A categorization of recent network approaches to analyse trophic interactions

Methods in Ecology and Evolution

Volumn 4, Issue 10, 2013, Pages 897-905

  Miranda, María ^a   Parrini, Francesca ^a   Dalerum, Fredrik ^b  

^a UNIVERSITY OF THE WITWATERSRAND   (South Africa)

^b UNIVERSITY OF PRETORIA   (South Africa)

Author keywords

Antagonism; Ecological interaction; Food web; Network analysis; Topology; Trophic network

Indexed keywords

EID: 84885599751     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/2041-210X.12092     Document Type: Review

References (86)

1. Abarca-Arenas, L.G., Franco-López, J., Peterson, M.S., Brown-Peterson, N.J. & Valero-Pacheco, E. (2007) Sociometric analysis of the role of penaeids in the continental shelf food web off Veracruz, Mexico based on by-catch. Fisheries Research, 87, 46-57.
2. Albert, R., Jeong, H. & Barabási, A.-L. (1999) Diameter of the world-wide web. Nature, 401, 130.
3. Almeida-Neto, M., Guimaraes, P.R. & Lewinsohn, T.M. (2007) On nestedness analyses: rethinking matrix temperature and anti-nestedness. Oikos, 116, 716-722.
4. Barabasi, A.L. & Albert, R. (1999) Emergence of scaling in random networks. Science, 286, 509-512.
5. Bascompte, J. (2007) Networks in ecology. Basic and Applied Ecology, 8, 485-490.
6. Batagelj, V. & Mrvar, A. (1998) Pajek - program for large network analysis. Connections, 21, 47-57.
7. Bersier, L.F., Banasek-Richter, C. & Cattin, M.F. (2002) Quantitative descriptors of food-web matrices. Ecology, 83, 2394-2407.
8. Caldarelli, G. (2007) Scale-Free Networks: Complex Webs in Nature and Technology. Oxford University Press, Oxford.
9. Caliman, A., Pires, A.F., Esteves, F.A., Bozelli, R.L. & Farjalla, V.F. (2010) The prominence of and biases in biodiversity and ecosystem functioning research. Biodiversity and Conservation, 19, 651-664.
10. Cardinale, B.J., Duffy, J.E., Gonzalez, A., Hooper, D.U., Perrings, C., Venail, P. et al. (2012) Biodiversity loss and its impact on humanity. Nature, 486, 59-67.
11. Cohen, J.E. (1977) Food webs and the dimensionality of trophic niche space. Proceedings of the National Academy of Sciences of the United States of America, 74, 4533-4536.
12. Cohen, J.E., Beaver, R.A., Cousins, S.H., De Angelis, D.L., Goldwasser, L., Heong, K.L. et al. (1993) Improving food webs. Ecology, 74, 252-258.
13. Dalerum, F., Cameron, E.Z., Kunkel, K.E. & Somers, M.J. (2012) Interactive effects of species richness and species traits on functional diversity and redundancy. Theoretical Ecology, 5, 129-139.
14. Digel, C., Riede, J.O. & Brose, U. (2011) Body sizes, cumulative and allometric degree distributions across natural food webs. Oikos, 120, 503-509.
15. Dobson, A. (2009) Food-web structure and ecosystem services: insights from the Serengeti. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 364, 1665-1682.
16. Dormann, C.F., Gruber, B. & Jochen, F. (2008) Introducing the bipartite package: analysing ecological networks. R News, Vol. 8/2, October 2008.
17. Dunne, J.A., Williams, R.J. & Martinez, N.D. (2002) Network structure and biodiversity loss in food webs: robustness increases with connectance. Ecology Letters, 5, 558-567.
18. Dunne, J.A., Williams, R.J., Martínez, N.D., Wood, R.A. & Erwin, D.H. (2008) Compilation and network analyses of Cambrian foodwebs. PLoS Biology, 6, e102, 693-708.
19. Dupont, Y.L., Trojelsgaard, K. & Olesen, J.M. (2011) Scaling down from species to individuals: a flower - visitation network between individual honeybees and thistle plants. Oikos, 120, 170-177.
20. Elton, C.S. (1927) Animal Ecology. Sidgwick & Jackson, London.
21. Euler, L. (1741) Solutio problematis ad geometriam situs pertinentis. Commentarii Academiae Scientiarum Petropolitanae, 8, 128-140.
22. Fedor, A. & Vasas, V. (2009) The robustness of keystone indices in food webs. Journal of Theoretical Biology, 260, 372-378.
23. Flynn, D.F.B., Mirotchnick, N., Jain, M., Palmer, M.I. & Naeem, S. (2011) Functional and phylogenetic diversity as predictors of biodiversity-ecosystem function relationships. Ecology, 92, 1573-1581.
24. Fontaine, C., Guimaraes, P.R., Kéfi, S., Loeuille, N., Memmott, J., van der Putten, W.H., van Veen, F.J.F. & Thébault, E. (2011) The ecological and evolutionary implications of merging different types of networks. Ecology Letters, 14, 1170-1181.
25. Fortuna, M.A., Stouffer, D.B., Olesen, J.M., Jordano, P., Mouillot, D., Krasnov, B.R., Pouiln, R. & Bascompte, J. (2010) Nestedness versus modularity in ecological networks: two sides of the same coin? Journal of Animal Ecology, 79, 811-817.
26. Goldwasser, L. & Roughgarden, J. (1997) Sampling effects and the estimation of food-web properties. Ecology, 78, 41-54.
27. Gómez, J.M. & Perfectti, F. (2012) Fitness consequences of centrality in mutualistic individual-based networks. Proceedings of the Royal Society. B, Biological Sciences, 279, 1754-1760.
28. Groves, C.R., Jensen, D.B., Valutis, L.L., Redford, K.H., Mark, L., Shaffer, J.M.S. et al. (2002) Planning for biodiversity conservation: putting conservation science into practice. BioScience, 52, 499-512.
29. Guimaraes, P.R. & Guimaraes, P. (2006) Improving the analyses of nestedness for large sets of matrices. Environmental Modelling & Software, 21, 1512-1513.
30. Hagen, E.M., McCluney, K.E., Wyant, K.A., Soykan, C.U., Keller, A.C., Luttermoser, K.C., Holmes, E.J., Mooore, J.C. & Sabo, J.L. (2012) A meta-analysis of the effects of detritus on primary producers and consumers in marine, freshwater, and terrestrial ecosystems. Oikos, 121, 1507-1515.
31. Harary, F. (1961) Who eats whom? General Systems, 6, 41-44.
32. Hegland, S.J., Dunne, J., Nielsen, A. & Memmott, J. (2010) How to monitor ecological communities cost-efficiently: the example of plant-pollinator networks. Biological Conservation, 143, 2092-2101.
33. Ings, T.C., Montoya, J.M., Bascompte, J., Blüthgen, N., Brown, L., Dormann, C.F. et al. (2009) Ecological networks-beyond food webs. Journal of Animal Ecology, 78, 253-269.
34. Joppa, L.N. & Williams, R. (2011) The influence of single elements on nested community structure. Methods in Ecology and Evolution, 2, 541-549.
35. Jordán, F. (2009) Keystone species and foodwebs. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 364, 1733-1741.
36. Jordán, F. & Osváth, G. (2009) The sensitivity of food web topology to temporal data aggregation. Ecological Modelling, 220, 3141-3146.
37. Jordán, F., Scheuring, I., Vasas, V. & Podani, J. (2006) Architectural classes of aquatic food webs based on link distribution. Community Ecology, 7, 81-90.
38. Kondoh, M., Kato, S. & Sakato, Y. (2010) Food webs are built up with nested subwebs. Ecology, 91, 3123-3130.
39. Krasnov, B.R., Fortuna, M.A., Mouillot, D., Khokhlova, I.S., Shenbrot, G.I. & Poulin, R. (2012) Phylogenetic signal in module composition and species connectivity in compartmentalized host-parasite networks. The American Naturalist, 179, 501-511.
40. Lafferty, K.D., Dobson, A.P. & Kuris, A.M. (2006) Parasites dominate food web links. Proceedings of the National Academy of Sciences of the United States of America, 103, 11211-11216.
41. Laliberté, E. & Tylianakis, J.M. (2010) Deforestation homogenizes tropical parasitoid-host networks. Ecology, 91, 1740-1747.
42. Lawton, J.H. (1989) Food webs. Ecological Concepts (ed. J. Cherrett ), pp. 43-78. Blackwell Scientific, Oxford.
43. Lindeman, R.J. (1942) The trophic-dynamic aspect of ecology. Ecology, 23, 399-418.
44. MacArthur, R. (1955) Fluctuations of animal populations and measure of community stability. Ecology, 36, 533-536.
45. Magurran, A.E. (2004) Measuring Biological Diversity. Blackwell Publishing, Oxford.
46. Martinez, N.D. (1991) Artifacts or attributes? Effects of resolution on the Little Rock Lake food web. Ecological Monographs, 61, 367-392.
47. May, R.M. (1972) Will a large complex system be stable? Nature, 238, 413-414.
48. May, R.M. (1973) Stability and Complexity in Model Ecosystems. Princeton University Press, Princeton.
49. McCann, K.S. (2000) The diversity-stability debate. Nature, 405, 228-233.
50. McCann, K.S. & Rooney, N. (2009) The more food webs change, the more they stay the same. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 364, 1789-1801.
51. Melián, C.J., Bascompte, J., Jordano, P. & Krivan, V. (2009) Diversity in a complex ecological networks with two interaction types. Oikos, 118, 122-130.
52. Memmott, J. (2009) Food webs: a ladder for picking strawberries or a practical tool for practical problems? Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 364, 1693-1699.
53. Meskens, C., McKenna, D., Hance, T. & Windsor, D. (2011) Host plant taxonomy and phenotype influence the structure of a neotropical host plant-hispine beetle food web. Ecological Entomology, 36, 480-489.
54. Montoya, J.M. & Raffaelli, D. (2010) Climate change, biotic interactions and ecosystem services. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 365, 2013-2018.
55. Montoya, J.M., Rodríguez, M.A. & Hawkings, B.A. (2003) Food web complexity and higher-level ecosystem services. Ecology Letters, 6, 587-593.
56. Montoya, J.M., Woodward, G., Emmerson, M.C. & Sole, R.V. (2009) Press perturbations and indirect effects in real food webs. Ecology, 90, 2426-2433.
57. Newman, M.E.J. (2001) Scientific collaboration networks. II. Shortest paths, weighted networks, and centrality. Physical Review E, 64, 016132.
58. Newman, M., Barabasi, A.-L. & Watts, D.J. (2006) The Structure and Dynamics of Networks. Princeton University Press, Princeton.
59. Odum, E.P. (1953) Fundamentals of Ecology. Saunders, Philadelphia.
60. Olesen, J.M., Bascompte, J., Elberling, H. & Jordano, P. (2008) Temporal dynamics in a pollination network. Ecology, 89, 1573-1582.
61. Olff, H., Alonso, D., Berg, M.P., Eriksson, K., Loreau, M., Piersma, T. & Rooney, N. (2009) Parallel ecological networks in ecosystems. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 364, 1755-1779.
62. Opsahl, T. (2009) Projecting two-mode networks onto weighted one-mode networks. http://toreopsahl.com/2009/05/01/projecting-two-mode-networks-onto-weighted-one-modenetworks (accessed 1 February 2013).
63. Pace, M.L., Cole, J.J., Carpenter, S.R. & Kitchell, J.F. (1999) Trophic cascades revealed in diverse ecosystems. Trends in Ecology and Evolution, 14, 483-488.
64. Pocock, M.J.O., Evans, D.M. & Memmott, J. (2012) The robustness and restoration of a network of ecological networks. Science, 335, 973-977.
65. R Development Core Team. (2012) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna. URL: http://www.R-project.org (accessed 1 December 2012).
66. Reiss, J., Bridle, J.R., Montoya, J.M. & Woodward, G. (2009) Emerging horizons in biodiversity and ecosystem function research. Trends in Ecology and Evolution, 24, 505-514.
67. Scheffer, M., Carpenter, S., Foley, J.A., Folke, C. & Walker, B. (2001) Catastrophic shifts in ecosystems. Nature, 413, 591-596.
68. Scotti, M. & Jordán, F. (2010) Relationships between centrality indices and trophic levels in food webs. Community Ecology, 11, 59-67.
69. Scotti, M., Podani, J. & Jordán, F. (2007) Weighting, scale dependence and indirect effects in ecological networks: a comparative study. Ecological Complexity, 4, 148-159.
70. Solé, R.V. & Montoya, J.M. (2001) Complexity and fragility in ecological networks. Proceedings of the Royal Society of London. Series B, 268, 2039-2045.
71. Stouffer, D.B. & Bascompte, J. (2011) Compartmentalization increases food-web persistence. Proceedings of the National Academy of Sciences of the United States of America, 108, 3648-3652.
72. Sugihara, G. (1984) Graph theory, homology and food webs. American Mathematical Society, 30, 83-101.
73. Sugihara, G., Schoenly, K. & Trombla, A. (1989) Scale invariance in food web properties. Science, 245, 48-52.
74. Thébault, E. & Fontaine, C. (2010) Stability of ecological communities and the architecture of mutualistic and trophic networks. Science, 329, 853-856.
75. Thompson, R.M., Brose, U., Dunne, J.A., Hall, R.O. Jr, Hladyz, S., Kitching, R.L. et al. (2012) Food webs: reconciling the structure and function of biodiversity. Trends in Ecology and Evolution, 27, 689-697.
76. Tylianakis, J.M., Laliberté, E., Nielsen, A. & Bascompte, J. (2010) Conservation of species interaction networks. Biological Conservation, 143, 2270-2279.
77. Van der Putten, W.H., de Ruiter, P.C., Bezemer, T.M., Harvey, J.A., Wassen, M. & Wolters, V. (2004) Trophic interactions in a changing world. Basic and Applied Ecology, 5, 487-494.
78. Verdu, M. & Valiente-Banuet, A. (2008) The nested assembly of plant facilitation networks prevents species extinctions. The American Naturalist, 172, 751-760.
79. de Visser, S.N., Freymann, B.P. & Olff, H. (2011) The Serengeti food web: empirical quantification and analysis of topological changes under increasing human impact. Journal of Animal Ecology, 80, 484-494.
80. Watts, D.J. & Strogatz, S.H. (1998) Collective dynamics in "small world" networks. Nature, 393, 440-442.
81. Wells, K. & O'Hara, R.B. (2013) Species interactions: estimating per-individual interaction strength and covariates before simplifying data into per-species ecological networks. Methods in Ecology and Evolution, 4, 1-8.
82. Williams, R.J. & Martínez, N.D. (2000) Simple rules yield complex food webs. Nature, 404, 180-183.
83. Wilson, E.O. & Peter, F.M. (1988) Biodiversity. National Academy Press, Washington, DC.
84. Winemiller, K.O. (1989) Must connectance decrease with species richness? The American Naturalist, 134, 960-968.
85. Woodward, G., Ebenman, B., Emmerson, M., Montoya, J.M., Olesen, J.M., Valido, A. & Warren, P. (2005) Body size in ecological networks. Trends in Ecology and Evolution, 20, 402-409.
86. Woodward, G., Papantoniou, G., Edwards, F. & Laurisen, R.B. (2008) Trophic trickles and cascades in a complex food web: impacts of a keystone predator on stream community structure and ecosystem processes. Oikos, 117, 683-692.