Data-based, synthesis-driven: Setting the agenda for computational ecology

Computational thinking is the integration of algorithms, software, and data, tosolve general questions in a field. Computation ecology has the potential totransform the way ecologists think about the integration of data and models. Asthe practice is gaining prominence as a way to conduct ecological research, itis important to reflect on what its agenda could be, and how it fits within thebroader landscape of ecological research. In this contribution, we suggest areasin which empirical ecologists, modellers, and the emerging community ofcomputational ecologists could engage in a constructive dialogue to build on oneanother's expertise; specifically, about the need to make predictions frommodels actionable, about the best standards to represent ecological data, andabout the proper ways to credit data collection and data reuse. We discuss howtraining can be amended to improve computational literacy.TP thanks the Canadian Institute for Ecology and Evolution for financial support. BIS is supported by the Natural Environment Research Council as part of the Cambridge Earth System Science NERC DTP (NE/L002507/1)

Landscape-level effects of forest on pollinators and fruit set of guava (<i>Psidium guajava</i> L.) in orchards across Southern Thailand

Pollination by wild pollinators is a key ecosystem service threatened by anthropogenic-induced land-use change. The proximity to natural habitat has previously been shown to positively affect pollinator communities and improve crop yield and quality but empirical evidence is limited from most parts of the World. Here, across six farms in Southern Thailand, we investigated the significance of landscape-level effects of natural habitat (proportion of and distance to evergreen forest) on both visitation rate and richness of pollinators as well as fruit set of guava (Psidium guajava L.), a local economically-important crop in the tropics. Overall, the most abundant pollinator was the Asian honey bee Apis cerana (39% of all visits) and different species of stingless bees (37%). We found that pollinator richness was unrelated to the proportion and distance to evergreen forest, however, the proportion of forest within a 1, 5 and 10 km radius had a significant positive impact on visitation rate of wild pollinators. Still, neither the various forest parameters nor pollinator visitation rate showed a significant impact on fruit set of guava, perhaps because guava self-pollinates. This illustrates that landscape-level degradation of natural habitat may negatively impact pollinator communities without diminishing the crop yield of the farmers

Estimating the risk of species interaction loss in mutualistic communities

Funder: Royal Commission for the Exhibition of 1851 (GB)Funder: Cambridge TrustFunder: Cambridge Depatment of ZoologyFunder: Grantham Foundation for the Protection of the Environment; funder-id: http://dx.doi.org/10.13039/100008118Funder: Kenneth Miller TrustFunder: ArcadiaInteractions between species generate the functions on which ecosystems and humans depend. However, we lack an understanding of the risk that interaction loss poses to ecological communities. Here, we quantify the risk of interaction loss for 4,330 species interactions from 41 empirical pollination and seed dispersal networks across 6 continents. We estimate risk as a function of interaction vulnerability to extinction (likelihood of loss) and contribution to network feasibility, a measure of how much an interaction helps a community tolerate environmental perturbations. Remarkably, we find that more vulnerable interactions have higher contributions to network feasibility. Furthermore, interactions tend to have more similar vulnerability and contribution to feasibility across networks than expected by chance, suggesting that vulnerability and feasibility contribution may be intrinsic properties of interactions, rather than only a function of ecological context. These results may provide a starting point for prioritising interactions for conservation in species interaction networks in the future

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

1. There is growing interest in understanding the functional outcomes of species interactions in ecological networks. For many mutualistic networks, including pollination and seed dispersal networks, interactions are generally sampled by recording animal foraging visits to plants. However, these visits may not reflect actual pollination or seed dispersal events, despite these typically being the ecological processes of interest. 2. Frugivorous animals can act as seed dispersers, by swallowing entire fruits and dispersing their seeds, or as pulp peckers or seed predators, by pecking fruits to consume pieces of pulp or seeds. These processes have opposing consequences for plant reproductive success. Therefore, equating visitation with seed dispersal could lead to biased inferences about the ecology, evolution and conservation of seed dispersal mutualisms. 3. Here we use natural history information on the functional outcomes of pairwise bird-plant interactions to examine changes in the structure of seven European plant-frugivore visitation networks after non-mutualistic interactions (pulp-pecking and seed predation) have been removed. Following existing knowledge of the contrasting structures of mutualistic and antagonistic networks, we hypothesised a number of changes following interaction removal, such as increased nestedness and lower specialisation. 4. Non-mutualistic interactions with pulp peckers and seed predators occurred in all seven networks, accounting for 21–48% of all interactions and 6–24% of total interaction frequency. When non-mutualistic interactions were removed, there were significant increases in network-level metrics such as connectance and nestedness, while robustness decreased. These changes were generally small, homogenous and driven by decreases in network size. Conversely, changes in species-level metrics were more variable and sometimes large, with significant decreases in plant degree, interaction frequency, specialisation and resilience to animal extinctions, and significant increases in frugivore species strength. 5. Visitation data can overestimate the actual frequency of seed dispersal services in plant-frugivore networks. We show here that incorporating natural history information on the functions of species interactions can bring us closer to understanding the processes and functions operating in ecological communities. Our categorical approach lays the foundation for future work quantifying functional interaction outcomes along a mutualism–antagonism continuum, as documented in other frugivore faunas.B.I.S. was supported by the Natural Environment Research Council as part of the Cambridge Earth System Science NERC DTP (NE/L002507/1). J.P.G.‐V. was funded by an Individual Fellowship from the Marie Sklodowska‐Curie Actions (H2020‐MSCA‐IF‐2014‐656572: MobileLinks). D.G. was funded by a grant from the Spanish MinECo (CGL2017‐82847‐P). W.J.S. is funded by Arcadia. N.F. thanks the administration of the Białowieża National Park, the forestry administrations of Białowieża, Hajnówka and Browsk and Polish authorities (Ministry of Environment, GDOS and RDOS) for the permissions to work in Białowieża Forest. J.A. was supported by the German Federal Foundation for Environment (DBU) and by the German Academic Exchange Service in the framework of a post‐doctorate fellowship grant (DAAD, No 91568794). L.V.D. was supported by the Natural Environment Research Council (grants NE/K015419/1 and NE/N014472/1)

Host- plasmid network structure in wastewater is linked to antimicrobial resistance genes

As mobile genetic elements, plasmids are central for our understanding of antimicrobial resistance spread in microbial communities. Plasmids can have varying fitness effects on their host bacteria, which will markedly impact their role as antimicrobial resistance vectors. Using a plasmid population model, we first show that beneficial plasmids interact with a higher number of hosts than costly plasmids when embedded in a community with multiple hosts and plasmids. We then analyse the network of a natural host-plasmid wastewater community from a Hi-C metagenomics dataset. As predicted by the model, we find that antimicrobial resistance encoding plasmids, which are likely to have positive fitness effects on their hosts in wastewater, interact with more bacterial taxa than non-antimicrobial resistance plasmids and are disproportionally important for connecting the entire network compared to non- antimicrobial resistance plasmids. This highlights the role of antimicrobials in restructuring host-plasmid networks by increasing the benefits of antimicrobial resistance carrying plasmids, which can have consequences for the spread of antimicrobial resistance genes through microbial networks. Furthermore, that antimicrobial resistance encoding plasmids are associated with a broader range of hosts implies that they will be more robust to turnover of bacterial strains

Refocusing multiple stressor research around the targets and scales of ecological impacts

Ecological communities face a variety of environmental and anthropogenic stressors acting simultaneously. Stressor impacts can combine additively or can interact, causing synergistic or antagonistic effects. Our knowledge of when and how interactions arise is limited, as most models and experiments only consider the effect of a small number of non-interacting stressors at one or few scales of ecological organization. This is concerning because it could lead to significant underestimations or overestimations of threats to biodiversity. Furthermore, stressors have been largely classified by their source rather than by the mechanisms and ecological scales at which they act (the target). Here, we argue, first, that a more nuanced classification of stressors by target and ecological scale can generate valuable new insights and hypotheses about stressor interactions. Second, that the predictability of multiple stressor effects, and consistent patterns in their impacts, can be evaluated by examining the distribution of stressor effects across targets and ecological scales. Third, that a variety of existing mechanistic and statistical modelling tools can play an important role in our framework and advance multiple stressor research

Plant-Frugivore Interactions Across the Caribbean Islands: Modularity, Invader Complexes and the Importance of Generalist Species

Aim: Mutualistic interactions between plants and animals are fundamental for the maintenance of natural communities and the ecosystem services they provide. However, particularly in human‐dominated island ecosystems, introduced species may alter mutualistic interactions. Based on an extensive dataset of plant–frugivore interactions, we mapped and analysed a meta‐network across the Caribbean archipelago. Specifically, we searched for subcommunity structure (modularity) and identified the types of species facilitating the integration of introduced species in the Caribbean meta‐network. Location: Caribbean archipelago (Lucayan archipelago, Greater Antilles, Lesser Antilles). Methods: We reviewed published scientific literature, unpublished theses and other nonpeer‐reviewed sources to compile an extensive dataset of plant–frugivore interactions. We visualized spatial patterns and conducted a modularity analysis of the cross‐island meta‐network. We also examined which species were most likely to interact with introduced species: (1) endemic, nonendemic native or introduced species, and (2) generalized or specialized species.We reported 3060 records of interactions between 486 plant and 178 frugivore species. Results: The Caribbean meta‐network was organized in 13 modules, driven by a combination of functional or taxonomic (modules dominated by certain groups of frugivores) and biogeographical (island‐specific modules) mechanisms. Few introduced species or interaction pairs were shared across islands, suggesting little homogenization of the plant–frugivore meta‐network at the regional scale. However, we found evidence of “invader complexes,” as introduced frugivores were more likely to interact with introduced plants than expected at random. Moreover, we found generalist species more likely to interact with introduced species than were specialized species. Main Conclusions: These results demonstrate that generalist species and “invader complexes” may facilitate the incorporation of introduced species into plant–frugivore communities. Despite the influx of introduced species, the meta‐network was structured into modules related to biogeographical and functional or taxonomic affinities. These findings reveal how introduced species become an integral part of mutualistic systems on tropical islands

The major barriers to evidence-informed conservation policy and possible solutions.

Conservation policy decisions can suffer from a lack of evidence, hindering effective decision-making. In nature conservation, studies investigating why policy is often not evidence-informed have tended to focus on Western democracies, with relatively small samples. To understand global variation and challenges better, we established a global survey aimed at identifying top barriers and solutions to the use of conservation science in policy. This obtained the views of 758 people in policy, practice, and research positions from 68 countries across six languages. Here we show that, contrary to popular belief, there is agreement between groups about how to incorporate conservation science into policy, and there is thus room for optimism. Barriers related to the low priority of conservation were considered to be important, while mainstreaming conservation was proposed as a key solution. Therefore, priorities should focus on convincing the public of the importance of conservation as an issue, which will then influence policy-makers to adopt pro-environmental long-term policies