FrogPond

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Overview

FrogPond lets you practice designing studies to determine the cause(s) of variation in a model population.

Consider three kinds of variation:

Genetic variation exists when individuals differ from each other due hereditary information received from their parents.
Environmental variation occurs when individuals differ because they have been exposed to different external conditions.
Genotype-by-environment interaction arises when individuals carry hereditary information that causes them to exhibit different patterns of phenotypic change across a range of environmental exposures.

You will investigate the variation among individuals in a simulated population. The population you will study is fictitious, but loosely based on a true story. Some years ago, in a variety of places in North America, school children, biologists, and ordinary people discovered populations of frogs with high frequencies of startling deformities—including extra legs. The suspected causes of deformity, some incriminated by stronger evidence than others, included UV radiation, water pollution, and a parasitic trematode worm, called Ribeiroia, whose larvae can encyst in the tissues of tadpoles and disrupt their development.

Your task is to discover the cause, or causes, of deformity in a population of frogs. The frogs vary in number of legs. Some have four legs; others have five.

The population is split across two ponds. You will first determine if there is a difference in the frequency of deformities in the two ponds. If there is a difference, you can take this a clue that will help you pinpoint the cause of deformity.

When there is a difference in the frequency of deformity in the two ponds, it could be due to parasitic worms, genetics, a combination of worms and genetics, or random chance. I know, because I wrote these causes into the different scenarios available in the simulation!

Use the tabs in this section for a quick look at what you can do with FrogPond. Please use this link for a detailed tutorial.

1) The Frogs

In the pane labeled The Frogs you should see a darker gray rectangle at the upper left, containing hundreds of dots. This rectangle is Top Pond. Each of the dots in Top Pond represents an individual. The larger, green dots are adult frogs. The smaller, gray dots are tadpoles. The orange dots are parasitic worms. To get a closer look at a frog or tadpole, click on its dot and hold.

When you click the Start button at the bottom right of the Frogs pane, you’ll see the individuals move around. The frogs will bump into each other and make babies. Eventually, they’ll get old and die. Go ahead and try it. When the simulation is running, the Start button turns into a Stop button—which does what you think!

You can drag individual frogs, tadpoles, or worms to any location in Top Pond. You can also drag them to Bottom Pond or any of the four holding tanks to the right of the ponds. By clicking and dragging inside one of the ponds or tanks—not on an animal it contains—you can select a group of frogs and/or tadpoles, then drag the group anywhere you’d like. (You can only move worms one at a time.)

If you drag animals or groups into the light gray area around the ponds and tanks, you’ll see the individuals fall to the open area below the tanks. You can drag individuals one at a time back into a pond or tank, But once you click Start, any individuals not in a pond or tank will vanish.

2) Phenotypes and Parasites

If you click on and examine enough individuals, you should notice that some of the adult frogs have four legs while others have five.

You should also notice that some of the adult frogs, and some of the tadpoles, have orange dots on them. Others do not have orange dots. The presence of an orange dot on a tadpole or frog indicates that the individual is infected with a parasite.

Note the following:

Infections can only be acquired by tadpoles—not by adult frogs. A tadpole becomes infected when it bumps into a parasite.
Once a tadpole becomes infected, it remains infected for life—even after it turns into a frog.
Infected frogs do not transmit their infection to their offspring. That means that every infected individual acquired its infection on its own—by bumping into a parasite.

Whether infection with the parasite has anything to do with a frog developing five legs varies from scenario to scenario—and is one of questions you will investigate.

3) Scenarios

At the bottom of the Frogs pane, you should see a set of radio buttons labeled Scenario. This determines the cause of deformity—that is, a fifth leg—in the frogs.

The cause of deformity is different in each of the four scenarios. Your challenge is conduct studies to learn the cause of deformity in each one. You can explore the scenarios in any order you like. I would suggest not starting with Scenario Four. In fact, taking the scenarios in order is a good strategy.

In all scenarios, always answer Question 1 first. If you skip straight to Question Two, you may waste a lot of time.

Note: You can reset the simulation any time by clicking on Reset at the upper right of the FrogPond window. This will create a new population of frogs and set the Scenario control to One. Please be aware that on a mobile device, the FrogPond window may refresh—and thus reset—if you open another app, then return to your web browser.

4) Q1

Is there a higher (or lower) frequency of deformed frogs in Top Pond than in Bottom Pond?

The frequency of deformed frogs is their proportional representation in the pond. If six out of ten frogs have an extra leg, then the frequency of deformed frogs is 6 / 10 = 0.6, or 60%.

To answer Question 1, survey the frogs. Start with Top Pond. Pick a frog at random and examine it. If it’= is deformed (has five legs), drag it to the upper left tank (Tank 1). If it’s normal (has four legs), drag it to the upper right tank (Tank 2). Now look at the pane labeled The Analyses. Make sure the Count Frogs tab is selected. This tab has a counter for each pond and tank.

After you have sorted a bunch of frogs, take the number of deformed frogs and divide it by the total number of deformed + normal frogs in Tanks 1 & 2. That will give you an estimate of the frequency of deformed frogs in Top Pond.

Sorting the entire population would be tedious. How many frogs do you think you need to survey to get a reasonably accurate estimate of the frequency of deformities? After you have an estimate you are comfortable with for Top pond, survey Bottom Pond.

Depending on the scenario, there may not be much difference in the frequency of deformity in Top versus Bottom Pond. Any apparent difference may be mostly due to chance—that is, luck-of-the-draw in the frogs you happened to survey. Do you think this is the case? Or is there really a difference between the frequency of deformity in Top versus Bottom Pond?

When finished with your survey, you can return the frogs to their ponds (see under Tab 1 - The Frogs).

If you think any apparent difference in the rate of deformity is just due to chance, your investigation is complete. Deformity just happens, and every frog has the same risk of growning an extra leg. Try a different scenario.

If you think there really is a substantial difference between Top versus Bottom Pond in the frequency of five-legged frogs, proceed to Question 2 (but first read Tab 5—Helper).

5) Helper

You will almost certainly not want to endure the tedium required to survey all the frogs in all ponds and tanks for every study you conduct. Fortunately, you have a devoted and efficient helper who will do the surveys for you. Select the Plot Histograms tab in the Analyses pane. This pane shows histograms revealing the total number of four- and five-legged frogs in every pond and tank.

Please don’t be too upset that I let you sort and count a whole lot of frogs by hand before telling you about the histograms! Having practiced collecting data yourself has given you a deeper appreciation for what the bars in the histograms mean—and why these graphs are useful.

6) Q2

If there is a difference in the frequency of deformed frogs in Top Pond versus Bottom Pond, then what is its cause?

Possible answers include:

Hypothesis 1: The deformities are caused by the worms, and one pond has more worms than the other. That is, the variation in number of legs is environmental—and genetics is irrelevant).
Hypothesis 2: The frogs in one pond are, on average, inherently more prone to deformity than the frogs in the other. That is, the variation in number of legs is genetic—and worms are irrelevant).

Your job is to design and conduct studies that will reveal which answer is correct. Your studies can be observational or experimental. Here are some things you might do:

Examine the frogs, and classify and count them.
Move frogs (and, if you like, worms) from the ponds to the smaller tanks. Run the simulation for a couple of generations. Then classify and count the frogs in your tanks.
Mate particular frogs with each other. Move two frogs to a tank. Encourage them to mate by making sure they are touching each other. Run the simulation for a short time. You will see the parents make tadpoles. Let the tadpoles grow up, then examine them.
Get rid of particular frogs (or worms) by dragging them out of a pond or tank. Then run the simulation.

You will have noticed that I have only told you pieces of what you might do during your studies. I haven’t told exactly what study designs to carry out. That is up to you. I will, however, offer three pieces of general advice. First, an effective way to proceed is to pick one of the two possible answers as your working hypothesis. I suggest you start by investigating Hypothesis 1. Then do something with the frogs. Predict what will happen if your hypothesis is right, and what will happen if it is wrong. Collect data to see what actually happened. Second, you may have to repeat a study a few times before a clear pattern emerges in the data. Third, if your study does not produce a clear outcome, try something different.

7) Apogee

The cause of deformity—of variation in number of legs—is different in each of the four scenarios. My hope is that you will conduct studies that will allow you to infer with confidence what’s going on in all of them—including Scenario Four, which is a little more complicated than the other three.

For more detailed suggestions on study designs, see the FrogPond Tutorial.

Here is the most ambitious challenge you can take on with FrogPond. There is at least one design for an experimental study that will give a different result under all four scenarios. In other words, this experimental design simultaneously tests all possible hypotheses. See if you can discover this experimental design and explain why it works the way it does.

License

I make no warranties or guarantees about the quality of FrogPond or the accuracy of the simulations it runs. Please have fun with it.

FrogPond is free to use. Please share the link. You may not copy, repost, re-use, or sell FrogPond.

If you use FrogPond, or if you have comments or suggestions, please let me know with an email to herronjc at uw.edu.

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