Network analysis in conservation biogeography: challenges and opportunities

Dissimilarity of vertebrate trophic interactions reveals spatial uniqueness but functional redundancy across Europe

Identifying areas that contain species assemblages not found elsewhere in a region is central to conservation planning.1,2 Species assemblages contain networks of species interactions that underpin species dynamics,3,4 ecosystem processes, and contributions to people.5,6,7 Yet the uniqueness of interaction networks in a regional context has rarely been assessed. Here, we estimated the spatial uniqueness of 10,000 terrestrial vertebrate trophic networks across Europe (1,164 species, 50,408 potential interactions8) based on the amount of similarity between all local networks mapped at a 10 km resolution. Our results revealed more unique networks in the Arctic bioregion, but also in southern Europe and isolated islands. We then contrasted the uniqueness of trophic networks with their vulnerability to human footprint and future climate change and measured their coverage within protected areas. This analysis revealed that unique networks situated in southern Europe were particularly exposed to human footprint and that unique networks in the Arctic might be at risk from future climate change. However, considering interaction networks at the level of trophic groups, rather than species, revealed that the general structure of trophic networks was redundant across the continent, in contrast to species' interactions. We argue that proactive European conservation strategies might gain relevance by turning their eyes toward interaction networks that are both unique and vulnerable.

Including animals in sociology

How do we include animals in sociology? Although sociology's initial avoidance of the nonhuman world may have been necessary to the field's development, recent scholarship - within mainstream sociology, environmental sociology and animal-centred research - is helping expand the field's horizons. With a focus on variety, this article reviews four key paths that researchers are taking to include animals in their research: (1) studying interspecies relations, (2) theorizing animals as an oppressed group, (3) investigating the social and ecological impacts of animal agriculture and (4) analysing social-ecological networks. This review shows how applying - and innovating - existing social theories and research methods allows researchers to include animals in their analyses and will be relevant to a variety of scholars, including mainstream and environmental sociologists, animal-focused researchers and social network analysts, to name a few.

Prioritizing management of high-risk routes and ports by vessel type to improve marine biosecurity efforts

The shipping industry constitutes the main vector of marine bioinvasions. Over 90,000 vessels world-wide create a highly complex shipping network that requires appropriate management tools. Here we characterized a novel vessel category, Ultra Large Container Vessels (ULCV), in terms of potential contribution to the dispersal of Non-Indigenous Species (NIS) in comparison to smaller vessels traveling similar routes. Such approach is essential for providing precise information-based risk analysis necessary to enforce biosecurity regulations and reduce the adverse global effects of marine NIS. We used Automatic Identification System (AIS) based websites to extract shipping data that will enable us to test for differences in two vessel behaviors linked to NIS dispersal: port visit durations and voyage sailing times. We then examined the geographic spread of ULCVs and small vessels, quantifying the accumulation of new port visits, countries, and ecoregions for each vessel category. Finally, Higher Order Network (HON) analysis revealed emergent patterns within shipping traffic, species flow, and invasion risk networks of these two categories. Compared to the smaller vessels, ULCVs spent significantly longer time in 20% of the ports and were more geographically constrained, with fewer port visits, countries, and regions. HON analysis revealed that the ULCV shipping species flow and invasion risk networks were more similar to each other than to those of the smaller vessels. However, HON port importance shifts were discernible for both vessel categories, with major shipping hubs not necessarily being major invasion hubs. Overall, compared to smaller vessels, ULCVs behave differently in ways that potentially increase biofouling risk, albeit in a smaller set of ports. Future studies using HON analysis of other dispersal vectors appears critical for prioritizing management of high-risk routes and ports.

The diversity of biotic interactions complements functional and phylogenetic facets of biodiversity

Taxonomic, functional, and phylogenetic diversities are important facets of biodiversity. Studying them together has improved our understanding of community dynamics, ecosystem functioning, and conservation values.^1-3 In contrast to species, traits, and phylogenies, the diversity of biotic interactions has so far been largely ignored as a biodiversity facet in large-scale studies. This neglect represents a crucial shortfall because biotic interactions shape community dynamics, drive important aspects of ecosystem functioning,^4-7 provide services to humans, and have intrinsic conservation value.^8,9 Hence, the diversity of interactions can provide crucial and unique information with respect to other diversity facets. Here, we leveraged large datasets of trophic interactions, functional traits, phylogenies, and spatial distributions of >1,000 terrestrial vertebrate species across Europe at a 10-km resolution. We computed the diversity of interactions (interaction diversity [ID]) in addition to functional diversity (FD) and phylogenetic diversity (PD). After controlling for species richness, surplus and deficits of ID were neither correlated with FD nor with PD, thus representing unique and complementary information to the commonly studied facets of diversity. A three-dimensional mapping allowed for visualizing different combinations of ID-FD-PD simultaneously. Interestingly, the spatial distribution of these diversity combinations closely matched the boundaries between 10 European biogeographic regions and revealed new interaction-rich areas in the European Boreal region and interaction-poor areas in Central Europe. Our study demonstrates that the diversity of interactions adds new and ecologically relevant information to multifacetted, large-scale diversity studies with implications for understanding eco-evolutionary processes and informing conservation planning.

Conceptualizing ecosystem services using social-ecological networks

Social-ecological networks (SENs) represent the complex relationships between ecological and social systems and are a useful tool for analyzing and managing ecosystem services. However, mainstreaming the application of SENs in ecosystem service research has been hindered by a lack of clarity about how to match research questions to ecosystem service conceptualizations in SEN (i.e., as nodes, links, attributes, or emergent properties). Building from different disciplines, we propose a typology to represent ecosystem service in SENs and identify opportunities and challenges of using SENs in ecosystem service research. Our typology provides guidance for this growing field to improve research design and increase the breadth of questions that can be addressed with SEN to understand human-nature interdependencies in a changing world.

Substrate type and plant phenolics influence epiphytic bacterial assembly during short-term succession

In natural ecosystems, large amounts of epiphytic bacteria live on the surfaces of submerged plants or non-biological substrates. Although it contributes greatly to host plant health or ecological functions in waters, little is known about the temporal dynamics and assembly mechanisms of epiphytic bacteria. To test whether host plant chemistry leads to divergent community dynamics, we investigated the fine scale temporal community successions of both epiphytic bacteria and the bacterioplankton of the surrounding water in two submerged plants and one non-biological artificial substance. We first observed differentiated epiphytic or surrounding water bacterial communities for different substrates in small spaces (approximately 1 m × 1 m). Selection played dominant roles in affecting the assembly of epiphytic bacteria in the high-phenolic plant Hydrilla verticillata, while for the artificial substance and the low-phenolic plant Vallisneria natans, drift and dispersal drove the assembly of both epiphytic bacteria and bacterioplankton. The higher selection may also contribute to higher turnover rates in both bacterioplankton and epiphytic communities of H. verticillata, with the latter changing drastically in approximately one week. Epiphytic bacteria in H. verticillata developed more complex networks with a higher proportion of positive links, suggesting that more intense interactions such as mutualism or facilitation may exist within epiphytic bacterial communities of the high-phenolic plant. Our results also implied that for the submerged macrophytes used in biological purification, the dynamics of epiphytic biofilm in the purification-related functional capacities might also be considered.

Dissolved organic matter (DOM) quality drives biogeographic patterns of soil bacterial communities and their association networks in semi-arid regions

It is of great interest to elucidate the biogeographic patterns of soil microorganisms and their driving forces, which is fundamental to predicting alterations in microbial-mediated functions arising from environment changes. Although dissolved organic matter (DOM) represents an important resource for soil microorganisms, knowledge of how its quality affects microbial biogeography is limited. Here, we characterized soil bacterial communities and DOM quality in 45 soil samples collected from a 1500-km sampling transect through semi-arid regions in northern China which are currently suffering great pressure from climate change, using Illumina Miseq sequencing and fluorescence spectroscopy, respectively. We found that DOM quality (i.e. the source of DOM and the humification degree of DOM) had profound shaping influence on the biogeographic patterns exhibited by bacterial diversity, community composition and association networks. Specifically, the composition of bacteria community closely associated with DOM quality. Plant-derived DOM sustained higher bacterial diversity relative to microbial-derived DOM. Meanwhile, bacterial diversity linearly increased with increasing humification degree of DOM. Additionally, plant-derived DOM was observed to foster more complex bacterial association networks with less competition. Together, our work contributes to the factors underlying biogeographic patterns not only of bacterial diversity, community composition but also of their association networks and reports previously undocumented important role of DOM quality in shaping these patterns.

Urban foraging: Land management policy, perspectives, and potential

Gathering of uncultivated food from green spaces, also known as foraging, is observed in urban areas across the world, but the literature focuses predominantly on the global north. Our study examines the existing urban land management structure and its approach to urban foraging in the eastern coastal region of South Africa. Through interviews with municipal officials in nine cities, we identified different stakeholders and their roles in urban green space management. We then used network analysis to represent interactions and influence of these stakeholders, and environmental worldviews to determine organisational and perceptual barriers to and enablers of foraging in urban green spaces. The policy on urban green space management, as well as land managers themselves are amenable to the concept of foraging in public spaces. Lack of knowledge on wild indigenous species and sustainable offtake, ambiguous, coarse, or lacking policy, and normative views of pristine nature may hinder foraging. We recommend pathways for policy and stakeholder partnerships to incorporate sustainable foraging in their biodiversity conservation and land stewardship strategies.

The capacity of wastewater treatment plants drives bacterial community structure and its assembly

Bacterial communities in wastewater treatment plants (WWTPs) affect plant functionality through their role in the removal of pollutants from wastewater. Bacterial communities vary extensively based on plant operating conditions and influent characteristics. The capacity of WWTPs can also affect the bacterial community via variations in the organic or nutrient composition of the influent. Despite the importance considering capacity, the characteristics that control bacterial community assembly are largely unknown. In this study, we discovered that bacterial communities in WWTPs in Korea and Vietnam, which differ remarkably in capacity, exhibit unique structures and interactions that are governed mainly by the capacity of WWTPs. Bacterial communities were analysed using 16S rRNA gene sequencing and exhibited clear differences between the two regions, with these differences being most pronounced in activated sludge. We found that capacity contributed the most to bacterial interactions and community structure, whereas other factors had less impact. Co-occurrence network analysis showed that microorganisms from high-capacity WWTPs are more interrelated than those from low-capacity WWTPs, which corresponds to the tighter clustering of bacterial communities in Korea. These results will contribute to the understanding of bacterial community assembly in activated sludge processing.

Social-ecological network analysis for sustainability sciences: a systematic review and innovative research agenda for the future

Social-ecological network (SEN) concepts and tools are increasingly used in human-environment and sustainability sciences. We take stock of this budding research area to further show the strength of SEN analysis for complex human-environment settings, identify future synergies between SEN and wider human-environment research, and provide guidance about when to use different kinds of SEN approaches and models. We characterize SEN research along a spectrum specifying the degree of explicit network representation of system components and dynamics. We then systematically review one end of this spectrum, what we term "fully articulated SEN" studies, which specifically model unique social and ecological units and relationships. Results show more focus on methodological advancement and applied ends. While there has been some development and testing of theories, this remains an area for future work and would help develop SENs as a unique field of research, not just a method. Authors have studied diverse systems, while mainly focused on the problem of social-ecological fit alongside a scattering of other topics. There is strong potential, however, to engage other issues central to human-environment studies. Analyzing the simultaneous effects of multiple social, environmental, and coupled processes, change over time, and linking network structures to outcomes are also areas for future advancement. This review provides a comprehensive assessment of (fully articulated) SEN research, a necessary step that can help scholars develop comparable cases and fill research gaps.

Implications of non-native species for mutualistic network resistance and resilience

Resilience theory aims to understand and predict ecosystem state changes resulting from disturbances. Non-native species are ubiquitous in ecological communities and integrated into many described ecological interaction networks, including mutualisms. By altering the fitness landscape and rewiring species interactions, such network invasion may carry important implications for ecosystem resistance and resilience under continued environmental change. Here, I hypothesize that the tendency of established non-native species to be generalists may make them more likely than natives to occupy central network roles and may link them to the resistance and resilience of the overall network. I use a quantitative research synthesis of 58 empirical pollination and seed dispersal networks, along with extinction simulations, to examine the roles of known non-natives in networks. I show that non-native species in networks enhance network redundancy and may thereby bolster the ecological resistance or functional persistence of ecosystems in the face of disturbance. At the same time, non-natives are unlikely to partner with specialist natives, thus failing to support the resilience of native species assemblages. Non-natives significantly exceed natives in network centrality, normalized degree, and Pollination Service Index. Networks containing non-natives exhibit lower connectance, more links on average, and higher generality and vulnerability than networks lacking non-natives. As environmental change progresses, specialists are particularly likely to be impacted, reducing species diversity in many communities and network types. This work implies that functional diversity may be retained but taxonomic diversity decline as non-native species become established in networks worldwide.

Social-ecological alignment and ecological conditions in coral reefs

Complex social-ecological interactions underpin many environmental problems. To help capture this complexity, we advance an interdisciplinary network modeling framework to identify important relationships between people and nature that can influence environmental conditions. Drawing on comprehensive social and ecological data from five coral reef fishing communities in Kenya; including interviews with 648 fishers, underwater visual census data of reef ecosystem condition, and time-series landings data; we show that positive ecological conditions are associated with ‘social-ecological network closure’ – i.e., fully linked and thus closed network structures between social actors and ecological resources. Our results suggest that when fishers facing common dilemmas form cooperative communication ties with direct resource competitors, they may achieve positive gains in reef fish biomass and functional richness. Our work provides key empirical insight to a growing body of research on social-ecological alignment, and helps to advance an integrative framework that can be applied empirically in different social-ecological contexts.

The relationships between people can have important consequences for the systems they depend on. Here the authors show that when coral reef fishers face commons dilemmas, the formation of cooperative communication with competitors can lead to positive gains in reef fish biomass and functional richness.

Responses of paddy soil bacterial community assembly to different long-term fertilizations in southeast China

Recent works have shown that long-term fertilization has a critical influence on soil microbial communities; however, the underlying ecological assemblage of microbial community as well as its linkage with soil fertility and crop yield are still poorly understood. In this study, using analysis of high-throughput sequencing of 16S rRNA gene amplicons, we investigate mean pairwise phylogenetic distance (MPD), nearest relative index (NRI), taxonomic compositions and network topological properties to evaluate the assembly of the soil microbial community developed in 30-year fertilized soils. The phylogenetic signal indicates that environmental filtering was a more important assembly process that structure the microbial community than the stochastic process. Increase of soil fertility indexes, such as cation exchange capacity (CEC), soil organic matter (SOM) and available P (AP), driven by balanced fertilizations and straw returning amendment, result in the decrease of environmental filtering on the bacterial community assembly. Network parameters show that the amendment of straw returning provides with more niches, which lead to more complex phylotype co-occurrence. Increase of crop yield under balanced fertilizations might due to the increase of soil microbial function traits, which is associated with decreasing influence of environmental filtering. The significantly increased bacterial genera, Candidatus Koribacter, Candidatus Solibacter, and Fimbriimonas, in straw returning treatments, might be the key species in the competition caused by long-term environmental filtering. These results are helpful for a unified understanding of the ecological processes for microbial communities in different fertilized agroecosystem and the development of sustainable agriculture.

Navigating protected areas networks for improving diffusion of conservation practices

The Natura 2000 protected area network is the cornerstone of European Union's biodiversity conservation strategy. These protected areas range across multiple biogeographic regions, and they include a diversity of species assemblages along with a diversity of managing organizations, altogether making difficult to pool relevant sites to facilitate the flow of knowledge significant to their management. Here we introduce an approach to navigating protected area networks that has the potential to foster systematic identification of key sites for facilitating the exchange of knowledge and diffusion of information within the network. To demonstrate our approach, we abstractly represented Romanian Natura 2000 network as a co-occurrence network, with individual sites as nodes and shared species as edges, further combining into our analysis network topology, community detection, and network reduction methods. We identified most representative Natura 2000 sites that may increase the transfer of information within the national network of protected areas, detected clusters of sites and key sites for maintaining network cohesiveness, and highlighted the subsample of sites that retain the characteristics of the entire network. Our analysis provides implications for protected area prioritization by proposing a network perspective approach to collaboration rooted in ecological principles.

Social-ecological network analysis of scale mismatches in estuary watershed restoration

Resource management boundaries seldom align with environmental systems, which can lead to social and ecological problems. Mapping and analyzing how resource management organizations in different areas collaborate can provide vital information to help overcome such misalignment. Few quantitative approaches exist, however, to analyze social collaborations alongside environmental patterns, especially among local and regional organizations (i.e., in multilevel governance settings). This paper develops and applies such an approach using social-ecological network analysis (SENA), which considers relationships among and between social and ecological units. The framework and methods are shown using an estuary restoration case from Puget Sound, United States. Collaboration patterns and quality are analyzed among local and regional organizations working in hydrologically connected areas. These patterns are correlated with restoration practitioners' assessments of the productivity of their collaborations to inform network theories for natural resource governance. The SENA is also combined with existing ecological data to jointly consider social and ecological restoration concerns. Results show potentially problematic areas in nearshore environments, where collaboration networks measured by density (percentage of possible network connections) and productivity are weakest. Many areas also have high centralization (a few nodes hold the network together), making network cohesion dependent on key organizations. Although centralization and productivity are inversely related, no clear relationship between density and productivity is observed. This research can help practitioners to identify where governance capacity needs strengthening and jointly consider social and ecological concerns. It advances SENA by developing a multilevel approach to assess social-ecological (or social-environmental) misalignments, also known as scale mismatches.

Microbial succession in response to pollutants in batch-enrichment culture

As a global problem, environmental pollution is an important factor to shape the microbial communities. The elucidation of the succession of microbial communities in response to pollutants is essential for developing bioremediation procedures. In the present study, ten batches of soil-enrichment subcultures were subjected to four treatments: phenanthrene, n-octadecane, phenanthrene + n-octadecane, or phenanthrene + n-octadecane + CdCl₂. Forty pollutant-degrading consortia, corresponding to each batch of the four treatments were obtained. High-throughput sequencing of the 16S rRNA gene revealed that the diversity, richness and evenness of the consortia decreased throughout the subculturing procedure. The well-known hydrocarbon degraders Acinetobacter, Gordonia, Sphingobium, Sphingopyxis, and Castellaniella and several other genera, including Niabella and Naxibacter, were detected in the enriched consortia. The predominant microbes varied and the microbial community in the consortia gradually changed during the successive subculturing depending on the treatment, indicating that the pollutants influenced the microbial successions. Comparison of the networks in the treatments indicated that organic pollutants and CdCl₂ affected the co-occurrence patterns in enriched consortia. In conclusion, single environmental factors, such as the addition of nutrients or selection pressure, can shape microbial communities and partially explain the extensive differences in microbial community structures among diverse environments.

PROMOTING RESILIENCE

Broadening contingents of ecologists and environmental scientists have recently begun to promote ecological resilience both as a conceptual framework and as a practical goal. As some critics have noted, this growing interest has brought with it a multiplication of notions of ecological resilience. This paper reviews how and why the notion of ecological resilience has been adopted, used, and defended in ecology since its introduction by C. S. Holling in 1973. We highlight the many faces of ecological resilience, but unlike other reviewers who see these as disunified and confused, we interpret ecological resilience as an evolving, multidimensional, theoretical concept unified by its role in guiding practical response to ecological and environmental challenges. This perspective informs a review of some of the factors often recognized as favoring resilience (structural and response diversity, functional redundancy, modularity, and spatial heterogeneity); we show how the roles and relationships of these factors can be clarified by considering them in the theoretical framework of Complex Adaptive Systems (CASs).

Coupling the Biophysical and Social Dimensions of Wildfire Risk to Improve Wildfire Mitigation Planning

We describe recent advances in biophysical and social aspects of risk and their potential combined contribution to improve mitigation planning on fire-prone landscapes. The methods and tools provide an improved method for defining the spatial extent of wildfire risk to communities compared to current planning processes. They also propose an expanded role for social science to improve understanding of community-wide risk perceptions and to predict property owners' capacities and willingness to mitigate risk by treating hazardous fuels and reducing the susceptibility of dwellings. In particular, we identify spatial scale mismatches in wildfire mitigation planning and their potential adverse impact on risk mitigation goals. Studies in other fire-prone regions suggest that these scale mismatches are widespread and contribute to continued wildfire dwelling losses. We discuss how risk perceptions and behavior contribute to scale mismatches and how they can be minimized through integrated analyses of landscape wildfire transmission and social factors that describe the potential for collaboration among landowners and land management agencies. These concepts are then used to outline an integrated socioecological planning framework to identify optimal strategies for local community risk mitigation and improve landscape-scale prioritization of fuel management investments by government entities.

Dispersal dynamics in food webs

Studies of food webs suggest that limited nonrandom dispersal can play an important role in structuring food webs. It is not clear, however, whether density-dependent dispersal fits empirical patterns of food webs better than density-independent dispersal. Here, we study a spatially distributed food web, using a series of population-dispersal models that contrast density-independent and density-dependent dispersal in landscapes where sampled sites are either homogeneously or heterogeneously distributed. These models are fitted to empirical data, allowing us to infer mechanisms that are consistent with the data. Our results show that models with density-dependent dispersal fit the α, β, and γ tritrophic richness observed in empirical data best. Our results also show that density-dependent dispersal leads to a critical distance threshold beyond which site similarity (i.e., β tritrophic richness) starts to decrease much faster. Such a threshold can also be detected in the empirical data. In contrast, models with density-independent dispersal do not predict such a threshold. Moreover, preferential dispersal from more centrally located sites to peripheral sites does not provide a better fit to empirical data when compared with symmetric dispersal between sites. Our results suggest that nonrandom dispersal in heterogeneous landscapes is an important driver that shapes local and regional richness (i.e., α and γ tritrophic richness, respectively) as well as the distance-decay relationship (i.e., β tritrophic richness) in food webs.

The potential for double-loop learning to enable landscape conservation efforts

As conservation increases its emphasis on implementing change at landscape-level scales, multi-agency, cross-boundary, and multi-stakeholder networks become more important. These elements complicate traditional notions of learning. To investigate this further, we examined structures of learning in the Landscape Conservation Cooperatives (LCCs), which include the entire US and its territories, as well as parts of Canada, Mexico, and Caribbean and Pacific island states. We used semi-structured interviews, transcribed and analyzed using NVivo, as well as a charrette-style workshop to understand the difference between the original stated goals of individual LCCs and the values and purposes expressed as the collaboration matured. We suggest double-loop learning as a theoretical framework appropriate to landscape-scale conservation, recognizing that concerns about accountability are among the valid points of view that must be considered in multi-stakeholder collaborations. Methods from the social sciences and public health sectors provide insights on how such learning might be actualized.

Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning

The mechanisms underlying community assembly and promoting temporal succession are often overlooked in microbial ecology. Here, we studied an undisturbed salt marsh chronosequence, spanning over a century of ecosystem development, to understand bacterial succession in soil. We used 16S rRNA gene-based quantitative PCR to determine bacterial abundance and multitag 454 pyrosequencing for community composition and diversity analyses. Despite 10-fold lower 16S rRNA gene abundances, the initial stages of soil development held higher phylogenetic diversities than the soil at late succession. Temporal variations in phylogenetic β-diversity were greater at initial stages of soil development, possibly as a result of the great dynamism imposed by the daily influence of the tide, promoting high immigration rates. Allogenic succession of bacterial communities was mostly driven by shifts in the soil physical structure, as well as variations in pH and salinity, which collectively explained 84.5% of the variation concerning community assemblage. The community assembly data for each successional stage were integrated into a network co-occurrence analysis, revealing higher complexity at initial stages, coinciding with great dynamism in turnover and environmental variability. Contrary to a spatial niche-based perspective of bacterial community assembly, we suggest temporal niche partitioning as the dominant mechanism of assembly (promoting more phylotype co-occurrence) in the initial stages of succession, where continuous environmental change results in the existence of multiple niches over short periods of time.

Exploring critical uncertainties in pathway assessments of human-assisted introductions of alien forest species in Canada

Long-distance introductions of alien species are often driven by socioeconomic factors, such that conventional "biological" invasion models may not be capable of estimating spread fully and reliably. In this study, we demonstrate a new technique for assessing and reconstructing human-mediated pathways of alien forest species entries to major settlements in Canada via commercial road transportation and domestic trade. We undertook our analysis in three steps. First, we used existing data on movement of commodities associated with bark- and wood-boring forest pests to build a probabilistic model of how the organisms may be moved from one location to another through a transportation network. We then used this model to generate multiple sets of predictions of species arrival rates at every location in the transportation network, and to identify the locations with the highest likelihood of new incursions. Finally, we evaluated the sensitivity of the species arrival rates to uncertainty in key model assumptions by testing the impact of additive and multiplicative errors (by respectively adding a uniform random variate or symmetric variation bounds to the arrival rate values) on the probabilities of pest transmission from one location to another, as well as the impact of the removal of one or more nodes and all connecting links to other nodes from the underlying transportation network. Overall, the identification of potential pest arrival hotspots is moderately robust to uncertainties in key modeling assumptions. Large urban areas and major border crossings that have the highest predicted species arrival rates have the lowest sensitivities to uncertainty in the pest transmission potential and to random changes in the structure of the transportation network. The roadside survey data appears to be sufficient to delineate major hubs and hotspots where pests are likely to arrive from other locations in the network via commercial truck transport. However, "pass-through" locations with few incoming and outgoing routes can be identified with lower precision. The arrival rates of alien forest pests appear to be highly sensitive to additive errors. Surprisingly, the impact of random changes in the structure of the transportation network was relatively low.

A network extension of species occupancy models in a patchy environment applied to the Yosemite Toad (Anaxyrus canorus)

A central challenge of conservation biology is using limited data to predict rare species occurrence and identify conservation areas that play a disproportionate role in regional persistence. Where species occupy discrete patches in a landscape, such predictions require data about environmental quality of individual patches and the connectivity among high quality patches. We present a novel extension to species occupancy modeling that blends traditional predictions of individual patch environmental quality with network analysis to estimate connectivity characteristics using limited survey data. We demonstrate this approach using environmental and geospatial attributes to predict observed occupancy patterns of the Yosemite toad (Anaxyrus (= Bufo) canorus) across >2,500 meadows in Yosemite National Park (USA). A. canorus, a Federal Proposed Species, breeds in shallow water associated with meadows. Our generalized linear model (GLM) accurately predicted ~84% of true presence-absence data on a subset of data withheld for testing. The predicted environmental quality of each meadow was iteratively ‘boosted’ by the quality of neighbors within dispersal distance. We used this park-wide meadow connectivity network to estimate the relative influence of an individual Meadow’s ‘environmental quality’ versus its ‘network quality’ to predict: a) clusters of high quality breeding meadows potentially linked by dispersal, b) breeding meadows with high environmental quality that are isolated from other such meadows, c) breeding meadows with lower environmental quality where long-term persistence may critically depend on the network neighborhood, and d) breeding meadows with the biggest impact on park-wide breeding patterns. Combined with targeted data on dispersal, genetics, disease, and other potential stressors, these results can guide designation of core conservation areas for A. canorus in Yosemite National Park.

The dissimilarity of species interaction networks

In a context of global changes, and amidst the perpetual modification of community structure undergone by most natural ecosystems, it is more important than ever to understand how species interactions vary through space and time. The integration of biogeography and network theory will yield important results and further our understanding of species interactions. It has, however, been hampered so far by the difficulty to quantify variation among interaction networks. Here, we propose a general framework to study the dissimilarity of species interaction networks over time, space or environments, allowing both the use of quantitative and qualitative data. We decompose network dissimilarity into interactions and species turnover components, so that it is immediately comparable to common measures of β-diversity. We emphasise that scaling up β-diversity of community composition to the β-diversity of interactions requires only a small methodological step, which we foresee will help empiricists adopt this method. We illustrate the framework with a large dataset of hosts and parasites interactions and highlight other possible usages. We discuss a research agenda towards a biogeographical theory of species interactions.

Predation risk shapes social networks in fission-fusion populations

Predation risk is often associated with group formation in prey, but recent advances in methods for analysing the social structure of animal societies make it possible to quantify the effects of risk on the complex dynamics of spatial and temporal organisation. In this paper we use social network analysis to investigate the impact of variation in predation risk on the social structure of guppy shoals and the frequency and duration of shoal splitting (fission) and merging (fusion) events. Our analyses revealed that variation in the level of predation risk was associated with divergent social dynamics, with fish in high-risk populations displaying a greater number of associations with overall greater strength and connectedness than those from low-risk sites. Temporal patterns of organisation also differed according to predation risk, with fission events more likely to occur over two short time periods (5 minutes and 20 minutes) in low-predation fish and over longer time scales (>1.5 hours) in high-predation fish. Our findings suggest that predation risk influences the fine-scale social structure of prey populations and that the temporal aspects of organisation play a key role in defining social systems.

Networks in plant epidemiology: from genes to landscapes, countries, and continents

There is increasing use of networks in ecology and epidemiology, but still relatively little application in phytopathology. Networks are sets of elements (nodes) connected in various ways by links (edges). Network analysis aims to understand system dynamics and outcomes in relation to network characteristics. Many existing natural, social, and technological networks have been shown to have small-world (local connectivity with short-cuts) and scale-free (presence of super-connected nodes) properties. In this review, we discuss how network concepts can be applied in plant pathology from the molecular to the landscape and global level. Wherever disease spread occurs not just because of passive/natural dispersion but also due to artificial movements, it makes sense to superimpose realistic models of the trade in plants on spatially explicit models of epidemic development. We provide an example of an emerging pathosystem (Phytophthora ramorum) where a theoretical network approach has proven particularly fruitful in analyzing the spread of disease in the UK plant trade. These studies can help in assessing the future threat posed by similar emerging pathogens. Networks have much potential in plant epidemiology and should become part of the standard curriculum.