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Bio481: AvidaLab

Background

Avida is a digital evolution research platform used to study evolution in real-time. Avida-Ed is a simplified version of the research-grade software intended for education.

In Avida, organisms develop, reproduce, and evolve within the confines of a computer program. Each organism (aka Avidian) has its own genetic code, which consists of simple computer instructions. Certain sequences of instructions allow the organism to perform certain skills, like replicate or metabolize a resource. You can allow resources (e.g. "Norose") in the world, and if an Avidaian evolves to utilize that resource, it gives the Avidian a boost to replication rate. As all Avidians in Avida-Ed are asexual, an increased replication rate means increased fitness. Some resources are more difficult (requiring longer specific sequence) to utilize, and hence have a larger reward for their metabolism.

Avida allows for fast, easy, and informative evolutionary experiments with only a computer needed. Of course, using results found from Avida need to be carefully interpreted before applying to other living systems.

Lab Overview

This lab consists of two parts, a replication of the Luria Delbruck experiment and the beginning of a group-directed research project. The research project will be continued in three additional lab sessions.

Lab Logistics:

This lab will take three lab sessions and may require out-of-class time depending on the experiment designed.

Day 1 (Tuesday)

Daily Overview:

You will recreate the Luria Delbruck experiment using Avida. Following which, you will design and implement a hypothesis-driven experiment.

Materials

• A computer running Windows or Mac OS-X 10.4 to 10.7.
• Avida-Ed software and manual (which can be downloaded from the creators website at http://avida-ed.msu.edu )
• A "Configued Dish" file containing the settings for the LD experiment. This can be downloaded by right-clicking this link and selecting "save link as..." and designating the Desktop as the location to save to.

Protocol

Luria Delbruck Revisited

1. In the Finder, go to Applications -> Biology 481. Drag the folder to the Desktop.
2. In the Biology 481 folder on the Desktop, double click on "Avida-ED" to open Avida-Ed.
3. In the top menu, select File -> New Workspace.
4. Designate the Desktop and the location, and name the file with your group's name. Then click save.
5. In the top menu, select File -> Import Item.
6. Designate the "Configued Dish" file (Desktop -> Biology 481 -> "LD_Settings.aex") and click open.
7. Drag from the "freezer" the configured dish named "LD_Settings".
8. If a dialog box opens, select the second option (Discard and Start New Experiment).
9. Click the play button at the bottom center of the screen.
10. The program should halt at 90 updates, at which time, you should record the number of organisms performing the function "Not". This value is displayed in the Population Statistics Window.
11. Repeat the previous 4 steps for twenty four iterations, taking care to record the number of organisms performing "Not" each time.
12. Each iteration is equivalent to one well from the LD Lab, with the number of organisms performing "Not" similar in principle to the number of Rifampicin-Resistant cells/colonies.

Hypothesis and Methods

1. The rest of the lab is dedicated to deciding upon an interesting question in ecology and/or evolutionary biology, which can be studied using the Avida system. Keep in mind the strengths and weaknesses of all model systems, and in particular, the capabilities of Avida itself.

Inputs to Avida-Ed:

• Adjustable Mutation Rate
• Adjustable Carrying Capacity (Population Size)
• Initial/Ancestral Organism(s)
• Spatial Structure
• Resources in Environment (of varying complexity and reward)
• Ability to "freeze" individuals and populations and reanimate them

Outputs from Avida-Ed:

• Evolved Populations and Individuals
• Abundance Data of Organisms which can consume various resources
• Fitness (and other phenotype information)

Example Experiments:

• Investigate the minimum population size to avoid Muller's Ratchet for different mutation rates
• Evolve individuals that can consume multiple resources and then evolve them in the absence of resources to study the cost of various abilities and their relation to complexity.
• Study specialization of populations evolved in different mutation rates, by competing an evolved individual from each mutation rate in arenas (which have different mutation rates).

Helpful Information

Importing and Exporting Data

Note: It is often useful to save evolved populations and/or individuals from an Avida-Ed experiment. Unfortunately, a number of compatibility issues can arise when moving files from one version of Avida-Ed to another or when changing Operating Systems (Windows versus Mac), so please test these steps with the computers involved before relying on them.

Exporting

Freezing the population:

1. Click on the snowflake icon (next to the play arrow) with the population you want to export showing
2. Name the population, select "Populated Dish" and click Freeze

Freezing an individual:

1. Drag an individual square from the population into the freezer (left of the population viewer).
2. Name individual and click freeze
3. Be sure to check that the individual frozen has the characteristics of interest (due to maternal inheritance of phenotype and fitness, the frozen individual may have mutations which affect its phenotype).

Exporting to file:

1. After an item (population or individual) is in the freezer, right click it.
2. Select export and click "Confirm"
3. Select the folder and the file name to export the item to. (Note the extension for the file will be ".aex").
4. The file can now be moved between computers (by email, flash drive, or telepathy).

Importing

Importing an item from a file:

1. Select the File menu (at the top) and click "Import Item"
2. Select the previously exported file (".aex" extension) and click open
3. The item should appear in the freezer with the same name as the file.