Predator Prey Scientific Paper by Using Netlogo Model

Predator Prey Scientific Paper by Using Netlogo Model

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Predator Prey Scientific Paper by Using Netlogo Model

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This assignment is done by observing the reading from a net logo model software which is attached with my moodle so I can provide you my moodle id and password to complete the assignment

Write a brief but insightful scientific paper, using the predator-prey model, evaluating the support for the hypothesis of your choice. In preparation to do so, consider what parameters of the model you will manipulate, and what response variables you will measure to evaluate your hypothesis. Consider how you will replicate your experiment to obtain confidence in your results. Use the following sections in your paper:

An appropriate, clever, and interesting title. Note that ‘Predator-prey dynamics’ is not a clever or interesting title!

In your abstract, provide a brief overview of your key results, interpretation and recommendations (150 words, maximum).

In your introduction, provide enough background and context so that the reader clearly understands the importance of the hypothesis you will test. A clear statement of your hypothesis should appear in the last paragraph of your introduction. Be sure to justify why you expect your hypotheses to be supported by the data. Refer to peer-reviewed literature to contextualize your results.

In your methods, briefly state how you manipulated the model. What parameter(s) did you vary, and over what range? How did you replicate your sampling? There is no need to describe the basis of the model itself. Nor are you required to use statistical tests. Doing so would be a nice addition, but is not required.

In the results, lay out your findings clearly, using figures, and if necessary, tables. The results section should present results suitable to evaluate the support for your hypothesis. Remember that a results section MUST include a text description of your key results. Use the text to highlight the key results shown in your figures. Be sure that your figures are legible, illustrate your findings, and include complete captions.

In the discussion, interpret your findings in terms of your hypothesis. Refer to peer-reviewed literature to interpret your results.

Use no more than 1200 words for ECOL203 (1500 words for ECOL403) in total (excluding abstract, captions, and references).  The rubric that provides the benchmarks against which your paper will be judged is available on Moodle.

Your report must be written in your own words. Write your report independently. Turn in this assignment by Moodle. Indicate your identity with your student number, and only your student number

ECOL203/403 – Ecology: Populations to Ecosystems Assignment 2: Predator-Prey Interactions

T1 2020

Figure 0. Tarantula Theraphosa blondi pulling a captured giant earthworm (presumably Rhinodrilus sp.) into its burrow in rainforest in French Guiana. Photo by C.E. Timothy Paine. Find more information about earthworm-eating tarantulas in Nyffler et. al. 2017. Journal of Arachnology 45:242–247.

Objective The purpose of this assignment is for you to run a manipulative experiment using a realistic predator-prey model. In so doing, you will

1. Explore how predators affect prey populations and vice versa 2. explore the linkages between ecological processes and their representations in models 3. design and execute an ecological experiment Introduction This assignment demonstrates how the actions of individuals compound to generate population dynamics.

We know that all populations can grow exponentially, and we also know that never occurs for long, as the resources available to populations eventually restrict their growth. In this practical, you will explore how and when this occurs. You will further explore conditions under which more complicated – and even interesting – population dynamics occur.

In simple models, one could assume that all predators had access to all prey at all times. In reality, however, populations have spatial structure, because individuals are located at specific locations in space. This has several effects on their ecology. First, an individual’s spatial location restricts the set of individuals that it can interact with to be those in its local neighborhood.

Second, space (together with the sensory organs of the organism in question) affects the detectability of predators and prey. Third, heterogeneity in the spatial distribution of resource availability, refuges, mates, and abiotic conditions (etc) can strongly influence ecological processes.

Finally, the viscosity (or ‘thickness’) of the environment, together with the dispersal abilities of the organism, affects how quickly they can move through space. All of these factors influence ecological interactions among organisms. A final consideration is the dimensionality of space.

For terrestrial organisms, the world is (to a first approximation) flat, whereas for aquatic, marine or airborne organisms it is three-dimensional. In the sky, a predator may be above you. In water, predators may lurk above or below you. In this model, we assume that the predators and prey exist in a flat (two- dimensional) homogeneous field.

Modeling platform You will use a modeling platform, NetLogo, in which the spatially explicit two- species model has been developed. NetLogo is a multi-agent programmable modeling environment used by tens of thousands of students, teachers and researchers worldwide.

Models are written in the NetLogo language, which provides a graphical user interface for users. Description of model ARENA: You will simulate predator-prey dynamics in a homogeneous, two- dimensional closed habitat. The habitat is rectangular, with dimensions you specify. The model is spatially explicit, with each individual having a set location. By joining the top and bottom edges of the arena, and the left and right edges, we create a torus (a donut). These manipulations make the spatial area of simulation endless.

Prey are shown as “bird” symbols, and predators as “cats”. These symbols were chosen to remind you of the devastating impact that feral cats have had on the native fauna of Australia. This is a general model, however. You can simulate ANY type of predators, and ANY type of prey, depending on the parameters you choose (see below). So don’t get trapped into thinking it’s only two particular species.

MOVEMENT: Prey move throughout the habitat at a speed you determine (“Prey_speed” Note: you can adjust all the parameters in italic text. See Figure 1 for an overview). They move in random directions, unless there is a predator within their “Dodge_distance”), in which case they move away from that predator.

Predators, likewise, move at a speed you determine (“Pred_speed”). They also move randomly, unless an individual prey comes within their “Search_distance”. When that happens, they move towards that prey. When a prey is located within the “Catch_distance” of a predator it is considered to be caught and eaten by that predator.

Note that the “Catch_distance” should never be larger than the “Search_distance”, as that would make no biological sense. If several predators catch a prey simultaneously, they share it. We assume that all prey contain the same level of resources, as far as the predator is concerned.

GROWTH: Individual prey grow by acquiring resources from the environment. This occurs at a constant rate. Individual predators, on the other hand, grow only by consuming prey.

REPRODUCTION: Prey and predators must obtain a threshold level of resources before they’re able to reproduce. Reproduction is by asexual budding: each new individual is generated at the same location as the parent, with a minimal level of resources. The threshold levels of resources necessary for reproduction by prey and predators (“Prey_energy_to_reproduce” and “Pred_energy_to_reproduce”) are set by you.

DEATH: Mortality for the prey occurs only when they are consumed by predators. Predators have a per-capita probability of death (“Pred_prob_death”) in every time-step.

INITIAL CONDITIONS: The indicates how many predators and prey are initially present in the habitat (“Pred_number_initial” and “Prey_number_initial”, respectively). Individuals are located randomly, with a random initial energy level.

Figure 1. Model parameters you can adjust. Parameters for the predators are on the left. Parameters for Prey are on the right. The length of the simulation is at the bottom. Note: The parameters provided here generate stable coexistence of predators and prey (for at least 10000 time-steps. If you find that your populations consistently go extinct, reset the parameters to these values!

Model outputs The model outputs several variables. First, you can watch the predators and prey as they move around the arena (Figure 2). Additionally, you can monitor the changes in the population size of predators and prey. This information is provided graphically over the course of the simulation, and the current population sizes for predators and prey are provided numerically (Figure 3).

You’ll see that, often, the predators drive the prey to extinction. Or, conversely, that the predators go extinct, allowing the prey population size to increase indefinitely. A key question of interest, therefore, is under what conditions the predator and prey populations can coexist stably.

We evaluate stability as the time of persistence of the two species. Furthermore, we can obtain from the model the mean population size of the prey and predators, as well as their ranges, which gives an indication of the degree of variation in population sizes.

Greater oscillations, and oscillations that grow larger through time, are indicators of instability, whereas small and damped oscillations indicate relative stability. In addition to population dynamics, we can observe the spatial patterning of predators and prey in the arena – are they all spread out?

Do predators hunt as a group? Do prey disperse from one another, or from the predators? Because this model allows individual predators and prey to move randomly around the arena, no two runs are identical. In other words, this model is stochastic. To evaluate its behavior, therefore, you need to observe multiple runs.

Use a minimum of 10 repetitions of every set of parameter values you evaluate, and record your response values after every replicate.

Figure 2. Example graphical output from the model. Prey are shown as blue birds and predators as black cats. Their size indicates their current level of resources.

Figure 3. Example output from the model, showing changes in population sizes through time, as well as numeric values of the population sizes.

Flexibility of the model You can explore a wide variety of predator prey interactions using this model. For example…

• You could create a plant-herbivore system by decreasing the speed of the prey to almost 0. (Don’t decrease it to 0, or new plants will be placed at exactly the same location as their parents)
• You could create sit-and-wait predators by making them extremely slow- moving. (Don’t decrease their speed to 0, or new predators will be placed at exactly the same location as their parent).

Hypotheses For your experiment, you can use one of the following hypotheses, or you can come up with your own. You can use this system to investigate a wide variety of ecological scenarios! If you use your own hypothesis, you MUST verify its suitability in writing with Dr Paine (timothy.paine@une.edu.au) prior to running your experiment.

1. The probability of prey survival decreases as their speed decreases. 2. The probability of prey survival decreases the speed of the predators increases. 3. Increasing the predator’s search radius decreases the likelihood of stable coexistence of the two species, whereas decreasing the search radius increases it.
2. Increasing the level of resources needed for prey reproduction increases the likelihood of stable coexistence.

How to evaluate the support for your hypothesis Students are often uncertain about what data they should collect in order to examine the support for their chosen hypothesis.

In general, the population dynamics, in other words, the changes in population size that occur during a single run of the model, are of less interest than is the final outcome: which species are present at the system at the end of the run. Ultimately, the data that you collect and present will depend on the hypothesis you test.

If, for example, you hypothesize that prey population sizes will be more variable as their speed increases, then you should report how strongly their population sizes vary. Or, if you choose to test Hypotheses 1 or 2, above, then you should report the percent of model runs in which the prey survive to the end of the model run.

In Hypotheses 3 and 4, above, the term ‘stable coexistence’ appears. By this, we mean the persistence of both the predator and the prey species until the end of the model run. A note on how to run the model By default, the model is set to run for 10,000 timesteps. You may find that running the time necessary for the model to run to 10,000 timesteps is too great.

Additionally, you may find that the two species almost never are able to stably coexist through 10,000 timesteps. In either of those cases, you should reduce the

“Max_simulation_duration” (Figure 1) to a smaller number. Don’t reduce it below 1,000 timesteps. If you do change this setting, be sure to explain that you do so, and why, in your methods section. Assignment Write a brief but insightful scientific paper, using the predator-prey model, evaluating the support for the hypothesis of your choice.

In preparation to do so, consider what parameters of the model you will manipulate, and what response variables you will measure to evaluate your hypothesis. As noted above, you must replicate your experiment to obtain confidence in your results. Use the following sections in your paper:

• An appropriate, clever, and interesting title. Note that ‘Predator-prey dynamics’ is not a clever or interesting title!
• In your abstract, provide a brief overview of your key results, interpretation and recommendations (150 words, maximum).
• In your introduction, provide enough background and context so that the reader clearly understands the importance of the hypothesis you will test. A clear statement of your hypothesis should appear in the last paragraph of your introduction. Be sure to justify why you expect your hypotheses to be supported by the data. Refer to peer-reviewed literature to contextualize your results.
• In your methods, briefly state how you manipulated the model. What parameter(s) did you vary, and over what range? How did you replicate your sampling? There is no need to describe the basis of the model itself. Nor are you required to use statistical tests. Doing so would be a nice addition, but is not required.
• In the results, lay out your findings clearly, using figures, and if necessary, tables. The results section should present results suitable to evaluate the support for your hypothesis. Remember that a results section MUST include a text description of your key results. Use the text to highlight the key results shown in your figures. Be sure that your figures are legible, illustrate your findings, and include complete captions.
• In the discussion, interpret your findings in terms of your hypothesis. Refer to peer-reviewed literature to interpret your results.

Use no more than 1200 words for ECOL203 (1500 words for ECOL403) in total (excluding abstract, captions, and references). The rubric that provides the benchmarks against which your paper will be judged is available on Moodle.

Your report must be written in your own words. Write your report independently. Turn in this assignment by Moodle. Indicate your identity with your student number, and only your student number.

Predator Prey Scientific Paper by Using Netlogo Model

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