Improved community detection in weighted bipartite networks

Beckett, Stephen J.

doi:10.1098/rsos.140536

Cited by 353 publications

(286 citation statements)

References 34 publications

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“…To explore whether hybrid network structure changed along the agricultural intensification gradient, we calculated species richness, connectance, nestedness and modularity of each of the 16 hybrid networks we created using the observed plant‐pollinator and plant‐herbivore interactions. We used weighted NODF (Almeida‐Neto & Ulrich ) to measure nestedness and Beckett’s weighted modularity, a label propagation algorithm, to measure modularity (Beckett ). We also calculated estimated species richness (Chao) to account for detection bias in species sampling.…”

Section: Methodsmentioning

confidence: 99%

Agricultural intensification drives changes in hybrid network robustness by modifying network structure

2019

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Within ecological communities, species engage in myriad interaction types, yet empirical examples of hybrid species interaction networks composed of multiple types of interactions are still scarce. A key knowledge gap is understanding how the structure and stability of such hybrid networks are affected by anthropogenic disturbance. Using 15,169 interaction observations, we constructed 16 hybrid herbivore‐plant‐pollinator networks along an agricultural intensification gradient to explore changes in network structure and robustness to local extinctions. We found that agricultural intensification led to declines in modularity but increases in nestedness and connectance. Notably, network connectance, a structural feature typically thought to increase robustness, caused declines in hybrid network robustness, but the directionality of changes in robustness along the gradient depended on the order of local species extinctions. Our results not only demonstrate the impacts of anthropogenic disturbance on hybrid network structure, but they also provide unexpected insights into the structure‐stability relationship of hybrid networks.

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Section: Methodsmentioning

confidence: 99%

Agricultural intensification drives changes in hybrid network robustness by modifying network structure

2019

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“…All network metrics and null models, except modularity, robustness and Resilience 75 , were calculated using the R package “bipartite” version 2.06.1 (Dormann, Fründ, Blüthgen, & Gruber, ; R Core Team, ). Modularity was calculated using the LPAwb+ code available on GitHub (https://github.com/sjbeckett/weighted-modularity-LPAwbPLUS; Beckett, ). For each modularity calculation, the LPAwb+ algorithm was run once.…”

Section: Methodsmentioning

confidence: 99%

Moving from frugivory to seed dispersal: Incorporating the functional outcomes of interactions in plant–frugivore networks

Simmons

Sutherland

Dicks

et al. 2018

Journal of Animal Ecology

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There is growing interest in understanding the functional outcomes of species interactions in ecological networks. For many mutualistic networks, including pollination and seed dispersal networks, interactions are generally sampled by recording animal foraging visits to plants. However, these visits may not reflect actual pollination or seed dispersal events, despite these typically being the ecological processes of interest. Frugivorous animals can act as seed dispersers, by swallowing entire fruits and dispersing their seeds, or as pulp peckers or seed predators, by pecking fruits to consume pieces of pulp or seeds. These processes have opposing consequences for plant reproductive success. Therefore, equating visitation with seed dispersal could lead to biased inferences about the ecology, evolution and conservation of seed dispersal mutualisms. Here, we use natural history information on the functional outcomes of pairwise bird-plant interactions to examine changes in the structure of seven European plant-frugivore visitation networks after non-mutualistic interactions (pulp pecking and seed predation) have been removed. Following existing knowledge of the contrasting structures of mutualistic and antagonistic networks, we hypothesized a number of changes following interaction removal, such as increased nestedness and lower specialization. Non-mutualistic interactions with pulp peckers and seed predators occurred in all seven networks, accounting for 21%-48% of all interactions and 6%-24% of total interaction frequency. When non-mutualistic interactions were removed, there were significant increases in network-level metrics such as connectance and nestedness, while robustness decreased. These changes were generally small, homogenous and driven by decreases in network size. Conversely, changes in species-level metrics were more variable and sometimes large, with significant decreases in plant degree, interaction frequency, specialization and resilience to animal extinctions and significant increases in frugivore species strength. Visitation data can overestimate the actual frequency of seed dispersal services in plant-frugivore networks. We show here that incorporating natural history information on the functions of species interactions can bring us closer to understanding the processes and functions operating in ecological communities. Our categorical approach lays the foundation for future work quantifying functional interaction outcomes along a mutualism-antagonism continuum, as documented in other frugivore faunas.

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“…Modularity values are computed by detecting the extent to which the number of interactions between modules is lower than expected based on random interactions. We calculated modularity Q with the algorithm proposed by Beckett () for weighted bipartite networks based on a single model run with 10 7 steps (Schleuning et al, ); five repeated runs yielded identical Q values. Finally, H 2 ′ measures the overall specialization within a network; that is, whether species in a network tend to partition or share their interaction partners (Blüthgen, Menzel, & Blüthgen, ).…”

Section: Methodsmentioning

confidence: 99%

Seed‐dispersal networks are more specialized in the Neotropics than in the Afrotropics

Dugger

Blendinger

Böhning‐Gaese

et al. 2018

Global Ecol Biogeogr

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Aim Biogeographical comparisons of interaction networks help to elucidate differences in ecological communities and ecosystem functioning at large scales. Neotropical ecosystems have higher diversity and a different composition of frugivores and fleshy‐fruited plants compared with Afrotropical systems, but a lack of intercontinental comparisons limits understanding of (a) whether plant–frugivore networks are structured in a similar manner, and (b) whether the same species traits define the roles of animals across continents. Location Afrotropics and Neotropics. Time period 1977–2015. Taxa Fleshy‐fruited plants and frugivorous vertebrates. Methods We compiled a dataset comprising 17 Afrotropical and 48 Neotropical weighted seed‐dispersal networks quantifying frugivory interactions between 1,091 fleshy‐fruited plant and 665 animal species, comprising in total 8,251 interaction links between plants and animals. In addition, we compiled information on the body mass of animals and their degree of frugivory. We compared four standard network‐level metrics related to interaction diversity and specialization, accounting for differences related to sampling effort and network location. Furthermore, we tested whether animal traits (body mass, degree of frugivory) differed between continents, whether these traits were related to the network roles of species and whether these relationships varied between continents. Results We found significant structural differences in networks between continents. Overall, Neotropical networks were less nested and more specialized than Afrotropical networks. At the species level, a higher body mass and degree of frugivory were associated with an increasing diversity of plant partners. Specialization of frugivores increased with the degree of frugivory, but only in the Neotropics. Main conclusions Our findings show that Afrotropical networks have a greater overlap in plant partners among vertebrate frugivores than the more diverse networks in the Neotropics that are characterized by a greater niche partitioning. Hence, the loss of frugivore species could have stronger impacts on ecosystem functioning in the more specialized Neotropical communities compared with the more generalized Afrotropical communities.

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Improved community detection in weighted bipartite networks

Cited by 353 publications

References 34 publications

Agricultural intensification drives changes in hybrid network robustness by modifying network structure

Agricultural intensification drives changes in hybrid network robustness by modifying network structure

Moving from frugivory to seed dispersal: Incorporating the functional outcomes of interactions in plant–frugivore networks

Seed‐dispersal networks are more specialized in the Neotropics than in the Afrotropics

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