formulated as a maximum rate exponentially dependent
on temperature, multiplied by a dimensionless, saturating
function
of
phytoplankton
biomass
(e.g., FOODLIM). Growth of larger animals such as
oysters, clams, and fish is typically formulated as an
allometric function of individual weight, followed by
scaling terms for temperature and food. Often, terms in
the governing equations are linked to other variables
being modeled, e.g., nutrients in the NUTLIM equation
or zooplankton biomass in the grazing rate formulation.
Bibliography
Baird, D., and Ulanowicz, R. E., 1989. The seasonal dynamics of
the Chesapeake Bay ecosystem. Ecological Monographs,
59(4), 329–364.
Baretta, J., and Ruardij, P. (eds.), 1988. Tidal Flat Estuaries: Simulation and Analysis of the Ems Estuary. Berlin: Springer.
Baretta-Bekker, J. G., 1995. European regional seas ecosystem
model-I. Netherlands Journal of Sea Research, 33(3–4).
Baretta-Bekker, J. G., and Baretta, J. W., 1997. European regional
seas ecosystem model II. Journal of Sea Research, 38(3–4).
Boynton, W. R., and Kemp, W. M., 2000. Influence of river flow
and nutrient loads on selected ecosystem processes: a synthesis
of Chesapeake Bay data. In Hobbie, J. E. (ed.), Estuarine Science: A Synthetic Approach to Research and Practice. Washington, DC: Island Press, pp. 269–298.
Boynton, W. R., and Nixon, S. W., 2012. Budget analyses of estuarine ecosystems. In Day, J. W., Jr., Crump, B. C., Kemp, W. M.,
and Yáñez-Arancibia, A. (eds.), Estuarine Ecology, 2nd edn.
Hoboken: Wiley, pp. 443–464.
Brush, M. J., and Harris, L. A., 2010. Advances in modeling estuarine and coastal ecosystems: approaches, validation, and applications (introduction). Ecological Modelling, 221(7), 965–968.
Canham, C. D., Cole, J. J., and Lauenroth, W. K. (eds.), 2003.
Models in Ecosystem Science. Princeton: Princeton University
Press.
Cerco, C. F., and Cole, T. M., 1994. Three-Dimensional Eutrophication Model of Chesapeake Bay, Vol. I: Main Report. Technical
report EL-94-4. Vicksburg: Waterways Experiment Station, US
Army Corps of Engineers.
Cerco, C. F., and Noel, M. R., 2004. The 2002 Chesapeake Bay
Eutrophication Model. Report 903-R-04-004. Annapolis: Chesapeake Bay Program Office, US Environmental Protection
Agency.
Cerco, C. F., and Noel, M. R., 2007. Can oyster restoration reverse
cultural eutrophication in Chesapeake Bay? Estuaries and
Coasts, 30(2), 331–343.
Chapra, S. C., 1997. Surface Water-Quality Modeling. New York:
McGraw-Hill.
Dame, J. K., and Christian, R. R., 2006. Uncertainty and the use of
network analysis for ecosystem-based fishery management.
Fisheries, 31(7), 331–341.
Dillon, P. J., and Rigler, F. H., 1974. The phosphorus-chlorophyll relationship in lakes. Limnology and Oceanography, 19, 767–773.
DiToro, D. M., 2001. Sediment Flux Modeling. New York: WileyInterscience.
DiToro, D. M., O’Connor, D. J., and Thomann, R. V., 1971.
A dynamic model of the phytoplankton population in the
Sacramento-San Joaquin Delta. In Hem, J. D. (ed.),
Nonequilibrium Systems in Natural Water Chemistry. Washington, DC: American Chemical Society. Advances in Chemistry
Series, Vol. 106, pp. 131–180.
Eppley, R. W., 1972. Temperature and phytoplankton growth in the
sea. Fishery Bulletin, 70(4), 1063–1085.
Fennel, W., and Neumann, T., 2004. Introduction to the Modelling
of Marine Ecosystems. Amsterdam: Elsevier.
Giblin, A. E., and Vallino, J. J., 2003. The role of models in
addressing coastal eutrophication. In Canham, C. D., Cole,
J. J., and Lauenroth, W. K. (eds.), Models in Ecosystem Science.
Princeton: Princeton University Press, pp. 327–343.
Haefner, J. W., 2005. Modeling Biological Systems: Principles and
Applications. New York: Springer.
Hall, C., and Day, J. (eds.), 1977. Ecosystem Modeling in Theory
and Practice: An Introduction with Case Histories. New York:
Wiley.
Harris, G. P., Bigelow, S. W., Cole, J. J., Cyr, H., Janus, L. L., Kinzig,
A. P., Kitchell, J. F., Likens, G. E., Reckhow, K. H., Scavia, D.,
Soto, D., Talbot, L. M., and Templer, P. H., 2003. The role of
models in ecosystem management. In Canham, C. D., Cole, J. J.,
and Lauenroth, W. K. (eds.), Models in Ecosystem Science.
Princeton: Princeton University Press, pp. 299–307.
Hofmann, E. E., 2000. Modeling for estuarine synthesis. In Hobbie,
J. E. (ed.), Estuarine Science: A Synthetic Approach to Research
and Practice. Washington, DC: Island Press, pp. 129–148.
Hopkinson, C. S., Wetzel, R. L., and Day, J. W., Jr., 1988. Simulation models of coastal wetland and estuarine systems: realization
of goals. In Mitsch, W. J., Straškraba, M., and Jørgensen, S. E.
(eds.), Wetland Modelling. Amsterdam: Elsevier, pp. 67–97.
HydroQual, Inc., 1987. A Steady-State Coupled Hydrodynamic/
Water Quality Model of the Eutrophication and Anoxia Process
in Chesapeake Bay. Mahwah: HydroQual.
HydroQual, Inc., 1991. Water Quality Modeling Analysis of Hypoxia in Long Island Sound. Mahwah: HydroQual.
HydroQual and Normandeau Associates, 1995. A Water Quality
Model for Massachusetts and Cape Cod Bays: Calibration of
the Bays Eutrophication Model (BEM). Report to the Massachusetts Water Resources Authority. Mahwah, NJ/Bedford, NH:
HydroQual/Normandeau Associates.
Kemp, W. M., and Boynton, W. R., 2012. Synthesis in estuarine and
coastal ecological research: what is it, why is it important, and
how do we teach it? Estuaries and Coasts, 35, 1–22.
Kremer, J. N., and Nixon, S. W., 1978. A Coastal Marine Ecosystem: Simulation and Analysis. New York: Springer.
Kremer, J. N., Kemp, W. M., Giblin, A. E., Valiela, I., Seitzinger,
S. P., and Hofmann, E. E., 2000. Linking biogeochemical processes to higher trophic levels. In Hobbie, J. E. (ed.), Estuarine
Science: A Synthetic Approach to Research and Practice. Washington, DC: Island Press, pp. 299–346.
Latour, R. J., Brush, M. J., and Bonzek, C. F., 2003. Toward
ecosystem-based fisheries management: strategies for
multispecies modeling and associated data requirements. Fisheries, 28(9), 10–22.
Levins, R., 1966. The strategy of model building in population biology. American Scientist, 54, 421–431.
Lotka, A. J., 1925. Elements of Physical Biology. Baltimore: Williams and Wilkins (reprinted 1956; as Elements of Mathematical
Biology. Mineola: Dover Publications).
Lotka, A. J., 1932. The growth of mixed populations: two species
competing for a common food supply. Journal of the Washington
Academy of Sciences, 22, 461–469.
Nixon, S. W., 1992. Quantifying the relationship between nitrogen
input and the productivity of marine ecosystems. In Takahashi,
M., Nakata, K., and Parsons, T. R. (eds.), Proceedings of
Advanced Marine Technology Conference. AMTEC, Vol. 5,
pp. 57–83.
Nixon, S. W., Oviatt, C. A., Frithsen, J., and Sullivan, B., 1986.
Nutrients and the productivity of estuarine and coastal marine
ecosystems. Journal of the Limnological Society of South Africa,
12(1/2), 43–71.
222
ECOLOGICAL MODELING
on temperature, multiplied by a dimensionless, saturating
function
of
phytoplankton
biomass
(e.g., FOODLIM). Growth of larger animals such as
oysters, clams, and fish is typically formulated as an
allometric function of individual weight, followed by
scaling terms for temperature and food. Often, terms in
the governing equations are linked to other variables
being modeled, e.g., nutrients in the NUTLIM equation
or zooplankton biomass in the grazing rate formulation.
Bibliography
Baird, D., and Ulanowicz, R. E., 1989. The seasonal dynamics of
the Chesapeake Bay ecosystem. Ecological Monographs,
59(4), 329–364.
Baretta, J., and Ruardij, P. (eds.), 1988. Tidal Flat Estuaries: Simulation and Analysis of the Ems Estuary. Berlin: Springer.
Baretta-Bekker, J. G., 1995. European regional seas ecosystem
model-I. Netherlands Journal of Sea Research, 33(3–4).
Baretta-Bekker, J. G., and Baretta, J. W., 1997. European regional
seas ecosystem model II. Journal of Sea Research, 38(3–4).
Boynton, W. R., and Kemp, W. M., 2000. Influence of river flow
and nutrient loads on selected ecosystem processes: a synthesis
of Chesapeake Bay data. In Hobbie, J. E. (ed.), Estuarine Science: A Synthetic Approach to Research and Practice. Washington, DC: Island Press, pp. 269–298.
Boynton, W. R., and Nixon, S. W., 2012. Budget analyses of estuarine ecosystems. In Day, J. W., Jr., Crump, B. C., Kemp, W. M.,
and Yáñez-Arancibia, A. (eds.), Estuarine Ecology, 2nd edn.
Hoboken: Wiley, pp. 443–464.
Brush, M. J., and Harris, L. A., 2010. Advances in modeling estuarine and coastal ecosystems: approaches, validation, and applications (introduction). Ecological Modelling, 221(7), 965–968.
Canham, C. D., Cole, J. J., and Lauenroth, W. K. (eds.), 2003.
Models in Ecosystem Science. Princeton: Princeton University
Press.
Cerco, C. F., and Cole, T. M., 1994. Three-Dimensional Eutrophication Model of Chesapeake Bay, Vol. I: Main Report. Technical
report EL-94-4. Vicksburg: Waterways Experiment Station, US
Army Corps of Engineers.
Cerco, C. F., and Noel, M. R., 2004. The 2002 Chesapeake Bay
Eutrophication Model. Report 903-R-04-004. Annapolis: Chesapeake Bay Program Office, US Environmental Protection
Agency.
Cerco, C. F., and Noel, M. R., 2007. Can oyster restoration reverse
cultural eutrophication in Chesapeake Bay? Estuaries and
Coasts, 30(2), 331–343.
Chapra, S. C., 1997. Surface Water-Quality Modeling. New York:
McGraw-Hill.
Dame, J. K., and Christian, R. R., 2006. Uncertainty and the use of
network analysis for ecosystem-based fishery management.
Fisheries, 31(7), 331–341.
Dillon, P. J., and Rigler, F. H., 1974. The phosphorus-chlorophyll relationship in lakes. Limnology and Oceanography, 19, 767–773.
DiToro, D. M., 2001. Sediment Flux Modeling. New York: WileyInterscience.
DiToro, D. M., O’Connor, D. J., and Thomann, R. V., 1971.
A dynamic model of the phytoplankton population in the
Sacramento-San Joaquin Delta. In Hem, J. D. (ed.),
Nonequilibrium Systems in Natural Water Chemistry. Washington, DC: American Chemical Society. Advances in Chemistry
Series, Vol. 106, pp. 131–180.
Eppley, R. W., 1972. Temperature and phytoplankton growth in the
sea. Fishery Bulletin, 70(4), 1063–1085.
Fennel, W., and Neumann, T., 2004. Introduction to the Modelling
of Marine Ecosystems. Amsterdam: Elsevier.
Giblin, A. E., and Vallino, J. J., 2003. The role of models in
addressing coastal eutrophication. In Canham, C. D., Cole,
J. J., and Lauenroth, W. K. (eds.), Models in Ecosystem Science.
Princeton: Princeton University Press, pp. 327–343.
Haefner, J. W., 2005. Modeling Biological Systems: Principles and
Applications. New York: Springer.
Hall, C., and Day, J. (eds.), 1977. Ecosystem Modeling in Theory
and Practice: An Introduction with Case Histories. New York:
Wiley.
Harris, G. P., Bigelow, S. W., Cole, J. J., Cyr, H., Janus, L. L., Kinzig,
A. P., Kitchell, J. F., Likens, G. E., Reckhow, K. H., Scavia, D.,
Soto, D., Talbot, L. M., and Templer, P. H., 2003. The role of
models in ecosystem management. In Canham, C. D., Cole, J. J.,
and Lauenroth, W. K. (eds.), Models in Ecosystem Science.
Princeton: Princeton University Press, pp. 299–307.
Hofmann, E. E., 2000. Modeling for estuarine synthesis. In Hobbie,
J. E. (ed.), Estuarine Science: A Synthetic Approach to Research
and Practice. Washington, DC: Island Press, pp. 129–148.
Hopkinson, C. S., Wetzel, R. L., and Day, J. W., Jr., 1988. Simulation models of coastal wetland and estuarine systems: realization
of goals. In Mitsch, W. J., Straškraba, M., and Jørgensen, S. E.
(eds.), Wetland Modelling. Amsterdam: Elsevier, pp. 67–97.
HydroQual, Inc., 1987. A Steady-State Coupled Hydrodynamic/
Water Quality Model of the Eutrophication and Anoxia Process
in Chesapeake Bay. Mahwah: HydroQual.
HydroQual, Inc., 1991. Water Quality Modeling Analysis of Hypoxia in Long Island Sound. Mahwah: HydroQual.
HydroQual and Normandeau Associates, 1995. A Water Quality
Model for Massachusetts and Cape Cod Bays: Calibration of
the Bays Eutrophication Model (BEM). Report to the Massachusetts Water Resources Authority. Mahwah, NJ/Bedford, NH:
HydroQual/Normandeau Associates.
Kemp, W. M., and Boynton, W. R., 2012. Synthesis in estuarine and
coastal ecological research: what is it, why is it important, and
how do we teach it? Estuaries and Coasts, 35, 1–22.
Kremer, J. N., and Nixon, S. W., 1978. A Coastal Marine Ecosystem: Simulation and Analysis. New York: Springer.
Kremer, J. N., Kemp, W. M., Giblin, A. E., Valiela, I., Seitzinger,
S. P., and Hofmann, E. E., 2000. Linking biogeochemical processes to higher trophic levels. In Hobbie, J. E. (ed.), Estuarine
Science: A Synthetic Approach to Research and Practice. Washington, DC: Island Press, pp. 299–346.
Latour, R. J., Brush, M. J., and Bonzek, C. F., 2003. Toward
ecosystem-based fisheries management: strategies for
multispecies modeling and associated data requirements. Fisheries, 28(9), 10–22.
Levins, R., 1966. The strategy of model building in population biology. American Scientist, 54, 421–431.
Lotka, A. J., 1925. Elements of Physical Biology. Baltimore: Williams and Wilkins (reprinted 1956; as Elements of Mathematical
Biology. Mineola: Dover Publications).
Lotka, A. J., 1932. The growth of mixed populations: two species
competing for a common food supply. Journal of the Washington
Academy of Sciences, 22, 461–469.
Nixon, S. W., 1992. Quantifying the relationship between nitrogen
input and the productivity of marine ecosystems. In Takahashi,
M., Nakata, K., and Parsons, T. R. (eds.), Proceedings of
Advanced Marine Technology Conference. AMTEC, Vol. 5,
pp. 57–83.
Nixon, S. W., Oviatt, C. A., Frithsen, J., and Sullivan, B., 1986.
Nutrients and the productivity of estuarine and coastal marine
ecosystems. Journal of the Limnological Society of South Africa,
12(1/2), 43–71.
222
ECOLOGICAL MODELING