Seeing networks for what they are in mycorrhizal ecology

Albert, 2000, Error and attack tolerance of complex networks, Nature, 406, 378, 10.1038/35019019 Bahram, 2015, Local-scale biogeography and spatiotemporal variability in communities of mycorrhizal fungi, New Phytol., 205, 1454, 10.1111/nph.13206 Barabási, 1999, Emergence of scaling in random networks, Science, 286, 509, 10.1126/science.286.5439.509 Bastolla, 2009, The architecture of mutualistic networks minimizes competition and increases biodiversity, Nature, 458, 1018, 10.1038/nature07950 Bever, 1996, Host-dependent sporulation and species diversity of arbuscular mycorrhizal fungi in a mown grassland, J. Ecol., 84, 71 Blake, 1991, Nested subsets and the distribution of birds on isolated woodlots, Conserv. Biol., 5, 58, 10.1111/j.1523-1739.1991.tb00388.x Borrelli, 2015, Selection on stability across ecological scales, Trends Ecol. Evol., 30, 417, 10.1016/j.tree.2015.05.001 Canard, 2014, Empirical evaluation of neutral interactions in host-parasite networks, Am. Nat., 183, 468, 10.1086/675363 Caruso, 2012, On the application of network theory to arbuscular mycorrhizal fungi – plant interactions: the importance of basic assumptions, New Phytol., 194, 891, 10.1111/j.1469-8137.2012.04163.x Chagnon, 2012, Using ecological network theory to evaluate the causes and consequences of arbuscular mycorrhizal community structure, New Phytol., 194, 307, 10.1111/j.1469-8137.2011.04044.x Chagnon, 2013, A trait-based framework to understand life history of mycorrhizal fungi, Trends Plant Sci., 18, 484, 10.1016/j.tplants.2013.05.001 Chagnon, 2014, Plant–fungal symbioses as ecological networks: the need to characterize more than just interaction patterns, Fungal Ecol., 12, 10, 10.1016/j.funeco.2014.05.002 Chagnon, 2015, Trait-based partner selection drives mycorrhizal network assembly, Oikos, 124, 1609, 10.1111/oik.01987 Chagnon, 2016, Interaction type influences ecological network structure more than local abiotic conditions: evidence from endophytic and endolichenic fungi at a continental scale, Oecologia, 180, 181, 10.1007/s00442-015-3457-5 Chamberlain, 2014, Traits and phylogenetic history contribute to network structure across Canadian plant-pollinator communities, Oecologia, 176, 545, 10.1007/s00442-014-3035-2 Clauset, 2004, Finding community structure in very large networks, Phys. Rev. E 70, 1 Connor, 2013, The checkered history of checkerboard distributions, Ecology, 94, 2403, 10.1890/12-1471.1 Dakos, 2014, Critical slowing down as early warning for the onset of collapse in mutualistic communities, Proc. Natl. Acad. Sci. U. S. A., 111, 17546, 10.1073/pnas.1406326111 Dáttilo, 2014, The structure of ant-plant ecological networks: is abundance enough?, Ecology, 95, 475, 10.1890/12-1647.1 Diamond, 1975, Assembly of species communities, 342 Díaz-Castelazo, 2010, Changes of a mutualistic network over time: reanalysis over a 10-year period, Ecology, 91, 793, 10.1890/08-1883.1 Dumbrell, 2010, Relative roles of niche and neutral processes in structuring a soil microbial community, ISME, 4, 337, 10.1038/ismej.2009.122 Encinas-Viso, 2016, Plant–mycorrhizal fungus co-occurrence network lacks substantial structure, Oikos, 125, 457, 10.1111/oik.02667 Eom, 2000, Host plant species effects on arbuscular mycorrhizal fungal communities in tallgrass prairie, Oecologia, 122, 435, 10.1007/s004420050050 Gorzelak, 2012, Community structure of ericoid mycorrhizas and root-associated fungi of Vaccinium membranaceum across an elevation gradient in the Canadian Rocky Mountains, Fungal Ecol., 5, 36, 10.1016/j.funeco.2011.08.008 Gotelli, 2002, Co-occurrence of ectoparasites of marine fishes: a null model analysis, Ecol. Lett., 5, 86, 10.1046/j.1461-0248.2002.00288.x Graham, 1997, Carbohydrate allocation patterns in citrus genotypes as affected by phosphorus nutrition, mycorrhizal colonization and mycorrhizal dependency, New Phytol., 135, 335, 10.1046/j.1469-8137.1997.00636.x Haug, 2013, Reforestation sites show similar and nested AMF communities to an adjacent pristine forest in a tropical mountain area of south Ecuador, PLoS One, 8, 10.1371/journal.pone.0063524 Husband, 2002, Molecular diversity of arbuscular mycorrhizal fungi and patterns of host association over time and space in a tropical forest, Mol. Ecol., 11, 2669, 10.1046/j.1365-294X.2002.01647.x Izzo, 2005, Detection of plot-level changes in ectomycorrhizal communities across years in an old-growth mixed-conifer forest, New Phytol., 166, 619, 10.1111/j.1469-8137.2005.01354.x Jacquemyn, 2011, Analysis of network architecture reveals phylogenetic constraints on mycorrhizal specificity in the genus Orchis (Orchidaceae), New Phytol., 192, 518, 10.1111/j.1469-8137.2011.03796.x Jacquemyn, 2015, Mycorrhizal networks and coexistence in species-rich orchid communities, New Phytol., 206, 1127, 10.1111/nph.13281 Johnson, 1997, Functioning of mycorrhizal associations along the mutualism-parasitism continuum, New Phytol., 135, 575, 10.1046/j.1469-8137.1997.00729.x Joppa, 2010, On nestedness in ecological networks, Evol. Ecol. Res., 12, 35 Junttila, 2011 Kaiser-Bunbury, 2014, Determinants of the microstructure of plant-pollinator networks, Ecology, 95, 3314, 10.1890/14-0024.1 Kennedy, 2014, Missing checkerboards: an absence of competitive signal in Alnus-associated ectomycorrhizal fungal communities, PeerJ, 2, e686, 10.7717/peerj.686 Klironomos, 2003, Variation in plant response to native and exotic arbuscular mycorrhizal fungi, Ecology, 84, 2292, 10.1890/02-0413 Krishna, 2008, A neutral-niche theory of nestedness in mutualistic networks, Oikos, 117, 1609, 10.1111/j.1600-0706.2008.16540.x Lázaro, 2010, Factors related to the inter-annual variation in plants' pollination generalization levels within a community, Oikos, 119, 825, 10.1111/j.1600-0706.2009.18017.x Leger, 2015, Clustering methods differ in their ability to detect patterns in ecological networks, Methods Ecol. Evol., 6, 474, 10.1111/2041-210X.12334 Leibold, 2002, Coherence, species turnover, and boundary clumping: elements of meta-community structure, Oikos, 97, 237, 10.1034/j.1600-0706.2002.970210.x Lever, 2014, The sudden collapse of pollinator communities, Ecol. Lett., 17, 350, 10.1111/ele.12236 Liiv, 2010, Review seriation and matrix reordering methods: an historical overview, Stat. Anal. Data Min., 10.1002/sam.10071 Maglianesi, 2014, Morphological traits determine specialization and resource use in plant – hummingbird networks in the neotropics, Ecology, 95, 3325, 10.1890/13-2261.1 Martín González, 2012, Drivers of compartmentalization in a Mediterranean pollination network, Oikos, 121, 2001, 10.1111/j.1600-0706.2012.20279.x Martos, 2012, The role of epiphytism in architecture and evolutionary constraint within mycorrhizal networks of tropical orchids, Mol. Ecol., 21, 5098, 10.1111/j.1365-294X.2012.05692.x McGill, 2007, Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework, Ecol. Lett., 10, 995, 10.1111/j.1461-0248.2007.01094.x Medan, 2007, Analysis and assembling of network structure in mutualistic systems, J. Theor. Biol., 246, 510, 10.1016/j.jtbi.2006.12.033 Mihaljevic, 2012, Linking metacommunity theory and symbiont evolutionary ecology, Trends Ecol. Evol., 10.1016/j.tree.2012.01.011 Miklós, 2005, Rearrangement of ecological data matrices via Markov chain Monte Carlo simulation, Ecology, 86, 3398, 10.1890/05-0027 Montesinos-Navarro, 2012, The network structure of plant-arbuscular mycorrhizal fungi, New Phytol., 194, 536, 10.1111/j.1469-8137.2011.04045.x Morales-Castilla, 2015, Inferring biotic interactions from proxies, Trends Ecol. Evol., 30, 347, 10.1016/j.tree.2015.03.014 Mummey, 2008, Spatial characterization of arbuscular mycorrhizal fungal molecular diversity at the submeter scale in a temperate grassland, FEMS Microbiol. Ecol., 64, 260, 10.1111/j.1574-6941.2008.00475.x Patterson, 1986, Nested subsets and the structure of insular mammalian faunas and archipelagos, Biol. J. Linn. Soc., 28, 65, 10.1111/j.1095-8312.1986.tb01749.x Petanidou, 2008, Long-term observation of a pollination network: fluctuation in species and interactions, relative invariance of network structure and implications for estimates of specialization, Ecol. Lett., 11, 564, 10.1111/j.1461-0248.2008.01170.x Pickles, 2012, Spatial analysis of ectomycorrhizal fungi reveals that root tip communities are structured by competitive interactions, Mol. Ecol., 21, 5110, 10.1111/j.1365-294X.2012.05739.x Stang, 2009, Size-specific interaction patterns and size matching in a plant-pollinator interaction web, Ann. Bot., 103, 1459, 10.1093/aob/mcp027 Stone, 1990, The checkerboard score and species distributions, Oecologia, 85, 74, 10.1007/BF00317345 Stouffer, 2006, A robust measure of food web intervality, Proc. Natl. Acad. Sci. U. S. A., 103, 19015, 10.1073/pnas.0603844103 Tang, 2014, Correlation between interaction strengths drives stability in large ecological networks, Ecol. Lett., 17, 1094, 10.1111/ele.12312 Taudiere, 2015, Beyond ectomycorrhizal bipartite networks: projected networks demonstrate contrasted patterns between early- and late-successional plants in Corsica, Front. Plant Sci., 6, 1, 10.3389/fpls.2015.00881 Thébault, 2010, Stability of ecological communities and the architecture of mutualistic and trophic networks, Science, 329, 853, 10.1126/science.1188321 Torrecillas, 2014, Modularity reveals the tendency of arbuscular mycorrhizal fungi to interact differently with generalist and specialist plant species in gypsum soils, Appl. Environ. Microbiol., 80, 5457, 10.1128/AEM.01358-14 Ulrich, 2009, A consumer's guide to nestedness analysis, Oikos, 118, 3, 10.1111/j.1600-0706.2008.17053.x Vacher, 2008, Architecture of an antagonistic tree/fungus network: the asymmetric influence of past evolutionary history, PLoS One, 3, 10.1371/annotation/c03a4beb-a3fa-4b78-8724-b3c8ce28c415 Vermaat, 2009, Major dimensions in food-web structure properties, Ecology, 90, 278, 10.1890/07-0978.1 Waser, 1996, Generalization in pollination and why it matters, Ecology, 77, 1043, 10.2307/2265575 Watts, 1998, Collective dynamics of “small-world” networks, Nature, 393, 440, 10.1038/30918 Wolfe, 2007, Small-scale spatial heterogeneity of arbuscular mycorrhizal fungal abundance and community composition in a wetland plant community, Mycorrhiza, 17, 175, 10.1007/s00572-006-0089-y