econullnetr: An r package using null models to analyse the structure of ecological networks and identify resource selection

Understanding Trophic Interactions in a Warming World by Bridging Foraging Ecology and Biomechanics with Network Science

Climate change will disrupt biological processes at every scale. Ecosystem functions and services vital to ecological resilience are set to shift, with consequences for how we manage land, natural resources, and food systems. Increasing temperatures cause morphological shifts, with concomitant implications for biomechanical performance metrics crucial to trophic interactions. Biomechanical performance, such as maximum bite force or running speed, determines the breadth of resources accessible to consumers, the outcome of interspecific interactions, and thus the structure of ecological networks. Climate change-induced impacts to ecosystem services and resilience are therefore on the horizon, mediated by disruptions of biomechanical performance and, consequently, trophic interactions across whole ecosystems. Here, we argue that there is an urgent need to investigate the complex interactions between climate change, biomechanical traits, and foraging ecology to help predict changes to ecological networks and ecosystem functioning. We discuss how these seemingly disparate disciplines can be connected through network science. Using an ant-plant network as an example, we illustrate how different data types could be integrated to investigate the interaction between warming, bite force, and trophic interactions, and discuss what such an integration will achieve. It is our hope that this integrative framework will help to identify a viable means to elucidate previously intractable impacts of climate change, with effective predictive potential to guide management and mitigation.

Does This Look Infected? Hidden Host Plant Infection by the Pathogen Botrytis cinerea Alters Interactions between Plants, Aphids and Their Natural Enemies in the Field

Few studies have considered whether hidden (asymptomatic) plant pathogen infection alters ecological interactions at the higher trophic levels, even though such infection still affects plant physiology. We explored this question in two field experiments, where two varieties of lettuce (Little Gem, Tom Thumb) infected with Botrytis cinerea were either (1) naturally colonised by aphids or (2) placed in the field with an established aphid colony. We then recorded plant traits and the numbers and species of aphids, their predators, parasitoids and hyperparasitoids. Infection significantly affected plant quality. In the first experiment, symptomatically infected plants had the fewest aphids and natural enemies of aphids. The diversity and abundance of aphids did not differ between asymptomatically infected and uninfected Little Gem plants, but infection affected the aphid assemblage for Tom Thumb plants. Aphids on asymptomatically infected plants were less attractive to predators and parasitoids than those on uninfected plants, while hyperparasitoids were not affected. In the second experiment, when we excluded natural enemies, aphid numbers were lower on asymptomatically and symptomatically infected plants, but when aphid natural enemies were present, this difference was removed, most likely because aphids on uninfected plants attracted more insect natural enemies. This suggests that hidden pathogen infection may have important consequences for multitrophic interactions.

Gut microbiota variation of a tropical oil-collecting bee species far exceeds that of the honeybee

Introduction

Interest for bee microbiota has recently been rising, alleviating the gap in knowledge in regard to drivers of solitary bee gut microbiota. However, no study has addressed the microbial acquisition routes of tropical solitary bees. For both social and solitary bees, the gut microbiota has several essential roles such as food processing and immune responses. While social bees such as honeybees maintain a constant gut microbiota by direct transmission from individuals of the same hive, solitary bees do not have direct contact between generations. They thus acquire their gut microbiota from the environment and/or the provision of their brood cell. To establish the role of life history in structuring the gut microbiota of solitary bees, we characterized the gut microbiota of Centris decolorata from a beach population in Mayagüez, Puerto Rico. Females provide the initial brood cell provision for the larvae, while males patrol the nest without any contact with it. We hypothesized that this behavior influences their gut microbiota, and that the origin of larval microbiota is from brood cell provisions.

Methods

We collected samples from adult females and males of C. decolorata (n = 10 each, n = 20), larvae (n = 4), and brood cell provisions (n = 10). For comparison purposes, we also sampled co-occurring female foragers of social Apis mellifera (n = 6). The samples were dissected, their DNA extracted, and gut microbiota sequenced using 16S rRNA genes. Pollen loads of A. mellifera and C. decolorata were analyzed and interactions between bee species and their plant resources were visualized using a pollination network.

Results

While we found the gut of A. mellifera contained the same phylotypes previously reported in the literature, we noted that the variability in the gut microbiota of solitary C. decolorata was significantly higher than that of social A. mellifera. Furthermore, the microbiota of adult C. decolorata mostly consisted of acetic acid bacteria whereas that of A. mellifera mostly had lactic acid bacteria. Among C. decolorata, we found significant differences in alpha and beta diversity between adults and their brood cell provisions (Shannon and Chao1 p < 0.05), due to the higher abundance of families such as Rhizobiaceae and Chitinophagaceae in the brood cells, and of Acetobacteraceae in adults. In addition, the pollination network analysis indicated that A. mellifera had a stronger interaction with Byrsonima sp. and a weaker interaction with Combretaceae while interactions between C. decolorata and its plant resources were constant with the null model.

Conclusion

Our data are consistent with the hypothesis that behavioral differences in brood provisioning between solitary and social bees is a factor leading to relatively high variation in the microbiota of the solitary bee.

Herbivorous dietary selection shown by hawfinch (Coccothraustes coccothraustes) within mixed woodland habitats

Knowledge of diet and dietary selectivity is vital, especially for the conservation of declining species. Accurately obtaining this information, however, is difficult, especially if the study species feeds on a wide range of food items within heterogeneous and inaccessible environments, such as the tree canopy. Hawfinches (Coccothraustes coccothraustes), like many woodland birds, are declining for reasons that are unclear. We investigated the possible role that dietary selection may have in these declines in the UK. Here, we used a combination of high-throughput sequencing of 261 hawfinch faecal samples assessed against tree occurrence data from quadrats sampled in three hawfinch population strongholds in the UK to test for evidence of selective foraging. This revealed that hawfinches show selective feeding and consume certain tree genera disproportionally to availability. Positive selection was shown for beech (Fagus), cherry (Prunus), hornbeam (Carpinus), maples (Acer) and oak (Quercus), while Hawfinch avoided ash (Fraxinus), birch (Betula), chestnut (Castanea), fir (Abies), hazel (Corylus), rowan (Sorbus) and lime (Tilia). This approach provided detailed information on hawfinch dietary choice and may be used to predict the effects of changing food resources on other declining passerines populations in the future.

Late Cenozoic cooling restructured global marine plankton communities

The geographic ranges of marine organisms, including planktonic foraminifera¹, diatoms, dinoflagellates², copepods³ and fish⁴, are shifting polewards owing to anthropogenic climate change⁵. However, the extent to which species will move and whether these poleward range shifts represent precursor signals that lead to extinction is unclear⁶. Understanding the development of marine biodiversity patterns over geological time and the factors that influence them are key to contextualizing these current trends. The fossil record of the macroperforate planktonic foraminifera provides a rich and phylogenetically resolved dataset that provides unique opportunities for understanding marine biogeography dynamics and how species distributions have responded to ancient climate changes. Here we apply a bipartite network approach to quantify group diversity, latitudinal specialization and latitudinal equitability for planktonic foraminifera over the past eight million years using Triton, a recently developed high-resolution global dataset of planktonic foraminiferal occurrences⁷. The results depict a global, clade-wide shift towards the Equator in ecological and morphological community equitability over the past eight million years in response to temperature changes during the late Cenozoic bipolar ice sheet formation. Collectively, the Triton data indicate the presence of a latitudinal equitability gradient among planktonic foraminiferal functional groups which is coupled to the latitudinal biodiversity gradient only through the geologically recent past (the past two million years). Before this time, latitudinal equitability gradients indicate that higher latitudes promoted community equitability across ecological and morphological groups. Observed range shifts among marine planktonic microorganisms^1,2,8 in the recent and geological past suggest substantial poleward expansion of marine communities even under the most conservative future global warming scenarios.

Structure and characteristics of the plant-frugivore bird network from the Guilin Botanical Garden

The interaction between plants and frugivores is crucial to ecosystem function and community diversity. However, little is known about the interaction between plants and frugivorous bird species in urban green spaces. We observed interactions between plants and frugivorous birds in the Guilin Botanical Garden for one year and determined the structure and characteristics of the interaction network. We also analyzed the impact of species traits on their network roles. Interactions between 14 frugivorous birds and 13 fruit plant species were recorded in the study area. Autumn interactions comprised 38.79% of the overall network, and winter interactions comprised 33.15%. The modularity (Q, z-score) of the network was higher in autumn; the weighted nestedness (wNODF, z-score) and interaction evenness (E₂ , z-score) of the network were higher in winter; the connectance (C, z-score) and interaction diversity (z-score) of the network were higher in spring; and the specialization (H₂', z-score) of the network was higher in summer. The observed network showed lower C, lower interaction H₂ , lower E₂ , lower wNODF, higher H₂' and higher Q when compared to the random networks. The bird species most important to network stability were Hemixos castanonotus, Parus venustulus, and Pycnonotus sinensis. The most important plant species were Alocasia macrorrhiza, Cinnamomum camphora, and Machilus nanmu. Of all the bird and plant traits included in this study, only plant color had a significant impact on species strength, with black fruit having a higher species strength. Our results suggest that interaction networks in urban green spaces can be temporally complex and variable and that a network approach can be an important monitoring tool for detecting the status of crucial ecosystem functions.

High Foraging Fidelity and Plant-Pollinator Network Dominance of Non-native Honeybees (Apis mellifera) in the Ecuadorian Andes

Pollinator foraging fidelity (i.e., consistent and repeated visitation to a particular plant species or area) is poorly understood for most bee species, but is important information for both the conservation of plant and pollinator species and the ecosystem services they provide to humans. We used plant-pollinator surveys and mark-recapture of floral-visiting Hymenoptera to study the foraging fidelity and species interaction network properties of a plant-pollinator community in the tropical Andes of southern Ecuador. After marking 92 bees visiting six plant taxa along four 100-m transects between July 16th and July 31st of 2019, only honeybees were resighted at a recapture rate of 47.7% (41/86). During our surveys, we observed nine bee and two wasp taxa feeding from the flowers of 10 morphospecies of plants, and we found significantly low network nestedness and significantly high network-level specialization. Specialization (d') was also significant for honeybees and bumblebees and for three plant taxa. Overall, our findings indicated that feral, non-native honeybees in this region dominated the local plant-pollinator network, yet this species is acting as a specialist forager at the individual level. Our results suggest that honeybees may be replacing the pollination services of some native bees and wasps in the region, but more research is needed to determine the effectiveness of honeybee pollination for the local plants.

Pollinator richness, pollination networks, and diet adjustment along local and landscape gradients of resource diversity

Loss of habitats and native species, introduction of invasive species, and changing climate regimes lead to the homogenization of landscapes and communities, affecting the availability of habitats and resources for economically important guilds, such as pollinators. Understanding how pollinators and their interactions vary along resource diversity gradients at different scales may help to determine their adaptability to the current diversity loss related to global change. We used data on 20 plant-pollinator communities along gradients of flower richness (local diversity) and landscape heterogeneity (landscape diversity) to understand how the diversity of resources at local and landscape scales affected (1) wild pollinator abundance and richness (accounting also for honey bee abundance), (2) the structure of plant-pollinator networks, (3) the proportion of actively selected interactions (those not occurring by neutral processes), and (4) pollinator diet breadth and species' specialization in networks. Wild pollinator abundance was higher overall in flower-rich and heterogeneous habitats, while wild pollinator richness increased with flower richness (more strongly for beetles and wild bees) and decreased with honeybee abundance. Network specialization (H₂ '), modularity, and functional complementarity were all positively related to floral richness and landscape heterogeneity, indicating niche segregation as the diversity of resources increases at both scales. Flower richness also increased the proportion of actively selected interactions (especially for wild bees and flies), whereas landscape heterogeneity had a weak negative effect on this variable. Overall, network-level metrics responded to larger landscape scales than pollinator-level metrics did. Higher floral richness resulted in a wider taxonomic and functional diet for all the study guilds, while functional diet increased mainly for beetles. Despite this, specialization in networks (d') increased with flower richness for all the study guilds, because pollinator species fed on a narrower subset of plants as communities became richer in species. Our study indicates that pollinators are able to adapt their diet to resource changes at local and landscape scales. However, resource homogenization might lead to poor and generalist pollinator communities, where functionally specialized interactions are lost. This study highlights the importance of including different scales to understand the effects of global change on pollination service through changes in resource diversity.

Seasonal and ontological variation in diet and age-related differences in prey choice, by an insectivorous songbird

The diet of an individual animal is subject to change over time, both in response to short-term food fluctuations and over longer time scales as an individual ages and meets different challenges over its life cycle. A metabarcoding approach was used to elucidate the diet of different life stages of a migratory songbird, the Eurasian reed warbler (Acrocephalus scirpaceus) over the 2017 summer breeding season in Somerset, the United Kingdom. The feces of adult, juvenile, and nestling warblers were screened for invertebrate DNA, enabling the identification of prey species. Dietary analysis was coupled with monitoring of Diptera in the field using yellow sticky traps. Seasonal changes in warbler diet were subtle, whereas age class had a greater influence on overall diet composition. Age classes showed high dietary overlap, but significant dietary differences were mediated through the selection of prey; (i) from different taxonomic groups, (ii) with different habitat origins (aquatic vs. terrestrial), and (iii) of different average approximate sizes. Our results highlight the value of metabarcoding data for enhancing ecological studies of insectivores in dynamic environments.

Oilseed Rape Shares Abundant and Generalized Pollinators with Its Co-Flowering Plant Species

Simple Summary

Plants in semi-natural areas provide food resources for pollinators that visit pollinator-dependent crop species, such as Oilseed Rape (OSR). Here, we study the patterns of pollinator visitation on OSR and its co-flowering plants in adjacent semi-natural areas. We find that OSR is visited by pollinators that are abundant in the community and that these pollinators also visit co-flowering plant species in semi-natural areas. OSR primarily influences the pollination of plant species which have similar floral traits (i.e., other disc flowers). Plant species that attract a high abundances of bumblebees, wild bees, flies, and beetles influence the pollination of OSR the most. Our results suggest that plant species in semi-natural areas that support the high abundances of common pollinators which are generalized in their visitation are most important to the pollination of OSR, and that such plant species do not necessarily have similar floral traits to OSR.

Abstract

Mass-flowering crops, such as Oilseed Rape (OSR), provide resources for pollinators and benefit from pollination services. Studies that observe the community of interactions between plants and pollinators are critical to understanding the resource needs of pollinators. We observed pollinators on OSR and wild plants in adjacent semi-natural areas in Sachsen-Anhalt, Germany to quantify (1) the co-flowering plants that share pollinators with OSR, (2) the identity and functional traits of plants and pollinators in the network module of OSR, and (3) the identity of the plants and pollinators that act as network connectors and hubs. We found that four common plants share a high percentage of their pollinators with OSR. OSR and these plants all attract abundant pollinators in the community, and the patterns of sharing were not more than would be expected by chance sampling. OSR acts as a module hub, and primarily influences the other plants in its module that have similar functional traits. However, the plants that most influence the pollination of OSR have different functional traits and are part of different modules. Our study demonstrates that supporting the pollination of OSR requires the presence of semi-natural areas with plants that can support a high abundances of generalist pollinators.

DNA diet profiles with high-resolution animal tracking data reveal levels of prey selection relative to habitat choice in a crepuscular insectivorous bird

Given the global decline of many invertebrate food resources, it is fundamental to understand the dietary requirements of insectivores. We give new insights into the functional relationship between the spatial habitat use, food availability, and diet of a crepuscular aerial insectivore, the European Nightjar (Caprimulgus europaeus) by relating spatial use data with high-throughput sequencing (HTS) combined with DNA metabarcoding. Our study supports the predictions that nightjars collect a substantial part of their daily nourishment from foraging locations, sometimes at considerable distance from nesting sites. Lepidopterans comprise 65% of nightjars' food source. Nightjars tend to select larger species of Lepidoptera (>19 mm) which suggests that nightjars optimize the efficiency of foraging trips by selecting the most energetically favorable-larger-prey items. We anticipate that our findings may shed additional light on the interactions between invertebrate communities and higher trophic levels, which is required to understand the repercussions of changing food resources on individual- and population-level processes.

Diversity and Distribution Patterns of Endolichenic Fungi in Jeju Island, South Korea

Lichens are symbiotic organisms containing diverse microorganisms. Endolichenic fungi (ELF) are one of the inhabitants living in lichen thalli, and have potential ecological and industrial applications due to their various secondary metabolites. As the function of endophytic fungi on the plant ecology and ecosystem sustainability, ELF may have an influence on the lichen diversity and the ecosystem, functioning similarly to the influence of endophytic fungi on plant ecology and ecosystem sustainability, which suggests the importance of understanding the diversity and community pattern of ELF. In this study, we investigated the diversity and the factors influencing the community structure of ELF in Jeju Island, South Korea by analyzing 619 fungal isolates from 79 lichen samples in Jeju Island. A total of 112 ELF species was identified and the most common species belonged to Xylariales in Sordariomycetes. The richness and community structure of ELF were significantly influenced by the host taxonomy, together with the photobiont types and environmental factors. Our results suggest that various lichen species in more diverse environments need to be analyzed to expand our knowledge of the diversity and ecology of ELF.

Characterizing ecological interaction networks to support risk assessment in classical biological control of weeds

A key element in weed biological control is the selection of a biological control agent that minimizes the risks of non-target attack and indirect effects on the recipient community. Network ecology is a promising approach that could help decipher tritrophic interactions in both the native and the invaded ranges, to complement quarantine-based host-specificity tests and gain insights on potential interactions of biological control agents. This review highlights practical questions addressed by networks, including 1) biological control agent selection, based on specialization indices, 2) risk assessment of biological control agent release into a novel environment, via particular patterns of association such as apparent competition between agent(s) and native herbivore(s), 3) network comparisons through structural metrics, 4) potential of network modelling and 5) limits of network construction methods.

Difficulties in benchmarking ecological null models: an assessment of current methods

Identifying species interactions and detecting when ecological communities are structured by them is an important problem in ecology and biogeography. Ecologists have developed specialized statistical hypothesis tests to detect patterns indicative of community-wide processes in their field data. In this respect, null model approaches have proved particularly popular. The freedom allowed in choosing the null model and statistic to construct a hypothesis test leads to a proliferation of possible hypothesis tests from which ecologists can choose to detect these processes. Here, we point out some serious shortcomings of a popular approach to choosing the best hypothesis for the ecological problem at hand that involves benchmarking different hypothesis tests by assessing their performance on artificially constructed data sets. Terminological errors concerning the use of Type I and Type II errors that underlie these approaches are discussed. We argue that the key benchmarking methods proposed in the literature are not a sound guide for selecting null hypothesis tests, and further, that there is no simple way to benchmark null hypothesis tests. Surprisingly, the basic problems identified here do not appear to have been addressed previously, and these methods are still being used to develop and test new null models and summary statistics, from quantifying community structure (e.g., nestedness and modularity) to analyzing ecological networks.

Plant species abundance and phylogeny explain the structure of recruitment networks

Established plants can affect the recruitment of young plants, filtering out some and allowing the recruitment of others, with profound effects on plant community dynamics. Recruitment networks (RNs) depict which species recruit under which others. We investigated whether species abundance and phylogenetic distance explain the structure of RNs across communities. We estimated the frequency of canopy-recruit interactions among woody plants in 10 forest assemblages to describe their RNs. For each RN, we determined the functional form (linear, power or exponential) best describing the relationship of interaction frequency with three predictors: canopy species abundance, recruit species abundance and phylogenetic distance. We fitted models with all combinations of predictor variables, from which we simulated RNs. The best functional form of each predictor was the same in most communities (linear for canopy species abundance, power for recruit species abundance and exponential for phylogenetic distance). The model including all predictor variables was consistently the best in explaining interaction frequency and showed the best performance in predicting RN structure. Our results suggest that mechanisms related to species abundance are necessary but insufficient to explain the assembly of RNs. Evolutionary processes affecting phylogenetic divergence are critical determinants of RN structure.

A systems approach reveals urban pollinator hotspots and conservation opportunities

Urban areas are often perceived to have lower biodiversity than the wider countryside, but a few small-scale studies suggest that some urban land uses can support substantial pollinator populations. We present a large-scale, well-replicated study of floral resources and pollinators in 360 sites incorporating all major land uses in four British cities. Using a systems approach, we developed Bayesian network models integrating pollinator dispersal and resource switching to estimate city-scale effects of management interventions on plant-pollinator community robustness to species loss. We show that residential gardens and allotments (community gardens) are pollinator ‘hotspots’: gardens due to their extensive area, and allotments due to their high pollinator diversity and leverage on city-scale plant-pollinator community robustness. Household income was positively associated with pollinator abundance in gardens, highlighting the influence of socio-economic factors. Our results underpin urban planning recommendations to enhance pollinator conservation, using increasing city-scale community robustness as our measure of success.

Seasonally varying marine influences on the coastal ecosystem detected through molecular gut analysis

Terrestrial predators on marine shores benefit from the inflow of organisms and matter from the marine ecosystem, often causing very high predator densities and indirectly affecting the abundance of other prey species on shores. This indirect effect may be particularly strong if predators shift diets between seasons. We therefore quantified the seasonal variation in diet of two wolf spider species that dominate the shoreline predator community, using molecular gut content analyses with general primers to detect the full prey range. Across the season, spider diets changed, with predominantly terrestrial prey from May until July and predominantly marine prey (mainly chironomids) from August until October. This pattern coincided with a change in the spider age and size structure, and prey abundance data and resource selection analyses suggest that the higher consumption of chironomids during autumn is due to an ontogenetic diet shift rather than to variation in prey abundance. The analyses suggested that small dipterans with a weak flight capacity, such as Chironomidae, Sphaeroceridae, Scatopsidae and Ephydridae, were overrepresented in the gut of small juvenile spiders during autumn, whereas larger, more robust prey, such as Lepidoptera, Anthomyidae and Dolichopodidae, were overrepresented in the diet of adult spiders during spring. The effect of the inflow may be that the survival and growth of juvenile spiders is higher in areas with high chironomid abundances, leading to higher densities of adult spiders and higher predation rates on the terrestrial prey next spring.