AlleleA1: Ducks & Gators

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Overview

The duck pond is home to a population of virtual ducks, as well as a small number of alligators. When you click the start button, the ducks will swim around. If a duck gets too close to a gator, the gator may eat the duck. Go ahead and try it.

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

1) Customize model ducks

You can customize the model duck population:

First, you can modify the genetic model—that is, you can change the relationship between genotype and phenotype. After ‘Duck phenotypes,’ use the three pop-up color menus to select a color (phenotype) for each duck genotype.
Second, under ‘Number of gators,’ you can set the overall intensity of predation by choosing from 0 to 12 gators. Note that the location of the gators changes along with the number. This means that every version of your model has slightly different predation rates.

2) Meausure fitness

Now you can measure how genotype affects Darwinian fitness in your model ducks:

Make sure the ‘Measure Fitness’ tab is selected.
Pick a genotype to assess using the radio buttons.
Click the ‘New ducks’ button to make sure your population contains 100 ducks.
Click the ‘Start’ button. The ducks will swim around the pond for 360 timesteps—which equals one generation. Some of the ducks will get eaten.
The fraction still alive when the simulation stops is a measure of the fitness of ducks with the genotype you are testing. Make a note of it.
Assess and make note of the fitnesses of the other two genotypes as well.
Note that if you change anything about your model—the phenotype associated with each genotype, the number of gators, or where the gators are sitting—the fitnesses of the genotypes will also change. This means you’ll have to measure them again.

3) Check prediction

You are now in a position to check how well the theory of population genetics can predict how your duck population will evolve across many generations:

Select the ‘Monitor Evolution’ tab. Adjust the starting frequency of Allele A1 in your ducks. You can also change the population size. You can get a new population by clicking on the ‘New ducks’ button.
The line on the graph in the ‘Analysical Model’ panel shows the prediction for how the duck population will evolve. This prediction is made using the arithmetic of the Hardy-Weinberg Equilibrium Principle.
- Set the starting frequency for the prediction to match what it is for your virtual ducks.
- Set the fitnesses of the three genotypes to match the values you measured for your ducks.
- Note whether the graph predicts that the frequency of A1 will rise or fall—and how quickly.
Finally, click the ‘Start’ button. Your ducks will swim around for 360 timesteps. Then the survivors will mate at random, lay eggs, and die. (To match the assumptions of the HWEP, we are assuming that generations do not overlap in our virtual ducks.) After a brief incubation period, the eggs will hatch into a new generation of ducks. The blue dots and dashed lines on the graph will show how the frequency of A1 actually changes across 15 generations.
How accurate was the prediction for your ducks? How might you improve it?

4) Gene drive

You may have noticed a small checkbox, near the lower-right corner of the duck pond, labeled ‘A1 is a gene drive.’ A gene drive is an engineered genetic construct that contains, among other things, genes for the components of the CRISPR-Cas9 gene editing machinery. Once inserted into a chromosome, the gene drive copies itself to the same location on any homologous chromosome that does not already contain it. In simpler language, a gene drive is an allele that cheats at the game of Mendelian inheritance. When it finds itself inside a heterozygote, it makes sure that all the gametes the heterozygote produces carry copies of the allele—not merely half of them. Try setting Allele A1 to behave like a gene drive. What effect does it have on how the population evolves? How important, in determining the outcome, are the fitnesses associated with the three genotypes?

Reset

If—at any point—you want to reset, click the ‘Reset’ link in the navigation bar. On some browsers, this may work better than refreshing the window.

License

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

Ducks & Gators is free to use. Please share the link. You may not copy, repost, reuse, or sell Ducks & Gators.

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

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Duck Pond

Analytical Model