Avida Lab Phase 1

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, such as replication or processing a resource by executing a (logic) task. You can allow resources (e.g. "Norose") in the world, and if an Avidian evolves to utilize that resource, it gives the Avidian a boost to its 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.

Getting Started with Avida

The Program

We will be using the web browser version of Avida-Ed. However, there are versions 3 and 4 available. We have tested version 3 (and that will be our default) but there are a few new features version 4 that might be interesting to check for certain experiments. Either version of Avida-Ed 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.)

Introduction Video

The developers of Avida-Ed have made nice introduction videos for AVIDA Version 3 and AVIDA Version 4 explaining Avida-Ed's features and how to use them. If you haven't already done so, please watch one or both of these short videos before coming to lab.

Lab Overview

This lab consists of four parts. In Phase 0, you will get familiar with Avida by conducting a simple experiment. 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. After opening the AVIDA platform on your browser, click the "Setup" button.
  2. Enter 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. Consider each of the following 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. Connect to the AVIDA 1 Worksheet. One of the members of your group will turn this AVIDA 1 Worksheet into the worksheet for the whole lab group. This individual should make a copy and label it with <Your group name>_AVIDA_1_Worksheet. Please include your group name and all group member's names at the top of the document. Then this worksheet link can be emailed to all the members of the group (granting editing permission to everyone).
  5. In this copy of the AVIDA 1 Worksheet, discuss the following as a group:
    • 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?
  6. Each member of the group should set the resources for Treatment A, click on the "Map" button, and then click "Run" (each run should only take a few minutes to complete).
  7. When the run is completed, record the following information (from the "Population Statistics" window) into this Google Sheet (you may have to scroll to the bottom of the sheet to find the first available empty row to enter your data):
    • Student name
    • Treatment (put "A" here)
    • Replicate (put "1" here)
    • Average fitness
    • The number of organisms executing each of the following functions: NOT, NAN, AND, ORN
  8. After your data is entered, click the "New" button and click "Discard" in the pop-up window. Next click the "Setup" button. You may need to drag the @ancestor into "Ancestor Organism:" box again and you may need to select the "when checked" option at the bottom again. Set the resources for Treatment B and double check that all of your settings match the specifications above. Click on the "Map" button, and then click "Run".
  9. Again when the run is completed, record the following information (from the "Population Statistics" window) into the same Google sheet as above (in a new row):
    • Student name
    • Treatment (put "B" here)
    • Replicate (put "1" here)
    • Average fitness
    • The number of organisms executing each of the following functions: NOT, NAN, AND, ORN
  10. Using the worksheet, discuss all of the class data in the Google Sheet in light of your predictions. (Please note that everyone in class will be adding to the same Google sheet during the Avida 0 lab, so if you'd like to wait to do your analysis until after the final lab on Tuesday, you will likely have more data). You are welcome to organize the class data and summarize the data in graphical form if you find that helpful for your discussion, but please make a copy of the Google Sheet before rearranging or editing. This completes the Phase 0 portion (please have this worksheet filled out and available for your peer facilitator to check at the beginning of the next lab).

PROTOCOL FOR PHASE 1

  1. Your PF will check that the group has finished the Phase 0 portion of the AVIDA 1 Worksheet.
  2. The TA will briefly discuss the class results from Phase 0.
  3. On your group's AVIDA 1 Worksheet, complete the Phase 1 portion. You may want to coordinate with at least one other lab group when you get to questions 4, 5, and 6, as it will be more efficient to complete runs with more laptop computers. This will be easiest to do if you make a single Google Sheet to share with all collaborating lab groups (after deciding who will run which treatments).
  4. Brainstorming about your own Avida experiments: Before you discuss possible questions, hypotheses, methods and predictions, please read the remaining sections of this protocol (especially "Inputs to Avida-Ed," "Outputs from Avida-Ed," and "Example Ideas Motivating Experiments").

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 Ideas Motivating Experiments:

  • Exploration of mutation rate:
    1. You have already explored whether there is an optimal rate of mutation. Are there other variables that you would like to vary to explore how the optimum (if one exists) may shift?
    2. Can a population adapt to a specific mutation rate? Does evolution lead to genotypes that are more "robust" to mutation for populations evolving under high mutation rates? Would genotypes evolved under one mutation rate fare worse when transplanted to an environment with a different mutation rate? How might you go about addressing such questions?
  • Exploration of historical contingency:
    1. Does rewarding moderate and hard functional abilities impact the ability of Avidians to evolve very hard or brutal functional abilities?
    2. For Avidians that have evolved moderate/hard functions, are very hard or brutal functions more likely to evolve with the moderate/hard functions continually rewarded (e.g., these simpler functions serving as building blocks) or with moderate/hard functions not rewarded (e.g, these simpler functions interfere with more complex function evolution)? How would you explore these possibilities? How would you use features of the Avida platform (e.g., freezing organisms or populations) to explore this?
  • Exploration of changing environments:
    1. Is there evidence of "local adaptation" in Avida? This is where adaptation to one environment (e.g., certain resources present) comes at an expense to adaptation to a different environment. How might you approach this topic?
    2. Is there a tradeoff between being a specialist and generalist in Avida? Are specialists able to outcompete generalists for the functions they specialize on? Do generalist perform better in environments rewarding a larger set of functions? How would you obtain specialists and generalists for such a study? How would you test for the possibility of tradeoffs?
  • Exploration of ecological feedback (note this question would require Avida version 4):
    1. Is the evolutionary trajectory of a population affected by whether the supply of a resource is limited (becomes exhausted when an Avidian executes the corresponding task) or is unlimited?
    2. What effects would resource limitation have on the evolution of diversity? The complexity of tasks that evolve? Does resource limitation affect the coexistence of distinct task strategies?

Helpful Information

Saving a Workspace

You can save your entire workspace, including the current population and all Freezer contents (saved configs, organisms, and populations) using File > Save Current Workspace. This will create a .zip folder with your workspace contents. Then you can later reload your workspace using File > Open Workspace and selecting the .zip folder that you saved.

Importing and Exporting Data

Exporting

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 cloud magic).

Importing

Importing an item from a file:

  1. Select the File menu (at the top) and click "Import Freezer 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.