Tutorial: Welcome to Anchovy Bay

Figure 1. Simplified basemap of Anchovy Bay from a spatial ecosystem model.
Colour gradient indicates depth and the black dots harbours.

The purpose of this tutorial is to introduce you to the Ecopath with Ecosim (EwE) software, explore what data is required, give examples of where you can get such data, and go through the steps that typically are required when constructing a model.

We acknowledge that if you are new to the subject area, you will struggle with this tutorial, but we've built is so that it takes you through it step by step with explanations as you go along, and we expect that you, with a bit of effort, will be able to work your way through it. Please take it as an introduction, when we later introduce and describe all the bits and pieces in detail, you'll have a better idea of how they fit together when you've done this tutorial.

Introduction to Anchovy Bay

Anchovy Bay is a popular tourist attraction with  its century-old fishing port. Fisheries have traditionally been the mainstay of the area, but catches have declined for decades and shifted from a focus on groundfish to being dominated by shrimp and pelagics.

In recent years, a whale-watching industry has developed linked with growing interest in eco-tourism and recovery of marine mammal populations after earlier periods of whaling and culling.

We will use Anchovy Bay as a "model ecosystem" throughout this textbook. Anchovy Bay is in many ways ideal for this as it is is well-studied – to the degree where we have excellent information about the resources in the bay, about how the environment has changed, and of how fisheries and other factors impacting the ecosystem have developed in recent history. The exercises will use variable amounts of information, starting simple (and thereby illustrating the impact of, e.g., missing important drivers) for gradually to include more and more data. This is to simplify the presentation and analysis, but also to illustrate that one can still work with incomplete information – even if it makes conclusions less reliable and leave more questions open for interpretation.

Build an ecosystem model

Anchovy Bay covers an area of 10,000 km². For this exercise, we assume that it is rather isolated from other marine systems, and that the populations stay in the bay year-round.

We want to create a model of the bay in 1970, with the following 11 groups:

Whales, seals, cod, whiting, mackerel, anchovy, shrimp, benthos, zooplankton, phytoplankton, detritus. [Hint: make a spreadsheet with these group names in rows, you’ll need to do more calculations later]

Start by opening EwE6, select Menu > File > New model. Browse to your preferred file location, and enter a name for the model. For instance, “Anchovy Bay”.  Now navigate on the Navigator (left panel) to Input data > Basic Input. The model will have one group, Detritus.

All models must have a detritus group, so we have entered it for you. Why? We need to be sure there is a group where we can send flows of excreted and egested material as well as dead organism. By default, they go to the detritus group.

On the Basic input form, select Define groups (also available from the menu on top: Ecopath > Define groups). Click Edit > Insert on the right side of the form that pops up. Continue clicking Insert  till you have 11 groups; then enter the group names, i.e., Whales in first row, Seals in second, etc. [Hint: you can cut and paste the names in one go from Excel, using Ctrl-C Ctrl-V]. When you have entered all, define that phytoplankton is a primary producer by clicking the Producer check mark in the phytoplankton row. On the right panel, you may also want to click the Colors > Alternate all, to get a better distribution of group colors (more distinguishable in Ecosim). Click OK.

We also need to define the fishing fleets. Click Ecopath > Input > Fishery on the Navigator to the left. Then click Fleets, and then Define fleets above the spreadsheet (or go Menu >Ecopath >Define fleets). We want five fleets: sealers, trawlers, seiners, bait boats, and shrimpers. We can enter catches at Ecopath > Input > Fishery > Landings; unit has to be t km^-2 year^-1. The sealers caught 1,500 seals in 1970 with an average weight of 30 kg. The fisheries catches were 4,500 t of cod and 2,000 t of whiting for the trawlers, 4,000 t of mackerel and 12,000 t of anchovy for the seiners, 2,000 t of anchovy for the bait boats, and 5,000 t of shrimp for the shrimpers. Calculate catches using the appropriate unit (t km^-2 year^-1), and enter in EwE.

The off-vessel landing prices (Ecopath > Input > Fishery > Off-vessel price) are seals $6 kg^-1; cod: $10 kg^-1; whiting $6 kg^-1; mackerel: $4 kg^-1; anchovy from seiners $2 kg^-1, and $3 kg^-1 for bait boats. Shrimps are $20 kg^-1. [While landings are in t, it is fine for now to enter landing prices in $/kg to avoid the extra ‘000s]. Prices are current prices (hence “are” instead of “were”) as we later will be using these for forward projections. If you lack catch or price information for your own models later, then search, check www.seaaroundus.org, ask around, or guess!

We now should enter the basic input parameters. Fortunately, there has been monitoring in the bay for decades, and we have some biomass survey estimates from 1970. The biomasses must be entered with the unit t km^-2. Whales: 50 individuals with an average weight of 16,000 kg. Seals: 20,300 individuals with an average weight of 30 kg. Cod: 30,000 t. Whiting 18,000 t. Mackerel: 12,000 t. Anchovy: 70,000 t. Shrimp: 0.8 t km^-2. Zooplankton: 14.8 t km^-2, detritus 10 t km^-2.

Next are production/biomass (P/B) ratios, which with certain assumptions (that we won’t worry about now) correspond to the total mortality, Z. The P/B are annual rates, so the unit is year^-1. We often can get Z from assessments, or, alternatively, we have Z = F + M (i.e. we can estimate total mortality as the sum of fishing mortality, F and natural (predation) mortality, M). So, if we have the catch (C) and the biomass (B), we can estimate F = C/B and add the total natural mortality, M, to get Z.

For fish, we can get estimates of M and Q/B from FishBase. On the FishBase landings page, search for the species, (Gadus morhua, Scomber scombrus, Engraulis encrasicolus), one by one. From the species info screen for each, go to Tools > Life-history tool, and extract the Q/B and M values for each. Estimate Z = F + M. For whiting (Merlangius merlangus), we have local estimates of P/B = 0.58 year^-1 and Q/B = 3.1 year^-1.

For estimating Z for exploited species, it is also an option to use an equation that was developed by Ray Beverton and Sidney Holt^[1]. It is implemented in the life-history tool table in FishBase. It relies on estimates of length at first capture (L_c), average length in the catch (L_mean), and asymptotic length (L_inf) to estimate Z. Try it for the three species here. Here are the lengths from the fishery in Anchovy Bay:

There is a close relationship between size and P/B; the bigger animals are, the lower the P/B. Here we have: Whales: P/B = 0.05 year^-1; seals: get F from catch, and M is 0.09 year^-1; shrimp P/B = 3 year^-1; benthos P/B = 3 year^-1; zooplankton: it is mainly small Acartia-sized plankton, with P/B = 35 year^-1.

Consumption/biomass (Q/B) ratios for the non-fish groups: for whales use 9 year^-1, and for seals 15 year^-1. For the invertebrates enter a P/Q ratio of 0.25 instead of entering a Q/B.

Finally, there is phytoplankton. We can often get primary production estimates from SeaWiFS satellite data. Here we have PP = 240 gC m^-2 year^-1. The conversion factor from gC to gWW is 9, so the total production, P, is 9 * 240 t km^-2 year^-1. You can set P/B to 120 year^-1, and calculate B. The 120 year^-1 is a guess, assuming that phytoplankton divides once per day in the productive part of the year (so less than 360/year), and is not very important as only the production, P = P/B * B is actually used in calculations. (Very high P/B values may, however, make Ecospace runs dizzy).

Next parameter is Ecotrophic Efficiency (EE), this is the part of the production that is used in the system (or rather, for which the model explains the fate of the production). In this model, we are missing a biomass estimate for benthos. We do not explain much of the mortality for this group, so we guess an EE = 0.6. For the other groups, we let Ecopath estimate the EEs, but bear in mind the definition of EE when you evaluate the estimated parameters.

In the Ecopath baseline year, the whale population had started to recover after whaling, but the seal population was still declining, so the Ecopath baseline model is not in steady state. We specify this on the Input data > Other production form by entering a biomass accumulation rate of 0.02 year^-1 for whales, and –0.05 year^-1 for seals.

Now it’s time for diets:

We now have the information that is needed to do mass-balance on this model. Select Output > Basic estimates, and check out the outcome. Save the model.