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Species interactions shape biodiversity patterns, community assemblage, and the dynamics of wildlife populations. Ecological theory posits that the strength of interspecific interactions is fundamentally underpinned by the population sizes of the involved species. Nonetheless, prevalent approaches for modeling species interactions predominantly center around occupancy states. Here, we use simulations to illuminate the inadequacies of modeling species interactions solely as a function of occupancy, as is common practice in ecology. We demonstrate erroneous inference into species interactions due to error in parameter estimates when considering species occupancy alone. To address this critical issue, we propose, develop, and demonstrate an abundance‐mediated interaction framework designed explicitly for modeling species interactions involving two or more species from detection/non‐detection data. We present Markov chain Monte Carlo (MCMC) samplers tailored for diverse ecological scenarios, including intraguild predation, disease‐ or predator‐mediated competition, and trophic cascades. Illustrating the practical implications of our approach, we compare inference from modeling the interactions in a three‐species network involving coyotes (Canis latrans), fishers (Pekania pennanti), and American marten (Martes americana) in North America as a function of occupancy states and as a function of abundance. When modeling interactions as a function of abundance rather than occupancy, we uncover previously unidentified interactions. Our study emphasizes that accounting for abundance‐mediated interactions rather than simple co‐occurrence patterns can fundamentally alter our comprehension of system dynamics. Through an empirical case study and comprehensive simulations, we demonstrate the importance of accounting for abundance when modeling species interactions, and we present a statistical framework equipped with MCMC samplers to achieve this paradigm shift in ecological research. [ABSTRACT FROM AUTHOR]

In the Neotropical biogeographic region, there are about 290 known species and subspecies of fleas, which have as their main hosts to the rodent subfamily Sigmodontinae. In Peru, more than 22 years have passed since the last list of known flea species was published. This study presents a review and update of the fleas recorded in Peru from 1908 to 2024. This list contains information on the flea species, including their known hosts, the localities in Peru where they were reported, the main references and some comments. In addition, the specificity of flea–host interactions was assessed using an interaction network approach. In the literature review, 86 flea species were found distributed among 9 families, 34 genera and 19 subspecies. These fleas were recorded parasitizing at least71 species of mammals and birds (14 orders, 28 families, 54 genera), 15 reported only at the genera level and seven undetermined ones. The flea–host interaction network exhibited a modular structure, indicating that these interactions tend to be specialized. A sigmodontine rodent (Akodon mollis) and a Rhopalopsyllidae flea (Polygenis litargus) were highly connected across modules and the overall network, and thus were important to maintain the structure. This review contributes to the knowledge of fleas in Peru, synthesizing the scattered information and providing information on the interaction they have with their hosts. [ABSTRACT FROM AUTHOR]

Understanding the behavior of migratory birds can help determine levels of connectivity and inform conservation actions for species of conservation concern. The common tern Sterna hirundo is a long‐distance migratory seabird that is considered a species of conservation concern in the North American Great Lakes region and that has experienced significant declines in breeding numbers across large lakes in Manitoba. To better understand the movement ecology of common terns, we used data from multiple tracking technologies (solar geolocation, GPS tracking, and Motus radio tracking) obtained from individuals (n = 83) across five breeding colonies on four inland lakes in North America. We identified key stopover regions used during southward migration and explored how demographics and social interactions influence connectivity. We identified three key stopover regions (Lake Erie, the southern Atlantic Coast, and Florida) and documented, for the first time, differences in post‐natal and post‐breeding migration for inland nesting terns. Juveniles arrived, on average, three weeks later than unrelated adults to their first major staging area. Although adult female arrival to and departure from Lake Erie was similar to adult males, female schedules became significantly earlier than males as southward migration progressed. Using a graph network to describe the spatiotemporal associations among adults from the same inland lake, individuals appeared to be highly connected, meeting up in different regions throughout the non‐breeding season, suggesting that social interactions may play an important role in maintaining spatial connectivity. Despite differences in migration schedules by sex and arrival to the first major staging area by age class, birds appeared to rely on the same key stopover regions during southward migration. The stopover regions identified in this study can help identify potential bottlenecks and guide future research aimed at assessing the impacts of climate change and human disturbance on common terns breeding in North America. [ABSTRACT FROM AUTHOR]

The separation of macro-level and microbial food webs is typical but has important limits. A multilayered food web conceptual model is needed because microbial food webs are nested within macro-organisms. These multilayered microbial food webs likely influence the network dynamics of macro-level food webs. A multilayered food webs model opens new avenues for empirical investigations into the complexity of ecological networks. The model can provide a new lens through which to view a network's response to ecosystem changes. Food webs are typically defined as being macro-organism-based (e.g., plants, mammals, birds) or microbial (e.g., bacteria, fungi, viruses). However, these characterizations have limits. We propose a multilayered food web conceptual model where microbial food webs are nested within food webs composed of macro-organisms. Nesting occurs through host–microbe interactions, which influence the health and behavior of host macro-organisms, such that host microbiomes likely alter population dynamics of interacting macro-organisms and vice versa. Here, we explore the theoretical underpinnings of multilayered food webs and the implications of this new conceptual model on food web ecology. Our framework opens avenues for new empirical investigations into complex ecological networks and provides a new lens through which to view a network's response to ecosystem changes. [ABSTRACT FROM AUTHOR]

Background: Cardiovascular diseases (CVDs) are major causes of mortality and morbidity worldwide; yet the understanding of their molecular basis is incomplete. Multi-omics studies have significant potential to uncover these mechanisms, but such studies are challenged by genetic and environmental confounding—a problem that can be effectively reduced by investigating intrapair differences in twins. Here, we linked data on all diagnoses of the circulatory system from the nationwide Danish Patient Registry (spanning 1977–2022) to a study population of 835 twins holding genome-wide DNA methylation and gene expression data. CVD diagnoses were divided into prevalent or incident cases (i.e., occurring before or after blood sample collection (2007–2011)). The diagnoses were classified into four groups: cerebrovascular diseases, coronary artery disease (CAD), arterial and other cardiovascular diseases (AOCDs), and diseases of the veins and lymphatic system. Statistical analyses were performed by linear (prevalent cases) or cox (incident cases) regression analyses at both the individual-level and twin pair-level. Significant genes (p < 0.05) in both types of biological data and at both levels were inspected by bioinformatic analyses, including gene set enrichment analysis and interaction network analysis. Results: In general, more genes were found for prevalent than for incident cases, and bioinformatic analyses primarily found pathways of the immune system, signal transduction and diseases for prevalent cases, and pathways of cell–cell communication, metabolisms of proteins and RNA, gene expression, and chromatin organization groups for incident cases. This potentially reflects biology related to response to CVD (prevalent cases) and mechanisms related to regulation and development of disease (incident cases). Of specific genes, Myosin 1E was found to be central for CAD, and DEAD-Box Helicase 5 for AOCD. These genes were observed in both the prevalent and the incident analyses, potentially reflecting that their DNA methylation and gene transcription levels change both because of disease (prevalent cases) and prior disease (incident cases). Conclusion: We present novel biomarkers for CVD by performing multi-omics analysis in twins, hereby lowering the confounding due to shared genetics and early life environment—a study design that is surprisingly rare in the field of CVD, and where additional studies are highly needed. [ABSTRACT FROM AUTHOR]

Background: Cardiovascular diseases (CVDs) are major causes of mortality and morbidity worldwide; yet the understanding of their molecular basis is incomplete. Multi-omics studies have significant potential to uncover these mechanisms, but such studies are challenged by genetic and environmental confounding—a problem that can be effectively reduced by investigating intrapair differences in twins. Here, we linked data on all diagnoses of the circulatory system from the nationwide Danish Patient Registry (spanning 1977–2022) to a study population of 835 twins holding genome-wide DNA methylation and gene expression data. CVD diagnoses were divided into prevalent or incident cases (i.e., occurring before or after blood sample collection (2007–2011)). The diagnoses were classified into four groups: cerebrovascular diseases, coronary artery disease (CAD), arterial and other cardiovascular diseases (AOCDs), and diseases of the veins and lymphatic system. Statistical analyses were performed by linear (prevalent cases) or cox (incident cases) regression analyses at both the individual-level and twin pair-level. Significant genes (p < 0.05) in both types of biological data and at both levels were inspected by bioinformatic analyses, including gene set enrichment analysis and interaction network analysis. Results: In general, more genes were found for prevalent than for incident cases, and bioinformatic analyses primarily found pathways of the immune system, signal transduction and diseases for prevalent cases, and pathways of cell–cell communication, metabolisms of proteins and RNA, gene expression, and chromatin organization groups for incident cases. This potentially reflects biology related to response to CVD (prevalent cases) and mechanisms related to regulation and development of disease (incident cases). Of specific genes, Myosin 1E was found to be central for CAD, and DEAD-Box Helicase 5 for AOCD. These genes were observed in both the prevalent and the incident analyses, potentially reflecting that their DNA methylation and gene transcription levels change both because of disease (prevalent cases) and prior disease (incident cases). Conclusion: We present novel biomarkers for CVD by performing multi-omics analysis in twins, hereby lowering the confounding due to shared genetics and early life environment—a study design that is surprisingly rare in the field of CVD, and where additional studies are highly needed. [ABSTRACT FROM AUTHOR]

Simple Summary: This research aimed to identify, through an in silico approach using interaction networks, a potential biomarker associated with HPV 16 integration in cervical cancer. MAGI-1 was selected, and the expression profiles and changes in subcellular localization in cell lines and samples were evaluated in patients with premalignant lesions and invasive squamous carcinoma with HPV 16 in an integrated state. MAGI-1 is a potential biomarker that differentiates a normal cell with integrated HPV 16 from early cervical lesions. HPV 16 integration is crucial for the onset and progression of premalignant lesions to invasive squamous cell carcinoma (ISCC) because it promotes the amplification of proto-oncogenes and the silencing of tumor suppressor genes; some of these are proteins with PDZ domains involved in homeostasis and cell polarity. Through a bioinformatics approach based on interaction networks, a group of proteins associated with HPV 16 infection, PDZ domains, and direct physical interaction with E6 and related to different hallmarks of cancer were identified. MAGI-1 was selected to evaluate the expression profile and subcellular localization changes in premalignant lesions and ISCC with HPV 16 in an integrated state in cervical cytology; the profile expression of MAGI-1 diminished according to lesion grade. Surprisingly, in cell lines CaSki and SiHa, the protein localization was cytoplasmic and nuclear. In contrast, in histological samples, a change in subcellular localization from the cytoplasm in low-grade squamous intraepithelial lesions (LSIL) to the nucleus in the high-grade squamous intraepithelial lesion (HSIL) was observed; in in situ carcinomas and ISCC, MAGI-1 expression was absent. In conclusion, MAGI-1 expression could be a potential biomarker for distinguishing those cells with normal morphology but with HPV 16 integrated from those showing morphology-related uterine cervical lesions associated with tumor progression. [ABSTRACT FROM AUTHOR]

Promoting urban green spaces is an effective strategy to increase biodiversity in cities. However, our understanding of how local and landscape factors influence trophic interactions in these urban contexts remains limited. Here, we sampled cavity-nesting bees and wasps and their natural enemies within 85 urban gardens in Zurich (Switzerland) to identify factors associated with the diversity and dissimilarity of antagonistic interactions in these communities. The proportions of built-up area and urban green area at small landscape scales (50 m radius), as well as the management intensity, sun exposure, plant richness and proportion of agricultural land at the landscape scale (250 m radius), were key drivers of interaction diversity. This increased interaction diversity resulted not only from the higher richness of host and natural enemy species, but also from species participating in more interactions. Furthermore, dissimilarity in community structure and interactions across gardens (beta-diversity) were primarily influenced by differences in built-up areas and urban green areas at the landscape scale, as well as by management intensity. Our study offers crucial insights for urban planning and conservation strategies, supporting sustainability goals by helping to understand the factors that shape insect communities and their trophic interactions in urban gardens. [ABSTRACT FROM AUTHOR]

Bats are the second‐most diverse group of mammals in the world, and bat flies are their main parasites. However, significant knowledge gaps remain regarding these antagonistic interactions, especially since diverse factors such as seasonality and host sex can affect their network structures. Here, we explore the influence of such factors by comparing species richness and composition of bat flies on host bats, as well as specialization and modularity of bat–bat fly interaction networks between seasons and adult host sexes. We captured bats and collected their ectoparasitic flies at 10 sampling sites in the savannahs of Amapá State, northeastern region of the Brazilian Amazon. Despite female bats being more parasitized and recording greater bat fly species richness in the wet season, neither relationship was statistically significant. The pooled network could be divided into 15 compartments with 54 links, and all subnetworks comprised >12 compartments. The total number of links ranged from 27 to 48 (for the dry and wet seasons, respectively), and female and male subnetworks had 44 and 41 links, respectively. Connectance values were very low for the pooled network and for all subnetworks. Our results revealed higher bat fly species richness and abundance in the wet season, whereas specialization and modularity were higher in the dry season. Moreover, the subnetwork for female bats displayed higher specialization and modularity than the male subnetwork. Therefore, both seasonality and host sex contribute in different ways to bat–bat fly network structure. Future studies should consider these factors when evaluating bat–bat fly interaction networks. [ABSTRACT FROM AUTHOR]

Background: The caffeoyl-CoA-O methyltransferase (CCoAOMT) family plays a crucial role in the oxidative methylation of phenolic substances and is involved in various plant processes, including growth, development, and stress response. However, there is a limited understanding of the interactions among CCoAOMT protein members in tea plants. Results: In this study, we identified 10 members of the CsCCoAOMT family in the genome of Camellia sinensis (cultivar 'HuangDan'), characterized by conserved gene structures and motifs. These CsCCoAOMT members were located on six different chromosomes (1, 2, 3, 4, 6, and 14). Based on phylogenetic analysis, CsCCoAOMT can be divided into two groups: I and II. Notably, the CsCCoAOMT members of group Ia are likely to be candidate genes involved in lignin biosynthesis. Moreover, through the yeast two-hybrid (Y2H) assay, we established protein interaction networks for the CsCCoAOMT family, revealing 9 pairs of members with interaction relationships. Conclusions: We identified the CCoAOMT gene family in Camellia sinensis and conducted a comprehensive analysis of their classifications, phylogenetic and synteny relationships, gene structures, protein interactions, tissue-specific expression patterns, and responses to various stresses. Our findings shed light on the evolution and composition of CsCCoAOMT. Notably, the observed interaction among CCoAOMT proteins suggests the potential formation of the O-methyltransferase (OMT) complex during the methylation modification process, expanding our understanding of the functional roles of this gene family in diverse biological processes. [ABSTRACT FROM AUTHOR]

Logical modeling is a powerful tool in biology, offering a system-level understanding of the complex interactions that govern biological processes. A gap that hinders the scalability of logical models is the need to specify the update function of every vertex in the network depending on the status of its predecessors. To address this, we introduce in this paper the concept of strong regulation, where a vertex is only updated to active/inactive if all its predecessors agree in their influences; otherwise, it is set to ambiguous. We explore the interplay between active, inactive, and ambiguous influences in a network. We discuss the existence of phenotype attractors in such networks, where the status of some of the variables is fixed to active/inactive, while the others can have an arbitrary status, including ambiguous. [ABSTRACT FROM AUTHOR]

Participants in mixed-species bird flocks (MSFs) have been shown to associate with species that are similar in body size, diet, and evolutionary history, suggesting that facilitation structures these assemblages. In addition, several studies have suggested that species in MSFs resemble each other in their plumage, but this question has not been systematically investigated for any MSF system. During the nonbreeding season of 2020 and 2021, we sampled 585 MSFs on 14 transects in 2 habitats of Tongbiguang Nature Reserve in western Yunnan Province, China. We performed social network analysis and the Multiple Regression Quadratic Assignment Procedure to evaluate the effect of 4 species traits (body size, overall plumage color, distinctive plumage patterns, and diet) and evolutionary history on species association strength at the whole-MSF and within-MSF levels. All 41 significant relationships showed that species with stronger associations were more similar in their various traits. Body size had the strongest effect on association strength, followed by phylogeny, plumage patterns, and plumage color; diet had the weakest effect. Our results are consistent with the hypotheses that the benefits of associating with phenotypically similar species outweigh the potential costs of interspecific competition, and that trait matching can occur in plumage characteristics, albeit more weakly than in other traits. Several explanations exist as to why similarities in plumage may occur in MSFs, including that they could reduce predators' ability to target phenotypically "odd" individuals. Whether trait matching in plumage occurs through assortative processes in ecological time or is influenced by co-evolution requires further study. [ABSTRACT FROM AUTHOR]

Stingless bees are important pollinators in tropical forests. Yet, we know little about their foraging behavior (e.g., their nutritional requirements or their floral sources visited for resource collection). Many stingless bees not only depend vitally on pollen and nectar for food but also on resin for nest building and/or defense. However, it is unclear whether the large effort devoted to collecting resin as a non‐food resource by certain stingless bees affects their foraging behavior. Therefore, in this study, we analyzed differences in foraging patterns (i.e., foraging activity, proportion of collected resources, and specialization in plants visited) and resource nutritional composition (i.e., sucrose amount in nectar and amino acids in pollen) of seven different stingless bee species (eleven wild colonies) in north‐western Ecuador with a particular focus on the role of resin collection. We found that species with a high resin intake tended to be more active than species with a low resin intake. The foragers per minute invested for pollen collection were similar across all species. Sucrose intake per minute differed between some species but was not affected by increased resin intake. Interestingly, high and low resin collectors partly differed in the plants visited for pollen collection. Pollen amino acid profiles largely, but not completely, overlapped between the two resin collection groups. Our findings show that the foraging patterns and plant choices of stingless bees may vary depending on their resin intake, highlighting the need for more research focusing on resin collection and use by stingless bees. [ABSTRACT FROM AUTHOR]

Beyond abiotic conditions, do population dynamics mostly depend on a species' direct predators, preys and conspecifics? Or can indirect feedback that ripples across the whole community be equally important? Determining where ecological communities sit on the spectrum between these two characterizations requires a metric able to capture the difference between them. Here we show that the spectral radius of a community's interaction matrix provides such a metric, thus a measure of ecological collectivity, which is accessible from imperfect knowledge of biotic interactions and related to observable signatures. This measure of collectivity integrates existing approaches to complexity, interaction structure and indirect interactions. Our work thus provides an original perspective on the question of to what degree communities are more than loose collections of species or simple interaction motifs and explains when pragmatic reductionist approaches ought to suffice or fail when applied to ecological communities. [ABSTRACT FROM AUTHOR]

Amyloid transthyretin (ATTR) amyloidosis caused by transthyretin misfolded into amyloid deposits in nerve and heart is a progressive rare disease. The unknown pathogenesis and the lack of therapy make the 5-year survival prognosis extremely poor. Currently available ATTR drugs can only relieve symptoms and slow down progression, but no drug has demonstrated curable effect for this disease. The growing volume of pharmacological data and large-scale genome and transcriptome data bring new opportunities to find potential new ATTR drugs through computational drug repositioning. We collected the ATTR-related in the disease pathogenesis and differentially expressed (DE) genes from five public databases and Gene Expression Omnibus expression profiles, respectively, then screened drug candidates by a corrected protein–protein network analysis of the ATTR-related genes as well as the drug targets from DrugBank database, and then filtered the drug candidates on the basis of gene expression data perturbed by compounds. We collected 139 and 56 ATTR-related genes from five public databases and transcriptome data, respectively, and performed functional enrichment analysis. We screened out 355 drug candidates based on the proximity to ATTR-related genes in the corrected interactome network, refined by graph neural networks. An Inverted Gene Set Enrichment analysis was further applied to estimate the effect of perturbations on ATTR-related and DE genes. High probability drug candidates were discussed. Drug repositioning using systematic computational processes on an interactome network with transcriptome data were performed to screen out several potential new drug candidates for ATTR. [ABSTRACT FROM AUTHOR]

In the present study, we investigated the effect of habitat heterogeneity, elevation gradient, and phylogenetic distance of host species on the abundance and richness of anuran endoparasites, assuming that parasites follow the distribution of their hosts independently of environmental variation. We collected 192 anurans distributed in three altitude ranges: 100–200 m, 400–500 m, and 700–800 m. We performed discriminant principal component analysis to analyze the interrelationships between environmental heterogeneity and the distribution of parasite and host species in the formation of species groups in each altitude range. We estimated the niche width and parasite overlap, using host species as a variable, and assessed whether parasite abundance is more influenced by historical (distance host phylogeny) or ecological effects in each altitude category and overall. Finally, we use network analyses to understand how interactions between parasites and hosts are formed along the altitude gradient. We found 22 parasite species, and the overall prevalence of infection was 74%. In our study, we did not identify environmental (altitude gradients and heterogeneity) or phylogenetic effects acting on the parasite species diversity. Overall, our results suggest that the parasites are distributed following the dispersal of their hosts and are dispersed among most anuran species. [ABSTRACT FROM AUTHOR]

Aim: As species' ranges shift poleward in response to anthropogenic change, they may lose antagonistic interactions if they move into less diverse communities, fail to interact with novel populations or species effectively, or if ancestral interacting populations or species fail to shift synchronously. We leveraged a poleward range expansion in a tractable insect host–enemy community to uncover mechanisms by which altered antagonistic interactions between native and recipient communities contributed to 'high niche opportunities' (limited biotic resistance) for a range‐expanding insect. Location: North America, Pacific Northwest. Methods: We created quantitative insect host–enemy interaction networks by sampling oak gall wasps on 400 trees of a dominant oak species in the native and expanded range of a range‐expanding gall wasp species. We compared host–enemy network structure between regions. We measured traits (phenology, morphology) of galls and interacting parasitoids, predicting greater trait divergence in the expanded range. We measured function relating to host control and explored if altered interactions and traits contributed to reduced function, or biotic resistance. Results: Interaction networks had fewer species in the expanded range and lower complementarity of parasitoid assemblages among host species. While networks were more generalized, interactions with the range‐expanding species were more specialized in the expanded range. Specialist enemies effectively tracked the range‐expanding host, and there was reduced apparent competition with co‐occurring hosts by shared generalist enemies. Phenological divergence of enemy assemblages interacting with the range‐expanding and co‐occurring hosts was greater in the expanded range, potentially contributing to weak apparent competition. Biotic resistance was lower in the expanded range, where fewer parasitoids emerged from galls of the range‐expanding host. Main Conclusions: Changes in interactions with generalist enemies created high niche opportunities, and limited biotic resistance, suggesting weak apparent competition may be a mechanism of enemy release for range‐expanding insects embedded within generalist enemy networks. [ABSTRACT FROM AUTHOR]

The current biodiversity crisis requires efficient approaches to address the ongoing impoverishment of natural communities and the depletion of ecosystem services and functions. In this sense, identifying key species that promote the functioning of ecological processes can be strategic to guide actions aiming at the conservation and restoration of biodiversity. Node‐level metrics in interaction networks can be helpful to identify those key species, as they measure the role each species plays in organizing the interactions. Moreover, ecological correlates of species structural roles may vary between local and global networks of interactions, reflecting distinct mechanisms acting at different spatial scales. By studying local seed dispersal networks and one global meta‐network combining those local networks, Moulatlet et al. identified the most important traits explaining bird species centrality at varying spatial scales. They found that body mass was the main trait explaining centrality at the local scale, whereas range size was the main predictor of species centrality at the global scale. In this contribution, besides assessing local interaction networks, Moulatlet et al. adopt a biogeographical perspective to seed dispersal systems, extending our knowledge about the possible mechanisms that underlie the organization of interacting assemblages when changing the spatial scale of observation. Future efforts on this field could include an intermediate scale, comprising the level of metacommunities, shedding light on the interplay between local and spatial processes, both embedded in biogeographical realms, when determining the organization of interactions and the ecological correlates of species roles. [ABSTRACT FROM AUTHOR]

Aim: Most biodiversity studies have considered species to be isolated entities, neglecting the fact that their biotic interactions and spatial variation are fundamental to their persistence across elevational gradients. Here, using a standardized sampling methodology, we evaluated how and why the composition of flower–visitor interactions (i.e. beta diversity) varies over an extensive elevational gradient. Specifically, we aimed to identify which biotic (species turnover) and abiotic factors (temperature, precipitation and primary productivity) inherent to elevational gradients can explain the distribution of floral visitor–plant interactions. Location: Mexican Transition Zone. Taxon: Angiosperms, Hymenoptera, Lepidoptera, Diptera, Hemiptera and Coleoptera. Methods: We sampled ecological interactions between floral visitors and flowering plants at 10 sites along an elevational gradient from 4 to 3425 m.a.s.l. We measured the additive partitioning of the beta diversity of species interactions and used generalized dissimilarity modelling to assess how spatial and environmental factors can explain the observed dissimilarity. Results: We found that the composition of interactions between floral visitors and plant species differs from lowlands to highlands mainly due to differences in temperature across the studied elevation gradient, rather than geographical distance or other environmental factors (i.e. mean annual precipitation and net primary productivity). We also observed that the main component of the beta diversity of interactions was interaction turnover driven by the turnover of both plants and floral visitors along the elevation gradient studied, which may be influenced by both temperature and the biogeographical affinity of biotas. Main Conclusions: We conclude that environmental filters play a crucial role in the establishment of novel interactions, as temperature can filter species and impact the behaviour and traits of floral visitors and plants across an elevational gradient. These findings underscore the importance of considering the role of abiotic factors in predicting and explaining the distribution of species interactions across different elevational gradients. [ABSTRACT FROM AUTHOR]

We present a framework called the Reasoning Engine, which implements Satisfiability Modulo Theories (SMT)-based methods within a unified computational environment to address diverse biological analysis problems. The Reasoning Engine was used to reproduce results from key scientific studies, as well as supporting new research in stem cell biology. The framework utilizes an intermediate language for encoding partially specified discrete dynamical systems, which bridges the gap between high-level domain-specific languages and low-level SMT solvers. We provide this framework as open source together with various biological case studies, illustrating the synthesis, enumeration, optimization, and reasoning over models consistent with experimental observations to reveal novel biological insights. [ABSTRACT FROM AUTHOR]

Frugivory and seed dispersal by fish is an important mutualistic interaction in complex and species-rich tropical rivers. The local ecological knowledge (LEK) held by fishers can provide new information on relationships between fishes and plants in less studied rivers. This study aims to investigate the feeding interactions between frugivorous fish and plants through interaction networks based on the fishers' LEK in three rivers in the Brazilian Amazon (Negro, Tapajós and Tocantins). A total of 418 fishers were interviewed in 24 communities (eight in each river). The studied fishes were tambaqui (Colossoma macropomum), matrinxã (Brycon spp.), pacu (Myloplus spp.), pacu manteiga (Mylossoma duriventre), pirapitinga (Piaractus brachypomus), and jaraqui (Semaprochilodus spp.). The interviewed fishers cited a total of 92 plants consumed by the six frugivorous fishes in the three rivers. The interaction networks showed a higher nestedness in the Tocantins, greater connectance and modularity in the Tapajós and more specialization in the Negro, where the protected areas may have contributed to a more complex and specialized interaction network. The more nested network in the Tocantins River indicated the loss of specialized interactions in disturbed communities. The Tapajós River network showed the highest number of interactions between fish and plants, but this river has been threatened by environmental changes. Fishers' LEK associated to network analyses can advance our understanding on ecological interactions. This approach can be also useful to evaluate and mitigate ecological effects from anthropic changes in the Amazon and other high diverse tropical rivers. [ABSTRACT FROM AUTHOR]

Arbuscular mycorrhizas are one of the most frequent mutualisms in terrestrial ecosystems. Although studies on plant mutualistic interaction networks suggest that they may leave their imprint on plant community structure and dynamics, this has not been explicitly assessed. Thus, in the context of plant‐fungi interactions, studies explicitly linking plant‐mycorrhizal fungi interaction networks with key ecological functions of plant communities, such as recruitment, are lacking.In this study, we analyse, in two Mediterranean forest communities of southern Iberian Peninsula, how plant‐arbuscular mycorrhizal fungi (AMF) networks modulate plant‐plant recruitment interaction networks. We use a new approach integrating plant‐AMF and plant recruitment networks into a single multilayer structure. We also develop a new metric (Interlayer Node Neighbourhood Integration, INNI) to explore the impact of a given node on the structure across layers.The similarity of plant species in their AMF communities is positively related to the observed frequency of recruitment interactions in the field. Results reveal that properties of plant‐AMF networks, such as plant degree and centrality, can explain about the properties of plant recruitment network, such as in‐ and out‐degree (i.e. sapling bank and canopy service) and its modular structure. However, these relationships differed between the two forest communities. Finally, we identify particular AMF that contribute to integrate the neighbourhood of recruitment interactions between plants.This multilayer network approach is useful to explore the role of plant‐AMF interactions on recruitment, a key ecosystem function enhanced by fungi. Results provide evidence that the complex structure of plant‐AMF interactions impacts functional and structurally plant‐plant interactions, which in turn may potentially influence plant community dynamics, through their effects on the structure of the recruitment network. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

It is not clear if mature secondary growth coniferous forests can support similar pollinator communities as old growth coniferous forests, or how active management (e.g., retention forestry) in mature secondary growth forests may affect pollinator communities. We compare the native bee community and plant‐bee interaction networks of old growth, naturally regenerating and actively managed (retention forestry) mature secondary growth forests of similar stand age. Old growth forests had a higher bee species richness and Shannon's diversity index, but not Simpson's diversity index, than both actively managed and naturally regenerating mature secondary forests. Forest type (old‐growth, naturally regenerating mature secondary growth, and actively managed mature secondary growth) had a significant effect on bee community composition. Redwood forest bee‐plant interaction networks were small in size and had lower complexity than expected and few connector species. While studies suggest that small‐scale timber harvest may increase bee biodiversity in the short‐term in other coniferous forest habitats, our study suggests that there may be long‐term negative effects of clear‐cutting that lower bee biodiversity in mature secondary growth forests as compared to mature old‐growth forests. [ABSTRACT FROM AUTHOR]

Flower‐vising bats are important components of tropical pollinator communities, yet little is known about the structure of their pollination networks and how resource availability through time (seasons) and space (habitat heterogeneity) affects the extent to which bats interact with plants within a community‐wide context. This information is key for the conservation of threatened nectarivore species, such as the Cerrado‐endemic Lonchophylla dekeyseri, for which data on its specialization on floral‐resources is scarce.Within a seasonal and heterogeneous savanna in the central Brazilian Cerrado, we performed a year‐round assessment of an inclusive assemblage of flower‐visiting bats (both nectarivores and other guilds that can also feed on nectar) within a savanna‐edge‐forest gradient, the phenological trends and spatial distribution of bat and their resource plants, and the resultant temporal and spatial interaction networks between bats and plants in order to associate network structure to resource availability.Clear spatiotemporal trends emerged in the community. Nectarivores dominated the flower‐visiting niche outside forests and were prolific floral visitors, resulting in networks with lower specialization and modularity. These bats diverged into savanna foragers active during the wet season and the wet‐dry transition, and edge foragers active mostly during the dry season. The latter group encompassed L. dekeyseri, which visited mostly Bauhinia species. Frugivores took over as main floral visitors within forests, as well as during peak dry season, when fewer fruits were available, resulting in more specialized and modular networks.Our work shows that the turnover of floral resources across seasons and vegetation types has a defining role in bat–plant interactions and relates to network structure, as bat trophic guilds interact with plants in distinct habitats and times of the year. Frugivores dominate the flower‐visiting niche in certain temporal and spatial subsets of the network, which calls for the inclusion of this guild in future studies. Moreover, the high visitation to Bauhinia species by L. dekeyseri during the dry season might reduce competition with other nectarivores and is relevant to the management of the species, although more data is needed on its resource consumption on a larger time frame and across its geographic range. [ABSTRACT FROM AUTHOR]

Moniliasis caused by the fungus Moniliophthora roreri is one of the most destructive cacao diseases in tropical America. In 2021, the presence of the pathogen was confirmed in cacao plantations in Brazil. This is the first proteomic study of the M. roreri protein profile of ungerminated spores and mycelium compared by 2D SDS‐PAGE (Two‐dimensional gel electrophoresis) associated with mass spectrometry. A total of 446 spots were detected on ungerminated spores gels and 402 spots on M. roreri mycelial gels. A total of 29 proteins were identified from the ungerminated spores, 21 of them were exclusive, and 53 were identified in the mycelium, 16 of them were exclusive. Most of the identified proteins at both development stages were categorized as being involved in metabolic processes, reduction/oxidation processes, and protein synthesis and folding. The interaction networks observed expand the known interactions of these proteins, resulting in eight functional clusters for proteins identified in ungerminated spores and seven clusters for mycelial proteins. In addition, a biological model of ungerminated spores and mycelium with cell location of proteins was constructed. The results contribute to a better understanding of the metabolic mechanisms of M. roreri during dormancy and vegetative development, which can support future studies for strategies to control moniliasis. [ABSTRACT FROM AUTHOR]

Plant‐pollinator interactions are fundamental to ecosystem functioning; however, the role that succession and phenology have on these interactions is poorly understood, particularly in endangered tropical ecosystems. In highly diverse ecosystems such as tropical dry forests (TDF), variation in water and food availability determines the life cycles of animal pollinators. Therefore, understanding patterns of flowering phenology and plant‐pollinator interactions across seasons in successional environments is key to maintaining and restoring TDF.We analysed the functional dynamics of plant‐floral visitor interactions at the community level across a successional gradient in a Mexican TDF. We evaluated changes in the diversity of blooming plant species and floral visitors, phenological patterns, interaction network metrics and beta diversity among early, intermediate and late successional stages, between dry and rainy seasons.We found a higher diversity of blooming plant species and a higher richness of animal species in the intermediate and late successional stages. Peak abundance of floral visitors overlapped with flowering peaks in the late successional stages, but this was not consistently the case in the early and intermediate stages. Plant‐floral visitors networks differed in structure according to successional stage and season, but specialisation metrics were higher in late successional stages. Interaction networks were more dissimilar between dry and rainy seasons within successional stages than within seasons between successional stages, suggesting connectivity across successional sites during each season. In addition, closely related plant species do not share the same pollination systems in any successional stage.Synthesis. Our results showed that plant‐floral visitor interactions are dynamic and vary with flowering phenology and with successional changes in plant and animal diversity. Plant‐floral visitor interactions were more diverse and specialised in the late successional stages. In the rainy season, differences in network structure among successional stages are due to interaction rewiring, while in the dry season, it is caused by species turnover. Our results demonstrate that seasonality plays a key role in community diversity and network structure and highlight the importance of conserving mature forests to ensure the maintenance of critical pollination interactions across all successional stages. [ABSTRACT FROM AUTHOR]

Detailed understanding of the mechanisms enabling or limiting the impacts of invasive generalist predators is needed. Harmonia axyridis is an invasive generalist coccinellid predator that may have destabilised coccinellid communities worldwide and is an excellent candidate for investigating invasion dynamics.We evaluated four hypotheses: (1) Nine years after being detected in Central Brazil, Ha. axyridis has dominated the coccinellid community. This is facilitated by (2) its broader aphid prey range than the other aphidophagous coccinellids, (3) its superiority as an asymmetrical intraguild predator, and (4) the invasibility of the present coccinellid community.We sampled the invertebrate communities associated with six organic vegetable farms in Brazil during 2017 and 2018, conducted a feeding trial to measure prey niche breadth and overlap, and estimated intra‐ and interspecific interaction strengths corresponding to first‐order Lotka‐Volterra parameters to evaluate the strength of intraguild predation and create a community matrix.We found (1) Ha. axyridis comprised ≤8.3% of the coccinellid community. (2) Hi. convergens had the broadest prey niche and dominated the prey niche of Ha. axyridis. (3) We could not determine from the population data if Ha. axyridis was the dominant intraguild predator because its density was too low and constant. (4) The community matrix indicated that the present‐day coccinellid community was stable.We conclude Ha. axyridis has not become invasive in Central Brazil, in part because it does not have the broadest prey niche breadth and the present coccinellid community is stable to the present perturbation of Ha. axyridis. [ABSTRACT FROM AUTHOR]

Introduction: Frugivory is a pivotal ecological process for the structure and regeneration of forests. In the tropics, where the diversity of plants and frugivorous animals is high, interspecific relationships in the interaction networks are complex and need study. Objective: To identify ecologically important plant species in two interaction networks, and the role of functional fruit traits in those interactions in a dry forest. Methods: We collected 10 fruits per plant from 10 plants of each species of interest in a Colombian dry forest, we calculated the Plant Importance Index based on the bird and mammal frugivores relevance for network structure. This relevance is directly related to the animal's potential as effective seed dispersers. We used generalized linear models to estimate the effect of fruit size, color, stratum, and type of pulp, on the index. Results: The most important plants are species of the genera Miconia, Ficus, Cecropia, Bursera, Casearia and Trichilia, also identified as important resources for tropical frugivores in other studies. Plants with small, red, and fleshy fruits are the best for seed dispersers. The plant importance index has a high variation; this suggests that the set of frugivore species benefited by each plant species has a differential contribution to the ecological processes derived from seed dispersal. Conclusions: Restoration programs for this kind of tropical dry forest should include a variety of plants, including species with small, red, and fleshy fruits. [ABSTRACT FROM AUTHOR]

Traits mediate mutualistic and antagonistic interactions between plants and animals, and should thus be useful for predicting trophic species interactions. Studies to date have examined the importance of morphological trait matching for plant–animal interactions, but have rarely explored the extent to which these interactions are shaped by matching between energetic provisions of plants and energetic demands of animals.We tested whether energetic and/or morphological trait matching shapes interactions between Protea plant species and their interacting animal mutualists and antagonists in the Cape Floristic Region, South Africa.We recorded interactions between 22 Protea species, pollinating insects and vertebrates as well as seed predators (endophagous insect larvae in protea cones) at 21 study sites. To relate species interactions to matching trait pairs, we measured key morphological traits (shape and size of flower heads and seed cones, and mouth part length as well as body length) and quantified the animals' energetic demands (metabolic rate) together with the plants' energetic provisions (nectar sugar amount, seed‐to‐cone mass ratio). We calculated log ratios of both energetic and morphological traits between animals and plants as predictor variables for the number of observed interactions between Protea species and their animal interaction partners.For both mutualistic and antagonistic interactions, we found significant effects of morphological and energetic trait ratios on the interactions between plants and animals. Trait ratios accounted for 11% to 22% of variation in species interactions. Consistent with energetic trait matching, we found a hump‐shaped relationship between interaction frequency and log ratios of energetic traits of animals and plants, indicating that interactions were most frequent at intermediate log ratios between energetic demand and provision. Effects of morphological trait ratios on interactions were statistically supported in most cases, but were variable in the magnitude and shape of the predicted relationships.Across animal taxa and interaction types, energetic traits had more consistent effects on interactions between plants and animals than morphological traits. This suggests that energy can function as an important interaction currency and facilitate the understanding and prediction of trophic species interactions. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

According to analytical studies of environmental impact assessment methodology, proposed nationally and internationally, it is of fundamental importance to incorporate a set of basic criteria in the current methods of analysis. The methodologies must be flexible, applicable at any stage of the planning and development process and must be constantly revised in the light of the results obtained and the experience gained. They must be suitable for an integrated, comprehensive, systematic and interdisciplinary analysis of the environment and its many components. Basically, the following methodological approaches have been developed for environmental impact assessment: Ad hoc methodologies; Check Lists; Interaction Matrices; Interaction Networks; Quantity Methodologies; Simulation Models; Overlay Maps; Scenario Projection, others. [ABSTRACT FROM AUTHOR]

Interaction prediction is a crucial task in the Social Internet of Things (SIoT), serving diverse applications including social network analysis and recommendation systems. However, the dynamic nature of items, users, and their interactions over time poses challenges in effectively capturing and analyzing these changes. Existing interaction prediction models often overlook the temporal aspect and lack the ability to model multi-relational user-item interactions over time. To address these limitations, in this paper, we propose a S tructure, F acticity, and T emporal information preservation e mbedding model (SFTe) to predict future interaction. Our model leverages the advantages of Temporal Knowledge Graphs (TKGs) that can capture both the multi-relations and evolution. We begin by modeling user-item interactions over time by constructing a Temporal Interaction Knowledge Graph (TIKG). We then employ Structure Embedding (SE), Facticity Embedding (FE), and Temporal Embedding (TE) to capture topological structure, facticity consistency, and temporal dependence, respectively. In SE, we focus on preserving the first-order relationships to capture the topological structure of TIKG. In the FE component, given the distinct nature of SIoT, we introduce an attention mechanism to capture the effect of entities with the same additional information for generating subgraph embeddings. Lastly, TE utilizes recurrent neural networks to model the temporal dependencies among subgraphs and capture the evolving dynamics of the interactions over time. Experimental results on standard future interaction prediction demonstrate the superiority of the SFTe model compared with the state-of-the-art methods. Our model effectively addresses the challenges of time-aware interaction prediction, showcasing the potential of TKGs to enhance prediction performance. [ABSTRACT FROM AUTHOR]

Keywords: arbuscular mycorrhizal fungi; Glomeromycotina; host-shift speciation; interaction networks; metabarcoding; mycoheterotrophy; phylogenetic signal; specialization EN arbuscular mycorrhizal fungi Glomeromycotina host-shift speciation interaction networks metabarcoding mycoheterotrophy phylogenetic signal specialization 836 841 6 07/04/22 20220801 NES 220801 Acknowledgements We thank Hiroaki Yamashita, Takaomi Sugimoto, and Syozi Hyodo for their fieldwork assistance and Makoto Taniguchi, Takako Shizuka, and Michiko Ishida for their technical assistance. S7 Associations between mycoheterotrophic plant species and VTXs.Methods S1 Methods used to investigate phylogenetic signals between three Oxygyne species and their mycorrhizal communities. Mycorrhizal symbiosis occurs most commonly between plants and arbuscular mycorrhizal fungi (AMFs), and I c i . 80% of land plant species establish mycorrhizas with members of Glomeromycotina (Wang & Qiu, 2006; Smith & Read, 2008; Spatafora I et al i ., 2016). Mycorrhizas constitute diffuse symbioses in which individual plants associate with multiple fungi simultaneously, and individual fungi associate with multiple plants simultaneously (Smith & Read, 2008; van der Heijden I et al i ., 2015). [Extracted from the article]

Since its inception, biodiversity has largely been understood as species diversity and assessed as such. Interactions among species or functional groups are gradually becoming part of an expanded concept of biodiversity. As a case study of the development of a research program in biodiversity, we summarize our multi-decade studies on interactions of Asteraceae and flowerhead-feeding insects in Brazil. Initially, host species were treated as independent replicates in order to assess the local and turnover components of their herbivore diversity. Research then expanded into sampling entire interactive communities of host plants and their associated herbivores in different localities and regions, enabling new research lines to be pursued. Interaction diversity could be assessed and factored into spatial and among-host components, suggesting a new field of interaction geography. Second, host specialization, a key component of interaction diversity, was reframed considering simultaneously relatedness and local availability of plant hosts. Third, with the influence of complex network theory, community-wide species interactions were probed for topological patterns. Having identified the modular structure of these plant-herbivore systems, later we demonstrated that they fit a compound hierarchical topology, in which interactions are nested within large-scale modules. In a brief survey of research funded by Fapesp, especially within the Biota-Fapesp program, we highlight several lines of internationally recognized research on interaction diversity, notably on plant-frugivore and plant-pollinator interactions, together with new theoretical models. The interplay of field studies with new theoretical and analytical approaches has established interaction diversity as an essential component for monitoring, conserving and restoring biodiversity in its broader sense. [ABSTRACT FROM AUTHOR]

The composition and richness of herbivore and plant assemblages change along climatic gradients, but knowledge about associated shifts in specialization is scarce and lacks controlling for the abundance and phylogeny of interaction partners. Thus, we aimed to test whether the specialization of phytophagous insects in insect‐plant interaction networks decreases toward cold habitats as predicted by the 'altitude niche‐breadth hypothesis' to forecast possible consequences of interaction rewiring under climate change. We used a non‐invasive, standardized metabarcoding approach to reconstruct dietary relationships of Orthoptera species as a major insect herbivore taxon along a broad temperature gradient (~12°C) in Southern Germany. Based on Orthoptera surveys, feeding observations, collection of fecal pellets from >3,000 individuals of 54 species, and parallel vegetation surveys on 41 grassland sites, we quantified plant resource availability and its use by herbivores. Herbivore assemblages were richer in species and individuals at sites with high summer temperatures, while plant richness peaked at intermediate temperatures. Corresponding interaction networks were most specialized in warm habitats. Considering phylogenetic relationships of plant resources, however, the specialization pattern was not linear but peaked at intermediate temperatures, mediated by herbivores feeding on a narrow range of phylogenetically related resources. Our study provides empirical evidence of resource specialization of insect herbivores along a climatic gradient, demonstrating that resource phylogeny, availability, and temperature interactively shape the specialization of herbivore assemblages. Instead of low specialization levels only in cold, harsh habitats, our results suggest increased generalist feeding due to intraspecific changes and compositional differences at both ends of the microclimatic gradient. We conclude that this nonlinear change of phylogeny‐based resource specialization questions predictions derived from the 'altitude‐niche breadth hypothesis' and highlights the currently limited understanding of how plant‐herbivore interactions will change under future climatic conditions. [ABSTRACT FROM AUTHOR]

Simple Summary: Species interactions are one of the main factors affecting community assembly, yet the role of such interactions remains mostly unknown. Here, we investigated roles of potential species associations in fish community assembly in the Qiupu River, China. Our results suggested that potential species associations might have been underestimated in stream fish community assembly. The contribution of potential species associations to fish community assembly can be reflected by interaction network structures. Omnivorous species play an important role in maintaining network structure as they may have more associations with other species. This study highlights the importance of capturing species associations in river ecosystems across different geographical and environmental settings. Environmental filtering, spatial factors and species interactions are fundamental ecological mechanisms for community organisation, yet the role of such interactions across different environmental and spatial settings remains mostly unknown. In this study, we investigated fish community organisation scenarios and seasonal species-to-species associations potentially reflecting biotic associations along the Qiupu River (China). Based on a latent variable approach and a tree-based method, we compared the relative contribution of the abiotic environment, spatial covariates and potential species associations for variation in the community structure, and assessed whether different assembly scenarios were modulated by concomitant changes in the interaction network structure of fish communities across seasons. We found that potential species associations might have been underestimated in community-based assessments of stream fish. Omnivore species, since they have more associations with other species, were found to be key components sustaining fish interaction networks across different stream orders. Hence, we suggest that species interactions, such as predation and competition, likely played a key role in community structure. For instance, indices accounting for network structure, such as connectance and nestedness, were strongly correlated with the unexplained residuals from our latent variable approach, thereby re-emphasising that biotic signals, potentially reflecting species interactions, may be of primary importance in determining stream fish communities across seasons. Overall, our findings indicate that interaction network structures are a powerful tool to reflect the contribution of potential species associations to community assembly. From an applied perspective, this study should encourage freshwater ecologists to empirically capture and manage biotic constraints in stream ecosystems across different geographical and environmental settings, especially in the context of the ever-increasing impacts of human-induced local extinction debts and species invasions. [ABSTRACT FROM AUTHOR]

Glycosaminoglycans (GAGs) are complex linear polysaccharides, which are covalently attached to core proteins (except for hyaluronan) to form proteoglycans. They play key roles in the organization of the extracellular matrix, and at the cell surface where they contribute to the regulation of cell signaling and of cell adhesion. To explore the mechanisms and pathways underlying their functions, we have generated an expanded dataset of 4,290 interactions corresponding to 3,464 unique GAG-binding proteins, four times more than the first version of the GAG interactome (Vallet, Clerc, and Ricard-Blum. J Histochem Cytochem 69: 93-104, 2021). The increased size of the GAG network is mostly due to the addition of GAG-binding proteins captured from cell lysates and biological fluids by affinity chromatography and identified by mass spectrometry. We review here the interaction repertoire of natural GAGs and of synthetic sulfated hyaluronan, the specificity and molecular functions of GAG-binding proteins, and the biological processes and pathways they are involved in. This dataset is also used to investigate the differences between proteins binding to iduronic acid-containing GAGs (dermatan sulfate and heparin/heparan sulfate) and those interacting with GAGs lacking iduronic acid (chondroitin sulfate, hyaluronan, and keratan sulfate). [ABSTRACT FROM AUTHOR]

Understanding how ecosystem functioning is impacted by global change drivers is a central topic in ecology and conservation science. We need to assess not only how environmental change affects species richness, but also how the distribution of functional traits (i.e. functional diversity) mediate the relationship between species richness and ecosystem functioning. However, most evidence about the capacity of functional diversity to explain ecosystem functioning has been developed from studies conducted at a single spatial scale. Here, we explore theory, expectations and evidence for why and how species richness and functional diversity relationships vary with spatial scale. Despite the importance of accounting for spatial processes at multiple scales, we show that most studies of the species richness–functional diversity relationship focus on single scale analyses that ignore spatial context. Thus, we discuss the need to establish a spatially explicit, multi‐scale framework for understanding the relationship between species richness and functional diversity. As a starting point to developing such a framework, we detail some expected trajectories and mechanisms by which the diversity of species and functional traits may change across increasing spatial scales. We also explore what is known about two important gaps in the literature about this relationship: 1) the influence of spatial autocorrelation on community assembly processes and 2) the variation in the structure of species interactions across spatial extents. We present some key challenges that could be addressed by integrating approaches from community and landscape ecology. This information will help improve our understanding of the relative influence of local and large‐scale processes on community structure, while providing a foundation for improving biodiversity monitoring, policy and ecosystem function based conservation. [ABSTRACT FROM AUTHOR]

Mammals are globally in decline, with habitat loss a primary driver. There are also human–wildlife conflicts, such as elephants destroying crops, which results in the ranges of many large mammal species being fenced off. Yet, how this activity affects functional associations of insects with large mammals has received little attention. Previous work suggests a generalised association with large mammals, as well as a strong response to landscape transformation.Here we assess how well dung beetle diversity tracks large African mammal herbivore diversity across a forestry plantation land use gradient by assessing how dung beetle taxonomic, phylogenetic and functional richness compares to large mammal diversity. We also determine how land use intensity affects dung beetle‐to‐mammal interaction networks.Dung beetles responded more intensively to an array of large mammals than to differences in land use intensity. Beetles also showed a strong preference for specific mammalian dung, with elephant dung being the most important factor for maintaining local dung beetle diversity.Large mammal abundance, functional diversity, dung beetle phylogenetic richness and number of realised mammal‐to‐dung beetle interactions were highest in the protected area. Land use intensity categories had distinct mammal and dung beetle assemblages. Transformed areas also have conservation value but provided that there is functional connectivity between remnant vegetation within the modified landscapes.Synthesis and applications. The loss of any native large mammal, especially African elephants, from transformed landscapes is likely to lead to a decline in biodiversity. This suggests that protected areas are essential for the conservation of native biodiversity and its interactions, while well‐designed and managed transformed areas can have additional conservation value. African conservation managers and landowners should be encouraged to maintain a diversity of large mammals on their properties to maintain functional diversity and ultimately ecological resilience. [ABSTRACT FROM AUTHOR]

1. Urban areas can host speciose bee communities due partially to the species‐rich combination of both native and alien plant species found in these landscapes. However, in intensively‐constructed zones, it could be expected to record a low plant diversity used by bees because of the high proportion of paved surfaces in these areas. 2. We investigated the influence of urbanisation on the cavity‐nesting bee‐plant community and interaction network structures in a medium‐sized city. The floral diversity used by nesting females in cell provisioning was retrieved from the pollen content obtained from trap‐nests collected in 11 sites located in an urban landscape gradient. 3. Eighty pollen types belonging to 20 families were identified in the 155 pollen samples analysed. At least seven alien plant species were identified in samples from all sampling points. The landscape analysis revealed a positive influence of the proportion of green areas on the pollen type richness, although the null model was also selected as best model. Likewise, all network metrics but connectance were not influenced by any of the landscape variables. 4. Our findings demonstrated that notwithstanding the sampling sites the floral diversity used by bees and the alien pollen type richness were similar. Likewise, the bee‐plant networks were modular, asymmetric, and highly specialised. The positive adaptation that cavity‐nesting bee species present in urban environments and the presence of bee species that can explore a diverse flora may indicate that the local variation in the landscape had little influence on their interactions with plants. [ABSTRACT FROM AUTHOR]

Simple Summary: Breast cancer involves changes in the healthy cells of the breast resulting in rapid and abnormal division of cells that later spread to other parts of the body through the process of metastasis, which involves epithelial mesenchymal transition (EMT). Ion channels play a significant role in the switch from epithelial to mesenchymal transition through their contributions to cellular motility, cell volume regulation and cell cycle progression. Comprehensive computational analyses were performed to understand the role of ion channels in tumor/metastatic samples of breast cancer and their correlation with EMT. Uncontrolled growth of breast cells due to altered gene expression is a key feature of breast cancer. Alterations in the expression of ion channels lead to variations in cellular activities, thus contributing to attributes of cancer hallmarks. Changes in the expression levels of ion channels were observed as a consequence of EMT. Additionally, ion channels were reported in the activation of EMT and maintenance of a mesenchymal phenotype. Here, to identify altered ion channels in breast cancer patients, differential gene expression and weighted gene co-expression network analyses were performed using transcriptomic data. Protein–protein interactions network analysis was carried out to determine the ion channels interacting with hub EMT-related genes in breast cancer. Thirty-two ion channels were found interacting with twenty-six hub EMT-related genes. The identified ion channels were further correlated with EMT scores, indicating mesenchymal phenotype. Further, the pathway map was generated to represent a snapshot of deregulated cellular processes by altered ion channels and EMT-related genes. Kaplan–Meier five-year survival analysis and Cox regressions indicated the expression of CACNA1B, ANO6, TRPV3, VDAC1 and VDAC2 to be potentially associated with poor survival. Deregulated ion channels correlate with EMT-related genes and have a crucial role in breast cancer-associated tumorigenesis. Most likely, they are potential candidates for the determination of prognosis in patients with breast cancer. [ABSTRACT FROM AUTHOR]

Interaction network structure reflects the ecological mechanisms acting within biological communities, which are affected by environmental conditions. In tropical forests, higher precipitation usually increases fruit production, which may lead frugivores to increase specialization, resulting in more modular and less nested animal–plant networks. In these ecosystems, El Niño is a major driver of precipitation, but we still lack knowledge of how species interactions change under this influence. To understand bat–plant network structure during an extreme El Niño‐Southern Oscillation event, we determined the links between plantivorous bat species and the plants they consume by DNA barcoding seeds and pulp in bat faeces. These interactions were recorded in the dry forest and rainforest of Costa Rica, during the dry and the wet seasons of an extreme El Niño year. From these we constructed seasonal and whole‐year bat–plant networks and analysed their structures and dissimilarities. In general, networks had low nestedness, had high modularity, and were dominated by one large compartment which included most species and interactions. Contrary to our expectations, networks were less nested and more modular in drier conditions, both in the comparison between forest types and between seasons. We suggest that increased competition, when resources are scarce during drier seasons and habitats, lead to higher resource partitioning among bats and thus higher modularity. Moreover, we have found similar network structures between dry and rainforests during El Niño and non‐El Niño years. Finally, most interaction dissimilarity among networks occurred due to interaction rewiring among species, potentially driven by seasonal changes in resource availability. [ABSTRACT FROM AUTHOR]

Approximately 20,000 species of flowering plant offer mainly pollen to their pollinators, generally bees. Stamen dimorphism, a floral trait commonly present in some pollen flowers, is thought to be associated with exclusive pollen provision for highly effective bee pollinators. Notwithstanding, little is known about how stamen dimorphism is related to other floral morphological traits and, consequently, plant–pollinator interactions at the community scale. Here we investigated the relationship between stamen dimorphism and other floral morphological traits, as well as the interactions with pollinators in plants of Melastomataceae.We characterized each plant species as stamen dimorphic or stamen isomorphic according to differences in size and shape between stamen sets. Data on interactions between the plants and their bee pollinators were analysed as quantitative bipartite networks.We found that petal and style size and shape were correlated to stamen dimorphism. Stamen dimorphic species present larger flowers and less variable style shapes than stamen isomorphic species. Furthermore, stamen dimorphism is associated with higher richness of visiting bees, i.e. higher ecological generalization.During the evolutionary history of Melastomataceae, the dependence on pollinators for fruit set has possibly favoured the evolution of larger flowers with dimorphic stamens, which in turn are able to make use of a larger spectrum of pollen‐collecting bees, leading to ecological generalization. [ABSTRACT FROM AUTHOR]

Mesenchymal stem cells are a continually expanding area in research and clinical applications. Their usefulness and capacity to differentiate into various cells, particularly neural types, has driven the research area for several years. Neural differentiation has considerable usefulness. There are several successful differentiation techniques of mesenchymal stem cells that employ the use of small molecules, growth factors and commercially available kits and supplements. Phenotyping, molecular biology, genomics and proteomics investigation revealed a wealth of data about these cells during neurogenic differentiation. However, there remain large gaps in the knowledge base, particularly related to cytokines and how their role, drive mechanisms and the downstream signalling processes change with their varied expression throughout the differentiation process. In this study, adult mesenchymal stem cells were induced with neurogenic differentiation media, the cellular changes monitored by live-cell microscopy and the changes in cytokine expression in the intracellular region, secretion into the media and in the extracellular vesicle cargo were examined and analysed bioinformatically. Through this analysis, the up-regulation of key cytokines was revealed, and several neuroprotective and neurotrophic roles were displayed. Statistically significant molecules IFN-G, IL1B, IL6, TNF-A, have roles in astrocyte development. Furthermore, the cytokine bioinformatics suggests the Janus Kinase/Signal Transducer and Activator of Transcription (JAK/STAT) pathway is upregulated, supporting differentiation toward an astroglial lineage. [ABSTRACT FROM AUTHOR]

Understanding the dynamics of larval habitat utilization by mosquito communities is crucial for the design of efficient environmental control strategies. The authors investigated the structure of mosquito communities found at hotel compounds in Zanzibar, networks of mosquito interactions with larval habitats and robustness of mosquito communities to elimination of larval habitats. A total of 23 698 mosquitoes comprising 26 species in six genera were found. Aedes aegypti (n = 16 207), Aedes bromeliae/Aedes lillie (n = 1340), Culex quinquefasciatus (n = 1300) and Eretmapodites quinquevitattus (n = 659) were the most dominant species. Ecological network analyses revealed the presence of dominant, larval habitat generalist species (e.g., A. aegypti), exploiting virtually all types of water holding containers and few larval habitat specialist species (e.g., Aedes natalensis, Orthopodomyia spp). Simulations of mosquito community robustness to systematic elimination of larval habitats indicate that mosquito populations are highly sensitive to elimination of larval habitats sustaining higher mosquito species diversity. This study provides insights on potential foci of future mosquito‐borne arboviral disease outbreaks in Zanzibar and underscores the need for detailed knowledge on the ecological function of larval habitats for effective mosquito control by larval sources management. [ABSTRACT FROM AUTHOR]

In most macaques, females are philopatric and males migrate from their natal ranges, which results in pronounced divergence of mitochondrial genomes within and among species. We therefore predicted that some nuclear genes would have to acquire compensatory mutations to preserve compatibility with diverged interaction partners from the mitochondria. We additionally expected that these sex-differences would have distinctive effects on gene flow in the X and autosomes. Using new genomic data from 29 individuals from eight species of Southeast Asian macaque, we identified evidence of natural selection associated with mitonuclear interactions, including extreme outliers of interspecies differentiation and metrics of positive selection, low intraspecies polymorphism and atypically long runs of homozygosity associated with nuclear-encoded genes that interact with mitochondria-encoded genes. In one individual with introgressed mitochondria, we detected a small but significant enrichment of autosomal introgression blocks from the source species of her mitochondria that contained genes which interact with mitochondria-encoded loci. Our analyses also demonstrate that sex-specific demography sculpts genetic exchange across multiple species boundaries. These findings show that behaviour can have profound but indirect effects on genome evolution by influencing how interacting components of different genomic compartments (mitochondria, the autosomes and the sex chromosomes) move through time and space. [ABSTRACT FROM AUTHOR]

The relationship between niche and distribution, and especially the role of biotic interactions in shaping species' geographic distributions, has gained increasing interest in the last two decades. Most ecological research has focused on negative species interactions, especially competition, predation and parasitism. Yet the relevance of positive interactions – mutualisms and commensalisms – have been brought to the fore in recent years by an increasing number of empirical studies exploring their impact on range limits. Based on a review of 73 studies from a Web of Science search, we found strong evidence that positive interactions can influence the extent of species' geographic or ecological ranges through a diversity of mechanisms. More specifically, we found that while obligate interactions, and especially obligate mutualisms, tend to constrain the ranges of one or both partners, facultative positive interactions tend to widen ranges. Nonetheless, there was more variation in effects of facultative interactions on range limits, pointing to important context‐dependencies. Therefore, we propose that conceptual development in this field will come from studying ecological interactions in the context of networks of many species across environmental gradients, since pairwise interactions alone might overlook the indirect and environmentally‐contingent effects that species have on each other in communities of many interacting species. Finally, our study also revealed key data gaps that limit our current understanding of the pervasiveness of effects that positive interactions have on species' ranges, highlighting potential avenues for future theoretical and experimental work. [ABSTRACT FROM AUTHOR]

Understanding spatiotemporal trends on insect‐plant interaction networks is essential to unveil the ecological and evolutionary processes driving herbivore specialisation. However, community studies accounting for temporal dynamics in host‐plant specialisation of herbivorous insects are surprisingly scarce. Here, we investigated how seasonality affects specialisation of a temperate forest herbivore community. A substantial body of literature suggests that young plant foliage tends to be more protected by defence mechanisms effective against generalist insect herbivores than mature leaves. We thus hypothesised that herbivore specialisation would be highest in the early season, when young leaves are available, and that the degree of dietary specialisation would decline with leaf maturation. To test this hypothesis, we sampled more than 4700 folivorous caterpillars associated with 16 tree species within a 0.2 ha deciduous forest stand in eastern North America. We further examined the dietary specialisation of exposed feeders versus shelter builders (e.g. leaf rollers, leaf tiers, webbers). Contrary to our prediction, we observed a significantly less specialised herbivore fauna in the early season than in the two subsequent summer seasons. We further found that the seasonal increase in specialisation was driven by a remarkable turnover in species composition rather than by shifts in guild structure or intraspecific changes in diet breadth of the herbivores. These findings run counter to the widespread belief that young leaves are less susceptible to generalist insect herbivores. Our study underscores the need to account for temporal dynamics when contrasting herbivore specialisation among sites with pronounced seasonality. [ABSTRACT FROM AUTHOR]

Maintaining the diversity of wild bees is a priority for preserving ecosystem function and promoting stability and productivity of agroecosystems. However, wild bee communities face many threats and beekeeping could be one of them, because honey bees may have a strong potential to outcompete wild pollinators when placed at high densities. Yet, we still know little about how beekeeping intensity affects wild bee diversity and their pollinator interactions. Here, we explore how honey bee density relates to wild bee diversity and the structure of their pollination networks in 41 sites on 13 Cycladic Islands (Greece) with similar landscapes but differing in beekeeping intensity. Our large‐scale study shows that increasing honey bee visitation rate had a negative effect on wild bee species richness and abundance, although the latter effect was relatively weak compared to the effect of other landscape variables. Competition for flowering resources (as indicated by a resource sharing index) increased with the abundance of honey bees, but the effect was more moderate for wild bees in family Apidae than for bees in other families, suggesting a stronger niche segregation in Apidae in response to honey bees. Honey bees also influenced the structure of wild bee pollination networks indirectly, through changes in wild bee richness. Low richness of wild bees in sites with high honey bee abundance resulted in wild bee networks with fewer links and lower linkage density. Our results warn against beekeeping intensification in these islands and similar hotspots of bee diversity, and shed light on how benefits to pollination services of introducing honey bees may be counterbalanced by detriments to wild bees and their ecosystem services. [ABSTRACT FROM AUTHOR]

• Borrelia, Rickettsia and Babesia were detected in the Orinoquia region, Colombia. • A total of 734 mammals (655 wild and 79 domestics) were analyzed. • Pathogen detection on 272 ticks collected while feeding from 96 mammals. • Pathogen detection in 93 mammals (blood, heart, liver, lung and kidney). • Interaction networks: 18 mammal and seven tick species, interacting with pathogens. The hard tick clade (Ixodidae) currently comprises 762 species worldwide (266 Prostriata and 496 Metastriata). A quarter of hard ticks are found in the Neotropical region, and 42 species have been documented in Colombia. Ixodidae species are important vectors of pathogens such as bacteria, helminths, protozoa, and viruses. In tick-borne diseases, vertebrate hosts perform an important role in the transmission, maintenance, and spread of pathogens. Colombia ranks sixth among countries with the highest mammal biodiversity, with a total of 548 species, where some of these species may be involved in pathogen transmission cycles with ticks as vectors. This research evaluated the presence of two genera of bacteria (Borrelia and Rickettsia) and the protozoan (Babesia) in ticks and mammals in the Orinoquia region of Colombia, establishing interaction networks. The information comes from 734 mammals (655 wild and 79 domestic), belonging to 59 species. Tick infestation (n = 1,805) was found with 14.85 % (n = 109) of the examined mammals and corresponds to nine tick species confirmed morphologically and molecularly. To detect pathogens 272 ticks were collected while feeding on 96 mammals; samples from 93 mammals were analyzed. The presence of borreliae from the relapsing fever group (RFG) and the Lyme disease group (LDG) were detected. Rickettsia spp. was detected in ticks and mammals, while Babesia bigemina was only detected in ticks. This research is the first to address the prevalence of zoonotic pathogens in domestic and wild mammals infested with hard ticks in the Department of Arauca, Colombia. Considering that reporting cases of infections with Babesia, Borrelia , and Rickettsia in Colombia is not mandatory, their impact on public health cannot be estimated. This highlights the importance of continuously detecting, confirming, and identifying these and other important pathogens within the "One Health" framework, as they have a significant economic and medical-veterinary impact globally. [Display omitted] [ABSTRACT FROM AUTHOR]

Species differ in their resource use and their interactions with other species and, consequently, they fulfil different functional roles in ecological processes. Species with specialized functional roles (specialists) are considered important for communities because they often interact with species with which few other species interact, thereby contributing complementary functional roles to ecological processes. However, the contribution of specialists could be low if they only interact with a small range of interaction partners. In contrast, species with unspecialized functional roles (generalists) often do not fulfil complementary roles but their contribution to ecological processes could be high because they interact with a large range of species.To investigate the importance of the functional roles of specialists versus generalists, we tested the relationship between species' degree of specialization and their contribution to functional‐role diversity for frugivorous birds in Andean seed‐dispersal networks. We used two measures for the specialization of birds—one based on the size, and one based on the position of their interaction niche—and measured their effect on the birds' contribution to functional‐role diversity and their functional complementarity, a measure of how much a species' functional role is complementary to those of the other species.In all networks, there were similar log‐normal distributions of species' contributions to functional‐role diversity and functional complementarity. Contribution to functional‐role diversity and functional complementarity increased with both increasing niche‐position specialization and increasing niche size, indicating that the composition of functional roles in the networks was determined by an interplay between specialization and generalization. There was a negative interaction between niche‐position specialization and niche size in both models, which showed that the positive effect of niche‐position specialization on functional‐role diversity and functional complementarity was stronger for species with a small niche size, and vice versa.Our results show that there is a continuum from specialized to generalized functional roles in species communities, and that both specialists and generalists fulfil important functional roles in ecological processes. Combining interaction networks with functional traits, as exemplified in this study, provides insight into the importance of an interplay of redundancy and complementarity in species' functional roles for ecosystem functioning. A free Plain‐Language Summary can be found within the Supporting Information of this article [ABSTRACT FROM AUTHOR]