Merging evolutionary history into species interaction networks

Functional Ecology

Volumn 30, Issue 12, 2016, Pages 1917-1925

  Peralta, Guadalupe ^a  

^a LABORATORIO DE ENTOMOLOGÍA   (Argentina)

Author keywords

antagonistic network; conservatism of interactions; module; mutualistic network; nestedness; network cohesion; phylogenetic signal; phylogeny

Indexed keywords

ANTAGONISM; COHESION; EVOLUTIONARY BIOLOGY; MANAGEMENT PRACTICE; METHODOLOGY; MUTUALISM; NESTEDNESS; PHYLOGENETICS; PHYLOGENY; SPECIES OCCURRENCE;

EID: 85006306792     PISSN: 02698463     EISSN: 13652435     Source Type: Journal    
DOI: 10.1111/1365-2435.12669     Document Type: Review

References (100)

1. Aizen, M.A., Gleiser, G., Sabatino, M., Gilarranz, L.J., Bascompte, J. & Verdu, M. (2016) The phylogenetic structure of plant–pollinator networks increases with habitat size and isolation. Ecology Letters, 19, 29–36.
2. Almeida-Neto, M., Guimarães, P., Guimarães, P.R.J., Loyola, R.D. & Ulrich, W. (2008) A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement. Oikos, 117, 1227–1239.
3. Baker, N.J., Kaartinen, R., Roslin, T. & Stouffer, D.B. (2015) Species’ roles in food webs show fidelity across a highly variable oak forest. Ecography, 38, 130–139.
4. Banasek-Richter, C., Cattin, M.F. & Bersier, L.F. (2004) Sampling effects and the robustness of quantitative and qualitative food-web descriptors. Journal of Theoretical Biology, 226, 23–32.
5. Bascompte, J., Jordano, P., Melian, C.J. & Olesen, J.M. (2003) The nested assembly of plant-animal mutualistic networks. Proceedings of the National Academy of Sciences of the United States of America, 100, 9383–9387.
6. Benson, D.A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. et al. (2013) GenBank. Nucleic Acids Research, 41, D36–D42.
7. Bersier, L.F. & Kehrli, P. (2008) The signature of phylogenetic constraints on food-web structure. Ecological Complexity, 5, 132–139.
8. Blomberg, S.P., Garland, T.J. & Ives, A.R. (2003) Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution, 57, 717–745.
9. Bluthgen, N., Menzel, F., Hovestadt, T., Fiala, B. & Bluthgen, N. (2007) Specialization, constraints, and conflicting interests in mutualistic networks. Current Biology, 17, 341–346.
10. Brodie, E.D. Jr, Ridenhour, B.J. & Iii, E.D.B. (2002) The evolutionary response of predators to dangerous prey: hotspots and coldspots in the geographic mosaic of coevolution between garter snakes and newts. Evolution, 56, 2067–2082.
11. Cadotte, M.W., Borer, E.T., Seabloom, E.W., Cavender-Bares, J., Harpole, W.S. & Cleland, E. (2010) Phylogenetic patterns differ for native and exotic plant communities across a richness gradient in Northern California. Diversity and Distributions, 16, 892–901.
12. Cagnolo, L., Salvo, A. & Valladares, G. (2011) Network topology: patterns and mechanisms in plant-herbivore and host-parasitoid food webs. Journal of Animal Ecology, 80, 342–351.
13. Cagnolo, L. & Tavella, J. (2015) The network structure of myrmecophilic interactions. Ecological Entomology, 40, 553–561.
14. Cahill, J.F.J., Kembel, S.W., Lamb, E.G. & Keddy, P.A. (2008) Does phylogenetic relatedness influence the strength of competition among vascular plants? Perspectives in Plant Ecology, Evolution and Systematics, 10, 41–50.
15. Cattin, M.-F., Bersier, L.-F., Banasek-Richter, C., Baltensperger, R. & Gabriel, J.-P. (2004) Phylogenetic constraints and adaptation explain food-web structure. Nature, 427, 835–839.
16. Cavender-Bares, J., Ackerly, D.D., Baum, D.A. & Bazzaz, F.A. (2004) Phylogenetic overdispersion in Floridian Oak communities. The American Naturalist, 163, 823–843.
17. Cavender-Bares, J., Kozak, K.H., Fine, P.V.A. & Kembel, S.W. (2009) The merging of community ecology and phylogenetic biology. Ecology Letters, 12, 693–715.
18. Chamberlain, S., Cartar, R.V., Worley, A.C., Semmler, S.J., Gielens, G., Elwell, S. et al. (2014a) Traits and phylogenetic history contribute to network structure across a Canadian plant-pollinator communities. Oecologia, 176, 545–556.
19. Chamberlain, S., Vazquez, D.P., Carvalheiro, L., Elle, E. & Vamosi, J.C. (2014b) Phylogenetic tree shape and the structure of mutualistic networks. Journal of Ecology, 102, 1234–1243.
20. Corbet, S.A. (2000) Conserving compartments in pollination webs. Conservation Biology, 14, 1229–1231.
21. Danieli-Silva, A., Tesserolli de Souza, J.M., Donatti, A.J., Pamplona Campos, R., Vicente-Silva, J., Freitas, L. et al. (2012) Do pollination syndromes cause modularity and predict interactions in a pollination network in tropical high-altitude grasslands? Oikos, 121, 35–43.
22. Dehling, D.M., Töpfer, T., Schaefer, H.M., Jordano, P., Böhning-Gaese, K. & Schleuning, M. (2014) Functional relationships beyond species richness patterns: trait matching in plant–bird mutualisms across scales. Global Ecology and Biogeography, 23, 1085–1093.
23. Donatti, C.I., Guimarães, P.R., Galetti, M., Pizo, M.A., Marquitti, F.M.D. & Dirzo, R. (2011) Analysis of a hyper-diverse seed dispersal network: modularity and underlying mechanisms. Ecology Letters, 14, 773–781.
24. Drummond, A.J. & Rambaut, A. (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
25. Dupont, Y.L. & Olesen, J.M. (2009) Ecological modules and roles of species in heathland plant-insect flower visitor networks. Journal of Animal Ecology, 78, 346–353.
26. Eklöf, A., Jacob, U., Kopp, J., Bosch, J., Castro-Urgal, R., Chacoff, N.P. et al. (2013) The dimensionality of ecological networks. Ecology Letters, 16, 577–583.
27. Elias, M., Fontaine, C. & van Veen, F.J.F. (2013) Evolutionary history and ecological processes shape a local multilevel antagonistic network. Current Biology, 23, 1355–1359.
28. Felsenstein, J. (1985) Phylogenies and the comparative method. The American Naturalist, 125, 1–15.
29. Fontaine, C. & Thébault, E. (2015) Comparing the conservatism of ecological interactions in plant-pollinator and plant-herbivore networks. Population Ecology, 57, 29–36.
30. Fontaine, C., Guimarães, P.R.J., Kéfi, S., Loeuille, N., Memmott, J., van der Putten, W.H. et al. (2011) The ecological and evolutionary implications of merging different types of networks. Ecology Letters, 14, 1170–1181.
31. Galvani, A.P. (2003) Epidemiology meets evolutionary ecology. Trends in Ecology & Evolution, 18, 132–139.
32. Garcia-Robledo, C., Erickson, D.L., Staines, C.L., Erwin, T.L. & Kress, W.J. (2013) Tropical plant-herbivore networks: reconstructing species interactions using DNA barcodes. PLoS ONE, 8, e52967.
33. Gómez, J.M., Verdú, M. & Perfectti, F. (2010) Ecological interactions are evolutionary conserved across the entire tree of life. Nature, 465, 918–921.
34. González-Castro, A., Yang, S., Nogales, A. & Carlo, T.A. (2015) Relative importance of phenotypic trait matching and species’ abundances in determining plant-avian seed dispersal interactions in a small insular community. AoB Plants, 7, plv017.
35. Gu, H., Goodale, E. & Chen, J. (2015) Emerging directions in the study of the ecology and evolution of plant-animal mutualistic networks: a review. Zoological Research, 36, 65–71.
36. Guimarães, P.R., Jordano, P. & Thompson, J.N. (2011) Evolution and coevolution in mutualistic networks. Ecology Letters, 14, 877–885.
37. Guimera, R. & Amaral, L.A.N. (2005) Functional cartography of complex metabolic networks. Nature, 433, 895–900.
38. Guimera, R., Sales-Pardo, M. & Amaral, L.A.N. (2007) Module identification in bipartite and directed networks. Physical Review E, 76, 036102.
39. Harvey, P.H. & Pagel, M.D. (1991) The Comparative Method in Evolutionary Biology. Oxford University Press, Oxford, UK.
40. Henneman, M.L. & Memmott, J. (2001) Infiltration of a Hawaiian community by introduced biological agents. Science, 293, 1314–1316.
41. Howarth, F.G. (1991) Environmental impacts of classical biological control. Annual Review of Entomology, 36, 485–509.
42. Ives, A.R. & Godfray, H.C.J. (2006) Phylogenetic analysis of trophic associations. The American Naturalist, 168, E1–E14.
43. Jacquemyn, H., Merckx, V., Brys, R., Tyteca, D., Cammue, B.P.A., Honnay, O. et al. (2011) Analysis of network architecture reveals phylogenetic constraints on mycorrhizal specificity in the genus Orchis (Orchidaceae). New Phytologist, 192, 518–528.
44. Johnson, K.P., Weckstein, J.D., Meyer, J.M. & Clayton, D.H. (2011) There and back again: switching between host orders by avian body lice (Ischnocera: Goniodidae). Biological Journal of the Linnean Society, 102, 614–625.
45. Jordano, P. (2010) Coevolution in multispecific interactions among free-living species. Evolution: Education and Outreach, 3, 40–46.
46. Jordano, P. (2015) Sampling networks of ecological interactions. bioRXiv. doi: 10.1101/025734.
47. Krasnov, B.R., Mouillot, D., Shenbrot, G.I., Khokhlova, I.S. & Poulin, R. (2004) Geographical variation in host specificity of fleas (Siphonaptera) parasitic on small mammals: the influence of phylogeny and local environmental conditions. Ecography, 27, 787–797.
48. 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.
49. Krause, A.E., Frank, K.A., Mason, D.M., Ulanowicz, R.E. & Taylor, W.W. (2003) Compartments revealed in food-web structure. Nature, 426, 282–285.
50. Lavandero, B. & Tylianakis, J.M. (2013) Genotype matching in a parasitoid–host genotypic food web: an approach for measuring effects of environmental change. Molecular Ecology, 22, 229–238.
51. Lavergne, S., Mouquet, N., Thuiller, W. & Ronce, O. (2010) Biodiversity and climate change: integrating evolutionary and ecological responses of species and communities. Annual Review of Ecology, Evolution and Systematics, 41, 321–350.
52. Leger, J.B., Daudin, J.J. & Vacher, C. (2015) Clustering methods differ in their ability to detect patterns in ecological networks. Methods in Ecology and Evolution, 64, 474–481.
53. Leppanen, S.A., Altenhofer, E., Liston, A.D. & Nyman, T. (2013) Ecological versus phylogenetic determinants of trophic associations in a plant-leafminer-parasitoid food web. Evolution, 67, 1493–1502.
54. Lima, D.P., Giacomini, H.C., Takemoto, R.M., Agostinho, A.A. & Bini, L.M. (2012) Patterns of interactions of a large fish–parasite network in a tropical floodplain. Journal of Animal Ecology, 81, 905–913.
55. Maddison, D.R. & Schulz, K.-S. (2007) The Tree of Life Web Project. http://tolweb.org.
56. Mantel, N. (1967) The detection of disease clustering and a generalized regression approach. Cancer Research, 27, 209–220.
57. Martinez, N.D., Hawkins, B.A., Dawah, H.A. & Feifarek, B.P. (1999) Effects of sampling effort on characterization of food-web structure. Ecology, 80, 1044–1055.
58. Mello, M.A.R., Marquitti, F.M.D., Guimarães, P.R.J., Kalko, E.K.V., Jordano, P. & Martinez de Aguiar, M.A. (2011) The missing part of seed dispersal networks: structure and robustness of bat-fruit interactions. PLoS ONE, 6, e17395.
59. Melo, A.S., Cianciaruso, M.V. & Almeida-Neto, M. (2014) treeNODF: nestedness to phylogenetic, functional and other tree-based diversity metrics. Methods in Ecology and Evolution, 5, 563–572.
60. Mielke, P.W. & Berry, K.J. (2001) Permutation Methods: A Distance Function Approach. Springer, New York, NY, USA.
61. Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D. & Alon, U. (2002) Network motifs: simple building blocks of complex networks. Science, 298, 824–827.
62. Montoya, D., Yallop, M.L. & Memmott, J. (2015) Functional group diversity increases with modularity in complex food webs. Nature Communications, 6, 7379.
63. Mooney, H.A. & Drake, J.A. (1986) Ecology of Biological Invasions of North America and Hawaii. Springer, New York, NY, USA.
64. Mouquet, N., Devictor, V., Meynard, C.N., Munoz, F., Bersier, L.F., Chave, J. et al. (2012) Ecophylogenetics: advances and perspectives. Biological Reviews, 87, 769–785.
65. Naisbit, R.E., Rohr, R.P., Rossberg, A.G., Kehrli, P. & Bersier, L.F. (2012) Phylogeny versus body size as determinants of food web structure. Proceedings of the Royal Society B, 279, 3291–3297.
66. Nielsen, A. & Bascompte, J. (2007) Ecological networks, nestedness and sampling effort. Journal of Ecology, 95, 1134–1141.
67. Nogales, M., Heleno, R., Rumeu, B., González-Castro, A., Traveset, A., Vargas, P. et al. (2015) Seed-dispersal netwoks on the Canaries and the Galapagos archipelagos: interaction modules as biogeographical entities. Global Ecology and Biogeography, 25, 912–922.
68. Peralta, G., Frost, C.M., Didham, R.K., Varsani, A. & Tylianakis, J.M. (2015) Phylogenetic diversity and co-evolutionary signals among trophic levels change across a habitat edge. Journal of Animal Ecology, 84, 364–372.
69. Perazzo, R.P.J., Hernandez, L., Ceva, H., Burgos, E. & Alvarez-Hamelin, J.I. (2014) Study of the influence of the phylogenetic distance on the interaction network of mutualistic ecosystems. Physica A, 394, 124–135.
70. Perez-Lozada, M.J., Hoeg, J.T. & Crandall, K.A. (2009) Remarkable convergent evolution in specialized parasitic Thecostraca (Crustaceae). BMC Biology, 7, 15.
71. Peterson, A.T., Soberón, J. & Sánchez-Cordero, V. (1999) Conservatism of ecological niches in evolutionary time. Science, 285, 1265–1267.
72. Poisot, T., Stouffer, D.B. & Gravel, D. (2015) Beyond species: why ecological interaction networks vary through space and time. Oikos, 124, 243–251.
73. Poisot, T., Thrall, P.H. & Hochberg, M.E. (2012) Trophic network structure emerges through antagonistic coevolution in temporally varying environments. Proceedings of the Royal Society B, 279, 299–308.
74. Polis, G. (1991) Complex trophic interactions in deserts: an empirical critique of food-web theory. The American Naturalist, 138, 123–155.
75. Poole, A.M., Stouffer, D.B. & Tylianakis, J.M. (2012) “Ecosystomics”: Ecology by sequencer. Trends in Ecology & Evolution, 27, 309–310.
76. Poulin, R., Krasnov, B.R., Pilosof, S. & Thieltger, D.W. (2013) Phylogeny determines the role of helminth parasites in intertidal food webs. Journal of Animal Ecology, 82, 1265–1275.
77. Proulx, S.R., Promislow, D.E. & Phillips, P.C. (2005) Network thinking in ecology and evolution. Trends in Ecology and Evolution, 20, 345–353.
78. Rezende, E.L., Jordano, P. & Bascompte, J. (2007) Effects of phenotypic complementarity and phylogeny on the nested structure of mutualistic networks. Oikos, 116, 1919–1929.
79. Rezende, E.L., Lavabre, J.E., Guimarães, P.R., Jordano, P. & Bascompte, J. (2007) Non-random coextinctions in phylogenetically structured mutualistic networks. Nature, 448, 925–928.
80. Rezende, E.L., Albert, E.M., Fortuna, M.A. & Bascompte, J. (2009) Compartments in a marine food web associated with phylogeny, body mass, and habitat structure. Ecology Letters, 12, 779–788.
81. Robinson, K.M., Hauzy, C., Loeuille, N. & Albrectsen, B.R. (2015) Relative impacts of environmental variation and evolutionary history on the nestedness and modularity of tree–herbivore networks. Ecology and Evolution, 5, 2898–2915.
82. Rohr, P.R. & Bascompte, J. (2014) Components of phylogenetic signal in antagonistic and mutualistic networks. The American Naturalist, 184, 556–564.
83. Rossberg, A.G., Matsuda, H., Amemiya, T. & Itoh, K. (2006) Food webs: experts consuming families of experts. Journal of Theoretical Biology, 241, 552–563.
84. Santamaria, L. & Rodriguez-Girones, M.A. (2007) Linkage rules for plant-pollinator networks: trait complementarity or exploitation barriers? PLoS ONE, 5, e31.
85. Schleuning, M., Ingmann, L., StrauB, R., Fritz, S.A., Dalsgaard, B., Dehling, D.M. et al. (2014) Ecological, historical and evolutionary determinants of modularity in weighted seed-dispersal networks. Ecology Letters, 17, 454–463.
86. Srivastava, D.S., Cadotte, M.W., MacDondald, A.M., Marushia, R.G. & Mirotchnick, N. (2012) Phylogenetic diversity and the functioning of ecosystems. Ecology Letters, 15, 637–648.
87. Stouffer, D.B., Rezende, E.L. & Amaral, L.A. (2011) The role of body mass in diet contiguity and food-web structure. Journal of Animal Ecology, 80, 632–639.
88. Stouffer, D.B., Sales-Pardo, M., Sirer, M.I. & Bascompte, J. (2012) Evolutionary conservation of species’ roles in food webs. Science, 335, 1489–1492.
89. Thébault, E. & Fontaine, C. (2010) Stability of ecological communities and the architecture of mutualistic and antagonistic networks. Science, 329, 853–856.
90. Thompson, J.N. (2005) The Geographic Mosaic of Coevolution. University of Chicago Press, Chicago, IL, USA.
91. Thompson, J.N. (2006) Mutualistic webs of species. Science, 312, 372–373.
92. Thompson, A.R., Adam, T.C., Hultgren, K.M. & Thacker, C.E. (2013) Ecology and evolution affect network structure in an intimate marine mutualism. The American Naturalist, 182, E58–E72.
93. Thuiller, W., Gallien, L., Boulangeat, I., de Bello, F., Münkemüller, T., Roquet, C. et al. (2010) Resolving Darwin's naturalization conundrum: a quest for evidence. Diversity and Distributions, 16, 461–475.
94. Ulrich, W., Almeida-Neto, M. & Gotelli, N.J. (2009) A consumer's guide to nestedness analysis. Oikos, 118, 3–17.
95. Vacher, C., Piou, D. & Desprez-Loustau, M.L. (2008) Architecture of an antagonistic tree/fungus network: the asymetric influence of past evolutionary history. PLoS ONE, 3, e1740.
96. Vázquez, D.P., Bluthgen, N., Cagnolo, L. & Chacoff, N.P. (2009) Uniting pattern and process in plant-animal mutualistic networks: a review. Annals of Botany, 103, 1445–1457.
97. Webb, C.O., Ackerly, D.D. & Kembel, S.W. (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics, 24, 2098–2100.
98. Webb, C.O. & Donoghue, M.J. (2005) Phylomatic: tree assembly for applied phylogenetics. Molecular Ecology Notes, 5, 181–183.
99. Webb, C.O., Ackerly, D.D., McPeek, M.A. & Donoghue, M.J. (2002) Phylogenies and community ecology. Annual Review of Ecology and Systematics, 33, 475–505.
100. Weiblen, G.D., Webb, C.O., Novotny, V., Basset, Y. & Miller, S.E. (2006) Phylogenetic dispersion of host use in a tropical insect herbivore community. Ecology, 87, S62–S75.