Quantitative Methods for Ecological Network Analysis and Its Application to Coastal Ecosystems

Treatise on Estuarine and Coastal Science

Volumn 9, Issue , 2012, Pages 35-57

  Ulanowicz, R E ^a,b  

^a UNIVERSITY OF FLORIDA   (United States)

^b UNIVERSITY OF MARYLAND CENTER FOR ENVIRONMENTAL SCIENCE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84961181556     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-12-374711-2.00904-9     Document Type: Chapter

References (106)

1. Abramson, N., 1963. Information Theory and Coding. McGraw-Hill, New York, 201 pp.
2. Allesina, S., Bodini, A., Bondavalli, C., 2005. Ecological subsystems via graph theory: the role of strongly connected components. Oikos 110 (1), 164-176.
3. Allesina, S., Bondavalli, C., 2003. Steady state of ecosystem flow networks: a comparison between balancing procedures. Ecological Modelling 165, 221-229.
4. Allesina, S., Ulanowicz, R.E., 2004. Cycling in ecological networks: Finn's index revisited. Computational Biology and Chemistry 28, 227-233.
5. Atlan, H., 1974. On a formal definition of organization. Journal of Theoretical Biology 45, 295-304.
6. Augustinovics, M., 1970. Methods of international and intertemporal comparison of structure. In: Carter, A.P., Brody, A. (Eds.), Contributions to Input-Output Analysis. North-Holland, Amsterdam, vol. I, pp. 249-269.
7. Barabási, A.-L., 2002. Linked: The New Science of Networks. Perseus, Cambridge, MA.
8. Baird, D., Christian, R.R., Peterson, C.H., Johnson, G.A., 2004. Consequences of hypoxia on Estuarine ecosystem function: energy diversion from consumers to microbes. Ecological Applications 14 (3), 805-822.
9. Baird, D., McGlade, J.M., Ulanowicz, R.E., 1991. The comparative ecology of six marine ecosystems. Philosophical Transactions of the Royal Society B 333, 15-29.
10. Baird, D., Ulanowicz, R.E., 1989. The seasonal dynamics of the Chesapeake Bay ecosystem. Ecological Monographs 59, 329-364.
11. Bateson, G., 1972. Steps to an Ecology of Mind. Ballantine Books, New York.
12. Bersier, L.-F., Banašek-Richter, C., Cattin, M.-F., 2002. Quantitative descriptors of food web matrices. Ecology 83, 2394-2407.
13. Biswas, A.K., 1981. Models for Water Quality Management. McGraw-Hill, New York, 348 pp.
14. Blachman, N.M., 1961. A Generalization of Mutual Information. Proceedings of the IRE 49 (8), 1331-1332.
15. Bondavalli, C., Ulanowicz, R.E., 1999. Unexpected effects of predators upon their prey: the case of the American alligator. Ecosystems 2, 49-63.
16. Caswell, H., 1989. Matrix Population Models. Sinauer, Sunderland, MA, 328 pp.
17. Christensen, V., Pauly, D., 1992. ECOPATH II-a software for balancing steady-state models and calculating network characteristics. Ecological Modelling 61, 169-185.
18. Christian, R.R., Dame, J.K., Johnson, G., Peterson, C.H., Baird, D., 2003. Monitoring and Modeling of the Neuse River Estuary, Phase 2: Functional Assessment of Environmental Phenomena through Network Analysis. UNC-WRRI 2003-343-E, Department of Biology, East Carolina University, Greenville, NC, 111 pp.
19. Christian, R.R., Luczkovich, J.J., 1999. Organizing and understanding a winter's seagrass foodweb network through effective trophic levels. Ecological Modelling 117, 99-124.
20. Cohen, J.E., Briand, F., Newman, C.M. (Eds.), 1990. Community Food Webs: Data and Theory. Biomathematics 20. Springer, Heidleberg, 308 pp.
21. Courant, R., 1936. Differential and Integral Calculus, Vol. II. Interscience, New York, 681 pp.
22. Cousins, S., 1985. Ecologists build pyramids again. New Scientist 107 (1463), 50-54.
23. Dame, R.F., Patten., B.C., 1981. Analysis of energy flows in an intertidal oyster reef. Marine Ecology Progress Series 5, 115-124.
24. DeAngelis, D.L., Gross, L.J. (Eds.), 1992. Individual-Based Models and Approaches in Ecology. Chapman and Hall, London, 525 pp.
25. Fath, B.D., Patten, B.C., 1998. Network synergism: emergence of positive relations in ecological systems. Ecological Modelling 107, 127-143.
26. Fath, B.D., Patten, B.C., 1999. Review of the foundations of network environ analysis. Ecosystems 2, 167-179.
27. Finn, J.T., 1976. Measures of ecosystem structure and function derived from analysis of flows. Journal of Theoretical Biology 56, 363-380.
28. Halfon, E.A., 1979. Theoretical Systems Ecology. Academic Press, New York, 516 pp.
29. Han, B.-P., 1997. On several measures concerning flow variables in ecosystems. Ecological Modelling 104, 289-302.
30. Hannon, B.M., 1973. The structure of ecosystems. Journal of Theoretical Biology 41, 535-546.
31. Hannon, B.M., Costanza, R., Ulanowicz, R.E., 1991. A general accounting framework for ecological systems: a functional taxonomy for connectivist ecology. Theoretical Population Biology 40, 78-104.
32. Heymans, J.J., 2003. Comparing the Newfoundland-Southern Labrador marine ecosystem models using information theory. In: Heymans, J.J. (Ed.), Ecosystem Models of Newfoundland and Southeastern Labrador (2J3KLNO): Additional Information and Analyses for "Back to the Future". Fisheries Centre Research Reports, The University of British Columbia, Vancouver, BC, vol. 11 (5), pp. 62-71.
33. Heymans, J.J., Guénette, S., Villy Christensen, V., 2007. Evaluating network analysis indicators of ecosystem status in the Gulf of Alaska. Ecosystems 10 (3), 488-502.
34. Higashi, M., Burns, T.D. (Eds.), 1991. Theoretical Studies of Ecosystems: The Network Perspective. Cambridge University Press, Cambridge, 364 pp.
35. Higashi, M., Patten, B.C., Burns, T.D., 1991. Network trophic dynamics: an emerging paradigm in ecosystems ecology. In: Higashi, M., Burns, T.D. (Eds.), Theoretical Studies of Ecosystems: The Network Perspective. Cambridge University Press, Cambridge, pp. 117-154.
36. Hillebrand, H., Shurin, J.B., 2005. Biodiversity and freshwater food webs. In: Belgrano, A., Scharler, U., Dunne, J., Ulanowicz, R.E. (Eds.), Aquatic Food Webs: An Ecosystem Approach. Oxford University Press, Oxford, ch. 14, pp. 184-197.
37. Holling, C.S., 1986. The resilience of terrestrial ecosystems: local surprise and global change. In: Clark, W.C., Munn, R.E. (Eds.), Sustainable Development of the Biosphere. Cambridge University Press, Cambridge, pp. 292-317.
38. Jassby, A.D., Platt, T.C., 1976. Mathematical formulation of the relationship between photosynthesis and light for phytoplankton. Limnology and Oceanography 21 (4), 540-547.
39. Karr, J.R., Fausch, K.D., Angermeier, P.L., Yant, P.R., Schlosser, I.J., 1986. Assessment of Biological Integrity in Running Water: A Method and Its Rationale. Illinois Natural History Survey, Publication 5, Champaign, IL.
40. Kavanagh, P., Newlands, N., Christensen, V., Pauly, D., 2004. Automated parameter optimization for Ecopath ecosystem models. Ecological Modelling 172, 141-149.
41. Kikawada, H., 1998. Applying Network Analysis to Simulated Ecological Landscape Dynamics. Master's Thesis, University of Maryland, College Park, MD, 181 pp.
42. Knuth, D.E., 1973. Fundamental Algorithms. Addison-Wesley, Reading, MA, vol. 1, 228 pp.
43. Krivov, S., Ulanowicz, R.E., 2003. Qunatitative measures of organization for multi-agent systems. BioSystems 69, 39-54.
44. Kullback, S., 1959. Information Theory and Statistics. Peter Smith, Gloucester, MA, 399 pp.
45. Latham, L.G., Scully, E.P., 2002. Quantifying constraint to assess development in ecological networks. Ecological Modelling 154, 25-44.
46. Leontief, W., 1951. The Structure of the American Economy, 1919-1939, Second ed. Oxford University Press, New York, 257 pp.
47. Levine, S., 1980. Several measures of trophic structure applicable to complex food webs. Journal of Theoretical Biology 83, 195-207.
48. Lewin, R., 1984. Why is development so illogical? Science 224, 1327-1329.
49. Liebig, J., 1854. Chemistry in Its Application to Agriculture and Physiology. Taylor and Walton, London, 401 pp.
50. Lotka, A.J., 1922. Contribution to the energetics of evolution. Proceedings of the National Academy of Sciences of the United States of America 8, 147-150.
51. MacArthur, R., 1955. Fluctuations of animal populations, and a measure of community stability. Ecology 36, 533-536.
52. Mateti, P., Deo, N., 1976. On algorithms for enumerating all the circuits of a graph. SIAM Journal on Scientific Computing 5, 90-99.
53. Matis, J.H., Patten, B.C., 1981. Environ analysis of linear compartmental systems: the static, time invariant case. Bulletin of the International Statistical Institute 48, 527-565.
54. Matis, J.H., Patten, B.C., White, G.C., 1979. Compartmental Analysis of Ecosystem Models. International Cooperative Publishing House, Fairland, MD, 368 pp.
55. May, R.M., 1972. Will a large complex system be stable? Nature 238, 413-414.
56. Mueller, F., Leupelt, M. (Eds.), 1998. Eco Targets, Goal Functions, and Orientors. Springer, Berlin, 619 pp.
57. Newell, R.I.E., 1988. Ecological Changes in Chesapeake Bay: are they the result of overharvesting the Eastern oyster (Crassostrea virginica)? In: Lynch, M.P., Krome, E.C. (Eds.), Understanding the Estuary: Advances in Chesapeake Bay Research. Chesapeake Research Consortium Publication 129 (CBP/TRS 24/88), Gloucester Point, VA, pp. 536-546.
58. NSF, 1999. Decision-making and Valuation for Environmental Policy. NSF Bulletin 99-14, National Science Foundation, Ballston, VA.
59. Odum, E.P., 1969. The strategy of ecosystem development. Science 164, 262-270.
60. Odum, H.T., 1971. Environment, Power and Society. Wiley, New York, 331 pp.
61. Pahl-Wostl, C., 1995. The Dynamic Nature of Ecosystems: Chaos and Order Entwined. Wiley, New York, 267 pp.
62. Patten, B.C., 1978. Systems approach to the concept of environment. Ohio Journal of Science 78, 206-222.
63. Patten, B.C., 1982. Environs: relativistic elementary particles for ecology. American Naturalist 119, 179-219.
64. Patten, B.C., Auble, G.T., 1981. System theory of the ecological niche. American Naturalist 117, 893-922.
65. Patten, B.C., Bosserman, R.W., Finn, J.T., Cale, W.G., 1976. Propagation of cause in ecosystems. In: Patten, B.C. (Ed.), Systems Analysis and Simulation in Ecology. Academic Press, New York, vol. 4, pp. 457-579.
66. Pauly, D., Christensen, V., Dalsgaard, J., Froese, R., Torres, F., 1998. Fishing Down Marine Food Webs. Science 279 (5352), 860-863.
67. Pimm, S.L., 1982. Food Webs. Chapman and Hall, London, 219 pp.
68. Pimm, S.L., Lawton, J.H., 1977. Number of trophic levels in ecological communities. Nature 268, 329-331.
69. Platt, T.C., Mann, K.H., Ulanowicz, R.E. (Eds.), 1981. Mathematical Models in Biological Oceanography. UNESCO Press, Paris, 157 pp.
70. Polis, G., Winemiller, K., 1995. Food Webs: Integration of Patterns and Dynamics. Chapman and Hall, New York, 472 pp.
71. Polovina, J.J., 1985. An approach to estimating an ecosystem box model. U.S. Fish Bulletin 83 (3), 457-460.
72. Rutledge, R.W., Basorre, B.L., Mulholland, R.J., 1976. Ecological stability: an information theory viewpoint. Journal of Theoretical Biology 57, 355-371.
73. Sanderson, J., Harris, L.D. (Eds.), 2000. Series in Landscape Ecology: A Top-Down Approach. Lewis, Boca Raton, FL.
74. Simon, H.A., Hawkins, D., 1949. Some conditions of macroeconomic stability. Econometrica 17, 245-248.
75. Szyrmer, J., Ulanowicz, R.E., 1987. Total flows in ecosystems. Ecological Modelling 35, 123-136.
76. Tarjan, R., 1972. Depth first search and linear graph algorithms. SIAM Journal of Computing 1, 146-160.
77. Tribus, M., McIrvine, E.C., 1971. Energy and information. Scientific American 225, 179-188.
78. Ulanowicz, R.E., 1980. An hypothesis on the development of natural communities. Journal of Theoretical Biology 85, 223-245.
79. Ulanowicz, R.E., 1983. Identifying the structure of cycling in ecosystems. Mathematical Biosciences 65, 219-237.
80. Ulanowicz, R.E., 1984. Community measures of marine food networks and their possible applications. In: Fasham, M.J.R. (Ed.), Flows of Energy and Materials in Marine Ecosystems. Plenum, London, pp. 23-47.
81. Ulanowicz, R.E., 1986. Growth and Development: Ecosystems Phenomenology. Springer, New York, 203 pp.
82. Ulanowicz, R.E., 1995. Ecosystem trophic foundations: Lindeman Exonerata. In: Patten, B.C., Jorgensen, S.E. (Eds.), Complex Ecology: The Part-Whole Relation in Ecosystems. Prentice Hall, Englewood Cliffs, NJ, pp. 549-560.
83. Ulanowicz, R.E., 1997. Ecology, the Ascendent Perspective. Columbia University Press, New York, 201 pp.
84. Ulanowicz, R.E., 2000a. Toward the measurement of ecological integrity. In: Pimentel, D., Westra, L., Noss, R.F. (Eds.), Ecological Integrity: Integrating Environment, Conservation and Health. Island Press, Washington, DC, pp. 99-113.
85. Ulanowicz, R.E., 2000b. Quantifying constraints upon trophic and migratory transfers in spatially heterogeneous ecosystems. In: Sanderson, J., Harris, L.D. (Eds.), Series in Landscape Ecology: A Top-Down Approach. Lewis, Boca Raton, FL (Eds.), pp. 113-142.
86. Ulanowicz, R.E., 2004. Quantitative methods for ecological network analysis. Computational Biology and Chemistry 28, 321-339.
87. Ulanowicz, R.E., 2009a. The Dual Nature of Ecosystem Dynamics. Ecological Modelling 220, 1886-1892.
88. Ulanowicz, R.E., 2009b. A Third Window: Natural Life beyond Newton and Darwin. Templeton Foundation Press, West Conshohocken, PA.
89. Ulanowicz, R.E., 2009c. Increasing entropy: Heat death or perpetual harmonies? International Journal of Design and Nature and Ecodynamics 42 (2), 83-96.
90. Ulanowicz, R.E., Abarca-Arenas, L.G., 1997. An informational synthesis of ecosystem structure and function. Ecological Modelling 95, 1-10.
91. Ulanowicz, R.E., Baird, D., 1999. Nutrient controls on ecosystem dynamics: The Chesapeake mesohaline community. Journal of Marine Systems 19, 159-172.
92. Ulanowicz, R.E., Goerner, S.J., Lietaer, B., Gomez, R., 2009. Quantifying sustainability: resilience, efficiency and the return of information theory. Ecological Complexity 6, 27-36.
93. Ulanowicz, R.E., Kemp, W.M., 1979. Toward canonical trophic aggregations. American Naturalist 114, 871-883.
94. Ulanowicz, R.E., Norden, J.S., 1990. Symmetrical overhead in flow networks. International Journal of Systems Science 1, 429-437.
95. Ulanowicz, R.E., Puccia, C.J., 1990. Mixed trophic impacts in ecosystems. Coenoses 5, 7-16.
96. Ulanowicz, R.E., Tuttle, J.H., 1992. The trophic consequences of oyster stock rehabilitation in Chesapeake Bay. Estuaries 15, 298-306.
97. Ulanowicz, R.E., Scharler, U.M., 2008. Least inference methods for constructing networks of trophic flows. Ecological Modelling 210, 278-286.
98. Ulanowicz, R.E., Wolff, W.F., 1991. Ecosystem flow networks: loaded dice? Mathematical Biosciences 103, 45-68.
99. Ulanowicz, R.E., Zickel, M.J., 2005. Using ecology to quantify fluid flows. In: Kleidon, A.M., Lorenz, R.D. (Eds.), Non-Equilibrium Thermodynamics and the Production of Entropy. Springer, Berlin, pp. 56-67.
100. Vezina, A.F., Platt, T.C., 1988. Food web dynamics in the ocean. I. Best-estimates of flow networks using inverse methods. Marine Ecology Progress Series 42, 269-287.
101. Wang, H.V., Johnson, B.J., 2000. Validation and application of the second generation three dimensional hydrodynamic model of Chesapeake Bay. Water Quality and Ecosystem Modeling 1, 51-90.
102. Whipple, S.J., Patten, B.C., 1993. The problem of nontrophic processes in trophic ecology: a network unfolding solution. Journal of Theoretical Biology 163, 393-411.
103. Woodwell, G.M., Smith, H.H. (Eds.), 1969. Diversity and Stability in Ecological Systems. U.S. Brookhaven Symposia in Biology, New York, vol. 22, 264 pp.
104. Wulff, F., Ulanowicz, R.E., 1989. A comparative anatomy of the Baltic Sea and Chesapeake Bay ecosystems. In: Wulff, F., Field, J.G., Mann, K.H. (Eds.), Flow Analysis of Marine Ecosystem. Springer, Berlin, pp. 232-256.
105. Yodzis, P., 1989. Patterns in food webs. Trends in Ecology and Evolution 4 (2), 49-50.
106. Zorach, A.C., Ulanowicz, R.E., 2003. Quantifying the complexity of flow networks: How many roles are there? Complexity 8 (3), 68-76.