{"id":869,"date":"2023-09-27T22:09:03","date_gmt":"2023-09-28T02:09:03","guid":{"rendered":"https:\/\/pressbooks.bccampus.ca\/ewemodel\/?post_type=chapter&p=869"},"modified":"2026-03-29T17:27:00","modified_gmt":"2026-03-29T21:27:00","slug":"welcome-to-anchovy-bay","status":"publish","type":"chapter","link":"https:\/\/pressbooks.bccampus.ca\/ewemodel\/chapter\/welcome-to-anchovy-bay\/","title":{"raw":"Tutorial: Welcome to Anchovy Bay","rendered":"Tutorial: Welcome to Anchovy Bay"},"content":{"raw":"
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Learning Objectives<\/p>\r\n\r\n<\/header>\r\n

\r\n\r\nBy the end of this tutorial, participants will be able to:\r\n
    \r\n \t
  1. Initiate and Configure a Basic Ecopath Model:<\/strong> Create a new EwE project, define essential functional groups (including primary producers and detritus), and establish relevant fishing fleets for a given ecosystem.<\/li>\r\n \t
  2. Parameterize an Ecopath Model with Diverse Dat<\/strong>a: Input ecological data, including biomass, production-to-biomass (P\/B), consumption-to-biomass (Q\/B) ratios, catch data, and diet compositions, using provided values and deriving estimates from external sources (e.g., FishBase, allometric relationships).<\/li>\r\n \t
  3. Achieve and Interpret Ecopath Mass Balance<\/strong>: Understand the underlying principles of mass balance in Ecopath and utilize the software's tools to iterate towards a balanced model, critically evaluating the estimated ecotrophic efficiencies (EEs) and other output parameters.<\/li>\r\n \t
  4. Perform Initial Model Diagnostics and Exploration<\/strong>: Generate and interpret basic Ecopath outputs, such as \"Basic estimates\" and \"Mixed Trophic Impact,\" to gain preliminary insights into ecosystem structure and trophic interactions.<\/li>\r\n \t
  5. Navigate the EwE Interface for Fundamental Operations<\/strong>: Use the Ecopath with Ecosim (EwE) software to create models, input data, access key diagnostic tools, and conduct simple exploratory changes to model parameters.<\/li>\r\n \t
  6. Recognize Data Requirements and Acquisition Strategies<\/strong>: Identify the specific data types required for Ecopath modeling and understand various practical approaches for acquiring or estimating these data, acknowledging limitations and uncertainties when information is incomplete.<\/li>\r\n<\/ol>\r\n<\/div>\r\n<\/div>\r\n

    \"This<\/p>\r\n

    Figure 1. Simplified basemap of Anchovy Bay from a spatial ecosystem model.\r\nColour gradient indicates depth and the black dots harbours.<\/strong><\/p>\r\nThe 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.\r\n\r\nWe 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.\r\n

    Introduction to Anchovy Bay<\/h2>\r\n

    [pb_glossary id=\"474\"]Anchovy Bay[\/pb_glossary] is a popular tourist attraction with \u00a0its 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.<\/p>\r\nIn 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.\r\n\r\nWe 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 \u2013 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 \u2013 even if it makes conclusions less reliable and leave more questions open for interpretation.\r\n

    Build an ecosystem model<\/h2>\r\n

    Anchovy Bay covers an area of 10,000 km2<\/sup>. For this exercise, we assume that it is rather isolated from other marine systems, and that the populations stay in the bay year-round.<\/span><\/p>\r\n\r\n

    \r\n\r\nAbout navigation in EwE:<\/strong>\r\n\r\nEcopath > Input > Fishery > Landings<\/em> indicates that you should find Ecopath<\/em> in the left-hand side Navigator, then Input<\/em>, then Fishery<\/em>, then the Landings<\/em> tab.\r\n\r\n<\/div>\r\nWe want to create a model of the bay in 1970, with the following 11 groups:\r\n\r\nWhales, seals, cod, whiting, mackerel, anchovy, shrimp, benthos, zooplankton, phytoplankton, detritus. [Hint: make a spreadsheet with these group names in rows, you\u2019ll need to do more calculations later]\r\n\r\nStart by opening EwE6, select Menu > File > New model<\/em>. Browse to your preferred file location, and enter a name for the model. For instance, \u201cAnchovy Bay\u201d. \u00a0Now navigate on the Navigator (left panel) to Input data > Basic Input<\/em>. The model will have one group, Detritus.\r\n\r\nAll 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.\r\n\r\nOn the Basic input form<\/em>, select Define groups<\/em>\u00a0(also available from the menu on top: Ecopath > Define groups<\/em>). Click Edit > Insert<\/em> on the right side of the form that pops up. Continue clicking Insert<\/em>\u00a0 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<\/em>]. When you have entered all, define that phytoplankton is a primary producer by clicking the Producer<\/em> check mark in the phytoplankton row. On the right panel, you may also want to click the Colors > Alternate all,<\/em> to get a better distribution of group colors (more distinguishable in Ecosim). Click OK<\/em>.\r\n
    \r\n\r\nYou can often cut\/paste values to EwE (Ctrl-C, Ctrl-V<\/em> usually works, cut-paste not always).\r\n\r\n<\/div>\r\nWe also need to define the fishing fleets. Click Ecopath > Input > Fishery<\/em> on the Navigator to the left. Then click Fleets<\/em>, and then Define fleets<\/em> above the spreadsheet (or go Menu >Ecopath >Define fleets<\/em>). We want five fleets: sealers, trawlers, seiners, bait boats, and shrimpers. We can enter catches at Ecopath > Input > Fishery > Landings<\/em>; unit has to be t km-2<\/sup> year-1<\/sup>. 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<\/sup> year-1<\/sup>), and enter in EwE.\r\n
    \r\n\r\nUnits are important<\/a>. We all make conversion errors occasionally. Be explicit and check your units (biomass t km-2<\/sup>, flows t km-2<\/sup> year-1<\/sup>). Conversion errors are the most common cause of problems with this tutorial.\r\n\r\n<\/div>\r\nThe off-vessel landing prices (Ecopath > Input > Fishery > Off-vessel price<\/em>) are seals $6 kg-1<\/sup>; cod: $10 kg-1<\/sup>; whiting $6 kg-1<\/sup>; mackerel: $4 kg-1<\/sup>; anchovy from seiners $2 kg-1<\/sup>, and $3 kg-1<\/sup> for bait boats. Shrimps are $20 kg-1<\/sup>. [While landings are in t, it is fine for now to enter landing prices in $\/kg to avoid the extra \u2018000s]. Prices are current prices (hence \u201care\u201d instead of \u201cwere\u201d) 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<\/a>, ask around, or guess!\r\n\r\nWe 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<\/sup>. 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<\/sup>. Zooplankton: 14.8 t km-2<\/sup>, detritus 10 t km-2<\/sup>.\r\n\r\nNext are production\/biomass (P\/B) ratios, which with certain assumptions (that we won\u2019t worry about now) correspond to the total mortality, Z.<\/em>\u00a0The P\/B are annual rates, so the unit is year-1<\/sup>. We often can get Z<\/em> from assessments, or, alternatively, we have Z = F + M<\/em> (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<\/em> and add the total natural mortality, M, to get Z<\/em>.\r\n\r\nFor fish, we can get estimates of M<\/em> and Q\/B<\/em> from FishBase<\/a>. On the FishBase landings page, search for the species, (Gadus morhua, Scomber scombrus, Engraulis encrasicolus<\/em>), one by one. From the species info screen for each, go to Tools > Life-history tool<\/em>, and extract the Q\/B<\/em> and M<\/em> values for each. Estimate Z = F + M<\/em>. For whiting (Merlangius merlangus<\/em>), we have local estimates of P\/B = 0.58 year-1 <\/sup>and Q\/B = 3.1 year-1<\/sup>.\r\n\r\nFor estimating Z<\/em> for exploited species, it is also an option to use an equation that was developed by Ray Beverton and Sidney Holt[footnote]Beverton, R.J.H. and Holt, S.J. 1957. On the dynamics of exploited fish populations. Fisheries Investigations, 19, 1-533.[\/footnote]. It is implemented in the life-history tool table in FishBase. It relies on estimates of length at first capture (Lc<\/sub><\/em>), average length in the catch (Lmean<\/sub><\/em>), and asymptotic length (Linf<\/sub><\/em>) to estimate Z<\/em>. Try it for the three species here. Here are the lengths from the fishery in Anchovy Bay:\r\n\r\n\r\n\r\n\r\n\r\n\r\n
    <\/td>\r\nLc<\/sub>\u00a0(cm)<\/td>\r\nLmean<\/sub> (cm)<\/td>\r\n<\/tr>\r\n
    Cod<\/td>\r\n52<\/td>\r\n72<\/td>\r\n<\/tr>\r\n
    Mackerel<\/td>\r\n18.9<\/td>\r\n26<\/td>\r\n<\/tr>\r\n
    Anchovy<\/td>\r\n6.8<\/td>\r\n10<\/td>\r\n<\/tr>\r\n<\/tbody>\r\n<\/table>\r\n
    \r\n\r\nCompare the P\/B = Z<\/em> estimates from the two methods (and consider = decide what to use). Maybe even try both estimates in Ecopath?\r\n\r\n<\/div>\r\n

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

    The inverse of <\/span>P\/B<\/em> (year<\/span>-1<\/sup>), i.e. <\/span>B\/P<\/em> has the unit year and expresses average longevity. As an example, whales with <\/span>P\/B<\/em> = 0.05 year<\/span>-1<\/sup>, have a <\/span>B\/P<\/em> ratio (and hence average longevity) of 20 years.<\/span><\/div>\r\n
    \r\n\r\nWe can get P\/B<\/em> for many invertebrates from Tom Brey\u2019s work (but don\u2019t need to for this tutorial). Check out: http:\/\/www.thomas-brey.de\/science\/virtualhandbook\/<\/a>. There is a neat collection of empirical relationships and conversion factors. \u00a0Also check SeaLifeBase<\/a>.\r\n\r\n<\/div>\r\n

    Consumption\/biomass (Q\/B) ratios for the non-fish groups: for whales use 9 year-1<\/sup>, and for seals 15 year-1<\/sup>. For the invertebrates enter a P\/Q<\/em> ratio of 0.25 instead of entering a Q\/B<\/em>.<\/p>\r\n\r\n

    \r\n\r\nSo, why enter P\/Q instead of Q\/B? When P\/Q is an input, Ecopath will estimate Q\/B = (P\/B)\/(P\/Q). \u00a0This makes it explicit that we haven't bothered to find a Q\/B, but instead use the reasonable assumption that Q\/B = 4 x P\/B. \u00a0We know that organisms only convert a fraction of their energy intake to production. For fish that fraction typically is 0.1-0.3, generally it relates to size where smaller organisms convert more efficiently than larger.\r\n\r\n<\/div>\r\n

    Finally, there is phytoplankton. We can often get primary production estimates from SeaWiFS satellite data. Here we have PP<\/em> = 240 gC m-2 <\/sup>year-1<\/sup>. The conversion factor from gC to gWW is 9, so the total production, P<\/em>, is 9 * 240 t km-2 <\/sup>year-1<\/sup>. You can set P\/B<\/em> to 120 year-1<\/sup>, and calculate B<\/em>. The 120 year-1<\/sup> 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<\/em> is actually used in calculations. (Very high P\/B<\/em> values may, however, make Ecospace runs dizzy).<\/p>\r\n

    Next parameter is Ecotrophic Efficiency<\/em> (EE<\/em>), 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<\/em> = 0.6. For the other groups, we let Ecopath estimate the EE<\/em>s, but bear in mind the definition of EE<\/em> when you evaluate the estimated parameters.<\/p>\r\n

    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<\/em> form by entering a biomass accumulation rate of 0.02 year-1<\/sup> for whales, and \u20130.05 year-1<\/sup> for seals.<\/p>\r\n

    Now it\u2019s time for diets:<\/p>\r\n[table id=17 \/]\r\n

    \r\n\r\nYou should be able to cut-paste (Ctrl-C, Ctrl-V<\/em>) from the spreadsheet above to the Ecopath diet screen. Or, you can download a spreadsheet with the diets from this link<\/a>.\r\n\r\n<\/div>\r\nWe now have the information that is needed to do mass-balance on this model. Select <\/span>Output > Basic estimates<\/em>, and check out the outcome. Save the model.<\/span>\r\n
    \r\n
    \r\n

    Try changing some of the input and see what happens. Don\u2019t save afterwards.<\/p>\r\n

    Check out Network analysis (Ecopath > Output > Tools > Network analysis<\/em>), especially, see the Mixed Trophic Impact<\/em> plot<\/p>\r\n

    Go to Ecosim > Output > Run Ecosim > Run<\/em>, and see what happens.<\/p>\r\n

    Explore the software.<\/p>\r\n\r\n<\/div>\r\nOptionally and time permitting, here are some suggestions for things to try.\r\n\r\n<\/div>\r\n

    \r\n

    Network analysis: Mixed Trophic Impact<\/p>\r\n\r\n<\/header>\r\n

    \r\n\r\nNetwork analysis<\/a> is a research field often categorizing networks based on stock and flow properties. Output is often indicators of ecosystem state, performance and function. \u00a0Explore the Network analysis available at Ecopath > Output > Tools > Network analysis\u00a0<\/em>for instance the Cycles and pathways, <\/em>which identifies all cycles and pathways in the model. \u00a0Or the Lindeman spline<\/em>.\r\n\r\nWe'll focus though on a key network module in EwE. the Mixed Trophic Impact<\/a> (MTI) analysis. MTI originates in the Nobel Prize work of Leontif[footnote]Leontief, W. W., 1951. The Structure of the U.S. Economy. Oxford University Press, New York.[\/footnote] to assess demand-supply and direct and indirect interactions in the economy of the USA, using what has since been called the Leontief matrix or input-output model. In Ecopath network analysis, we have incorporated a derived approach developed by Ulanowicz and Puccia,[footnote]Ulanowicz, R. E., and Puccia, C. J. 1990. Mixed trophic impacts in ecosystems. Coenoses, 5:7-16.[\/footnote] to quantify direct and indirect trophic impacts in an ecosystem.\r\n\r\nYou can find the MTI analysis at Ecopath > Output > Tools > Network analysis > Mixed Trophic Impacts > Mixed trophic impact plot<\/em> where\u00a0Options<\/em> let you change Data<\/em> to Colours<\/em> and\u00a0Plot > Fit to available area<\/em> as options.\r\n\r\nIn the plot, red colours indicate negative competition effects and blue colours positive. The effects are relative and comparable across the ecosystems (fleets included). \u00a0You can think of the effects as addressing the question: \"if we were to change the biomass of the groups mentioned to the right of each row and infinitesimal[footnote]\"infinitesimal\" to indicate a small change that doesn't impact food availability noticeably.[\/footnote] amount, what impact would this have on the groups listed above each column?\"\r\n\r\nTrace the simple connections between predators and prey to find direct impacts, notice how the diagonal indicates within-group competition.\r\n\r\nCan you find any examples of what Sheila Heymans called \"beneficial predation\", i.e where a group preys on another group but still has a positive impact on the prey?[footnote]Spoiler alert: check whales' or mackerel's MTI and diet [\/footnote]\r\n