Incorporating alternative interaction modes, forbidden links and trait‐based mechanisms increases the minimum trait dimensionality of ecological networks

1. Individual-level traits mediate interaction outcomes and community structure. It is important, therefore, to identify the minimum number of traits that characterise ecological networks, that is, their ‘minimum dimensionality’. Existing methods for estimating minimum dimensionality often lack three features associated with in- creased trait numbers: alternative interaction modes (e.g. feeding strategies such as active vs. sit-and-wait feeding), trait-mediated ‘forbidden links’ and a mechanistic description of interactions. Omitting these features can underestimate the trait numbers involved, and therefore, minimum dimensionality. We develop a ‘mini- mum mechanistic dimensionality’ measure, accounting for these three features.2. The only input our method requires is the network of interaction outcomes. We assume how traits are mechanistically involved in alternative interaction modes. These unidentified traits are contrasted using pairwise performance inequalities between interacting species. For example, if a predator feeds upon a prey spe- cies via a typical predation mode, in each step of the predation sequence, the predator's performance must be greater than the prey's. We construct a system of inequalities from all observed outcomes, which we attempt to solve with mixed integer linear programming. The number of traits required for a feasible system of inequalities provides our minimum dimensionality estimate.3. We applied our method to 658 published empirical ecological networks includ- ing primary consumption, predator–prey, parasitism, pollination, seed dispersal and animal dominance networks, to compare with minimum dimensionality estimates when the three focal features are missing. Minimum dimensionality was typically higher when including alternative interaction modes (54% of empirical networks), ‘forbidden interactions’ as trait-mediated interaction outcomes (92%) or a mechanistic perspective (81%), compared to estimates missing these features. Additionally, we tested minimum dimensionality estimates on simulated networks with known dimensionality. Our method typically estimated a higher minimum dimensionality, closer to the actual dimensionality, while avoiding the overestimation associated with a previous method.4. Our method can reduce the risk of omitting traits involved in different interaction modes, in failure outcomes or mechanistically. More accurate estimates will allow us to parameterise models of theoretical networks with more realistic structure at the interaction outcome level. Thus, we hope our method can improve predictions of community structure and structure-dependent dynamics

Twitter: More than Tweets for Undergraduate Student Researchers

During the COVID-19 pandemic, biology educators were forced to think of ways to communicate with their students, engaging them in science and with the scientific community. For educators using course-based undergraduate research experiences (CUREs), the challenge to have students perform real science, analyze their work, and present their results to a larger scientific audience was difficult as the world moved online. Many instructors were able to adapt CUREs utilizing online data analysis and virtual meeting software for class discussions and synchronous learning. However, interaction with the larger scientific community, an integral component of making science relevant for students and allowing them to network with other young scientists and experts in their fields, was still missing. Even before COVID-19, a subset of students would travel to regional or national meetings to present their work, but most did not have these opportunities. With over 300 million active users, Twitter provided a unique platform for students to present their work to a large and varied audience. The Cell Biology Education Consortium hosted an innovative scientific poster session entirely on Twitter to engage undergraduate researchers with one another and with the much broader community. The format for posting on this popular social media platform challenged students to simplify their science and make their points using only a few words and slides. Nineteen institutions and over one hundred students participated in this event. Even though these practices emerged as a necessity during the COVID-19 pandemic, the Twitter presentation strategy shared in this paper can be used widely

Boom‐bust dynamics in biological invasions: towards an improved application of the concept

Boom‐bust dynamics – the rise of a population to outbreak levels, followed by a dramatic decline – have been associated with biological invasions and offered as a reason not to manage troublesome invaders. However, boom‐bust dynamics rarely have been critically defined, analyzed, or interpreted. Here, we define boom‐bust dynamics and provide specific suggestions for improving the application of the boom‐bust concept. Boom‐bust dynamics can arise from many causes, some closely associated with invasions, but others occurring across a wide range of ecological settings, especially when environmental conditions are changing rapidly. As a result, it is difficult to infer cause or predict future trajectories merely by observing the dynamic. We use tests with simulated data to show that a common metric for detecting and describing boom‐bust dynamics, decline from an observed peak to a subsequent trough, tends to severely overestimate the frequency and severity of busts, and should be used cautiously if at all. We review and test other metrics that are better suited to describe boom‐bust dynamics. Understanding the frequency and importance of boom‐bust dynamics requires empirical studies of large, representative, long‐term data sets that use clear definitions of boom‐bust, appropriate analytical methods, and careful interpretations

Grazing reduces bee abundance and diversity in saltmarshes by suppressing flowering of key plant species

Global declines in pollinator populations and associated services make it imperative to identify and sensitively manage valuable habitats. Coastal habitats such as saltmarshes can support extensive flowering meadows, but their importance for pollinators, and how this varies with land-use intensity, is poorly understood. We hypothesised that saltmarshes provide important bee foraging habitat, and that livestock grazing either suppresses or enhances its value by reducing the abundance - or increasing the diversity - of flowering plants. To test these hypotheses, we surveyed 11 saltmarshes in Wales (UK) under varying grazing management (long-term ungrazed, extensively grazed, intensively grazed) over three summers and investigated causal pathways linking grazing intensity with bee abundance and diversity using a series of linear mixed models. We also compared observed bee abundances to 11 common terrestrial habitats using national survey data. Grazing reduced bee abundance and richness via reductions in the flower cover of the two key food plants: sea aster Tripolium pannonicum and sea lavender Limonium spp. Grazing also increased flowering plant richness, but the positive effects of flower richness did not compensate for the negative effects of reduced flower cover on bees. Bee abundances were approximately halved in extensively grazed marshes (relative to ungrazed) and halved again in intensively grazed marshes. Saltmarsh flowers were primarily visited by honeybees Apis mellifera and bumblebees Bombus spp. in mid and late summer. Compared to other broad habitat types in Wales, ungrazed saltmarshes ranked highly for honeybees and bumblebees in July-August, but were relatively unimportant for solitary bees. Intensively grazed saltmarshes were amongst the least valuable habitats for all bee types. Under appropriate grazing management, saltmarshes provide a valuable and previously overlooked foraging habitat for bees. The strong effects of livestock grazing identified here are likely to extend geographically given that both livestock grazing and key grazing-sensitive plants are widespread in European saltmarshes. We recommend that long-term ungrazed saltmarshes are protected from grazing, and that grazing is maintained at extensive levels on grazed marshes. In this way, saltmarshes can provide forage for wild and managed bee populations and support ecosystem services

Metabolic responses of two pioneer wood decay fungi to diurnally cycling temperature

Decomposition of lignin-rich wood by fungi drives nutrient recycling in woodland ecosystems. Fluctuating abiotic conditions are known to promote the functioning of ecological communities and ecosystems. In the context of wood decay, fluctuating temperature increases decomposition rates. Metabolomics, in tandem with other ‘omics tools, can highlight the metabolic processes affected by experimental treatments, even in the absence of genome sequences and annotations. Globally, natural wood decay communities are dominated by the phylum Basidiomycota. We examined the metabolic responses of Mucidula mucida, a dominant constituent of pioneer communities in beech branches in British woodlands, and Exidia glandulosa, a stress-selected constituent of the same communities, in response to constant and diurnally cycling temperature. We applied untargeted metabolomics and proteomics to beech wood blocks, colonised by M. mucida or E. glandulosa and exposed to either diurnally cycling (mean 15 ± 10°C) or constant (15°C) temperature, in a fully factorial design. Metabolites and proteins linked to lignin breakdown, the citric acid cycle, pentose phosphate pathway, carbohydrate metabolism, fatty acid metabolism and protein biosynthesis and turnover were under-enriched in fluctuating, compared to stable temperatures, in the generalist M. mucida. Conversely, E. glandulosa showed little differential response to the experimental treatments. Synthesis. By demonstrating temperature-dependant metabolic signatures related to nutrient acquisition in a generalist wood decay fungus, we provide new insights into how abiotic conditions can affect community-mediated decomposition and carbon turnover in forests. We show that mechanisms underpinning important biogeochemical processes can be highlighted using untargeted metabolomics and proteomics in the absence of well-annotated genomes

Clinical characteristics, risk factors and outcomes in patients with severe COVID-19 registered in the International Severe Acute Respiratory and Emerging Infection Consortium WHO clinical characterisation protocol: a prospective, multinational, multicentre, observational study

Respiratory infections and tuberculosisInfecciones respiratorias y tuberculosisInfeccions respiratòries i tuberculosiDue to the large number of patients with severe coronavirus disease 2019 (COVID-19), many were treated outside the traditional walls of the intensive care unit (ICU), and in many cases, by personnel who were not trained in critical care. The clinical characteristics and the relative impact of caring for severe COVID-19 patients outside the ICU is unknown. This was a multinational, multicentre, prospective cohort study embedded in the International Severe Acute Respiratory and Emerging Infection Consortium World Health Organization COVID-19 platform. Severe COVID-19 patients were identified as those admitted to an ICU and/or those treated with one of the following treatments: invasive or noninvasive mechanical ventilation, high-flow nasal cannula, inotropes or vasopressors. A logistic generalised additive model was used to compare clinical outcomes among patients admitted or not to the ICU. A total of 40 440 patients from 43 countries and six continents were included in this analysis. Severe COVID-19 patients were frequently male (62.9%), older adults (median (interquartile range (IQR), 67 (55–78) years), and with at least one comorbidity (63.2%). The overall median (IQR) length of hospital stay was 10 (5–19) days and was longer in patients admitted to an ICU than in those who were cared for outside the ICU (12 (6–23) days versus 8 (4–15) days, p<0.0001). The 28-day fatality ratio was lower in ICU-admitted patients (30.7% (5797 out of 18 831) versus 39.0% (7532 out of 19 295), p<0.0001). Patients admitted to an ICU had a significantly lower probability of death than those who were not (adjusted OR 0.70, 95% CI 0.65–0.75; p<0.0001). Patients with severe COVID-19 admitted to an ICU had significantly lower 28-day fatality ratio than those cared for outside an ICU.This work was supported by the UK Foreign, Commonwealth and Development Office and Wellcome (215091/Z/18/Z), the Bill and Melinda Gates Foundation (OPP1209135), Canadian Institutes of Health Research Coronavirus Rapid Research Funding Opportunity OV2170359, grants from Rapid European COVID-19 Emergency Response Research (Horizon 2020 project 101003589), the European Clinical Research Alliance on Infectious Diseases (965313), The Imperial National Institute for Health Research (NIHR) Biomedical Research Centre, and The Cambridge NIHR Biomedical Research Centre; and endorsed by the Irish Critical Care Clinical Trials Group, co-ordinated in Ireland by the Irish Critical Care Clinical Trials Network at University College Dublin and funded by the Health Research Board of Ireland (CTN-2014-12). Data and Material provision was supported by grants from: the NIHR (award CO-CIN-01), the Medical Research Council (grant MC_PC_19059), the NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool in partnership with Public Health England (PHE) (award 200907), Wellcome Trust (Turtle, Lance-fellowship 205228/Z/16/Z), NIHR HPRU in Respiratory Infections at Imperial College London with PHE (award 200927), Liverpool Experimental Cancer Medicine Centre (grant C18616/A25153), NIHR Biomedical Research Centre at Imperial College London (award IS-BRC-1215-20013), and NIHR Clinical Research Network providing infrastructure support. This work was by Research Council of Norway grant number 312780, and a philanthropic donation from Vivaldi Invest A/S owned by Jon Stephenson von Tetzchner

Multiple trait dimensions mediate stress gradient effects on plant biomass allocation, with implications for coastal ecosystem services

The plant economic spectrum (PES) predicts a suite of correlated traits in a continuum from resource conservation to rapid resource acquisition. In addition to competing for resources, plants need to cope with other environmental stresses to persist and reproduce. Yet, it is unclear how multiple strategies (i.e. traits uncorrelated with the PES) affect plant biomass allocation, hindering our ability to connect environmental gradients to ecosystem services.We examined intraspecific dimensionality of leaf and root traits in the salt marsh pioneer species Spartina anglica across salinity, redox and sand content gradients, and related them to above-ground and below-ground plant biomass—properties associated with wave attenuation and sediment stabilization in coastal marshes.Through principal component analysis, we did not find support for a single PES trait dimension (strategy), but instead identified four trait dimensions: (a) leaf economic spectrum (LES, leaf analogue of PES); (b) fine roots-rhizomes; (c) coarse roots; and (d) salt extrusion. Structural equation modelling showed a shift towards the conservative side of the LES under increasing salinity, while redox had a positive influence on the coarse roots dimension. In turn, these trait dimensions were strongly associated with above-ground and below-ground biomass (BLW biomass) allocation.These results indicate that under high salinity, plants will adopt a conservative strategy and will invest more in BLW biomass. Yet, high sediment redox would still allow plants to invest in above-ground biomass. Therefore, plants' trait-mediated biomass allocation depends on the specific combination of abiotic factors experienced at the local scale.Synthesis. Our study highlights the importance of considering multiple ecological strategies for understanding the effect of the environment on plants. Abiotic stresses can influence multiple trait strategy-dimensions, with consequences for ecosystem functioning

Testing for effects of climate change on competitive relationships and coexistence between two bird species

Nils Christian Stenseth et al.© 2015 The Author(s) Published by the Royal Society. Climate change is expected to have profound ecological effects, yet shifts in competitive abilities among species are rarely studied in this context. Blue tits (Cyanistes caeruleus) and great tits (Parus major) compete for food and roosting sites, yet coexist across much of their range. Climate change might thus change the competitive relationships and coexistence between these two species. Analysing four of the highest-quality, long-term datasets available on these species across Europe, we extend the textbook example of coexistence between competing species to include the dynamic effects of long-term climate variation. Using threshold time-series statistical modelling, we demonstrate that long-term climate variation affects species demography through different influences on density-dependent and density-independent processes. The competitive interaction between blue tits and great tits has shifted in one of the studied sites, creating conditions that alter the relative equilibrium densities between the two species, potentially disrupting longterm coexistence. Our analyses show that long-term climate change can, but does not always, generate local differences in the equilibrium conditions of spatially structured species assemblages. We demonstrate how long-term data can be used to better understand whether (and how), for instance, climate change might change the relationships between coexisting species. However, the studied populations are rather robust against competitive exclusion.Peer Reviewe

Social recovery therapy: a treatment manual

Social Recovery Therapy is an individual psychosocial therapy developed for people with psychosis. The therapy aims to improve social recovery through increasing the amount of time individuals spend in meaningful structured activity. Social Recovery Therapy draws on our model of social disability arising as functional patterns of withdrawal in response to early socio-emotional difficulties and compounded by low hopefulness, self-agency and motivation. The core components of Social Recovery Therapy include using an assertive outreach approach to promote a positive therapeutic relationship, with the focus of the intervention on using active behavioural work conducted outside the clinical room and promoting hope, values, meaning, and positive schema. The therapy draws on traditional Cognitive Behavioural Therapy techniques but differs with respect to the increased use of behavioural and multi-systemic work, the focus on the development of hopefulness and positive self, and the inclusion of elements of case management and supported employment. Our treatment trials provide evidence for the therapy leading to clinically meaningful increases in structured activity for individuals experiencing first episode and longer-term psychosis. In this paper, we present the core intervention components with examples in order to facilitate evaluation and implementation of the approach

Evolution of Siderian juvenile crust to Rhyacian high Ba-Sr magmatism in the Mineiro Belt, southern S?o Francisco Craton.

Plutonic rocks from the Mineiro Belt, Brazil record a delayed onset of the transition from TTG to sanukitoid-type magmatism (high Ba-Sr), starting during the Siderian magmatic lull when little juvenile magma was added to the continental crust. Rocks mostly belong to the calc-alkaline series, meta- to peraluminous and originally ?I-type?, meaning that oxidized magmas were formed by partial melting of subducted material. The temporal distribution and apparent secular changes of the magmas are consistent with the onset of subduction-driven plate tectonics due to an increase of the subduction angle and opening of the mantle wedge. New isotopic analyses (Sm-Nd whole rock and Lu-Hf in zircon) corroborate the restricted juvenile nature of the Mineiro Belt and confirm the genetic link between the Lagoa Dourada Suite, a rare ca. 2350 Ma high-Al tonalite-trondhjemite magmatic event, and the sanukitoid-type ca. 2130 Ma Alto Maranh?o Suite. U-Pb dating of zircon and titanite constrain the crystallisation history of plutonic bodies; coupled with major and trace element analyses of the host rocks, they distinguish evolutionary trends in the Mineiro Belt. Several plutons in the region have ages close to 2130 Ma but are distinguished by the lower concentration of compatible elements in the juvenile high Ba-Sr suite