Open Science principles for accelerating trait-based science across the Tree of Life

The AusTraits plant dictionary

Traits with intuitive names, a clear scope and explicit description are essential for all trait databases. The lack of unified, comprehensive, and machine-readable plant trait definitions limits the utility of trait databases, including reanalysis of data from a single database, or analyses that integrate data across multiple databases. Both can only occur if researchers are confident the trait concepts are consistent within and across sources. Here we describe the AusTraits Plant Dictionary (APD), a new data source of terms that extends the trait definitions included in a recent trait database, AusTraits. The development process of the APD included three steps: review and formalisation of the scope of each trait and the accompanying trait description; addition of trait metadata; and publication in both human and machine-readable forms. Trait definitions include keywords, references, and links to related trait concepts in other databases, enabling integration of AusTraits with other sources. The APD will both improve the usability of AusTraits and foster the integration of trait data across global and regional plant trait databases.

A scoping review on what constitutes a good research culture

Background

The crisis in research culture is well documented, covering issues such as a tendency for quantity over quality, unhealthy competitive environments, and assessment based on publications, journal prestige and funding. In response, research institutions need to assess their own practices to promote and advocate for change in the current research ecosystem. The purpose of the scoping review was to explore ' What does the evidence say about the 'problem' with 'poor' research culture, what are the benefits of 'good' research culture, and what does 'good' look like?'

Aims

To examine the peer-reviewed and grey literature to explore the interplay between research culture, open research, career paths, recognition and rewards, and equality, diversity, and inclusion, as part of a larger programme of activity for a research institution.

Methods

A scoping review was undertaken. Six databases were searched along with grey literature. Eligible literature had relevance to academic research institutions, addressed research culture, and were published between January 2017 to May 2022. Evidence was mapped and themed to specific categories. The search strategy, screening and analysis took place between April-May 2022.

Results

1666 titles and abstracts, and 924 full text articles were assessed for eligibility. Of these, 253 articles met the eligibility criteria for inclusion. A purposive sampling of relevant websites was drawn from to complement the review, resulting in 102 records included in the review. Key areas for consideration were identified across the four themes of job security, wellbeing and equality of opportunity, teamwork and interdisciplinary, and research quality and accountability.

Conclusions

There are opportunities for research institutions to improve their own practice, however institutional solutions cannot act in isolation. Research institutions and research funders need to work together to build a more sustainable and inclusive research culture that is diverse in nature and supports individuals' well-being, career progression and performance.

Different sets of traits determine transition of alien species along the invasion continuum

Invasive alien species are currently considered as one of the dominant drivers of global environmental change. Till now, the majority of studies have focused on single or a few traits of alien species that facilitate their invasion. Also inclusion of all the traits which determine the transition of aliens along the different stages of invasion continuum (casual, naturalised and invasive) has remained largely overlooked. In this study, we collected a comprehensive trait dataset on 144 alien plant species of Kashmir Himalaya - a global biodiversity hotspot region. To test which traits of alien species, individually or in combination along with anthropogenic factors, determine their transition along the invasion continuum, we employed chi-square tests, boosted regression trees and phylogenetic methods. We found the perennial life span, longer residence time, greater number of introduced regions, and better seed dispersal mechanism were critical in determining the transition from casual to naturalised. The herbaceous growth form, therophyte Raunkiaer life-form, annual life span, achene fruit, longer residence time and broader introduced range were the species' traits determining transition from naturalised to invasive. Aliens introduced as ornamentals have more propensity to become naturalised; whereas aliens introduced unintentionally show overrepresentation at the invasive stage. Phylogeny alone showed mixed results indicating both clustering and dispersion; however, in combination with other traits, it plays a significant role in determining the stage of invasion. Overall, our study disentangles the individual and interactive roles of multiple traits that determine the transition of alien species' along the invasion continuum. Further, we foresee the potential applicability of our findings in designing robust invasion risk analysis protocols and stage-specific invasion management strategies in this Himalayan region, with learnings for elsewhere in the world.

A slow-fast trait continuum at the whole community level in relation to land-use intensification

Organismal functional strategies form a continuum from slow- to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, whether there is synchronisation of these strategies at the entire community level is unclear. Here, we combine trait data for >2800 above- and belowground taxa from 14 trophic guilds spanning a disturbance and resource availability gradient in German grasslands. The results indicate that most guilds consistently respond to these drivers through both direct and trophically mediated effects, resulting in a 'slow-fast' axis at the level of the entire community. Using 15 indicators of carbon and nutrient fluxes, biomass production and decomposition, we also show that fast trait communities are associated with faster rates of ecosystem functioning. These findings demonstrate that 'slow' and 'fast' strategies can be manifested at the level of whole communities, opening new avenues of ecosystem-level functional classification.

DEBBIES Dataset to study Life Histories across Ectotherms

Demographic models are used to explore how life history traits structure life history strategies across species. This study presents the DEBBIES dataset that contains estimates of eight life history traits (length at birth, puberty and maximum length, maximum reproduction rate, fraction energy allocated to respiration versus reproduction, von Bertalanffy growth rate, mortality rates) for 185 ectotherm species. The dataset can be used to parameterise dynamic energy budget integral projection models (DEB-IPMs) to calculate key demographic quantities like population growth rate and demographic resilience, but also link to conservation status or biogeographical characteristics. Our technical validation shows a satisfactory agreement between observed and predicted longevity, generation time, age at maturity across all species. Compared to existing datasets, DEBBIES accommodates (i) easy cross-taxonomical comparisons, (ii) many data-deficient species, and (iii) population forecasts to novel conditions because DEB-IPMs include a mechanistic description of the trade-off between growth and reproduction. This dataset has the potential for biologists to unlock general predictions on ectotherm population responses from only a few key life history traits.

The Pelagic Species Trait Database, an open data resource to support trait-based ocean research

Trait-based frameworks are increasingly used for predicting how ecological communities respond to ongoing global change. As species range shifts result in novel encounters between predators and prey, identifying prey 'guilds', based on a suite of shared traits, can distill complex species interactions, and aid in predicting food web dynamics. To support advances in trait-based research in open-ocean systems, we present the Pelagic Species Trait Database, an extensive resource documenting functional traits of 529 pelagic fish and invertebrate species in a single, open-source repository. We synthesized literature sources and online resources, conducted morphometric analysis of species images, as well as laboratory analyses of trawl-captured specimens to collate traits describing 1) habitat use and behavior, 2) morphology, 3) nutritional quality, and 4) population status information. Species in the dataset primarily inhabit the California Current system and broader NE Pacific Ocean, but also includes pelagic species known to be consumed by top ocean predators from other ocean basins. The aim of this dataset is to enhance the use of trait-based approaches in marine ecosystems and for predator populations worldwide.

Improper data practices erode the quality of global ecological databases and impede the progress of ecological research

The scientific community has entered an era of big data. However, with big data comes big responsibilities, and best practices for how data are contributed to databases have not kept pace with the collection, aggregation, and analysis of big data. Here, we rigorously assess the quantity of data for specific leaf area (SLA) available within the largest and most frequently used global plant trait database, the TRY Plant Trait Database, exploring how much of the data were applicable (i.e., original, representative, logical, and comparable) and traceable (i.e., published, cited, and consistent). Over three-quarters of the SLA data in TRY either lacked applicability or traceability, leaving only 22.9% of the original data usable compared with the 64.9% typically deemed usable by standard data cleaning protocols. The remaining usable data differed markedly from the original for many species, which led to altered interpretation of ecological analyses. Though the data we consider here make up only 4.5% of SLA data within TRY, similar issues of applicability and traceability likely apply to SLA data for other species as well as other commonly measured, uploaded, and downloaded plant traits. We end with suggested steps forward for global ecological databases, including suggestions for both uploaders to and curators of databases with the hope that, through addressing the issues raised here, we can increase data quality and integrity within the ecological community.

A roadmap to define and select aquatic biological traits at different scales of analysis

Trait-based approaches are a powerful tool, as they not only improve understanding of ecological complexity and functioning but also allow comparison across different ecosystems and biogeographical regions. They may be used to unveil ecosystem processes and assess community structures, but their great potential becomes limited when dealing with scattered trait data and historically unstandardised trait nomenclature. The lack of standardisation allows authors to use the terminology of their preference, which inevitably leads to ambiguous misunderstandings and limits comparison between different studies. There have been some attempts to organise the trait vocabulary, but even these are mostly created from the perspective of a single ecosystem, which limits their applicability. In this work, we conducted a systematic literature review that identified and compiled 1127 traits across 37 datasets of fishes, invertebrates and zooplankton from freshwater, marine and transitional ecosystems. This dataset was then used to build on the Marine Species Traits Wiki and to propose a new, unified approach to a trait vocabulary based directly on readily available trait data. We propose a single standardised designation for all the different traits identified and provide a list of all the different synonyms commonly used for these traits. A roadmap to help the trait selection process is also provided, offering a guide through four main steps and important questions for choosing an adequate set of traits at the beginning of any study, which constitutes one of the main challenges in functional ecology research. Overall, this proposal will provide a solid baseline for tackling gaps in trait nomenclature and ensuring a clearer future for functional ecology studies.

Seasonal and sex-specific changes in the gastrointestinal tracts of Peromyscus maniculatus

Functional traits are phenotypic characteristics that contribute to fitness of individuals in dynamic and changing environments. In mammals, both categorical and continuous (e.g., quantitative) functional traits have been extensively utilized as proxies for diet, locomotion, and other aspects of species ecology, but there has been less focus on form and function of soft tissues. This is particularly true for the digestive system, which varies in size and complexity across Class Mammalia and plays a major role in the energetics of species. To guide more effective utilization of gastrointestinal (GI) morphology as a functional proxy in small mammal ecology, we examined how GI tracts (lengths and masses of four GI sections) varied within a population of deer mice (Peromyscus maniculatus) in the Southern Appalachian Mountains of North Carolina, United States. We collected samples of adult P. maniculatus monthly for 1 year and measured GI tracts to quantify variation with respect to seasonality and trophic level, providing insight into plasticity in this soft tissue trait over time. We found that season had a significant effect on the total length and wet mass of the GI tract, with January mice having the longest GI tracts and lengths being shortest in the summer. The relative shortening of the GI tract in summer corresponded with a partial trophic increase detected by stable isotope signatures. GI length and wet mass also were affected by reproduction, but males and females responded in sex-specific ways to demands of reproduction, with reproductively active males having shorter and lighter GI tracts than nonreproductively active males. Our study provides proof-of-concept for understanding population-level plasticity in a rarely collected soft tissue trait, which may also be complementary to standard craniodental measurements as a functional dietary proxy to understand mammalian ecology and community assembly.

The seafloor from a trait perspective. A comprehensive life history dataset of soft sediment macrozoobenthos

Biological trait analysis (BTA) is a valuable tool for evaluating changes in community diversity and its link to ecosystem processes as well as environmental and anthropogenic perturbations. Trait-based analytical techniques like BTA rely on standardised datasets of species traits. However, there are currently only a limited number of datasets available for marine macrobenthos that contain trait data across multiple taxonomic groups. Here, we present an open-access dataset of 16 traits for 235 macrozoobenthic species recorded throughout multiple sampling campaigns of the Dutch Wadden Sea; a dynamic soft bottom system where humans have long played a substantial role in shaping the coastal environment. The trait categories included in this dataset cover a variety of life history strategies that are tightly linked to ecosystem functioning and the resilience of communities to (anthropogenic) perturbations and can advance our understanding of environmental changes and human impacts on the functioning of soft bottom systems.

A global assessment of the Raunkiaeran shortfall in plants: geographic biases in our knowledge of plant traits

This article is part of the Special Collection ‘Global plant diversity and distribution’. See https://www.newphytologist.org/global-plant-diversity for more details.

An ecologist's guide for studying DNA methylation variation in wild vertebrates

The field of molecular biology is advancing fast with new powerful technologies, sequencing methods and analysis software being developed constantly. Commonly used tools originally developed for research on humans and model species are now regularly used in ecological and evolutionary research. There is also a growing interest in the causes and consequences of epigenetic variation in natural populations. Studying ecological epigenetics is currently challenging, especially for vertebrate systems, because of the required technical expertise, complications with analyses and interpretation, and limitations in acquiring sufficiently high sample sizes. Importantly, neglecting the limitations of the experimental setup, technology and analyses may affect the reliability and reproducibility, and the extent to which unbiased conclusions can be drawn from these studies. Here, we provide a practical guide for researchers aiming to study DNA methylation variation in wild vertebrates. We review the technical aspects of epigenetic research, concentrating on DNA methylation using bisulfite sequencing, discuss the limitations and possible pitfalls, and how to overcome them through rigid and reproducible data analysis. This review provides a solid foundation for the proper design of epigenetic studies, a clear roadmap on the best practices for correct data analysis and a realistic view on the limitations for studying ecological epigenetics in vertebrates. This review will help researchers studying the ecological and evolutionary implications of epigenetic variation in wild populations.

Unified and pluralistic ideals for data sharing and reuse in biodiversity

How should billions of species observations worldwide be shared and made reusable? Many biodiversity scientists assume the ideal solution is to standardize all datasets according to a single, universal classification and aggregate them into a centralized, global repository. This ideal has known practical and theoretical limitations, however, which justifies investigating alternatives. To support better community deliberation and normative evaluation, we develop a novel conceptual framework showing how different organizational models, regulative ideals and heuristic strategies are combined to form shared infrastructures supporting data reuse. The framework is anchored in a general definition of data pooling as an activity of making a taxonomically standardized body of information available for community reuse via digital infrastructure. We describe and illustrate unified and pluralistic ideals for biodiversity data pooling and show how communities may advance toward these ideals using different heuristic strategies. We present evidence for the strengths and limitations of the unification and pluralistic ideals based on systemic relationships of power, responsibility and benefit they establish among stakeholders, and we conclude the pluralistic ideal is better suited for biodiversity data.

MOSAIC - A Unified Trait Database to Complement Structured Population Models

Despite exponential growth in ecological data availability, broader interoperability amongst datasets is needed to unlock the potential of open access. Our understanding of the interface of demography and functional traits is well-positioned to benefit from such interoperability. Here, we introduce MOSAIC, an open-access trait database that unlocks the demographic potential stored in the COMADRE, COMPADRE, and PADRINO open-access databases. MOSAIC data were digitised and curated through a combination of existing datasets and new trait records sourced from primary literature. In its first release, MOSAIC (v. 1.0.0) includes 14 trait fields for 300 animal and plant species: biomass, height, growth determination, regeneration, sexual dimorphism, mating system, hermaphrodism, sequential hermaphrodism, dispersal capacity, type of dispersal, mode of dispersal, dispersal classes, volancy, and aquatic habitat dependency. MOSAIC includes species-level phylogenies for 1,359 species and population-specific climate data. We identify how database integration can improve our understanding of traits well-quantified in existing repositories and those that are poorly quantified (e.g., growth determination, modularity). MOSAIC highlights emerging challenges associated with standardising databases and demographic measures.

A species-level trait dataset of bats in Europe and beyond

Knowledge of species' functional traits is essential for understanding biodiversity patterns, predicting the impacts of global environmental changes, and assessing the efficiency of conservation measures. Bats are major components of mammalian diversity and occupy a variety of ecological niches and geographic distributions. However, an extensive compilation of their functional traits and ecological attributes is still missing. Here we present EuroBaTrait 1.0, the most comprehensive and up-to-date trait dataset covering 47 European bat species. The dataset includes data on 118 traits including genetic composition, physiology, morphology, acoustic signature, climatic associations, foraging habitat, roost type, diet, spatial behaviour, life history, pathogens, phenology, and distribution. We compiled the bat trait data obtained from three main sources: (i) a systematic literature and dataset search, (ii) unpublished data from European bat experts, and (iii) observations from large-scale monitoring programs. EuroBaTrait is designed to provide an important data source for comparative and trait-based analyses at the species or community level. The dataset also exposes knowledge gaps in species, geographic and trait coverage, highlighting priorities for future data collection.

Publication bias impacts on effect size, statistical power, and magnitude (Type M) and sign (Type S) errors in ecology and evolutionary biology

Collaborative efforts to directly replicate empirical studies in the medical and social sciences have revealed alarmingly low rates of replicability, a phenomenon dubbed the 'replication crisis'. Poor replicability has spurred cultural changes targeted at improving reliability in these disciplines. Given the absence of equivalent replication projects in ecology and evolutionary biology, two inter-related indicators offer the opportunity to retrospectively assess replicability: publication bias and statistical power. This registered report assesses the prevalence and severity of small-study (i.e., smaller studies reporting larger effect sizes) and decline effects (i.e., effect sizes decreasing over time) across ecology and evolutionary biology using 87 meta-analyses comprising 4,250 primary studies and 17,638 effect sizes. Further, we estimate how publication bias might distort the estimation of effect sizes, statistical power, and errors in magnitude (Type M or exaggeration ratio) and sign (Type S). We show strong evidence for the pervasiveness of both small-study and decline effects in ecology and evolution. There was widespread prevalence of publication bias that resulted in meta-analytic means being over-estimated by (at least) 0.12 standard deviations. The prevalence of publication bias distorted confidence in meta-analytic results, with 66% of initially statistically significant meta-analytic means becoming non-significant after correcting for publication bias. Ecological and evolutionary studies consistently had low statistical power (15%) with a 4-fold exaggeration of effects on average (Type M error rates = 4.4). Notably, publication bias reduced power from 23% to 15% and increased type M error rates from 2.7 to 4.4 because it creates a non-random sample of effect size evidence. The sign errors of effect sizes (Type S error) increased from 5% to 8% because of publication bias. Our research provides clear evidence that many published ecological and evolutionary findings are inflated. Our results highlight the importance of designing high-power empirical studies (e.g., via collaborative team science), promoting and encouraging replication studies, testing and correcting for publication bias in meta-analyses, and adopting open and transparent research practices, such as (pre)registration, data- and code-sharing, and transparent reporting.

Conceptual methodological framework for the resilience of biogeochemical services to heavy metals stress

The idea of linking stressors, services providing units (SPUs), and ecosystem services (ES) is ubiquitous in the literature, although is currently not applied in areas contaminated with heavy metals (HMs), This integrative literature review introduces the general form of a deterministic conceptual model of the cross-scale effect of HMs on biogeochemical services by SPUs with a feedback loop, a cross-scale heuristic concept of resilience, and develops a method for applying the conceptual model. The objectives are 1) to identify the clusters of existing research about HMs effects on ES, biodiversity, and resilience to HMs stress, 2) to map the scientific fields needed for the conceptual model's implementation, identify institutional constraints for inter-disciplinary cooperation, and propose solutions to surpass them, 3) to describe how the complexity of the cause-effect chain is reflected in the research hypotheses and objectives and extract methodological consequences, and 4) to describe how the conceptual model can be implemented. A nested analysis by CiteSpace of a set of 16,176 articles extracted from the Web of Science shows that at the highest level of data aggregation there is a clear separation between the topics of functional traits, stoichiometry, and regulating services from the typical issues of the literature about HMs, biodiversity, and ES. Most of the resilience to HMs stress agenda focuses on microbial communities. General topics such as the biodiversity-ecosystem function relationship in contaminated areas are no longer dominant in the current research, as well as large-scale problems like watershed management. The number of Web of Science domains that include the analyzed articles is large (26 up to 87 domains with at least ten articles, depending on the sub-set), but thirteen domains account for 70-80% of the literature. The complexity of approaches regarding the cause-effect chain, the stressors, the biological and ecological hierarchical level and the management objectives was characterized by a detailed analysis of 60 selected reviews and 121 primary articles. Most primary articles approach short causal chains, and the number of hypotheses or objectives by article tends to be low, pointing out the need for portfolios of complementary research projects in coherent inter-disciplinary programs and innovation ecosystems to couple the ES and resilience problems in areas contaminated with HMs. One provides triggers for developing innovation ecosystems, examples of complementary research hypotheses, and an example of technology transfer. Finally one proposes operationalizing the conceptual methodological model in contaminated socio-ecological systems by a calibration, a sensitivity analysis, and a validation phase.

Research on the relationships between discourse leading indicators and citations: perspectives from altmetrics indicators of international multidisciplinary academic journals

Purpose

This paper aims to analyze the relationships between discourse leading indicators and citations from perspectives of integrating altmetrics indicators and tries to provide references for comprehending the quantitative indicators of scientific communication in the era of open science, constructing the evaluation indicator system of the discourse leading for academic journals and then improving the discourse leading of academic journals.

Design/methodology/approach

Based on the theory of communication and the new pattern of scientific communication, this paper explores the formation process of academic journals' discourse leading. This paper obtains 874,119 citations and 6,378,843 altmetrics indicators data from 65 international multidisciplinary academic journals. The relationships between indicators of discourse leading (altmetrics) and citations are studied by using descriptive statistical analysis, correlation analysis, principal component analysis, negative binomial regression analysis and marginal effects analysis. Meanwhile, the connotation and essential characteristics of the indicators, the strength and influence of the relationships are further analyzed and explored. It is proposed that academic journals' discourse leading is composed of news discourse leading, social media discourse leading, peer review discourse leading, encyclopedic discourse leading, video discourse leading and policy discourse leading.

Findings

It is discovered that the 15 altmetrics indicators data have a low degree of centralization to the center and a high degree of polarization dispersion overall; their distribution patterns do not follow the normal distributions, and their distributions have the characteristics of long-tailed right-peaked curves. Overall, 15 indicators show positive correlations and wide gaps exist in the number of mentions and coverage. The academic journals' discourse leading significantly affects total cites. When altmetrics indicators of international mainstream academic and social media platforms are used to explore the connotation and characteristics of academic journals' discourse leading, the influence or contribution of social media discourse, news discourse, video discourse, policy discourse, peer review discourse and encyclopedia discourse on the citations decreases in turn.

Originality/value

This study is innovative from the academic journal level to analyze the deep relationships between altmetrics indicators and citations from the perspective of correlation. First, this paper explores the formation process of academic journals' discourse leading. Second, this paper integrates altmetrics indicators to study the correlation between discourse leading indicators and citations. This study will help to enrich and improve basic theoretical issues and indicators’ composition, provide theoretical support for the construction of the discourse leading evaluation system for academic journals and provide ideas for the evaluation practice activities.

Close to open-Factors that hinder and promote open science in ecology research and education

The Open Science (OS) movement is rapidly gaining traction among policy-makers, research funders, scientific journals and individual scientists. Despite these tendencies, the pace of implementing OS throughout the scientific process and across the scientific community remains slow. Thus, a better understanding of the conditions that affect OS engagement, and in particular, of how practitioners learn, use, conduct and share research openly can guide those seeking to implement OS more broadly. We surveyed participants at an OS workshop hosted by the Living Norway Ecological Data Network in 2020 to learn how they perceived OS and its importance in their research, supervision and teaching. Further, we wanted to know what OS practices they had encountered in their education and what they saw as hindering or helping their engagement with OS. The survey contained scaled-response and open-ended questions, allowing for a mixed-methods approach. We obtained survey responses from 60 out of 128 workshop participants (47%). Responses indicated that usage and sharing of open data and code, as well as open access publication, were the most frequent OS practices. Only a minority of respondents reported having encountered OS in their formal education. A majority also viewed OS as less important in their teaching than in their research and supervisory roles. The respondents' suggestions for what would facilitate greater OS engagement in the future included knowledge, guidelines, and resources, but also social and structural support. These are aspects that could be strengthened by promoting explicit implementation of OS practices in higher education and by nurturing a more inclusive and equitable OS culture. We argue that incorporating OS in teaching and learning of science can yield substantial benefits to the research community, student learning, and ultimately, to the wider societal objectives of science and higher education.

The China plant trait database version 2

Plant functional traits represent adaptive strategies to the environment, linked to biophysical and biogeochemical processes and ecosystem functioning. Compilations of trait data facilitate research in multiple fields from plant ecology through to land-surface modelling. Here we present version 2 of the China Plant Trait Database, which contains information on morphometric, physical, chemical, photosynthetic and hydraulic traits from 1529 unique species in 140 sites spanning a diversity of vegetation types. Version 2 has five improvements compared to the previous version: (1) new data from a 4-km elevation transect on the edge of Tibetan Plateau, including alpine vegetation types not sampled previously; (2) inclusion of traits related to hydraulic processes, including specific sapwood conductance, the area ratio of sapwood to leaf, wood density and turgor loss point; (3) inclusion of information on soil properties to complement the existing data on climate and vegetation (4) assessments and flagging the reliability of individual trait measurements; and (5) inclusion of standardized templates for systematical field sampling and measurements.

Habitat loss estimation for assessing terrestrial mammalian species extinction risk: an open data framework

Terrestrial mammals face a severe crisis of habitat loss worldwide. Therefore, assessing information on habitat loss throughout different time periods is crucial for assessing species' conservation statuses based on the IUCN Red List system. To support the national extinction risk assessment in Brazil (2016-2022), we developed a script that uses the MapBiomas Project 6.0 data source of land cover and land use (annual maps at 30 m scale) within the Google Earth Engine (GEE) platform to calculate habitat loss. We defined suitable habitats from the MapBiomas Project land cover classification for 190 mammalian taxa, according to each species range map and ecological characteristics. We considered a period of three generation lengths to assess habitat loss in accordance with the Red List assessment criteria. We used the script to estimate changes in available habitat throughout the analyzed period within the species' known ranges. The results indicated that habitat loss occurred within 94.3% of the analyzed taxa range, with the Carnivora order suffering the greatest habitat loss, followed by the Cingulata order. These analyses may be decisive for applying criteria, defining categories during the assessment of at least 17 species (9%), enriching discussions, and raising new questions for several other species. We considered the outcome of estimating habitat loss for various taxa when applying criterion A, which refers to population reduction, thus supporting more accurate inferences about past population declines.

Indigenous and introduced Collembola differ in desiccation resistance but not its plasticity in response to temperature

Biological invasions have significant ecological and economic impacts. Much attention is therefore focussed on predicting establishment and invasion success. Trait-based approaches are showing much promise, but are mostly restricted to investigations of plants. Although the application of these approaches to animals is growing rapidly, it is rare for arthropods and restricted mostly to investigations of thermal tolerance. Here we study the extent to which desiccation tolerance and its phenotypic plasticity differ between introduced (nine species) and indigenous (seven species) Collembola, specifically testing predictions of the 'ideal weed' and 'phenotypic plasticity' hypotheses of invasion biology. We do so on the F2 generation of adults in a full factorial design across two temperatures, to elicit desiccation responses, for the phenotypic plasticity trials. We also determine whether basal desiccation resistance responds to thermal laboratory natural selection. We first show experimentally that acclimation to different temperatures elicits changes to cuticular structure and function that are typically associated with water balance, justifying our experimental approach. Our main findings reveal that basal desiccation resistance differs, on average, between the indigenous and introduced species, but that this difference is weaker at higher temperatures, and is driven by particular taxa, as revealed by phylogenetic generalised least squares approaches. By contrast, the extent or form of phenotypic plasticity does not differ between the two groups, with a 'hotter is better' response being most common. Beneficial acclimation is characteristic of only a single species. Laboratory natural selection had little influence on desiccation resistance over 8-12 generations, suggesting that environmental filtering rather than adaptation to new environments may be an important factor influencing Collembola invasions.

To harness traits for ecology, let’s abandon ‘functionality’

Traits are measurable features of organisms. Functional traits aspire to more. They quantify an organism's ecology and, ultimately, predict ecosystem functions based on local communities. Such predictions are useful, but only if 'functional' really means 'ecologically relevant'. Unfortunately, many 'functional' traits seem to be characterized primarily by availability and implied importance - not by their ecological information content. Better traits are needed, but a prevailing trend is to 'functionalize' existing traits. The key may be to invert the process, that is, to identify functions of interest first and then identify traits as quantifiable proxies. We propose two distinct, yet complementary, perspectives on traits and provide a 'taxonomy of traits', a conceptual compass to navigate the diverse applications of traits in ecology.

Trait-mediated competition drives an ant invasion and alters functional diversity

The assumption that differences in species' traits reflect their different niches has long influenced how ecologists infer processes from assemblage patterns. For instance, many assess the importance of environmental filtering versus classical limiting-similarity competition in driving biological invasions by examining whether invaders' traits are similar or dissimilar to those of residents, respectively. However, mounting evidence suggests that hierarchical differences between species' trait values can distinguish their competitive abilities (e.g. for the same resource) instead of their niches. Whether such trait-mediated hierarchical competition explains invasions and structures assemblages is less explored. We integrate morphological, dietary, physiological and behavioural trait analyses to test whether environmental filtering, limiting-similarity competition or hierarchical competition explain invasions by fire ants on ant assemblages. We detect both competition mechanisms; invasion success is not only explained by limiting similarity in body size and thermal tolerance (presumably allowing the invader to exploit different niches from residents), but also by the invader's superior position in trait hierarchies reflecting competition for common trophic resources. We find that the two mechanisms generate complex assemblage-level functional diversity patterns-overdispersion in some traits, clustering in others-suggesting their effects are likely missed by analyses restricted to a few traits and composite trait diversity measures.

AnimalTraits - a curated animal trait database for body mass, metabolic rate and brain size

Trait databases have become important resources for large-scale comparative studies in ecology and evolution. Here we introduce the AnimalTraits database, a curated database of body mass, metabolic rate and brain size, in standardised units, for terrestrial animals. The database has broad taxonomic breadth, including tetrapods, arthropods, molluscs and annelids from almost 2000 species and 1000 genera. All data recorded in the database are sourced from their original empirical publication, and the original metrics and measurements are included with each record. This allows for subsequent data transformations as required. We have included rich metadata to allow users to filter the dataset. The additional R scripts we provide will assist researchers with aggregating standardised observations into species-level trait values. Our goals are to provide this resource without restrictions, to keep the AnimalTraits database current, and to grow the number of relevant traits in the future.

Measurement(s)	metabolic rate quantification • body mass • brain size
Technology Type(s)	metabolic rate measurement • body mass quantification • brain mass brain volume

Past and future uses of text mining in ecology and evolution

Ecology and evolutionary biology, like other scientific fields, are experiencing an exponential growth of academic manuscripts. As domain knowledge accumulates, scientists will need new computational approaches for identifying relevant literature to read and include in formal literature reviews and meta-analyses. Importantly, these approaches can also facilitate automated, large-scale data synthesis tasks and build structured databases from the information in the texts of primary journal articles, books, grey literature, and websites. The increasing availability of digital text, computational resources, and machine-learning based language models have led to a revolution in text analysis and natural language processing (NLP) in recent years. NLP has been widely adopted across the biomedical sciences but is rarely used in ecology and evolutionary biology. Applying computational tools from text mining and NLP will increase the efficiency of data synthesis, improve the reproducibility of literature reviews, formalize analyses of research biases and knowledge gaps, and promote data-driven discovery of patterns across ecology and evolutionary biology. Here we present recent use cases from ecology and evolution, and discuss future applications, limitations and ethical issues.

Assistência Farmacêutica e governança global da saúde em tempos de Covid-19

RESUMO Este ensaio aborda como e em que níveis a Assistência Farmacêutica é atravessada pela dinâmica da governança global da saúde, e como se relaciona com aspectos geopolíticos e socioeconômicos. Tenta-se ir além do acesso a medicamentos e produtos para saúde, abordando também o uso racional de medicamentos, seu impacto na resistência aos antimicrobianos e na saúde dos povos. Além disso, discute como a Assistência Farmacêutica pode ser vista nesse contexto.

Pharmaceutical Services and global health governance in times of COVID-19

ABSTRACT This essay addresses how and at what levels Pharmaceutical Services is affected by the dynamics of global health governance, and how it correlates with geopolitical and socioeconomic aspects. It attempts to go beyond access to medicines and health products, as well as to address the rational use of medicines, the impact in antimicrobial resistance and in people’s health. Furthermore, it debates how Pharmaceutical Services can be seen in this context.

Trait-based approaches to global change ecology: moving from description to prediction

Trait-based approaches are increasingly recognized as a tool for understanding ecosystem re-assembly and function under intensifying global change. Here we synthesize trait-based research globally (n = 865 studies) to examine the contexts in which traits may be used for global change prediction. We find that exponential growth in the field over the last decade remains dominated by descriptive studies of terrestrial plant morphology, highlighting significant opportunities to expand trait-based thinking across systems and taxa. Very few studies (less than 3%) focus on predicting ecological effects of global change, mostly in the past 5 years and via singular traits that mediate abiotic limits on species distribution. Beyond organism size (the most examined trait), we identify over 2500 other morphological, physiological, behavioural and life-history traits known to mediate environmental filters of species' range and abundance as candidates for future predictive global change work. Though uncommon, spatially explicit process models—which mechanistically link traits to changes in organism distributions and abundance—are among the most promising frameworks for holistic global change prediction at scales relevant for conservation decision-making. Further progress towards trait-based forecasting requires addressing persistent barriers including (1) matching scales of multivariate trait and environment data to focal processes disrupted by global change, and (2) propagating variation in trait and environmental parameters throughout process model functions using simulation.

Best practices for building and curating databases for comparative analyses

Comparative analyses have a long history of macro-ecological and -evolutionary approaches to understand structure, function, mechanism and constraint. As the pace of science accelerates, there is ever-increasing access to diverse types of data and open access databases that are enabling and inspiring new research. Whether conducting a species-level trait-based analysis or a formal meta-analysis of study effect sizes, comparative approaches share a common reliance on reliable, carefully curated databases. Unlike many scientific endeavors, building a database is a process that many researchers undertake infrequently and in which we are not formally trained. This Commentary provides an introduction to building databases for comparative analyses and highlights challenges and solutions that the authors of this Commentary have faced in their own experiences. We focus on four major tips: (1) carefully strategizing the literature search; (2) structuring databases for multiple use; (3) establishing version control within (and beyond) your study; and (4) the importance of making databases accessible. We highlight how one's approach to these tasks often depends on the goal of the study and the nature of the data. Finally, we assert that the curation of single-question databases has several disadvantages: it limits the possibility of using databases for multiple purposes and decreases efficiency due to independent researchers repeatedly sifting through large volumes of raw information. We argue that curating databases that are broader than one research question can provide a large return on investment, and that research fields could increase efficiency if community curation of databases was established.

AVONET: morphological, ecological and geographical data for all birds

Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species-level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity.

Profiling insular vertebrates prone to biological invasions: What makes them vulnerable?

Invasive alien species (IAS) are a major threat to insular vertebrates, although the ecological characteristics that make insular communities vulnerable to IAS are poorly understood. After describing the ecological strategies of 6015 insular amphibians, birds, lizards, and mammals, we assessed the functional and ecological features of vertebrates exposed to IAS. We found that at least 50% of insular amphibian functional richness was hosted by IAS-threatened amphibians and up to 29% for birds. Moreover, all IAS-threatened groups except birds harbored a higher functional richness than species groups threatened by other threats. Disentangling the ecological strategies threatened by IAS, compared to those associated with other threats, we showed that birds, lizards, and mammals were more likely to be terrestrial foragers and amphibians to have larval development. By contrast, large-bodied species and habitat specialists were universally threatened. By considering the functional aspect of threatened insular diversity, our work improves our understanding of global IAS impacts. This new dimension proves essential for undertaking relevant and effective conservation actions.

Low statistical power and overestimated anthropogenic impacts, exacerbated by publication bias, dominate field studies in global change biology

Field studies are essential to reliably quantify ecological responses to global change because they are exposed to realistic climate manipulations. Yet such studies are limited in replicates, resulting in less power and, therefore, potentially unreliable effect estimates. Furthermore, while manipulative field experiments are assumed to be more powerful than non-manipulative observations, it has rarely been scrutinized using extensive data. Here, using 3847 field experiments that were designed to estimate the effect of environmental stressors on ecosystems, we systematically quantified their statistical power and magnitude (Type M) and sign (Type S) errors. Our investigations focused upon the reliability of field experiments to assess the effect of stressors on both ecosystem's response magnitude and variability. When controlling for publication bias, single experiments were underpowered to detect response magnitude (median power: 18%-38% depending on effect sizes). Single experiments also had much lower power to detect response variability (6%-12% depending on effect sizes) than response magnitude. Such underpowered studies could exaggerate estimates of response magnitude by 2-3 times (Type M errors) and variability by 4-10 times. Type S errors were comparatively rare. These observations indicate that low power, coupled with publication bias, inflates the estimates of anthropogenic impacts. Importantly, we found that meta-analyses largely mitigated the issues of low power and exaggerated effect size estimates. Rather surprisingly, manipulative experiments and non-manipulative observations had very similar results in terms of their power, Type M and S errors. Therefore, the previous assumption about the superiority of manipulative experiments in terms of power is overstated. These results call for highly powered field studies to reliably inform theory building and policymaking, via more collaboration and team science, and large-scale ecosystem facilities. Future studies also require transparent reporting and open science practices to approach reproducible and reliable empirical work and evidence synthesis.

Sub-critical limits are viable alternatives to critical thermal limits

Thermal traits are frequently used to explain variation in species distributions, abundance, and sensitivity to climate change. Due to their utility and ease of measurement, critical thermal limits in particular have proliferated across the ecophysiological literature. Critical limit assays can, however, have deleterious or even lethal effects on individuals and there is growing recognition that intermediate metrics of performance can provide a further, nuanced understanding of how species interact with their environments. Meanwhile, the scarcity of data describing sub-critical or voluntary limits, which have been proposed as alternatives to critical limits and can be collected under less extreme conditions, reduces their value in comparative analyses and broad-scale syntheses. To overcome these limitations and determine if sub-critical limits are viable proxies for upper and lower critical thermal limits we measured and compared the critical and sub-critical thermal limits of 2023 ants representing 51 species. Sub-critical limits in isolation were a satisfactory linear predictor for both individual and species critical limits and when species identity was also considered there were substantial gains in variance explained. These gains indicate that a species-specific conversion factor can further improve estimates of critical traits using sub-critical proxies. Sub-critical limits can, therefore, be integrated into broader syntheses of critical limits and confidently used to calculate common ecological metrics, such as warming tolerance, so long as uncertainty in estimates is explicitly acknowledged. Although lower thermal traits exhibited more variation than their upper counterparts, the stronger phylogenetic signal of lower thermal traits indicates that appropriate conversions for lower thermal traits can be inferred from congenerics or other closely related taxa.

Crowdsourcing Global Perspectives in Ecology Using Social Media

Transparent, open, and reproducible research is still far from routine, and the full potential of open science has not yet been realized. Crowdsourcing–defined as the usage of a flexible open call to a heterogeneous group of individuals to recruit volunteers for a task –is an emerging scientific model that encourages larger and more outwardly transparent collaborations. While crowdsourcing, particularly through citizen- or community-based science, has been increasing over the last decade in ecological research, it remains infrequently used as a means of generating scientific knowledge in comparison to more traditional approaches. We explored a new implementation of crowdsourcing by using an open call on social media to assess its utility to address fundamental ecological questions. We specifically focused on pervasive challenges in predicting, mitigating, and understanding the consequences of disturbances. In this paper, we briefly review open science concepts and their benefits, and then focus on the new methods we used to generate a scientific publication. We share our approach, lessons learned, and potential pathways forward for expanding open science. Our model is based on the beliefs that social media can be a powerful tool for idea generation and that open collaborative writing processes can enhance scientific outcomes. We structured the project in five phases: (1) draft idea generation, (2) leadership team recruitment and project development, (3) open collaborator recruitment via social media, (4) iterative paper development, and (5) final editing, authorship assignment, and submission by the leadership team. We observed benefits including: facilitating connections between unusual networks of scientists, providing opportunities for early career and underrepresented groups of scientists, and rapid knowledge exchange that generated multidisciplinary ideas. We also identified areas for improvement, highlighting biases in the individuals that self-selected participation and acknowledging remaining barriers to contributing new or incompletely formed ideas into a public document. While shifting scientific paradigms to completely open science is a long-term process, our hope in publishing this work is to encourage others to build upon and improve our efforts in new and creative ways.

Strategic traits of bacteria and archaea vary widely within substrate-use groups

Quantitative traits such as maximum growth rate and cell radial diameter are one facet of ecological strategy variation across bacteria and archaea. Another facet is substrate-use pathways, such as iron reduction or methylotrophy. Here, we ask how these two facets intersect, using a large compilation of data for culturable species and examining seven quantitative traits (genome size, signal transduction protein count, histidine kinase count, growth temperature, temperature-adjusted maximum growth rate, cell radial diameter and 16S rRNA operon copy number). Overall, quantitative trait variation within groups of organisms possessing a particular substrate-use pathway was very broad, outweighing differences between substrate-use groups. Although some substrate-use groups had significantly different means for some quantitative traits, standard deviation of quantitative trait values within each substrate-use pathway mostly averaged between 1.6 and 1.8 times larger than standard deviation across group means. Most likely, this wide variation reflects ecological strategy: for example, fast maximum growth rate is likely to express an early successional or copiotrophic strategy, and maximum growth varies widely within most substrate-use pathways. In general, it appears that these quantitative traits express different and complementary information about ecological strategy, compared with substrate use.

Creating accessible evidence bases: Opportunities through the integration of interactive tools into literature review synthesis

The COVID-19 pandemic has shown that an immediate access to relevant information is key for timely interventions and forming of public opinion and discourse. In this regard, dashboards present themselves as invaluable tools for the democratization of data and for the creation of accessible evidence bases. Building on this momentum, it is proposed to integrate interactive means such as dashboards into academic literature review synthesis, in order to support the summarization, narration, and dissemination of findings, and furthermore, to increase transparency and support the transferability and comparability of findings. Exemplified for a systematic literature review on urban forests as nature-based solutions,•

Key functionalities, requirements and design considerations for the development of dashboards for use in academic literature reviews synthesis are identified.

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An application architecture that embeds dashboard development into an R workflow is presented, with emphasis on the steps needed to transform the data collected during the review process into a structured form.

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Technical and methodological means for the actual dashboard implementation are highlighted, considering the identified key functionalities and requirements.

Why Are Species’ Traits Weak Predictors of Range Shifts?

We examine the evidence linking species’ traits to contemporary range shifts and find they are poor predictors of range shifts that have occurred over decades to a century. We then discuss reasons for the poor performance of traits for describing interspecific variation in range shifts from two perspectives: ( a) factors associated with species’ traits that degrade range-shift signals stemming from the measures used for species’ traits, traits that are typically not analyzed, and the influence of phylogeny on range-shift potential and ( b) issues in quantifying range shifts and relating them to species’ traits due to imperfect detection of species, differences in the responses of altitudinal and latitudinal ranges, and emphasis on testing linear relationships between traits and range shifts instead of nonlinear responses. Improving trait-based approaches requires a recognition that traits within individuals interact in unexpected ways and that different combinations of traits may be functionally equivalent.

Ten simple rules for training yourself in an emerging field

The opportunity to participate in and contribute to emerging fields is increasingly prevalent in science. However, simply thinking about stepping outside of your academic silo can leave many students reeling from the uncertainty. Here, we describe 10 simple rules to successfully train yourself in an emerging field, based on our experience as students in the emerging field of ecological forecasting. Our advice begins with setting and revisiting specific goals to achieve your academic and career objectives and includes several useful rules for engaging with and contributing to an emerging field.

The World Spider Trait database: a centralized global open repository for curated data on spider traits

Spiders are a highly diversified group of arthropods and play an important role in terrestrial ecosystems as ubiquitous predators, which makes them a suitable group to test a variety of eco-evolutionary hypotheses. For this purpose, knowledge of a diverse range of species traits is required. Until now, data on spider traits have been scattered across thousands of publications produced for over two centuries and written in diverse languages. To facilitate access to such data, we developed an online database for archiving and accessing spider traits at a global scale. The database has been designed to accommodate a great variety of traits (e.g. ecological, behavioural and morphological) measured at individual, species or higher taxonomic levels. Records are accompanied by extensive metadata (e.g. location and method). The database is curated by an expert team, regularly updated and open to any user. A future goal of the growing database is to include all published and unpublished data on spider traits provided by experts worldwide and to facilitate broad cross-taxon assays in functional ecology and comparative biology. Database URL:https://spidertraits.sci.muni.cz/.

For flux's sake: General considerations for energy-flux calculations in ecological communities

Global change alters ecological communities with consequences for ecosystem processes. Such processes and functions are a central aspect of ecological research and vital to understanding and mitigating the consequences of global change, but also those of other drivers of change in organism communities. In this context, the concept of energy flux through trophic networks integrates food-web theory and biodiversity-ecosystem functioning theory and connects biodiversity to multitrophic ecosystem functioning. As such, the energy-flux approach is a strikingly effective tool to answer central questions in ecology and global-change research. This might seem straight forward, given that the theoretical background and software to efficiently calculate energy flux are readily available. However, the implementation of such calculations is not always straight forward, especially for those who are new to the topic and not familiar with concepts central to this line of research, such as food-web theory or metabolic theory. To facilitate wider use of energy flux in ecological research, we thus provide a guide to adopting energy-flux calculations for people new to the method, struggling with its implementation, or simply looking for background reading, important resources, and standard solutions to the problems everyone faces when starting to quantify energy fluxes for their community data. First, we introduce energy flux and its use in community and ecosystem ecology. Then, we provide a comprehensive explanation of the single steps towards calculating energy flux for community data. Finally, we discuss remaining challenges and exciting research frontiers for future energy-flux research.

AusTraits, a curated plant trait database for the Australian flora

We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.