We will, once again, use the ecosystem model of Anchovy Bay that we constructed in a previous tutorial (if need be, you can download it from this link). The purpose of this exercise is to incorporate non-trophic effects through mediation.

Mediation

Ecosim can incorporate non-trophic effects through what we call ‘mediation’. Ecospace can use such mediation functions that are defined in Ecosim as they are non-spatial. Examples can be that phytoplankton causes shading that may have negative impact on kelp, or that bottom trawls can smash bivalves, and thus make them accessible to, e.g., crabs.

Open the Anchovy Bay model, then open a new scenario in Ecosim, (and name it, e.g., “mediation”). Go to Ecosim > Output > Run Ecosim, and run the model. Does the model run show whales increasing and seals decreasing? It should; it’s because of the biomass accumulation rates, we provided. Next load the Anchovy Bay time series (saved version is fine, if not available then read in the Anchovy Bay time series file again^[1]). Run the Ecosim model again, and check that seals are now increasing (due to stop of sealing). Take note of the end biomass of adult mackerel and of anchovy, (you can get it from Ecosim > Output > Ecosim results). Also, on the Ecosim run form, click Show multiple runs on the bar above the graph, and do another run. Ecosim will now keep the runs in memory to make it easy to compare trends between runs.

We now pretend that seals somehow scare mackerel away so that they have less access to anchovy as prey. Perhaps the seals hang around the anchovy schools to feed on approaching mackerel schools? (It’s not a very realistic example of mediation, but it can illustrate the principles only). We will set up this mechanism in Ecosim next.

Go Ecosim > Input > Mediation. There should be one mediation shape (1: Mediation shape 1 – you can change the name to something more instructive by clicking on Values (or double clicking the name) and then write another name, e.g., seal-mackerel-anchovy). We’ll set this up so that the X-axis is relative biomass of seals, and Y-axis is the relative feeding rate of ad. mackerel on anchovy. The stippled vertical line represents the Ecopath baseline, so unity (relative value of 1) is where this stippled line is placed (you can move it). Now click Change shape, select Sigmoid, and it’s probably fine as is. If not play with numbers). Click OK to close the form. Next click Define mediating groups and fleets, click seals and the arrow to the right to move Seals over to Assigned groups and fleets). Click OK.

Next, we need to define what it is that seals are impacting through mediation. For this, click Mediation (consumer), and click on the cell with adult mackerel as predator and anchovy as prey. Select the 1: seal-mackerel-anchovy mediation function, click the arrow to the right, to assign this shape to the mackerel – anchovy interaction. Leave the Apply multiplier to: on Search rate (a), this will impact the search rate of adult mackerel, and with this their consumption rate of anchovy as seals biomass changes. Click OK.

Run Ecosim again, and compare the end biomass of adult mackerel and of anchovy without and with mediation.

Try experimenting with different shapes and try moving the vertical blue dotted line (the Ecopath baseline reference) and check for what impact it makes. How can one go about getting shapes for mediation functions in a “real” application?

Optional:

Add a new group to the Anchovy Bay model: kelp. Use a P/B of 7 year^-1, and a B of 5 t km^-2, and add a new fleet “kelpers” that harvest kelp at a rate of 1 t km^-2 year^-1. Kelp serves as refugia and foraging arena for juvenile fish and some invertebrates. For illustration of the method, assume that shrimp hide for cod in the kelp. Create a new mediation function and define it as we did in the tutorial above.

Then try to increase fishing for the kelpers, and evaluate the impact this has on shrimp.

Try alternative mediation shapes and reflect on what you consider a reasonable shape to use.