Tutorial 1: Anchovy Bay model

Anchovy Bay: an imaginary ecosystem model
The purpose of this exercise is to introduce you to the Ecopath with Ecosim software, version 6 (EwE6), explore what data is required, and give examples of where you can get such data.
Anchovy Bay is a popular tourist attraction due to its century-old fishing port and its newer whale-watching industry. The fisheries have declined over the last decades, and have shifted from a focus on groundfish to being dominated by shrimp and pelagic fisheries.
The bay covers an area of 100 km2 and is rather isolated from other marine systems, and we can assume that the populations stay in the bay year-round. We here create a model of the bay in 1970, and we will in later exercises model the period from 1970 up to the present, as well as explore spatial modeling. But first we need to create a model. Our model will have 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 some more calculations later]
Start by opening EwE6, select File, New model. Browse to your preferred file location, and enter a name for the model. For instance, “Anchovy Bay”. 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 excreted and egested material as well as dead organism. By default they go to the detritus group.
Select Ecopath from the menu on top, and then Edit groups. Click Insert on the right side of the form that pops up. Continue clicking 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 from Excel, using Ctrl-C and Ctrl-V]. When you have entered all, click 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. Click OK.
We also need to define our fishing fleets. Click Fishery on the Navigator to the left. Then click Definition of fleets, and then Edit fleets above the spreadsheet (or click Ecopath on the top menu, and then Edit fleets). We need five fleets: sealers, trawlers, seiners, bait boats, and shrimpers. We can enter catches while we are here; unit has to be t/km2/year. The sealers caught 15 seals in 1970 with an average weight of 30 kg. The fisheries catches were 45 t of cod and 20 to of whiting for the trawlers, 40 t of mackerel and 120 t of anchovy for the seiners, 20 t of anchovy for the bait boats, and 50 t of shrimp for the shrimpers. Calculate catches using the appropriate unit, and enter in EwE.
The off-vessel landing prices are seals $6/kg; cod: $10/kg; whiting$6/kg; mackerel: $4/kg; anchovy from seiners $2/kg, and $3 /kg for bait boats. Shrimps are $20/kg. 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 check
We now should enter the basic input parameters. Fortunately, the biologists have been busy, and we have some survey estimates from 1970 of biomasses in the bay. The biomasses must be entered with the unit: t/km2.
Whales: 10 individuals with an average weight of 800 kg. Seals: 203 individuals with an average weight of 30 kg. Cod: 300 t. Whiting 180 t. Mackerel: 120 t. Anchovy: 700 t. Shrimp: 0.8 t/km2. Zooplankton: 14.8 t/km2. Detritus 10t/km2.
Next are production/biomass ratios, which with certain assumptions (that we don’t worry about now) correspond to the total mortality, Z. The unit is year-1, and we can often get Z from assessments. Alternatively, we have Z = F + M, so if we have the catch and the biomass, we can estimate F = C/B and add the total natural mortality to get Z.
We do this for the fish where we can get an estimate of M and Q/B from FishBase, (try or (Note also that has information for non-fish species.) Search for the species, (Gadusmorhua, Merlangiusmerlangus, Scomberscombrus, Engraulisencrasicolus), find the life-history table, and extract the values. Estimate Z = F + M.
It is also an option for exploited species to use an equation for estimation of Z that was developed by Beverton and Holt (1957). It is implemented in the life-history table in FishBase. It relies on estimates of length at first capture (Lc), average length in the catch (Lmean), and asymptotic length (Linf) to estimate Z. Try it for the four fish species in our model. Here are the lengths from the fishery in Anchovy Bay:
Lc(cm) / Lmean (cm)
Cod / 52 / 72
Whiting / 17.1 / 26.5
Mackerel / 18.9 / 26
Anchovy / 6.8 / 10
Compare the Z estimates from the two methods (and consider).
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.
We can get P/B for many invertebrates from Tom Brey’s work (but don’t need to for this tutorial). Check out: There is a neat collection of empirical relationships and conversion factors.Tom Brey's spreadsheet is available on this website for download (EmpRelat04.xls)
Consumption/biomass 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/m2/year. The conversion factor from gC to gWW is 9, so an easy way to parameterize this is to enter a biomass of 9 t/km2 for phytoplankton and a P/B of 240/year. EwE only uses the product of these, so it doesn’t really matter how they are distributed, but the P/B indicates a turnover of less than once per day, which is reasonable.
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 the start situation the whale population had started to recover after whaling, but the seal population was still declining. We specify this by entering an EE of 0.4 for whales and of 0.35 for seals. When we run the parameterization later, EwE will ask if you want to estimate biomass accumulation for these groups; you do. For benthos, we are missing a biomass estimate. We do not explain much of the mortality for this group, so guess an EE = 0.6.
Now it’s time for diets:
Prey \ predator 12 3 4 5 6 7 8 9
1 Whales
2 Seals
3 Cod.1 .04 .05
4 Whiting .1 .05 .05 .05
5 Mackerel .2 .05
6 Anchovy.5 .1 .45.5
7 Shrimp.01 .01 .01
8 Benthos.1 .9 .84 .44 1 .1
9 Zooplankton.45 1 .1
10 Phytoplankton.1 .9
11 Detritus.7 .1
[note that predators are listed by column, and that the diets some to 1. For instance, #1 whales eat 0.10 cod, 0.10 whiting, 0.20 mackereland so on]
We now have the information that is needed to do mass-balance on this model. Select Parameterization, Basic estimates, and check out the outcome. Save the model.
Try changing some of the input and see what happens. Don't save afterwards.
Go to Time dynamic (Ecosim), Output, RunEcosim. Click Run, and see what happens.