For this workshop, you will be using a simulator of coupled populations of hosts and their parasites.
Create a new document to complete this exercise in. You may work alone or with your tablemates. If working together, you can collaborate using a shared Google Doc.
The simulation was inspired by the Red Queen Game created by Amanda K. Gibson, Devin M. Drown, and Curtis M. Lively (2015)
This is a simulation of a population of host organisms coupled with a population of parasites that infect them.
Hosts and parasites have ‘genotypes’ that consist of one allele.
When host and parasite alleles match, the parasite has a chance to infect and kill a host. When the alleles are mismatched, the host wins and the parasite dies.
Take a moment to read the ‘About the Model’ section of the simulator page.
Read sections 1, 2a, and 2b of Brockhurst et al. (2014) to review the basics of the Red Queen hypothesis and three modes of Red Queen dynamics. Note the summary and comparison of the three mechanisms in Table 1.
Discuss with your neighbors and write down the answers in your workshop document.
Click here to open the simulator in a new tab.
Notice that the simulation initializes with a population of size 12, 4 alleles, 90% infection mortality, host fertility of 1 and parasite fertility of 2.
Using the default settings, click the play button and observe the patterns that develop in the output plot over several generations. You should evolve the simulation for 50 generations.
Save an image of the output plot and paste it into your workshop document (Figure 1).
Reset the simulator and run another simulation. Save this image and paste it into your document as well (Figure 2).
What do you notice about the dynamics of hosts and parasites in the two simulations?
What is similar and different about the plots of the two simulations? Think qualitatively and quantitatively:
Now see what happens when you increase the population size to 100, keeping all other parameters the same.
Let’s explore what happens when we adjust the reproductive rates of the hosts and parasites.
Using a population size of 100, first see what happens when you increase the fertility of hosts. Paste a figure into your document (Figure 3).
Now, reset the host fertility to 1 and see what happens when you increase the fertility of the parasites Paste a figure into your document (Figure 4).
Next, set the fertility rate to zero for both hosts and parasites, run a simulation, and save a figure (Figure 5).
Reset the fertility rates to the default values and adjust the mortality rate to 50% and save a figure in your document (Figure 6).
Finally, decrease the mortality rate to 30% and rerun the simulation. You may want to run the simulation for more than 50 generations, possibly up to 500 or more. Save another figure (Figure 7).
Compare the figures from your simulations (Figures 3 - 7) and answer the following, comparing your simulations to simulations using the default parameters (Figures 1 and 2).
Now explore different parameter combinations on your own and see what different kinds of dynamics are produced in the system.
After you have explored the parameters, select a simulation with an interesting pattern, paste a figure into your report (Figure 8) and describe (in plain English) what you observed in the simulation.
Interpret the patterns in Figure 8 in terms of the coevolutionary trajectory of the host and parasite species.
Refer back to the table 1 in the Brockhurst et al. paper. Which of the three types of Red Queen dynamics best matches what you observe in the simulations in this workshop? Explain your answer.