biomass of primary producers. This happens because the ocean's primary producers are tiny phytoplankton which grow and reproduce rapidly, so a small mass can have a fast rate of primary production. In contrast, many significant terrestrial primary producers, such as mature forests, grow and reproduce slowly, so a much larger mass is needed to achieve the same rate of primary production.
The ecology of fear is a conceptual framework describing the psychological impact that predator-induced stress experienced by animals has on populations and ecosystems. Within ecology, the impact of predators has been traditionally viewed as limited to the animals that they directly kill, while the ecology of fear advances evidence that predators may have a far more substantial impact on the individuals that they predate, reducing fecundity, survival and population sizes. To avoid being killed, animals that are preyed upon will employ anti-predator defenses which aid survival but may carry substantial costs.
Eco-evolutionary dynamics refers to the reciprocal effects that ecology and evolution have on each other. The effects of ecology on evolutionary processes are commonly observed in studies, but the realization that evolutionary changes can be rapid led to the emergence of eco-evolutionary dynamics. The idea that evolutionary processes can occur quickly and on one timescale with ecological processes led scientists to begin studying the influence evolution has on ecology along with the affects ecology has on evolution. Recent studies have documented eco-evolutionary dynamics and feedback, which is the cyclic interaction between evolution and ecology, in natural and laboratory systems at different levels of biological organization, such as populations, communities, and ecosystems.
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