Machine learning algorithms to infer trait-matching and predict species interactions in ecological networks

Ecologists have long suspected that species are more likely to interact if their traits match in a particular way. For example, a pollination interaction may be more likely if the proportions of a bee's tongue fit a plant's flower shape. Empirical estimates of the importance of trait‐matching for determining species interactions, however, vary significantly among different types of ecological networks. Here, we show that ambiguity among empirical trait‐matching studies may have arisen at least in parts from using overly simple statistical models. Using simulated and real data, we contrast conventional generalized linear models (GLM) with more flexible Machine Learning (ML) models (Random Forest, Boosted Regression Trees, Deep Neural Networks, Convolutional Neural Networks, Support Vector Machines, naïve Bayes, and k‐Nearest‐Neighbor), testing their ability to predict species interactions based on traits, and infer trait combinations causally responsible for species interactions. We found that the best ML models can successfully predict species interactions in plant–pollinator networks, outperforming GLMs by a substantial margin. Our results also demonstrate that ML models can better identify the causally responsible trait‐matching combinations than GLMs. In two case studies, the best ML models successfully predicted species interactions in a global plant–pollinator database and inferred ecologically plausible trait‐matching rules for a plant–hummingbird network from Costa Rica, without any prior assumptions about the system. We conclude that flexible ML models offer many advantages over traditional regression models for understanding interaction networks. We anticipate that these results extrapolate to other ecological network types. More generally, our results highlight the potential of machine learning and artificial intelligence for inference in ecology, beyond standard tasks such as image or pattern recognition

Linking farmer and beekeeper preferences with ecological knowledge to improve crop pollination

1. Pollination by insects is a key input into many crops, with managed honeybees often being hired to support pollination services. Despite substantial research into pollination management, no European studies have yet explored how and why farmers managed pollination services and few have explored why beekeepers use certain crops. 2. Using paired surveys of beekeepers and farmers in 10 European countries, this study examines beekeeper and farmer perceptions and motivations surrounding crop pollination. 3. Almost half of the farmers surveyed believed they had pollination service deficits in one or more of their crops. 4. Less than a third of farmers hired managed pollinators, however most undertook at least one form of agri-environment management known to benefit pollinators, although few did so to promote pollinators. 5. Beekeepers were ambivalent towards many mass flowering crops, with some beekeepers using crops for their honey that other beekeepers avoid because of perceived pesticide risks. 6. The findings highlight a number of largely overlooked knowledge gaps that will affect knowledge exchange and co-operation between the two groups

Apple pollination: demand depends on variety and supply depends on pollinator identity

Insect pollination underpins apple production but the extent to which different pollinator guilds supply this service, particularly across different apple varieties, is unknown. Such information is essential if appropriate orchard management practices are to be targeted and proportional to the potential benefits pollinator species may provide. Here we use a novel combination of pollinator effectiveness assays (floral visit effectiveness), orchard field surveys (flower visitation rate) and pollinator dependence manipulations (pollinator exclusion experiments) to quantify the supply of pollination services provided by four different pollinator guilds to the production of four commercial varieties of apple. We show that not all pollinators are equally effective at pollinating apples, with hoverflies being less effective than solitary bees and bumblebees, and the relative abundance of different pollinator guilds visiting apple flowers of different varieties varies significantly. Based on this, the taxa specific economic benefits to UK apple production have been established. The contribution of insect pollinators to the economic output in all varieties was estimated to be £92.1M across the UK, with contributions varying widely across taxa: solitary bees (£51.4M), honeybees (£21.4M), bumblebees (£18.6M) and hoverflies (£0.7M). This research highlights the differences in the economic benefits of four insect pollinator guilds to four major apple varieties in the UK. This information is essential to underpin appropriate investment in pollination services management and provides a model that can be used in other entomolophilous crops to improve our understanding of crop pollination ecology

Management-dependent effects of pollinator functional diversity on apple pollination services: A response–effect trait approach

Data available via the Dryad Digital Repository https://doi.org/10.5061/dryad.63xsj3v39 (Roquer-Beni et al., 2021).Functional traits mediate the response of communities to disturbances (response traits) and their contribution to ecosystem functions (effect traits). To predict how anthropogenic disturbances influence ecosystem services requires a dual approach including both trait concepts. Here, we used a response–effect trait conceptual framework to understand how local and landscape features affect pollinator functional diversity and pollination services in apple orchards. We worked in 110 apple orchards across four European regions. Orchards differed in management practices. Low-intensity (LI) orchards were certified organic or followed close-to-organic practices. High-intensity (HI) orchards followed integrated pest management practices. Within each management type, orchards encompassed a range of local (flower diversity, agri-environmental structures) and landscape features (orchard and pollinator-friendly habitat cover). We measured pollinator visitation rates and calculated trait composition metrics based on 10 pollinator traits. We used initial fruit set as a measure of pollination service. Some pollinator traits (body size and hairiness) were negatively related to orchard cover and positively affected by pollinator-friendly habitat cover. Bee functional diversity was lower in HI orchards and decreased with increased landscape orchard cover. Pollination service was not associated with any particular trait but increased with pollinator trait diversity in LI orchards. As a result, LI orchards with high pollinator trait diversity reached levels of pollination service similar to those of HI orchards. Synthesis and applications. Pollinator functional diversity enables pollinator communities to respond to agricultural intensification and to increase pollination function. Our results show that efforts to promote biodiversity provide greater returns in low-intensity than in high-intensity orchards. The fact that low-intensity orchards with high pollinator functional diversity reach levels of pollination services similar to those of high-intensity orchards provides a compelling argument for the conversion of high-intensity into low-intensity farms.This research (EcoFruit project) was funded through the 2013–2014 BiodivERsA/FACCE-JPI joint call (2014-74), Spanish MinECo (PCIN-2014-145-C02), German BMBF (PT-DLR/BMBF, 01LC1403) and Swedish Research Council Formas (2014-1784) by Formas (2013-934 to M.T.), Stiftelsen Lantbruksforskning (H1256150 to M.P.), INIA (RTA2013-00039-C03-00 to G.A. and M.M.), MinECo/FEDER (CGL2015-68963-C2-2-R to D.G.), FI-AGAUR (to L.R.-B.) and MinECo (RYC-2015-18448 to X.A.)

Proportion of extended-spectrum ß-lactamase-producing Enterobacteriaceae in community setting in Ngaoundere, Cameroon

BACKGROUND: There is no information regarding the resistance mechanisms of extended-spectrum ß-lactamase (ESBL)-producing Enterobacteriaceae in community setting in Cameroon. The current study aimed to determine the proportion of ESBLs in Enterobacteriaceae isolated in the community and to analyse some risk factors associated with ESBL carriage. METHODS: Faecal samples were collected from 208 different outpatients and 150 healthy student volunteers between 3 January and 3 April 2009. Enterobacterial isolates resistant to third-generation cephalosporins were screened for ESBL production by the double-disk synergy test. Presumptive ESBL-producing isolates with positive synergy test were identified by Mass Spectrometry using the BioTyper MALDI-TOF. For such ESBL positive isolates, antibiotic susceptibility was determined by the Vitek 2 system. PCR and sequencing were performed for the detection of different types of ESBL genes in presumptive ESBL-producing isolates. Statistical methods were used for the univariate calculation of risk factors. RESULTS: During the study period, a total of 358 faecal samples were analysed; 58 of such samples (16%) showed an ESBL phenotype and were confirmed by PCR. The proportion of ESBL producers in faecal carriage was statistically different between outpatients and student volunteers (23.1% vs. 6.7%: p < 0.000). According to a univariate analysis, previous use of antibiotics (ciprofloxacin) appeared to be a risk factor for ESBL carriage (p < 0.05).Escherichia coli was the species most frequently isolated among the ESBL producers in outpatients (66.7%) and student volunteers (90%). Isolates showed additional resistance to gentamicin, ciprofloxacin and trimethoprim/sulfamethoxazole but none of them was resistant to temocillin, amikacin or meropenem. Most of the strains (97%) produced a CTX-M group 1 enzymes [CTX-M-15 (98%) or CTX-M-1 (2%)] and the remaining strains produced SHV-12 enzyme (3%). CONCLUSIONS: The use of drugs such as amoxicillin, ciprofloxacin and trimethoprim/sulfamethoxazole does not seem appropriate for empirical treatment because of emerging resistance. The implementation in Cameroon or in other African countries of methods of screening ESBL-producing organisms in routine laboratories is of great importance in order for us to offer patients appropriate treatment and for infection control efforts to succeed

A global synthesis reveals biodiversity-mediated benefits for crop production

Human land use threatens global biodiversity and compromises multiple ecosystem functions critical to food production. Whether crop yield-related ecosystem services can be maintained by a few dominant species or rely on high richness remains unclear. Using a global database from 89 studies (with 1475 locations), we partition the relative importance of species richness, abundance, and dominance for pollination; biological pest control; and final yields in the context of ongoing land-use change. Pollinator and enemy richness directly supported ecosystem services in addition to and independent of abundance and dominance. Up to 50% of the negative effects of landscape simplification on ecosystem services was due to richness losses of service-providing organisms, with negative consequences for crop yields. Maintaining the biodiversity of ecosystem service providers is therefore vital to sustain the flow of key agroecosystem benefits to society

A global synthesis reveals biodiversity-mediated benefits for crop production

Human land use threatens global biodiversity and compromises multiple ecosystem functions critical to food production. Whether crop yield-related ecosystem services can be maintained by a few dominant species or rely on high richness remains unclear. Using a global database from 89 studies (with 1475 locations), we partition the relative importance of species richness, abundance, and dominance for pollination; biological pest control; and final yields in the context of ongoing land-use change. Pollinator and enemy richness directly supported ecosystem services in addition to and independent of abundance and dominance. Up to 50% of the negative effects of landscape simplification on ecosystem services was due to richness losses of service-providing organisms, with negative consequences for crop yields. Maintaining the biodiversity of ecosystem service providers is therefore vital to sustain the flow of key agroecosystem benefits to society. [Abstract copyright: Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

Incorporating the social dimension into hydrogeochemical investigations for rural development: the Bir Al-Nas approach for socio-hydrogeology

A replicable multidisciplinary approach is presented for science-based groundwater management practices: Bir Al-Nas (Bottom-up IntegRated Approach for sustainabLe grouNdwater mAnagement in rural areaS). This approach provides a practical example of the concept of “socio-hydrogeology”, a way of incorporating the social dimension into hydrogeological investigations, as reinforced by the translation of the Arabic bir al-nas: “the people’s well”. To achieve this, hydrogeologists act as “social hydrologists” during their monitoring activities, which often bring them into contact with local communities and end users (and polluters) of water. Not only can they retrieve reliable information about traditional know-how and local issues, but they can also change the public perception of science/scientists to create the basis for mutual collaboration and understanding in view of implementing improved integrated groundwater management. The final outcomes are expected to be an increased awareness of communities at the local level and a clear understanding of their water issues and needs from the very early stages of the investigation. Although the importance of using such methods in groundwater analysis and management is widely recognized, hydrogeological investigations are currently dominated by sectorial approaches that are easier to implement but less sustainable. The pressure of population growth, the shift towards more water-dependent economies, climate change and its impact on water availability will require scientists to use a more integrated approach, such as Bir Al-Nas, when dealing with increasing water pollution and water-scarcity issues.A replicable multidisciplinary approach is presented for science-based groundwater management practices: Bir Al-Nas (Bottom-up IntegRated Approach for sustainabLe grouNdwater mAnagement in rural areaS). This approach provides a practical example of the concept of "socio-hydrogeology", a way of incorporating the social dimension into hydrogeological investigations, as reinforced by the translation of the Arabic bir al-nas: "the people's well". To achieve this, hydrogeologists act as "social hydrologists" during their monitoring activities, which often bring them into contact with local communities and end users (and polluters) of water. Not only can they retrieve reliable information about traditional know-how and local issues, but they can also change the public perception of science/scientists to create the basis for mutual collaboration and understanding in view of implementing improved integrated groundwater management. The final outcomes are expected to be an increased awareness of communities at the local level and a clear understanding of their water issues and needs from the very early stages of the investigation. Although the importance of using such methods in groundwater analysis and management is widely recognized, hydrogeological investigations are currently dominated by sectorial approaches that are easier to implement but less sustainable. The pressure of population growth, the shift towards more water-dependent economies, climate change and its impact on water availability will require scientists to use a more integrated approach, such as Bir Al-Nas, when dealing with increasing water pollution and water-scarcity issues