🐎 mop up section

index.qmd

@@ -130,7 +130,7 @@ This is perhaps the most developed group of models; with a variety of approaches
 
 ## Models that predict realised networks (realised interactions)
 
-In order to construct realised networks models need to incorporate *both* the feasibility of interactions (*i.e.,* determine the entire diet breadth of a species) as well as then determine which interactions are realised (*i.e.,* incorporate the 'cost' of interactions). As far as we are aware there is no model that explicitly accounts for both of these 'rules' and rather *only* account for processes that determine the realisation of an interaction (*i.e.,* abundance, predator choice, or non-trophic interactions). Although the use of allometry *i.e.,* body size [*e.g.,* @valdovinosBioenergeticFrameworkAboveground2023; @beckermanForagingBiologyPredicts2006] may represent a first step in capturing 'evolutionary compatibility' alongside more energy (predator choice) driven processes we still need to account for other traits that determine feeding compatibility [*e.g.,* @vandewalleArthropodFoodWebs2023 show how incorporating prey defensive properties alongside body size improves predictions]. In terms of constructing realised networks, diet models [@beckermanForagingBiologyPredicts2006; @petcheySizeForagingFood2008] have been used construct networks based on both predator choice (as determined by the handling time, energy content, and predator attack rate) as well as abundance (prey density) and progress has also been made in understanding the compartmentation of energy in networks and how this influences energy acquisition [@woottonModularTheoryTrophic2023; @krauseCompartmentsRevealedFoodweb2003]. As realised networks are are build on the concept of dynamic processes (the abundance of species will always be in flux) these networks are valuable for understanding the behaviour of networks over time or their response to change [@lajaaitiEcologicalNetworksDynamicsJlJulia2024; @delmasSimulationsBiomassDynamics2017; @curtsdotterEcosystemFunctionPredator2019]. However, the are 'costly' to construct (requiring data about the entire community as it is the behaviour of the system that determines the behaviour of the part) and also lack the larger context afforded by metawebs.
+In order to construct realised networks models need to incorporate *both* the feasibility of interactions (*i.e.,* determine the entire diet breadth of a species) as well as then determine which interactions are realised (*i.e.,* incorporate the 'cost' of interactions). As far as we are aware there is no model that explicitly accounts for both of these 'rules' (although see @olivierExploringTemporalVariability2019) and rather *only* account for processes that determine the realisation of an interaction (*i.e.,* abundance, predator choice, or non-trophic interactions). Although the use of allometry *i.e.,* body size [*e.g.,* @valdovinosBioenergeticFrameworkAboveground2023; @beckermanForagingBiologyPredicts2006] may represent a first step in capturing 'evolutionary compatibility' alongside more energy (predator choice) driven processes we still need to account for other traits that determine feeding compatibility [*e.g.,* @vandewalleArthropodFoodWebs2023 show how incorporating prey defensive properties alongside body size improves predictions]. In terms of constructing realised networks, diet models [@beckermanForagingBiologyPredicts2006; @petcheySizeForagingFood2008] have been used construct networks based on both predator choice (as determined by the handling time, energy content, and predator attack rate) as well as abundance (prey density) and progress has also been made in understanding the compartmentation of energy in networks and how this influences energy acquisition [@woottonModularTheoryTrophic2023; @krauseCompartmentsRevealedFoodweb2003]. As realised networks are are build on the concept of dynamic processes (the abundance of species will always be in flux) these networks are valuable for understanding the behaviour of networks over time or their response to change [@lajaaitiEcologicalNetworksDynamicsJlJulia2024; @delmasSimulationsBiomassDynamics2017; @curtsdotterEcosystemFunctionPredator2019]. However, they are 'costly' to construct (requiring data about the entire community as it is the behaviour of the system that determines the behaviour of the part) and also lack the larger diet niche context afforded by metawebs.
 
 ## Models that predict structure (interaction agnostic)
 

references.bib

@@ -15,6 +15,25 @@ @article{adhuryaNovelMethodPredicting2024
   file = {/Users/tanyastrydom/Zotero/storage/6MDYZGGG/Adhurya and Park - A novel method for predicting ecological interacti.pdf;/Users/tanyastrydom/Zotero/storage/EGHM9LFC/2041-210X.html}
 }
 
+@article{albouyMarineFishFood2019,
+  title = {The Marine Fish Food Web Is Globally Connected},
+  author = {Albouy, Camille and Archambault, Philippe and Appeltans, Ward and Ara{\'u}jo, Miguel B. and Beauchesne, David and Cazelles, Kevin and Cirtwill, Alyssa R. and Fortin, Marie-Jos{\'e}e and Galiana, Nuria and Leroux, Shawn J. and Pellissier, Lo{\"i}c and Poisot, Timoth{\'e}e and Stouffer, Daniel B. and Wood, Spencer A. and Gravel, Dominique},
+  year = {2019},
+  month = aug,
+  journal = {Nature Ecology \& Evolution},
+  volume = {3},
+  number = {8},
+  pages = {1153--1161},
+  publisher = {Nature Publishing Group},
+  issn = {2397-334X},
+  doi = {10.1038/s41559-019-0950-y},
+  urldate = {2021-05-14},
+  abstract = {The productivity of marine ecosystems and the services they provide to humans are largely dependent on complex interactions between prey and predators. These are embedded in a diverse network of trophic interactions, resulting in a cascade of events following perturbations such as species extinction. The sheer scale of oceans, however, precludes the characterization of marine feeding networks through de novo sampling. This effort ought instead to rely on a combination of extensive data and inference. Here we investigate how the distribution of trophic interactions at the global scale shapes the marine fish food web structure. We hypothesize that the heterogeneous distribution of species ranges in biogeographic regions should concentrate interactions in the warmest areas and within species groups. We find that the inferred global metaweb of marine fish---that is, all possible potential feeding links between co-occurring species---is highly connected geographically with a low degree of spatial modularity. Metrics of network structure correlate with sea surface temperature and tend to peak towards the tropics. In contrast to open-water communities, coastal food webs have greater interaction redundancy, which may confer robustness to species extinction. Our results suggest that marine ecosystems are connected yet display some resistance to perturbations because of high robustness at most locations.},
+  copyright = {2019 The Author(s), under exclusive licence to Springer Nature Limited},
+  langid = {english},
+  file = {/Users/tanyastrydom/Zotero/storage/2QX9YAVK/s41559-019-0950-y.html}
+}
+
 @article{allesinaFoodWebModels2009,
   title = {Food Web Models: A Plea for Groups},
   shorttitle = {Food Web Models},
@@ -1858,6 +1877,24 @@ @article{ohlmannMappingImprintBiotic2018
   file = {/Users/tanyastrydom/Zotero/storage/RUPS3ATP/Ohlmann et al. - 2018 - Mapping the imprint of biotic interactions on β-di.pdf;/Users/tanyastrydom/Zotero/storage/K3R3BHFT/ele.html}
 }
 
+@article{olivierExploringTemporalVariability2019,
+  title = {Exploring the Temporal Variability of a Food Web Using Long-Term Biomonitoring Data},
+  author = {Olivier, Pierre and Frelat, Romain and Bonsdorff, Erik and Kortsch, Susanne and Kr{\"o}ncke, Ingrid and M{\"o}llmann, Christian and Neumann, Hermann and Sell, Anne F. and Nordstr{\"o}m, Marie C.},
+  year = {2019},
+  journal = {Ecography},
+  volume = {42},
+  number = {12},
+  pages = {2107--2121},
+  issn = {1600-0587},
+  doi = {10.1111/ecog.04461},
+  urldate = {2024-10-10},
+  abstract = {Ecological communities are constantly being reshaped in the face of environmental change and anthropogenic pressures. Yet, how food webs change over time remains poorly understood. Food web science is characterized by a trade-off between complexity (in terms of the number of species and feeding links) and dynamics. Topological analysis can use complex, highly resolved empirical food web models to explore the architecture of feeding interactions but is limited to a static view, whereas ecosystem models can be dynamic but use highly aggregated food webs. Here, we explore the temporal dynamics of a highly resolved empirical food web over a time period of 18 years, using the German Bight fish and benthic epifauna community as our case study. We relied on long-term monitoring ecosystem surveys (from 1998 to 2015) to build a metaweb, i.e. the meta food web containing all species recorded over the time span of our study. We then combined time series of species abundances with topological network analysis to construct annual food web snapshots. We developed a new approach, `node-weighted' food web metrics by including species abundances to represent the temporal dynamics of food web structure, focusing on generality and vulnerability. Our results suggest that structural food web properties change through time; however, binary food web structural properties may not be as temporally variable as the underlying changes in species composition. Further, the node-weighted metrics enabled us to detect that food web structure was influenced by changes in species composition during the first half of the time series and more strongly by changes in species dominance during the second half. Our results demonstrate how ecosystem surveys can be used to monitor temporal changes in food web structure, which are important ecosystem indicators for building marine management and conservation plans.},
+  copyright = {{\copyright} 2019 The Authors. Ecography published by John Wiley \& Sons on behalf of Nordic Society Oikos},
+  langid = {english},
+  keywords = {food web structure,temporal variability,topology},
+  file = {/Users/tanyastrydom/Zotero/storage/C6YX4CZH/Olivier et al. - 2019 - Exploring the temporal variability of a food web u.pdf;/Users/tanyastrydom/Zotero/storage/J73S5VIF/ecog.html}
+}
+
 @article{ovaskainenUsingLatentVariable2016,
   title = {Using Latent Variable Models to Identify Large Networks of Species-to-Species Associations at Different Spatial Scales},
   author = {Ovaskainen, Otso and Abrego, Nerea and Halme, Panu and Dunson, David},