Network analyses support the role of prey preferences in shaping resource use patterns within five animal populations

Using individual-based trait frequency distributions to forecast plant-pollinator network responses to environmental change

Determining how and why organisms interact is fundamental to understanding ecosystem responses to future environmental change. To assess the impact on plant-pollinator interactions, recent studies have examined how the effects of environmental change on individual interactions accumulate to generate species-level responses. Here, we review recent developments in using plant-pollinator networks of interacting individuals along with their functional traits, where individuals are nested within species nodes. We highlight how these individual-level, trait-based networks connect intraspecific trait variation (as frequency distributions of multiple traits) with dynamic responses within plant-pollinator communities. This approach can better explain interaction plasticity, and changes to interaction probabilities and network structure over spatiotemporal or other environmental gradients. We argue that only through appreciating such trait-based interaction plasticity can we accurately forecast the potential vulnerability of interactions to future environmental change. We follow this with general guidance on how future studies can collect and analyse high-resolution interaction and trait data, with the hope of improving predictions of future plant-pollinator network responses for targeted and effective conservation.

Rare and Hungry: Feeding Ecology of the Golden Alpine Salamander, an Endangered Amphibian in the Alps

Amphibians are considered critical species in the nutrient flow within and across ecosystems, and knowledge on their trophic ecology and niches is crucial for their conservation. For the first time we studied the trophic ecology of the rare and endemic Salamandra atra aurorae in a mixed temperate forest in northern Italy. We aimed to define the realized trophic niche, investigate the prey selectivity and explore possible levels of individual specialization. In summer 2022 we obtained stomach contents from 53 salamanders by stomach flushing and prey availability using pitfall traps. We used the Costello graphical method to analyse the realized trophic niche, and the relativized electivity index to study prey selectivity. Our results show that the Golden Alpine salamander adopts a generalist feeding strategy with positive selection of few prey categories (e.g., Myriapoda, Hymenoptera except Formicidae). Food preference seems to be driven by size, movement ability and chitinization of the prey. A high degree of inter-individual diet variation, modularity and clustering was found, describing a scenario that can be framed in a Distinct Preference model framework. This study gives new insights on the trophic ecology of the Alpine salamander complex, whose subspecies appear to adopt similar feeding strategies.

Global trends in the trophic specialisation of flower-visitor networks are explained by current and historical climate

Trophic specialisation is known to vary across space, but the environmental factors explaining such variation remain elusive. Here we used a global dataset of flower-visitor networks to evaluate how trophic specialisation varies between latitudinal zones (tropical and temperate) and across elevation gradients, while considering the environmental variation inherent in these spatial gradients. Specifically, we assessed the role of current (i.e., net primary productivity, temperature, and precipitation) and historical (i.e., temperature and precipitation stability) environmental factors in structuring the trophic specialisation of floral visitors. Spatial variations in trophic specialisation were not explained by latitudinal zones or elevation. Moreover, regardless of network location on the spatial gradient, there was a tendency for higher trophic specialisation in sites with high productivity and precipitation, whereas historical temperature stability was related to lower trophic specialisation. We highlight that both energetic constraints in animal foraging imposed by climate and resource availability may drive the global variation in trophic specialisation.

Weighted individual-resource networks in prey-predator systems: the role of prey availability on the emergence of modular structures

Ecological networks, usually depicting interactions among species, have been recently down-scaled to the individual level, permitting description of patterns of inter-individual resource variation that are usually hindered at the species level. Optimal diet theory (ODT) models, applied to prey-predator systems, predict different patterns of nestedness and modularity in the network, depending on the available resources and intra-specific competition. The effect of resource availability on the emergence of networks structures, and ODT framework, has not yet fully been clarified. Here, we analyzed the structural patterns of individual-resource networks in 3 species of Mediterranean salamanders, in relation to changes in prey availability. We used weighted individual-resource network metrics to interpret the observed patterns, according to 3 ODT models. We found significant nestedness recurring in our study system, indicating that both selective and opportunistic individuals occur in the same population. Prey diversity, rather than abundance, was apparently related to inter-individual resource variation and promoted the emergence of significant modularity within all networks. The observed patterns of nestedness and modularity, together with the variation in resource diversity and intra-specific competition, are in agreement with the distinct preferences model of ODT. These findings suggest that in the focal prey-predator systems, individuals were able to perceive changes in prey diversity and to exploit in different ways the variations in composition of available resources, shifting their diet assembly rules accordingly. Our findings also confirm that the use of weighted individual-resource networks, in prey-predator systems, allows to disclose dynamics that are masked at the species or population level.

The Structure of Ecological Networks Across Levels of Organization

Interactions connect the units of ecological systems, forming networks. Individual-based networks characterize variation in niches among individuals within populations. These individual-based networks merge with each other, forming species-based networks and food webs that describe the architecture of ecological communities. Networks at broader spatiotemporal scales portray the structure of ecological interactions across landscapes and over macroevolutionary time. Here, I review the patterns observed in ecological networks across multiple levels of biological organization. A fundamental challenge is to understand the amount of interdependence as we move from individual-based networks to species-based networks and beyond. Despite the uneven distribution of studies, regularities in network structure emerge across scales due to the fundamental architectural patterns shared by complex networks and the interplay between traits and numerical effects. I illustrate the integration of these organizational scales by exploring the consequences of the emergence of highly connected species for network structures across scales.

Diet composition of the lizard Podarcis lilfordi (Lacertidae) on 2 small islands: an individual-resource network approach

Despite it is widely accepted that intrapopulation variation is fundamental to ecological and evolutionary processes, this level of information has only recently been included into network analysis of species/population interactions. When done, it has revealed non-random patterns in the distribution of trophic resources. Nestedness in resource use among individuals is the most recurrent observed pattern, often accompanied by an absence of modularity, but no previous studies examine bipartite modularity. We use network analysis to describe the diet composition of the Balearic endemic lizard Podarcis lilfordi in 2 islets at population and individual levels, based on the occurrence of food items in fecal samples. Our objectives are to 1) compare niche structure at both levels, 2) characterize niche partition using nestedness and modularity, and 3) assess how size, sex, season, and spatial location influence niche structure. At population-level niche width was wide, but narrow at the level of the individual. Both islet networks were nested, indicating similar ranking of the food preferences among individuals, but also modular, which was partially explained by seasonality. Sex and body size did not notably affect diet composition. Large niche overlap and therefore possibly relaxed competition were observed among females in one of the islets and during spring on both islets. Likewise, higher modularity in autumn suggests that higher competition could lead to specialization in both populations, because resources are usually scarce in this season. The absence of spatial location influence on niche might respond to fine-grained spatio-temporally distribution of food resources. Behavioral traits, not included in this study, could also influence resource partitioning.

Availability of food resources and habitat structure shape the individual-resource network of a Neotropical marsupial

Spatial and temporal variation in networks has been reported in different studies. However, the many effects of habitat structure and food resource availability variation on network structures have remained poorly investigated, especially in individual-based networks. This approach can shed light on individual specialization of resource use and how habitat variations shape trophic interactions.To test hypotheses related to habitat variability on trophic interactions, we investigated seasonal and spatial variation in network structure of four populations of the marsupial Gracilinanus agilis in the highly seasonal tropical savannas of the Brazilian Cerrado.We evaluated such variation with network nestedness and modularity considering both cool-dry and warm-wet seasons, and related such variations with food resource availability and habitat structure (considered in the present study as environmental variation) in four sites of savanna woodland forest.Network analyses showed that modularity (but not nestedness) was consistently lower during the cool-dry season in all G. agilis populations. Our results indicated that nestedness is related to habitat structure, showing that this metric increases in sites with thick and spaced trees. On the other hand, modularity was positively related to diversity of arthropods and abundance of fruits.We propose that the relationship between nestedness and habitat structure is an outcome of individual variation in the vertical space and food resource use by G. agilis in sites with thick and spaced trees. Moreover, individual specialization in resource-rich and population-dense periods possibly increased the network modularity of G. agilis. Therefore, our study reveals that environment variability considering spatial and temporal components is important for shaping network structure of populations.

Analysing ecological networks of species interactions

Network approaches to ecological questions have been increasingly used, particularly in recent decades. The abstraction of ecological systems - such as communities - through networks of interactions between their components indeed provides a way to summarize this information with single objects. The methodological framework derived from graph theory also provides numerous approaches and measures to analyze these objects and can offer new perspectives on established ecological theories as well as tools to address new challenges. However, prior to using these methods to test ecological hypotheses, it is necessary that we understand, adapt, and use them in ways that both allow us to deliver their full potential and account for their limitations. Here, we attempt to increase the accessibility of network approaches by providing a review of the tools that have been developed so far, with - what we believe to be - their appropriate uses and potential limitations. This is not an exhaustive review of all methods and metrics, but rather, an overview of tools that are robust, informative, and ecologically sound. After providing a brief presentation of species interaction networks and how to build them in order to summarize ecological information of different types, we then classify methods and metrics by the types of ecological questions that they can be used to answer from global to local scales, including methods for hypothesis testing and future perspectives. Specifically, we show how the organization of species interactions in a community yields different network structures (e.g., more or less dense, modular or nested), how different measures can be used to describe and quantify these emerging structures, and how to compare communities based on these differences in structures. Within networks, we illustrate metrics that can be used to describe and compare the functional and dynamic roles of species based on their position in the network and the organization of their interactions as well as associated new methods to test the significance of these results. Lastly, we describe potential fruitful avenues for new methodological developments to address novel ecological questions.

Interaction paths promote module integration and network-level robustness of spliceosome to cascading effects

The functionality of distinct types of protein networks depends on the patterns of protein-protein interactions. A problem to solve is understanding the fragility of protein networks to predict system malfunctioning due to mutations and other errors. Spectral graph theory provides tools to understand the structural and dynamical properties of a system based on the mathematical properties of matrices associated with the networks. We combined two of such tools to explore the fragility to cascading effects of the network describing protein interactions within a key macromolecular complex, the spliceosome. Using S. cerevisiae as a model system we show that the spliceosome network has more indirect paths connecting proteins than random networks. Such multiplicity of paths may promote routes to cascading effects to propagate across the network. However, the modular network structure concentrates paths within modules, thus constraining the propagation of such cascading effects, as indicated by analytical results from the spectral graph theory and by numerical simulations of a minimal mathematical model parameterized with the spliceosome network. We hypothesize that the concentration of paths within modules favors robustness of the spliceosome against failure, but may lead to a higher vulnerability of functional subunits, which may affect the temporal assembly of the spliceosome. Our results illustrate the utility of spectral graph theory for identifying fragile spots in biological systems and predicting their implications.