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Bio481: AvidaLabPhase0

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 functions, 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 more complex genetic instructions) to utilize, and hence have a larger reward for their metabolism.

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

If you are interested in learning more about how Avida works and how it is used in research, you can check out the Avida wiki and a selection of related papers.

Before the lab section on Tuesday, please connect to the web-based Avida platform and watch the introduction video. You can also feel free to play around with the platform a bit if you have time.

Getting Started with Avida

The Program

We will be using the web browser version of Avida-Ed. This version should work on any computer using a recent version of Chrome or Firefox; no software needs to be installed on your machine. (There are also desktop versions of Avida-Ed and Avida for research, but you aren't expected to use these.)

• Click here to launch the Avida-Ed Application
• Avida-Ed website for support and information about the program

Introduction Video

The developers of Avida-Ed have made a nice introduction video explaining Avida-Ed's features and how to use them. Please watch this short video before coming to lab.

• Avida-Ed Introduction Video

Lab Overview

This lab consists of four parts. In Phase 0, you will get familiar with Avida by conducting a simple experiment (which foreshadows your upcoming reading). In Phase 1, you will complete a worksheet on a more involved experiment and you will start to brainstorm with your group about designing your own experiment in Avida. In Phase 2, you will propose a full experiment before lab (via a worksheet; specifying your question, hypotheses, methods, and predictions) and you will receive feedback and make clear plans for conducting the experiment (you will start running your experiment during lab). Finally, in Phase 3, you will consider the hypotheses motivating your original experiment in light of your data and potentially re-design your experiment and/or re-work your hypotheses.

Materials

• A computer with either Chrome or Firefox installed (other browsers probably work, but aren't recommended by the developers). We will be working in a large conference room (LSB 401), and, if possible, you should bring your personal computer to get familiar with using Avida-Ed on your own machine. If you do not have access to a laptop, please inform your TA and we will provide one for you.

PROTOCOL FOR PHASE 0

1. Your TA will go over the basics of Avida and the settings that you can change.

• Please note that all of the steps below (in red) were not executed during the Data Analysis Lab (due to time constraints). Thus, these steps are being transplanted to the AVIDA 1 protocol () and some of these will be part of the AVIDA 1 Worksheet. These AVIDA 0 steps should be completed before lab session on Tuesday.

1. Each member of your group should click the "Set Up" button on their own laptop.
2. Each person should use the following settings:
   • Dish size: 30 x 30
   • Per site mutation rate: 2%
   • Ancestral organism: Drag in the @ancestor into the box from the Organisms panel to the left
   • Place offspring: Near their parent
   • Repeatability mode: Experimental
   • Pause run at: 1000 (and make sure to check the "when checked" option)
3. Each group member should pick one of the following treatments. As a group, you will want to run each treatment at least four times (thus, you could have everyone run each treatment once, or have different lab members run a few replicates of the different treatments).
   • [Treatment A] Moderate Available Resources: check only andose and ornose
   • [Treatment B] Easy and Moderate Available Resources: check notose, nanose, andose and ornose
4. Before running any treatments, discuss a few predictions with your group. In particular:
   • Do you think Avidians will more easily evolve to use andose and ornose in treatment A or treatment B? Why?
   • Do you think Avidians will evolve higher fitness in treatment A or treatment B? Why?
5. Click on the "Map" button and then hit "Run" (each run should only take a few minutes to complete).
6. When the run is completed, record the following information (from the "Population Statistics" window) into the class Google Sheet:
   • Average fitness
   • The number of organisms executing each of the following functions: NOT, NAN, AND, ORN
7. After collecting all the results from your group together, discuss your data (and other data from other groups in the class) in light of your predictions.
8. The TA will briefly lead a short discussion on class results.