A comparison of network, neighborhood, and node levels of analyses in two models of nitrogen cycling in the Cape Fear River Estuary

Ecological Modelling

Volumn 293, Issue , 2014, Pages 210-220

  Hines, David E ^a   Borrett, Stuart R ^a  

^a UNIVERSITY OF NORTH CAROLINA WILMINGTON   (United States)

Author keywords

Ascendency; Centrality; Ecological buffer capacity; Ecological network analysis; Hierarchy; Network environ analysis

Indexed keywords

ALGORITHMS; ECOSYSTEMS; NITROGEN;

ASCENDENCY; BUFFER CAPACITY; CENTRALITY; ECOLOGICAL NETWORK ANALYSIS; HIERARCHY; NETWORK ENVIRON ANALYSIS;

ECOLOGY;

ALGORITHM; ECOLOGICAL MODELING; ECOSYSTEM FUNCTION; HIERARCHICAL SYSTEM; NEIGHBORHOOD; NETWORK ANALYSIS; NITROGEN CYCLE; PHYTOPLANKTON; SALINITY;

CAPE FEAR ESTUARY; NORTH CAROLINA; UNITED STATES;

EID: 84910683227     PISSN: 03043800     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecolmodel.2013.11.013     Document Type: Article

References (88)

1. Ahl V., Allen T.F. Hierarchy Theory: A Vision, Vocabulary, and Epistemology 1996, Columbia University Press, New York.
2. Allen T., Tainter J.A., Pires J.C., Hoekstra T.W. Dragnet ecology - "just the facts, ma'am": the privilege of science in a postmodern world. Bioscience 2001, 51:475-485.
3. Allesina S., Bondavalli C. Steady state of ecosystem flow networks. A comparison between balancing procedures. Ecol. Model. 2003, 165:221-229.
4. Allesina S., Bodini A., Bondavalli C. Ecological subsystems via graph theory: the role of strongly connected components. Oikos 2005, 110:164-176.
5. Baird D., Ulanowicz R.E. The seasonal dynamics of the Chesapeake Bay ecosystem. Ecol. Monogr. 1989, 59:329-364.
6. Baird D., Ulanowicz R.E. Comparative study on the trophic structure, cycling and ecosystem properties of four tidal estuaries. Mar. Ecol. Prog. Ser. 1993, 99:221-237.
7. Baird D., McGlade J.M., Ulanowicz R.E. The comparative ecology of six marine ecosystems. Philos. Trans. R. Soc. Lond. B 1991, 333:15-29.
8. Bersier L.F., Banašek-Richter C., Cattin M.F. Quantitative descriptors of food-web matrices. Ecology 2002, 83:2394-2407.
9. Bonacich P. Power and centrality: a family of measures. Am. J. Sociol. 1987, 92:1170-1182.
10. Bondavalli C., Ulanowicz R.E. Unexpected effects of predators upon their prey: the case of the American alligator. Ecosystems 1999, 2:49-63.
11. Borgatti S.P., Everett M.G. A graph-theoretic perspective on centrality. Social Netw. 2006, 28:466-484.
12. Borrett S.R. Throughflow centrality is a global indicator of the functional importance of species in ecosystems. Ecol. Indic. 2013, 32:182-196.
13. Borrett S.R., Freeze M.A. Reconnecting environs to their environment. Ecol. Model. 2011, 222:2393-2403.
14. Borrett S.R., Fath B.D., Patten B.C. Functional integration of ecological networks through pathway proliferation. J. Theor. Biol. 2007, 245:98-111.
15. Borrett S.R., Moody J., Edelmann A. The rise of network ecology: maps of the topic diversity and scientific collaboration. Ecol. Model. 2013, (in this issue). arxiv:1311.1785.
16. Bosserman R.W., Harary F. Demiarcs, creaons and genons. J. Theor. Biol. 1981, 92:241-254.
17. Brandes U., Erlebach T. Network Analysis: Methodological Foundations 2005, vol. 3418. Springer, New York.
18. Carpenter S.R., Kraft C.E., Wright R., He X., Soranno P.A., Hodgson J.R. Resilience and resistance of a lake phosphorus cycle before and after food web manipulation. Am. Nat. 1992, 781-798.
19. Christian R.R., Thomas C.R. Network analysis of nitrogen inputs and cycling in the Neuse River Estuary, North Carolina, USA. Estuaries 2003, 26:815-828.
20. Craft C., Clough J., Ehman J., Joye S., Park R., Pennings S., Guo H., Machmuller M. Forecasting the effects of accelerated sea-level rise on tidal marsh ecosystem services. Front. Ecol. Environ. 2008, 7:73-78.
21. Dame R.F., Patten B.C. Analysis of energy flows in an intertidal oyster reef. Mar. Ecol. Prog. Ser. 1981, 5:115-124.
22. DeAngelis D.L., Bartell S.M., Brenkert A.L. Effects of nutrient recycling and food-chain length on resilience. Am. Nat. 1989, 778-805.
23. Dong L.F., Thornton D.C.O., Nedwell D.B., Underwood G.J.C. Denitrification in sediments of the River Colne estuary, England. Mar. Ecol. Prog. Ser. 2000, 203:109-122.
24. Estrada E. Characterization of topological keystone species: local, global and "meso-scale" centralities in food webs. Ecol. Complex. 2007, 4:48-57.
25. Estrada E. Generalized walks-based centrality measures for complex biological networks. J. Theor. Biol. 2010, 263:556-565.
26. Estrada E., Bodin O. Using network centrality measures to manage landscape connectivity. Ecol. Appl. 2008, 18:1810-1825.
27. Fath B.D., Borrett S.R. A Matlab© function for network environ analysis. Environ. Model. Softw. 2006, 21:375-405.
28. Fath B.D., Patten B.C. Quantifying resource homogenization using network flow analysis. Ecol. Model. 1999, 107:193-205.
29. Fath B.D., Patten B.C. Review of the foundations of network environ analysis. Ecosystems 1999, 2:167-179.
30. Fath B.D., Patten B.C., Choi J.S. Complementarity of ecological goal functions. J. Theor. Biol. 2001, 208:493-506.
31. Fath B.D., Scharler U.M., Ulanowicz R.E., Hannon B. Ecological network analysis: network construction. Ecol. Model. 2007, 208:49-55.
32. Fath B.D., Scharler U.M., Baird D. Dependence of network metrics on model aggregation and throughflow calculations. Demonstration using the Sylt-Rømø Bight Ecosystem. Ecol. Model. 2012, 252:214-219.
33. Finn J.T. Measures of ecosystem structure and function derived from analysis of flows. J. Theor. Biol. 1976, 56:363-380.
34. Finn J.T. Flow analysis of models of the Hubbard Brook ecosystem. Ecology 1980, 61:562-571.
35. Gardner W.S., Seitzinger S.P., Malczyk J.M. The effects of sea salts on the forms of nitrogen released from estuarine and freshwater sediments: does ion pairing affect ammonium flux?. Estuaries 1991, 14:157-166.
36. Gattie D.K., Schramski J.R., Bata S.A. Analysis of microdynamic environ flows in an ecological network. Ecol. Eng. 2006, 28:187-204.
37. Gattie D.K., Schramski J.R., Borrett S.R., Patten B.C., Bata S.A., Whipple S.J. Indirect effects and distributed control in ecosystems: network environ analysis of a seven-compartment model of nitrogen flow in the Neuse River Estuary, USA-steady-state analysis. Ecol. Model. 2006, 194:162-177.
38. Higashi M., Patten B.C. Further aspects of the analysis of indirect effects in ecosystems. Ecol. Model. 1986, 31:69-77.
39. Higashi M., Patten B.C. Dominance of indirect causality in ecosystems. Am. Nat. 1989, 133:288-302.
40. Hines D.E., Lisa J.A., Song B., Tobias C.R., Borrett S.R. A network model shows the importance of coupled processes in the microbial N cycle in the Cape Fear River Estuary. Estuar. Coast. Shelf Sci. 2012, 45-57.
41. Hines, D.E., Lisa, J.A., Song, B., Tobias, C.R., Borrett, S.R., 2013. Estimating the effects of sea level rise on coupled estuarine nitrogen cycling processes through comparative network analysis. (submitted for publication). arxiv:1311.1171.
42. Holling C.S. Engineering resilience versus ecological resilience. Engineering with Ecological Constraints 1996, 31-44. National Academy Press, Washington, DC. P.C. Schulze (Ed.).
43. Hou L., Liu M., Jiang H., Xu S., Ou D., Liu Q., Zhang B. Ammonium adsorption by tidal flat surface sediments from the Yangtze Estuary. Environ. Geol. 2003, 45:72-78.
44. Jordan F., Jørgensen S.E. Models of the Ecological Hierarchy: From Molecules to the Ecosphere 2012, vol. 25. Elsevier, Amsterdam.
45. Jordán F., Liu W.C., Davis A.J. Topological keystone species: measures of positional importance in food webs. Oikos 2006, 112:535-546.
46. Jørgensen S.E. Introduction to Systems Ecology 2012, CRC Press, Boca Raton.
47. Jørgensen S.E., Mejer H. Ecological buffer capacity. Ecol. Model. 1977, 3:39-61.
48. Jørgensen S.E., Patten B.C., Straškraba M. Ecosystems emerging: 4. Growth. Ecol. Model. 2000, 126:249-284.
49. Jørgensen S.E., Fath B., Bastianoni S., Marques J.C., Muller F., Nielsen S.N., Patten B.D., Tiezzi E., Ulanowicz R.E. A New Ecology: Systems Perspective 2011, Elsevier Science, Amsterdam.
50. Krause A.E., Frank K.A., Mason D.M., Ulanowicz R.E., Taylor W.W. Compartments revealed in food-web structure. Nature 2003, 426:282-285.
51. Lau M.K., Borrett S.R., Hines D.E. enaR: Tools ecological network analysis. R package version 2.0 2013.
52. Li S., Zhang Y., Yang Z., Liu H., Zhang J. Ecological relationship analysis of the urban metabolic system of Beijing, China. Environ. Pollut. 2012, 170:169-176.
53. Mageau M.T., Costanza R., Ulanowicz R.E. Quantifying the trends expected in developing ecosystems. Ecol. Model. 1998, 112:1-22.
54. Margalef R. Perspectives in Ecological Theory 1968, The University of Chicago Press, Chicago.
55. Patrício J., Ulanowicz R., Pardal M., Marques J. Ascendency as an ecological indicator: a case study of estuarine pulse eutrophication. Estuar. Coast. Shelf Sci. 2004, 60:23-35.
56. Patten B.C. Systems approach to the concept of environment. Ohio J. Sci. 1978, 78:206-222.
57. Patten B.C. Environs: the superniches of ecosystems. Am. Zool. 1981, 21:845-852.
58. Patten B.C. Environs: relativistic elementary particles for ecology. Am. Nat. 1982, 119:179-219.
59. Patten B.C. On the quantitative dominance of indirect effects in ecosystems. Analysis of Ecological Systems: State-of-the-art in Ecological Modelling 1983, 27-37. Elsevier, Amsterdam. W.K. Lauenroth, G.V. Skogerboe, M. Flug (Eds.).
60. Patten B.C. Network ecology: indirect determination of the life-environment relationship in ecosystems. Theoretical Studies of Ecosystems: The Network Perspective 1991, 288-351. Cambridge University Press, New York. M. Higashi, T. Burns (Eds.).
61. Pocock M.J., Johnson O., Wasiuk D. Succinctly assessing the topological importance of species in flower-pollinator networks. Ecol. Complex. 2011, 8:265-272.
62. Rysgaard S., Thastum P., Dalsgaard T.B.C.P., Sloth N.P. Effects of salinity on NH4+ adsorption, nitrification, and denitrification in Danish estuarine sediments. Estuaries 1999, 22:21-30.
63. Salas A.K., Borrett S.R. Evidence for dominance of indirect effects in 50 trophic ecosystem networks. Ecol. Model. 2011, 222:1192-1204.
64. Samuelson P.A. Economics: An Introductory Analysis 1948, McGraw-Hill Book Co., New York.
65. Scharler U.M., Baird D. A comparison of selected ecosystem attributes of three South African estuaries with different freshwater inflow regimes, using network analysis. J. Mar. Syst. 2005, 56:283-308.
66. Schramski J.R., Gattie D.K., Patten B.C., Borrett S.R., Fath B.D., Thomas C.R., Whipple S.J. Indirect effects and distributed control in ecosystems: Distributed control in the environ networks of a seven-compartment model of nitrogen flow in the Neuse River Estuary, USA-steady-state analysis. Ecol. Model. 2006, 194:189-201.
67. Schramski J.R., Kazanci C., Tollner E.W. Network environ theory, simulation and Econet© 2.0. Environ. Model. Softw. 2010, 26:419-428.
68. Scotti M. Development capacity. Ecol. Indic. 2008, 2:911-920.
69. Scotti M., Podani J., Jordán F. Weighting, scale dependence and indirect effects in ecological networks: a comparative study. Ecol. Complex. 2007, 4:148-159.
70. Skiena S. Strong and weak connectivity. Implementing Discrete Mathematics: Combinatorics and Graph Theory with Mathematica 1990, 172-174.
71. Small G.E., Sterner R.W., Finlay J.C. An ecological network analysis of nitrogen cycling in the Laurentian Great Lakes. Ecol. Model. 2013, (in this issue).
72. Ulanowicz R.E. An hypothesis on the development of natural communities. J. Theor. Biol. 1980, 85:223-245.
73. Ulanowicz R.E. Identifying the structure of cycling in ecosystems. Math. Biosci. 1983, 65:219-237.
74. Ulanowicz R.E. Community measures of marine food networks and their possible applications. Flows of Energy and Materials in Marine Ecosystems: Theory and Practice 1984, 23-47. Plenum Press, New York. M.J.R. Fasham (Ed.).
75. Ulanowicz R.E. Growth and Development: Ecosystems Phenomenology 1986, Springer-Verlag, New York.
76. Ulanowicz R.E. Trophic flow networks as indicators of ecosystem stress. Food Webs: Integration of Patterns and Dynamics 1996, 358-368. Chapman-Hall, New York.
77. Ulanowicz R.E. Ecology, the Ascendent Perspective 1997, Columbia University Press, New York.
78. Ulanowicz R.E. Ascendancy: a measure of ecosystem performance. Handbook of Ecosystyms: Theories and Management 2000, 303-315. Lewis Publishers, Boca Raton, FL. S.E. Jørgensen, F. Müller (Eds.).
79. Ulanowicz R.E. Quantitative methods for ecological network analysis. Comput. Biol. Chem. 2004, 28:321-339.
80. Ulanowicz R.E., Puccia C.J. Mixed trophic impacts in ecosystems. Coenoses 1990, 5:7-16.
81. Ulanowicz R.E., Jørgensen S.E., Fath B.D. Exergy, information and aggradation: an ecosystems reconciliation. Ecol. Model. 2006, 198:520-524.
82. Wasserman S., Faust K. Social Network Analysis: Methods and Applications 1994, Cambridge University Press, Cambridge/New York.
83. Whipple S.J., Borrett S.R., Patten B.C., Gattie D.K., Schramski J.R., Bata S.A. Indirect effects and distributed control in ecosystems: comparative network environ analysis of a seven-compartment model of nitrogen flow in the Neuse River Estuary, USA-time series analysis. Ecol. Model. 2007, 206:1-17.
84. Whipple S.J., Patten B.C., Borrett S.R. Indirect effects and distributed control in ecosystems - comparative network environ analysis of a seven-compartment model of nitrogen storage in the Neuse River estuary, USA: time series analysis. Ecol. Model. 2013, (in this issue).
85. Whittaker R.J., Willis K.J., Field R. Scale and species richness: towards a general, hierarchical theory of species diversity. J. Biogeogr. 2001, 28:453-470.
86. Wootton J.T. The nature and consequences of indirect effects in ecological communities. Annu. Rev. Ecol. Evol. Syst. 1994, 25:443-466.
87. Wu J., David J.L. A spatially explicit hierarchical approach to modeling complex ecological systems. Theory and applications. Ecol. Model. 2002, 153:7-26.
88. Wulff F., Ulanowicz R.E. A comparative anatomy of the Baltic Sea and Chesapeake Bay ecosystems. Coast. Estuar. Stud. 1989, 32:232-256.