Avida-ED Lab Book

Fall 2016

Avidians in Action

Avida-ED Project Curriculum Development Team

Wendy Johnson, Cory Kohn, Amy Lark, Louise Mead,
Robert T. Pennock, Jim Smith, Michael Wiser
http://avida-ed.msu.edu
http://bit.do/avida-ed
 This material is based in part upon work supported by the National Science Foundation
under NSF-IUSE (NSF Grant # 1432563), "Active LENS: Learning Evolution and the
Nature of Science using Evolution in Action", Robert T. Pennock, PI, Richard Lenski,
Louise Mead, Charles Ofria, James J. Smith, co-PIs. Any opinions, findings, and
conclusions or recommendations expressed in this material are those of the author(s) and
do not necessarily reflect the views of the National Science Foundation.

Expenses associated with workshop presentations were subsidized, in part, by funds

from HHMI Grant Award #52008102 Leveraging Engagement and Vision to
Encourage Retention in STEM
Robert T. Pennock, Jon Stricklen, co-PIs, to Michigan State University.
 Getting the Avida-ED software

Avida-ED 3.0 beta is the current version of the software and its use remains free of
charge. The public beta was released on June 18, 2016. Avida-ED 3 now runs in a
browser window instead of as a stand-alone application. This solves the problem of
developing and maintaining separate applications for MacOS, Windows and other
operating systems. Eventually, it will run fully in all major browsers, but at the moment full
functionality requires Firefox or Chrome. It will remain in beta status through the end of
2016, and will be regularly updated as bugs are uncovered and squashed.

ccess the latest software, curriculum and news from the Avida-ED home page:
http://avida-ed.msu.edu/

The direct URL for Avida-ED 3.0 is:

https://avida-ed.beacon-center.org/app/AvidaED.html

We also have two mirror locations:

http://avida-ed-mirror1.beacon-center.org/AvidaED.html
or
http://bit.do/avida-ed

Once Avida-
not on any remote server. That means it requires an internet connection initially to load,
but not to run.

For users who want to keep a local copy on their computers for occasions when they
have no internet access at all, the Avida-ED web site also has links for self-hosted
versions for Macs and PCs.

Note: Previous stand-alone versions of the software Avida-ED 2.0 and 1.2 for Mac OSX
and Avida-ED 1.2 for Windows are no longer maintained but remain available for
historical reference.

a. Go to http://avida-ed.msu.edu/.

c. Select the radio button for the version you want to download.
-
e. Open the file and drag the Avida-ED icon to your desktop. Open the application.

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Introduction - Avida-ED and Digital Evolution
Avida-ED is adapted from Avida, a software platform created by a group of computer
scientists and software engineers interested in the experimental study of digital organisms
in order to better understand how biological evolution works. Both programs provide an
instance of evolution in a model environment. The evolution itself is real; the digital
organisms are subject to the same processes as biological organisms, such as mutation,
replication, and selection. Scientists can study how digital organisms evolve, and examine
questions related to the evolution of complex features, sex, intelligence, cooperation, and
foraging behavior. Avida has even been used to confirm the outcomes of ongoing
biological experiments. This is possible because the process of ev
variation,
inheritance, and selection evolution will inevitably result.

Using this powerful tool, you will be able to design and perform your own experiments to
test hypotheses about evolution in much the same way that researchers use Avida.

Driving Questions
What is Avida-ED (how does it work)?

Can we observe evolution? How?

Can we study evolution by doing experiments? What kinds?
How is Avida a useful tool for biologists? What are the strengths and limitations of
such an approach?

Tasks
Discover
Magazine in 2005. The article can be found immediately following this Introduction or
will be made available by your instructor.
2. Start Avida-ED. The program now runs in a web browser. Navigate to https://avida-
ed.beacon-center.org/app/AvidaED.html. Please note that the program may take a
minute or two to load, be patient.
3. Watch the Avida-ED video tutorial found in the support section of the Avida-ED website
or on YouTube: https://www.youtube.com/watch?v=mJwtg0so4BA&feature=youtu.be
U

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Using Avida-ED
The Avida-ED workspace includes:

1. (view mode buttons) allows you to switch among three

modes:
a. Population the organisms evolving in the virtual Petri dish and the
experimental set-up;
b. Organism
c. Analysis allows comparisons of population variables (e.g. average fitness)
over time.

2. saved materials)

a. Configured dishes settings, no organisms;

b. Organisms
dragging or saving to the freezer; and
c. Populated Dishes settings and organisms saved by freezing populations.

3. Lab Bench (where things happen)

place where your Avidians will grow and multiply (Figure 1). You can access the
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size (30x30 is default), mutation rate (2.0% is default), whether or not functions are
rewarded (default is all nine rewarded), and other options.

Figure 1. Screen shot of the Avida-ED Workspace map view.

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Figure 2. Screen shot of the Avida-
Several parameters of the experimental set-up can be manipulated.

To run an Avida-ED experiment, drag an organism from the freezer to the virtual Petri
dish (if in Map view) or to the Ancestral
in Map view or

be placed in the center of the virtual Petri dish. To examine a single Avidian, click on

The genome is
circular and represented by colored letters. Each letter is a specific command. Notice that
-
commands and here essentially serve as placeholders).

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Part I: Examining an Avidian Individual and Observing Replication
The digital organisms in Avida are referred to as Avidians, and are defined by a series of
commands, which are simple computer instructions (Figure 3). During an experiment, the
Avida-ED application reads t

genome of 50 letters, which includes a sequence of instructions for replication.

Follow the steps below to observe Avidian replication.

1. The lab bench becomes an empty

rectangle with a set of buttons at the bottom.
2. Drag the default organism ( @ancestor ) from the freezer panel to the lab bench
area. A set of circles with letters inside them appears (see Figure 3).
3. -ED. At
a certain point, you will notice that the organism replicates. Click the button
and repeat this step a number of times. You can observe the code being read and
read
head forward one instruction at a time. When paused, you can get the instruction
number by clicking on an instruction.

questions by entering your responses in the space provided.

instructions?

Mutations in the offspring appear as an instruction with a black circle. Record the
mutations for a single round of replication.

Position 1 10 20 30 40 50
Ancestor wzcagcccccccccccccccccccccccccccccccccccczvfcaxgab
Mutations

Total # of mutated sites _______

Locations of mutated sites ________________

If a mutation occurred within the sequence of replication instructions what do you

think would happen ?

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 If you wanted to determine the function of each letter (command) of the code, where
would you find that information?

How does the offspring Avidian compare to its parent? In other words, how many
differences are there in the set of 50 commands, and where are the differences

Part II: Observing the Frequency and Location of Mutations that Occur
During Replication
1. Under Settings (still in Organism view), find the mutation rate that you used above,
and record it.
2. the per site mutation rate to 2% by moving the slider or
If you use the slider to change the mutation rate, look
carefully at the placement of the decimal to verify you have set it to
(approximately) 2% and not 0.20%. You can either press the enter key, or click
elsewhere on the screen, and the mutation rate will update. Then click on the x in
the upper right corner of this box.
3. Then click play or drag the slider to watch the organism run through its code.

Please respond to the following questions by entering your responses in the spaces
provided.

There are 50 commands. How many sites do you expect will have a mutation given
a 2% per site mutation rate?

How does your replicated offspring compare to the parent?

How did your offspring (replicated with the 2% mutation rate) compare to your
g (also replicated with a 2% mutation rate)? Did they have the
same number and/or type of mutations?

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Storing an Avidian Individual in the Freezer

1. Click and drag the offspring genome into the Freezer Panel.
2.
name you like, but we suggest something descriptive, perhaps indicating the
mutation rate, or what tasks it can perform.

Part III: Evolving a Population

Avidians replicate in the virtual Petri dish, much the way bacteria replicate when plated on
a medium. The virtual dish is divided into a grid in which each box holds one Avidian.
When an Avidian replicates, the offspring are placed in a box adjacent to the parent (the
default setting) or randomly on the grid. As we have seen above, if there is mutation,
offspring will not be exactly like the parent.

Figure 4. Screen shot of the panels displaying population and individual statistics. The upper
right panel shows basic population statistics, plus how many individuals in the population perform
each function. The panel just to its left does the same for a selected individual. The lower panel
graphs a number of population parameters as the run progresses.

Carrying out the set of numbered tasks below will result in the growth of an Avidian
population, with each individual in that population having descended from a single
ancestral Avidian. At the end of the run, you will save the Petri plate containing your
Avidians to the Freezer, as well as saving a single Avidian with relatively high fitness.

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 1. The lab bench changes back to the
Petri dish.
2. Click on Setup . Drag the default organism ( @ancestor ) from the freezer panel
Set the world size to 30 x 30 cells and the per site
mutation rate to 2.0%. Make sure the Near their parent
Place Offspring panel (should be the default). Turn off all resources (i.e., notose,
nanose, etc.) by clicking in the box so that it is not checked. All other default
settings should remain unchanged. [Note: resources, when made available, provide
additional energy to Avidians that evolve the ability to use these resources.]
3. the drop
down menu below the Petri dish. Use the slider below the Petri dish to increase the
view size.
4. Push the Run button below the Petri dish and watch as the ancestor and
subsequent descendants start multiplying. Each grid square represents an
organism.
5. As you watch the Avidians multiply, notice that the information in the Population
Statistics box and the graph change. When the dish looks full, click to stop
the growth in the Petri dish.
6. Click on an organism (a grid square). The information for the Avidian in this grid
square appears in the Selected Organism Type panel (Figure 4). Click on a few
other organisms and notice how their information differs. You may click on different
individuals during the run to observe their characteristics in the organism
information box.
7. Information on the population is displayed in the Population Statistics panel, and in
the graph below this panel. Click the play button again and observe the dish and the
population statistics boxes as the run proceeds.
8. Pause the run when there have been about 1,000 updates (unit of time for Avida-
ED). The update number can be found under the bottom left corner of the Petri dish.
Before proceeding with the next step, save the entire plate by clicking the Freeze
button at the bottom and saving the population to the Freezer. You will be prompted
whether you wish to save the Configuration, Organism, or Population; here you
should save the Population. We recommend using a labeling system that keeps
track of the mutation rate and world size (i.e., m2-w30x30-number of updates, but
you can use any naming system that makes sense to you).
9. Click on individual organisms, one at a time, to find an individual with a high fitness.
To do this, use the fitness scale below the Petri dish, as well as looking in the
organism info panel for each organism.
10. Drag an organism with a relatively high fitness to the freezer panel. In the box, type
a name for this organism followed by the fitness value.

Please respond to the following questions by entering your responses in the spaces
provided.

measured in Avida-ED?

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Choose two Avidians in your population with different fitness and explain how
differences in these Avidians contribute to differences in their fitness.

Based on what you observed in the Population Statistics and the Organism Type
boxes during the run, what do you think accounts for changes in individual fitness
and changes in the average fitness in the population?

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Exploring the Effects of Mutation Rate
on Individuals

Left: Pale grass blue butterfly (Z. maha) with normal fore and hind wings.
Right: Mutated butterfly with stunted wings.

Background

On March 11, 2011 the largest earthquake ever to hit Japan, and one of the five largest in

tsunami that produced waves with heights up to 133 feet (40.5 m) that traveled as much as
6 miles (10 km) inland, causing extensive damage to property and significant loss of human
life. Among the infrastructure casualties was the Fukushima Daiichi Nuclear Power Plant
complex. Three reactors sustained heavy damage, resulting in the worst nuclear accident
since Chernobyl in 1986. The area within a 20-mile (~30 km) radius of the Fukushima plant
was determined to have dangerously high levels of radiation, with the highest levels up to 2
miles (3 km) from the plant. The Japanese government prohibited access to this area and
ordered the evacuation of anyone living between 2 and 12 miles (3 and 20 km) of the plant.
People living between 12 and 20 miles (20 and 30 km) away were put on high alert and also
encouraged to evacuate.

The disaster at Fukushima has provided scientists with an opportunity to investigate the
biological impact of radiation on organisms. One species in particular, the pale grass blue
butterfly (Zizeeria maha), is helping researchers pursue questions about the immediate and
long-term effects of radiation at various doses (Hiyama et al., Scientific Reports 2 Article
570, 2012). Butterflies collected closer to the power plant experienced larger doses of
radiation than those farther away, and the scientists found that larger doses were
associated with increased infertility, mortality, and incidence of physiological abnormalities.
Many of these abnormalities were inherited and amplified in offspring of butterflies that had
been exposed to the radiation initially as overwintering larvae. The researchers concluded
are produced by random

assuming that higher doses of radiation are associated with increased mutation rates, can
exposure to radiation account for the adverse biological effects reported in the study?

By Amy Lark
Avida-ED Project http://avida-ed.msu.edu
STUDENT MATERIALS
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 Exploring the Effects of Mutation Rate on Individuals

Assignment Tasks

Predict: What will

mutation rates (low, medium and high)?

Test: Follow the instructions carefully. Use the table provided to record your data.
1.) In the Organism viewer, drag an ancestral all_functions
viewing pane. Under the Settings, set the per site mutation rate to 1%.
2.) Click on the Run button and allow the ancestor to replicate. Note: After clicking Run
you can skip visualizing the replication process by clicking End.
3.) On your data sheet, record the number of mutations in the offspring (circled in
black).
4.) Drag the offspring to the freezer. Name it in a way that will allow you to match it to
Click the Reset button.
5.) Repeat steps 2 4 ten times, completely filling out the first of
your data sheet.
6.) Drag your first saved offspring from the freezer into the Organism viewing pane.
Click Run and record the number of functions (9 metabolic functions and the ability
to replicate) it has lost. Repeat this for all remaining offspring until you have
completely filled out the column of your data sheet. Note:
After clicking Run you can skip visualizing the replication process by clicking End.
7.) Repeat steps 2 6 at 5%, 10%, and 15% mutation rates, recording data in the
appropriate spaces on your data table.
8.) Use your data to calculate the average number of mutations and percentage of
abnormalities for each of the four mutation rates.

Results: Were your predictions confirmed or disconfirmed by the data you collected?

Discussion: What do your tests reveal about the relationships between mutation rate,
frequency of mutations, and physiological abnormalities?

Does the evidence from your study support

that the abnormal phenotypes observed are produced by random mutations caused by
How?

By Amy Lark
Avida-ED Project http://avida-ed.msu.edu
STUDENT MATERIALS 2
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8
7
6
5
4
3
2
1

10
Offspring

Average
Mutations
number of
(n)
mutations

By Amy Lark
1%
Abnormality Abnormalities
rate (n)

Average
Mutations
number of
(n)
mutations

Avida-ED Project http://avida-ed.msu.edu

5%

Abnormality Abnormalities
rate (n)

Average
Mutations
number of
Mutation Rate

(n)
mutations
10%
Exploring the Effects of Mutation Rate on Individuals

Abnormality Abnormalities
rate (n)

Average
Mutations
number of
(n)
mutations
Data Table. Keep track of your experimental observations in the table provided.

15%

STUDENT MATERIALS
Abnormality Abnormalities
rate (n)

3
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 Exploring the Effects of Mutation Rate on Individuals

Data Chart. Plot your data to reveal patterns.

100 10

90 9

80 8
Abnormality Rate (%)

70 7

Average # Mutations
60 6

50 5

40 4

30 3

20 2

10 1

0 0
1% 5% 10% 15%
Mutation Rate

By Amy Lark
Avida-ED Project http://avida-ed.msu.edu
STUDENT MATERIALS 4
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