Multilayer networks reveal the spatial structure of seed-dispersal interactions across the Great Rift landscapes

The propagation of disturbances in ecological networks

Despite the development of network science, we lack clear heuristics for how far different disturbance types propagate within and across species interaction networks. We discuss the mechanisms of disturbance propagation in ecological networks, and propose that disturbances can be categorized into structural, functional, and transmission types according to their spread and effect on network structure and functioning. We describe the properties of species and their interaction networks and metanetworks that determine the indirect, spatial, and temporal extent of propagation. We argue that the sampling scale of ecological studies may have impeded predictions regarding the rate and extent that a disturbance spreads, and discuss directions to help ecologists to move towards a predictive understanding of the propagation of impacts across interacting communities and ecosystems.

Local people enhance our understanding of Afrotropical frugivory networks

Afrotropical forests are undergoing massive change caused by defaunation, i.e., the human-induced decline of animal species,1 most of which are frugivorous species.1,2,3 Frugivores' depletion and their functional disappearance are expected to cascade on tree dispersal and forest structure via interaction networks,4,5,6,7 as the majority of tree species depend on frugivores for their dispersal.8 However, frugivory networks remain largely unknown, especially in Afrotropical areas,9,10,11 which considerably limits our ability to predict changes in forest dynamics and structures using network analysis.12,13,14,15 While the academic workforce may be inadequate to fill this knowledge gap before it is too late, local ecological knowledge appears as a valuable source of ecological information and could significantly contribute to our understanding of such crucial interactions for tropical forests.16,17,18,19,20,21 To investigate potential synergies between local ecological knowledge and academic knowledge,20,21 we compiled frugivory interactions linking 286 trees to 100 frugivore species from the academic literature and local ecological knowledge coming from interviews of Gabonese forest-dependent people. Here, we showed that local ecological knowledge on frugivory interactions was substantial and original, with 39% of these interactions unknown by science. We demonstrated that combining academic and local ecological knowledge affects the functional relationship linking frugivore body mass to seed size, as well as the network structure. Our results highlight the benefits of bridging knowledge systems between academics and local communities for a better understanding of the functioning and response to perturbations of Afrotropical forests.

Multilayer Networks Assisting to Untangle Direct and Indirect Pathogen Transmission in Bats

The importance of species that connect the different types of interactions is becoming increasingly recognized, and this role may be related to specific attributes of these species. Multilayer networks have two or more layers, which represent different types of interactions, for example, between different parasites and hosts that are nonetheless connected. The understanding of the ecological relationship between bats, ectoparasites, and vector-borne bacteria could shed some light on the complex transmission cycles of these pathogens. In this study, we investigated a multilayer network in Brazil formed by interactions between bat-bacteria, bat-ectoparasite, and ectoparasite-bacteria, and asked how these interactions overlap considering different groups and transmission modes. The multilayer network was composed of 31 nodes (12 bat species, 14 ectoparasite species, and five bacteria genera) and 334 links, distributed over three layers. The multilayer network has low modularity and shows a core-periphery organization, that is, composed of a few generalist species with many interactions and many specialist species participating in few interactions in the multilayer network. The three layers were needed to accurately describe the multilayer structure, while aggregation leads to loss of information. Our findings also demonstrated that the multilayer network is influenced by a specific set of species that can easily be connected to the behavior, life cycle, and type of existing interactions of these species. Four bat species (Artibeus lituratus, A. planirostris, Phyllostomus discolor, and Platyrrhinus lineatus), one ectoparasite species (Steatonyssus) and three bacteria genera (Ehrlichia, hemotropic Mycoplasma and Neorickettsia) are the most important species for the multilayer network structure. Finally, our study brings an ecological perspective under a multilayer network approach on the interactions between bats, ectoparasites, and pathogens. By using a multilayer approach (different types of interactions), it was possible to better understand these different ecological interactions and how they affect each other, advancing our knowledge on the role of bats and ectoparasites as potential pathogen vectors and reservoirs, as well as the modes of transmission of these pathogens.

Frugivore Population Biomass, but Not Density, Affect Seed Dispersal Interactions in a Hyper-Diverse Frugivory Network

Mutualistic interactions are regulated by plant and animal traits, including animal body size and population density. In seed dispersal networks, frugivore body size determines the interaction outcome, and species population density determines interaction probability through encounter rates. To date, most studies examining the relative role of body size and population density in seed dispersal networks have examined animal guilds encompassing a narrow range of body sizes (e.g., birds only). Given non-random, body-size dependent defaunation, understanding the relative role of these traits is important to predict and, ideally, mitigate the effects of defaunation. We analyzed a hyper-diverse seed dispersal network composed of birds and mammals that cover a wide range of body sizes and population densities in the Brazilian Pantanal. Animal density per se did not significantly explain interaction patterns. Instead, population biomass, which represents the combination of body size and population density, was the most important predictor for most interaction network metrics. Population biomass was strongly correlated with body size, but not with density. Thus, larger frugivore species dispersed more plant species and were involved in more unique pairwise interactions than smaller species. Moreover, species with larger population biomass had the strongest influence (i.e., as indicated by measures of centrality) on other species in the network and were more generalist, interacting with a broader set of species, compared to species with lower population biomass. We posit that the increased abundance of small-sized frugivores resulting from the pervasive defaunation of large vertebrates would not compensate for the loss-of-function of the latter and the inherent disruption of seed dispersal networks.

Road-based line distance surveys overestimate densities of olive baboons

Estimating population density and population dynamics is essential for understanding primate ecology and relies on robust methods. While distance sampling theory provides a robust framework for estimating animal abundance, implementing a constrained, non-systematic transect design could bias density estimates. Here, we assessed potential bias associated with line distance sampling surveys along roads based on a case study with olive baboons (Papio anubis) in Lake Manyara National Park (Tanzania). This was achieved by comparing density estimates of olive baboons derived from road transect surveys with density estimates derived from estimating the maximum number of social groups (via sleeping site counts) and multiplying this metric with the estimated average size of social groups. From 2011 to 2019, we counted olive baboons along road transects, estimated survey-specific densities in a distance sampling framework, and assessed temporal population trends. Based on the fitted half-normal detection function, the mean density was 132.5 baboons km^-2 (95% CI: 110.4–159.2), however, detection models did not fit well due to heaping of sightings on and near the transects. Density estimates were associated with relatively wide confidence intervals that were mostly caused by encounter rate variance. Based on a generalized additive model, baboon densities were greater during the rainy seasons compared to the dry seasons but did not show marked annual trends. Compared to estimates derived from the alternative method (sleeping site survey), distance sampling along road transects overestimated the abundance of baboons more than threefold. Possibly, this overestimation was caused by the preferred use of roads by baboons. While being a frequently used technique (due to its relative ease of implementation compared to spatially randomized survey techniques), inferring population density of baboons (and possibly other species) based on road transects should be treated with caution. Beyond these methodological concerns and considering only the most conservative estimates, baboon densities in LMNP are among the highest across their geographic distribution range.

The impact of habitat loss on pollination services for a threatened dune endemic plant

Habitat loss is currently a major threat to biodiversity, affecting species interactions, such as plant-pollinator interactions. This is particularly important in self-incompatible plants relying on pollinators to reproduce and sustain their populations. Here, we evaluated how habitat loss affects the pollination system, plant individual-pollinator species interaction network, and plant reproductive fitness of the self-incompatible Jasione maritima var. sabularia, a threatened taxon from dune systems. This plant is a pollinator generalist, visited by 108 species from distinct taxonomic groups. Results suggest that increasing habitat loss led to a significant decline in pollinator richness, increased pollen limitation, and a decrease in reproductive fitness of J. maritima var. sabularia. Visitation rate per individual did not significantly change with available area, indicating that the quality of pollen differed across populations. The topology of the network between J. maritima var. sabularia individuals and its pollinator species did not change, which may be attributed to the stability in the core of pollinator species. This suggests that the lower fitness of plants with increasing habitat degradation may be explained not only by the lower richness of peripheral pollinators but also by the genetic structure of the plant populations, as there is a possible higher transference of less quality pollen by pollinators, ultimately compromising the persistence of plant populations. Our study highlights the need of future studies to integrate the fine details provided by individual-level networks, which will increase our understanding of the pattern of species interactions and its consequences for the fitness of threatened plant populations.

Network ecology in dynamic landscapes

Network ecology is an emerging field that allows researchers to conceptualize and analyse ecological networks and their dynamics. Here, we focus on the dynamics of ecological networks in response to environmental changes. Specifically, we formalize how network topologies constrain the dynamics of ecological systems into a unifying framework in network ecology that we refer to as the 'ecological network dynamics framework'. This framework stresses that the interplay between species interaction networks and the spatial layout of habitat patches is key to identifying which network properties (number and weights of nodes and links) and trade-offs among them are needed to maintain species interactions in dynamic landscapes. We conclude that to be functional, ecological networks should be scaled according to species dispersal abilities in response to landscape heterogeneity. Determining how such effective ecological networks change through space and time can help reveal their complex dynamics in a changing world.

Ecological plasticity governs ecosystem services in multilayer networks

Agriculture is under pressure to achieve sustainable development goals for biodiversity and ecosystem services. Services in agro-ecosystems are typically driven by key species, and changes in the community composition and species abundance can have multifaceted effects. Assessment of individual services overlooks co-variance between different, but related, services coupled by a common group of species. This partial view ignores how effects propagate through an ecosystem. We conduct an analysis of 374 agricultural multilayer networks of two related services of weed seed regulation and gastropod mollusc predation delivered by carabid beetles. We found that weed seed regulation increased with the herbivore predation interaction frequency, computed from the network of trophic links between carabids and weed seeds in the herbivore layer. Weed seed regulation and herbivore interaction frequencies declined as the interaction frequencies between carabids and molluscs in the carnivore layer increased. This suggests that carabids can switch to gastropod predation with community change, and that link turnover rewires the herbivore and carnivore network layers affecting seed regulation. Our study reveals that ecosystem services are governed by ecological plasticity in structurally complex, multi-layer networks. Sustainable management therefore needs to go beyond the autecological approaches to ecosystem services that predominate, particularly in agriculture.

Species functional traits and abundance as drivers of multiplex ecological networks: first empirical quantification of inter-layer edge weights

Many vertebrate species act as both plant pollinators and seed-dispersers, thus interconnecting these processes, particularly on islands. Ecological multilayer networks are a powerful tool to explore interdependencies between processes; however, quantifying the links between species engaging in different types of interactions (i.e. inter-layer edges) remains a great challenge. Here, we empirically measured inter-layer edge weights by quantifying the role of individually marked birds as both pollinators and seed-dispersers of Galápagos plant species over an entire year. Although most species (80%) engaged in both functions, we show that only a small proportion of individuals actually linked the two processes, highlighting the need to further consider intra-specific variability in individuals' functional roles. Furthermore, we found a high variation among species in linking both processes, i.e. some species contribute more than others to the modular organization of the multilayer network. Small and abundant species are particularly important for the cohesion of pollinator seed-dispersal networks, demonstrating the interplay between species traits and neutral processes structuring natural communities.

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.

Frugivore species maintain their structural role in the trophic and spatial networks of seed dispersal interactions

Trophic relationships have inherent spatial dimensions associated with the sites where species interactions, or their delayed effects, occur. Trophic networks among interacting species may thus be coupled with spatial networks linking species and habitats whereby animals connect patches across the landscape thanks to their high mobility. This trophic and spatial duality is especially inherent in processes like seed dispersal by animals, where frugivores consume fruit species and deposit seeds across habitats. We analysed the frugivore-plant interactions and seed deposition patterns of a diverse assemblage of frugivores in a heterogeneous landscape in order to determine whether the roles of frugivores in network topology are correlated across trophic and spatial networks of seed dispersal. We recorded fruit consumption and seed deposition by birds and mammals during 2 years in the Cantabrian Range (N Spain). We then constructed two networks of trophic (i.e. frugivore-plant) and spatial (i.e. frugivore-seed deposition habitat) interactions and estimated the contributions of each frugivore species to the network structure in terms of nestedness, modularity and complementary specialization. We tested whether the structural role of frugivore species was correlated across the trophic and spatial networks, and evaluated the influence of each frugivore abundance and body mass in that relationship. Both the trophic and the spatial networks were modular and specialized. Trophic modules matched medium-sized birds with fleshy-fruited trees, and small bird and mammals with small-fruit trees and shrubs. Spatial modules associated birds with woody canopies, and mammals with open habitats. Frugivore species maintained their structural role across the trophic and spatial networks of seed dispersal, even after accounting for frugivore abundance and body mass. The modularity found in our system points to complementarity between birds and mammals in the seed dispersal process, a fact that may trigger landscape-scale secondary succession. Our results open up the possibility of predicting the consumption pattern of a diverse frugivore community, and its ecological consequences, from the uneven distribution of fleshy-fruit resources in the landscape.

The functional roles of species in metacommunities, as revealed by metanetwork analyses of bird-plant frugivory networks

Understanding how biodiversity and interaction networks change across environmental gradients is a major challenge in ecology. We integrated metacommunity and metanetwork perspectives to test species' functional roles in bird-plant frugivory interactions in a fragmented forest landscape in Southwest China, with consequences for seed dispersal. Availability of fruit resources both on and under trees created vertical feeding stratification for frugivorous birds. Bird-plant interactions involving birds feeding only on-the-tree or both on and under-the-tree (shared) had a higher centrality and contributed more to metanetwork organisation than interactions involving birds feeding only under-the-tree. Moreover, bird-plant interactions associated with large-seeded plants disproportionately contributed to metanetwork organisation and centrality. Consequently, on-the-tree and shared birds contributed more to metanetwork organisation whereas under-the-tree birds were more involved in local processes. We would expect that species' roles in the metanetwork will translate into different conservation values for maintaining functioning of seed-dispersal networks.

An integrative approach to discern the seed dispersal role of frugivorous guilds in a Mediterranean semiarid priority habitat

Seed dispersal is an essential process to maintain the viability of plant populations, and understanding this ecological process allows management strategies to be developed to conserve ecosystems. European Union priority habitat 5220* is defined as "Mediterranean arborescent shrubland with Ziziphus lotus" and it represents a favorable microclimate within the severe climatic conditions typical of the semiarid south-eastern region of the Iberian Peninsula. Therefore, the study of seed dispersal in this priority habitat by different frugivorous guilds, is a challenge for its conservation. In this study, we have characterized a mutualistic network of seed dispersal that is mediated by vertebrates (mammals and birds) in the protected habitat 5220*. The aims of this study were to: (i) identify the seed disperser community; (ii) analyze the relative role of key species in the dispersal process; and (iii) compare the functional ecology of the seed dispersal process between mammals and birds. As such, we collected animal faeces to determine seed dispersers taxonomy, identifying the mammals through the visual aspect of the faeces and the birds by DNA barcoding. In the case of birds, we also collected regurgitated seeds in which the disperser species was also identified through molecular techniques. This allowed us to build-up a mutualistic network and to identify the relative role of these animals in seed dispersal. Our results showed that mammals and birds fulfilled complementary roles in seed dispersal, with birds representing the main dispersers of key plants within the 5220* habitat, and mammals the main dispersers of human-cultivated plants. Herein, we provide a useful approach with relevant information that can be used to propose management policies that focus on restoring the threatened 5220* habitat, promoting the role of birds to disperse key species that structure plant communities of this priority habitat.

Interdomain ecological networks between plants and microbes

While macroscopic interkingdom relationships have been intensively investigated in various ecosystems, the above-belowground ecology in natural ecosystems has been poorly understood, especially for the plant-microbe associations at a regional scale. In this study, we proposed a workflow to construct interdomain ecological networks (IDEN) between multiple plants and various microbes (bacteria and archaea in this study). Across 30 latitudinal forests in China, the regional IDEN showed particular topological features, including high connectance, nested structure, asymmetric specialization and modularity. Also, plant species exhibited strong preference to specific microbial groups, and the observed network was significantly different from randomly rewired networks. Network module analysis indicated that a majority of microbes associated with plants within modules rather than across modules, suggesting specialized associations between plants and microorganisms. Consistent plant-microbe associations were captured via IDENs constructed within individual forest locations, which reinforced the validity of IDEN analysis. In addition, the plant-forest link distribution showed the geographical distribution of plants had higher endemicity than that of microorganisms. With cautious experimental design and data processing, this study shows interdomain species associations between plants and microbes in natural forest ecosystems and provides new insights into our understanding of meta-communities across different domain species.

Seed dispersal by dispersing juvenile animals: a source of functional connectivity in fragmented landscapes

Juvenile animals generally disperse from their birthplace to their future breeding territories. In fragmented landscapes, habitat-specialist species must disperse through the anthropogenic matrix where remnant habitats are embedded. Here, we test the hypothesis that dispersing juvenile frugivores leave a footprint in the form of seed deposition through the matrix of fragmented landscapes. We focused on the Sardinian warbler ( Sylvia melanocephala), a resident frugivorous passerine. We used data from field sampling of bird-dispersed seeds in the forest and matrix of a fragmented landscape, subsequent disperser identification through DNA-barcoding analysis, and data from a national bird-ringing programme. Seed dispersal by Sardinian warblers was confined to the forest most of the year, but warblers contributed a peak of seed-dispersal events in the matrix between July and October, mainly attributable to dispersing juveniles. Our study uniquely connects animal and plant dispersal, demonstrating that juveniles of habitat-specialist frugivores can provide mobile-link functions transiently, but in a seasonally predictable way.

Reshaping our understanding of species' roles in landscape-scale networks

In network ecology, landscape-scale processes are often overlooked, yet there is increasing evidence that species and interactions spill over between habitats, calling for further study of interhabitat dependencies. Here, we investigate how species connect a mosaic of habitats based on the spatial variation of their mutualistic and antagonistic interactions using two multilayer networks, combining pollination, herbivory and parasitism in the UK and New Zealand. Developing novel methods of network analysis for landscape-scale ecological networks, we discovered that few plant and pollinator species acted as connectors or hubs, both within and among habitats, whereas herbivores and parasitoids typically have more peripheral network roles. Insect species' roles depend on factors other than just the abundance of taxa in the lower trophic level, exemplified by larger Hymenoptera connecting networks of different habitats and insects relying on different resources across different habitats. Our findings provide a broader perspective for landscape-scale management and ecological community conservation.

Integrating plant species contribution to mycorrhizal and seed dispersal mutualistic networks

Mutualistic interactions like those established between plants and mycorrhizal fungi or seed dispersers are key drivers of plant population dynamics and ecosystem functioning; however, these interactions have rarely been explored together. We assembled a tripartite fungi-plant-disperser network in the Gorongosa National Park-Mozambique, to test (1) if diversity and importance of plant mutualists above- and belowground are correlated, and (2) whether biotically and abiotically dispersed plants are associated with distinct arbuscular mycorrhizal fungi (AMF). We quantified seed dispersal by animals for 1 year and characterized the AMF of 26 common plant species. Sixteen plant species were dispersed by 15 animals and colonized by 48 AMF virtual taxa (VT), while the remaining 10 plant species were not dispersed by animals and associated with 34 AMF VT. We found no evidence for a correlation between the number of plant partners above- and belowground or on plant specialization on both types of partners. We also found no evidence for differentiation of AMF communities between biotically and abiotically dispersed plants. Our results suggest that the establishment of plant interactions with seed dispersers and mycorrhizal fungi is largely independent and that both biotically and abiotically dispersed plants seem to associate with similar communities of AMF.

Proximity of restored hedgerows interacts with local floral diversity and species' traits to shape long-term pollinator metacommunity dynamics

Disconnected habitat fragments are poor at supporting population and community persistence; restoration ecologists, therefore, advocate for the establishment of habitat networks across landscapes. Few empirical studies, however, have considered how networks of restored habitat patches affect metacommunity dynamics. Here, using a 10-year study on restored hedgerows and unrestored field margins within an intensive agricultural landscape, we integrate occupancy modelling with network theory to examine the interaction between local and landscape characteristics, habitat selection and dispersal in shaping pollinator metacommunity dynamics. We show that surrounding hedgerows and remnant habitat patches interact with the local floral diversity, bee diet breadth and bee body size to influence site occupancy, via colonisation and persistence dynamics. Florally diverse sites and generalist, small-bodied species are most important for maintaining metacommunity connectivity. By providing the first in-depth assessment of how a network of restored habitat influences long-term population dynamics, we confirm the conservation benefit of hedgerows for pollinator populations and demonstrate the importance of restoring and maintaining habitat networks within an inhospitable matrix.

Localization of multilayer networks by optimized single-layer rewiring

We study localization properties of principal eigenvectors (PEVs) of multilayer networks (MNs). Starting with a multilayer network corresponding to a delocalized PEV, we rewire the network edges using an optimization technique such that the PEV of the rewired multilayer network becomes more localized. The framework allows us to scrutinize structural and spectral properties of the networks at various localization points during the rewiring process. We show that rewiring only one layer is enough to attain a MN having a highly localized PEV. Our investigation reveals that a single edge rewiring of the optimized MN can lead to the complete delocalization of a highly localized PEV. This sensitivity in the localization behavior of PEVs is accompanied with the second largest eigenvalue lying very close to the largest one. This observation opens an avenue to gain a deeper insight into the origin of PEV localization of networks. Furthermore, analysis of multilayer networks constructed using real-world social and biological data shows that the localization properties of these real-world multilayer networks are in good agreement with the simulation results for the model multilayer network. This paper is relevant to applications that require understanding propagation of perturbation in multilayer networks.

Connectivity and complex systems: learning from a multi-disciplinary perspective

In recent years, parallel developments in disparate disciplines have focused on what has come to be termed connectivity; a concept used in understanding and describing complex systems. Conceptualisations and operationalisations of connectivity have evolved largely within their disciplinary boundaries, yet similarities in this concept and its application among disciplines are evident. However, any implementation of the concept of connectivity carries with it both ontological and epistemological constraints, which leads us to ask if there is one type or set of approach(es) to connectivity that might be applied to all disciplines. In this review we explore four ontological and epistemological challenges in using connectivity to understand complex systems from the standpoint of widely different disciplines. These are: (i) defining the fundamental unit for the study of connectivity; (ii) separating structural connectivity from functional connectivity; (iii) understanding emergent behaviour; and (iv) measuring connectivity. We draw upon discipline-specific insights from Computational Neuroscience, Ecology, Geomorphology, Neuroscience, Social Network Science and Systems Biology to explore the use of connectivity among these disciplines. We evaluate how a connectivity-based approach has generated new understanding of structural-functional relationships that characterise complex systems and propose a 'common toolbox' underpinned by network-based approaches that can advance connectivity studies by overcoming existing constraints.