Ecosystem models review

1. Ecopath with Ecosim (EwE) models

  • Recommendation from Desiree Tommasi: Laura Koehn’s 2016 paper and project GitHub repository

    • The authors developed a food web model with high taxonomic resolution of forage fish and their predators in the California Current

    • The study comprehensively described trophic linkages involving forage fish and examine the ecological role of forage fish in the ecosystem

    • The authors used Ecopath model with 92 living functional groups and used a Monte Carlo approach to characterize parameter uncertainty

    • The model can be used to support generalized equilibrium trade-off analysis or dynamic modeling to identify specific predators that would be of conservation concern under conditions of future forage fish depletion

  • Other available EwE models from EcoBase: a database of Ecopath with Ecosim models

    • model.country is “United States”, “united States of America”, or “United States of America”

    • model.ecosim is TRUE or NA

    • model.fisheries is TRUE or NA

Table 1. Ecosystem information of available EwE models.
model.model_number model.model_name model.country model.ecosystem_type model.num_group model.model_year model.model_period
2 Alaska, Prince William Sound United States of America bay/fjord 19 1980 9
252 Aleutian Islands United States of America continental shelf 40 1963 0
768 Apalachicola Bay United States Estuary 54 2000 50
34 Chesapeake United States of America bay/fjord 45 1950 0
35 Chesapeake present United States of America bay/fjord 45 2002 0
183 Eastern Bering Sea United States of America open ocean 25 1979 6
16 Eastern Bering Sea 1950 United States of America open ocean 25 1955 5
764 Florida Bay United States Estuary 47 2006 11
442 Heymans_1963_EAleutians_CGulfAlaska United States of America open ocean 40 1963 0
269 Looe Key National Marine Sanctuary United States of America coral reef 20 1980 9
753 Narragansett Bay food web United States Estuary 15 1994 25
521 Northern Californian Current United States of America upwelling 65 1990 10
279 Prince William Sound United States of America bay/fjord 48 1994 2
438 South East Alaska United States of America continental shelf 40 1963 0
729 Tampa Bay United States Estuary 74 2005 5
153 Tampa Bay United States of America bay/fjord 52 1950 54
173 West Florida Shelf United States of America continental shelf 59 1997 1
755 West Florida Shelf United States of America continental shelf 83 1985 33
727 West Florida Shelf Historic Model United States Continental shelf 70 1950 60
Table 2. Model information of available EwE models.
model.model_number model.model_name model.ecosim model.ecospace model.whole_food_web model.fisheries model.aquaculture model.environment_variability model.ecosyst_functioning model.pollution model.dissemination_allow model.is_fitted model.other_impact_assessment
2 Alaska, Prince William Sound true false true true false false false false true false false
252 Aleutian Islands true false true NA NA NA NA NA true NA NA
768 Apalachicola Bay true true false true false true false false true true false
34 Chesapeake true false true NA NA NA NA NA true NA NA
35 Chesapeake present true false true true false false false false false NA NA
183 Eastern Bering Sea true false true NA NA NA NA NA true NA NA
16 Eastern Bering Sea 1950 true false true true false false true false false NA NA
764 Florida Bay true false false true false true true false true false false
442 Heymans_1963_EAleutians_CGulfAlaska true false true true false false true false false NA NA
269 Looe Key National Marine Sanctuary true false true true false false false false true false false
753 Narragansett Bay food web true false false true true true true false true true false
521 Northern Californian Current true false true true false false false false true false false
279 Prince William Sound true true true NA NA NA NA NA true false NA
438 South East Alaska true false true NA NA NA NA NA true NA NA
729 Tampa Bay true false false true false true false false true true true
153 Tampa Bay true true true NA NA NA NA NA true NA NA
173 West Florida Shelf true false true true false true true false false NA NA
755 West Florida Shelf true true false true false false false false true true true
727 West Florida Shelf Historic Model true false false true false false false false true true false
Table 3. Conatact information of available EwE models.
model.model_number model.model_name model.author model.contact model.reference model.url model.doi
2 Alaska, Prince William Sound Dalsgaard, J. Dalsgaard J.,Pauly D.,Okey T.A.(1997). Preliminary mass-balance model of Prince William Sound, Alaska, for the pre-spill period, 1980-1989 Fisheries Centre Research Reports http://publications.oceans.ubc.ca/node/3840 NA
252 Aleutian Islands Guénette, S. Guénette S.,Heymans S.J.J.,Christensen V.,Trites A.W.(2006). Ecosystem models show combined effects of fishing, predation, competition, and ocean productivity on Steller sea lions (Eumetopias jubatus) in Alaska Canadian Journal of Fisheries and Aquatic Sciences. pp 2495-2517 http://www.nrcresearchpress.com/doi/abs/10.1139/f06-136 NA
768 Apalachicola Bay Kira Allen Allen 2022 https://stars.library.ucf.edu/etd2020/1355/ NA
34 Chesapeake Christensen, V. Christensen V.,Beattie A.,Buchanan C.,Hongguang M.,Martell S.J.D.,Latour R.J.,Preikshot D.,Sigrist M.B.,Uphoff J.H.,Walters C.J.,Wood R.J.,Townsend H.(2009). Fisheries Ecosystem Model of the Chesapeake Bay: Methodology, Parameterization, and Model Exploration NOAA Technical Memorandum http://spo.nmfs.noaa.gov/tm/TM106%20FINAL.pdf NA
35 Chesapeake present Christensen, V. Christensen V.,Beattie A.,Buchanan C.,Hongguang M.,Martell S.J.D.,Latour R.J.,Preikshot D.,Sigrist M.B.,Uphoff J.H.,Walters C.J.,Wood R.J.,Townsend H.(2009). Fisheries Ecosystem Model of the Chesapeake Bay: Methodology, Parameterization, and Model Exploration NOAA Technical Memorandum http://spo.nmfs.noaa.gov/tm/TM106%20FINAL.pdf NA
183 Eastern Bering Sea Trites, A.W. Trites A.W.,Livingston P.A.,Mackinson S.,Vasconcellos M.C.,Springer A.M.,Pauly D.(1999). Ecosystem Change and the Decline of Marine Mammals the Eastern Bering Sea: Testing the Ecosystem Shift and Commercial Whaling Hypotheses Fisheries Centre Research Reports http://publications.oceans.ubc.ca/node/3831 NA
16 Eastern Bering Sea 1950 Trites, A.W. Trites A.W.,Livingston P.A.,Mackinson S.,Vasconcellos M.C.,Springer A.M.,Pauly D.(1999). Ecosystem Change and the Decline of Marine Mammals the Eastern Bering Sea: Testing the Ecosystem Shift and Commercial Whaling Hypotheses Fisheries Centre Research Reports http://publications.oceans.ubc.ca/node/3831 NA
764 Florida Bay Mason Smith Smith, M., Chagaris, D., Paperno, R. and Markwith, S., 2020. Ecosystem structure and resilience of the Florida Bay Estuary: an original ecosystem model with implications for everglades restoration https://www.publish.csiro.au/mf/MF20125 https://doi.org/10.1071/MF20125
442 Heymans_1963_EAleutians_CGulfAlaska Heymans, S.J.J. Heymans S.J.J.,Heymans S.J.J.(2005). Ecosystem model of the eastern Aleutians and central Gulf of Alaska in 1963 Food web models and data for studying fisheries and environmental impacts on Eastern Pacific ecosystems. pp 83-105. In Guenette S.,Christensen V. http://publications.oceans.ubc.ca/node/3797 NA
269 Looe Key National Marine Sanctuary McCormick Venier, J. McCormick Venier J.(1997). Seasonal ecosystem models of the Looe Key National Marine Sanctuary, Florida https://circle.ubc.ca/handle/2429/7662 NA
753 Narragansett Bay food web Austin Humphries Innes-Gold, A., Heinichen, M., Gorospe, K., Truesdale, C., Collie, J., & Humphries, A. (2020). Model https://www.int-res.com/abstracts/meps/v654/p17-33/ https://doi.org/10.3354/meps13505
521 Northern Californian Current Field, J.C. Field J.(2004). Application of ecosystem-based fishery management approaches in the northern California Current http://weber.s.uw.edu/research/publications/ms_phd/Field_John_PhD_Su04.pdf NA
279 Prince William Sound Okey, T.A. Okey T.A.,Wright B.A.(2004). Toward ecosystem-based extraction policies for Prince William Sound, Alaska: integrating conflicting objectives and rebuilding Pinnipeds Bulletin of Marine Science. pp 727-747 http://www.ingentaconnect.com/content/umrsmas/bullmar/2004/00000074/00000003/art00017 NA
438 South East Alaska Guénette, S. Guénette S.,Heymans S.J.J.,Christensen V.,Trites A.W.(2006). Ecosystem models show combined effects of fishing, predation, competition, and ocean productivity on Steller sea lions (Eumetopias jubatus) in Alaska Canadian Journal of Fisheries and Aquatic Sciences. pp 2495-2517 http://www.seaaroundus.org/doc/publications/books-and-reports/2005/Guenette-and-Christensene-food-web-models-eastern-pacific-ecosystems.pdf NA
729 Tampa Bay Chagaris, David D. Chagaris & B. Mahmoudi, 2010. Assessing the influence of bottom-up and top-down processes in Tampa Bay using Ecopath with Ecosim. In: Cooper, S.T. (ed.). Proceedings, Tampa Bay Area Scientific Information Symposium, BASIS 5: 20-23 October 2009. St. Petersburg, FL. pp 263-274. http://www.tbrpc.org/events/basis5/ NA
153 Tampa Bay Walters, C.J. Walters C.,Martell S.J.D.,Christensen V.,Mahmoudi B.(2008). An Ecosim Model for Exploring Gulf of Mexico Ecosystem Management Options: Implications of Including Multistanza Life-History Models for Policy Predictions Bulletin of Marine Science. pp 251-271 http://www.ingentaconnect.com/content/umrsmas/bullmar/2008/00000083/00000001/art00014 NA
173 West Florida Shelf Okey, T.A. Okey T.A.,Mahmoudi B.(2002). An Ecosystem model of the West Florida Shelf for use in Fisheries Management and Ecological Research: Volume II: Model Construction http://www.safmc.net/Library/Ecosystem/WFSmodel.pdf NA
755 West Florida Shelf David Chagaris Vilas, Daniel, David Chagaris, and Joe Buszowski. 2020. Red tide mortality on gag grouper from 2002- http://sedarweb.org/docs/wpapers/S72_WP_01_red_tide_Mortality_Ecospace_v3.pdf NA
727 West Florida Shelf Historic Model Chagaris, David Chagaris, D., B. Mahmoudi, C. Walters, and M. Allen. 2015. Simulating the trophic impacts of fishery NA http://dx.doi.org/10.1080/19425120.2014.966216

2. Atlantis models