In this lesson, you will explore a computational model of bacterial population to understand the idea of genetic grift and influence of carrying capacity in the process of genetic drift.

Click here to download the model.

Follow the instructions below to get started:

Open NetLogo folder and click on NetLogo Logging.

Open the Genetic Switch NetLogo Model that you downloaded earlier.

This is a model of a population of bacterial cells, E. coli.

The model starts with different colored E. coli cells, randomly distributed across the world. The E. coli cells move around the world and eat sugar if it’s available to them where they are present. Grey patches (in the image below) contain sugar. Eating sugar increases the energy of an E. coli cell, whereas movement and basic metabolic processes decrease its energy. When the energy of a cell doubles, it reproduces to form two daughter cells of its type (of the same color). If the energy of an E.coli cell reduces to zero, the cell dies.

Different colored cells do not have any ‘advantage’ over other cells in terms of growth rate or sugar consumption.

Components of the model:

How to run the model:

• Click ‘SETUP’ to set the initial population of the bacterial cells.
• Click ‘Go’ to run the model.

This model simulates the growth of a bacterial population. As the model progresses the cells move around. If they are at a patch that has sugar, they eat it.

• Number of types:

Use this slider to set the initial number of types (colors) of bacteria in the world.

• Maximum initial population:

Use this slider to set the maximum number of bacteria of all colors in the initial population in the world.

• Carrying capacity:

Use this slider to set the carrying capacity of the world. Carrying capacity is the maximum population that can be sustained in the world. This slider changes the availability of sugar in the world and thus controls the maximum population.

This is a model simulating the growth of a bacterial population in an environment containing sugar. Bacteria eat sugar and divide. Thus, the population of bacteria grow.

Start the simulation with one type of bacteria.

Let's investigate how the bacterial population changes over time.

Prediction time!

Set the carrying capacity to medium. Set the number of types of bacteria to ‘two’. Set maximum initial population to 10. Do NOT run the model, yet. Answer the questions below first.

Design a computational experiment to test your predictions.

Increase the number of types of bacteria to 6 or 7. How do you think the results will be different than when you had 2 types? Make a prediction. Do NOT run the model yet. Write your prediction first.

Let’s investigate the effects of carrying capacity on this process of genetic drift.

Genetic drift is the process of one color surviving without having any selective advantage. How would the process of genetic drift differ at high and low carrying capacities? Make a prediction.

NetLogo’s logging facility allows researchers to record student actions for later analysis.

Use the following information to find a logging file on your computer.

Logs are stored in the OS-specific temp directory. On most Unix-like systems that is /tmp. On Windows computers the logs can be found in c:\Users\<user>\AppData\Local\Temp, where <user> is the logged in user.

On Mac OS X, the temp directory varies for each user. You can determine your temp directory by opening the Terminal application and typing echo $TMPDIR at the prompt.

After you find the log files (.xml format), check for the file names that correspond to the date today. Upload those files.