Showing papers in "Trends in Ecology and Evolution in 2021"

Rewriting results sections in the language of evidence

Abstract: Despite much criticism, black-or-white null-hypothesis significance testing with an arbitrary P-value cutoff still is the standard way to report scientific findings. One obstacle to progress is likely a lack of knowledge about suitable alternatives. Here, we suggest language of evidence that allows for a more nuanced approach to communicate scientific findings as a simple and intuitive alternative to statistical significance testing. We provide examples for rewriting results sections in research papers accordingly. Language of evidence has previously been suggested in medical statistics, and it is consistent with reporting approaches of international research networks, like the Intergovernmental Panel on Climate Change, for example. Instead of re-inventing the wheel, ecology and evolution might benefit from adopting some of the 'good practices' that exist in other fields.

Beyond organic farming - harnessing biodiversity-friendly landscapes.

Abstract: We challenge the widespread appraisal that organic farming is the fundamental alternative to conventional farming for harnessing biodiversity in agricultural landscapes. Certification of organic production is largely restricted to banning synthetic agrochemicals, resulting in limited benefits for biodiversity but high yield losses despite ongoing intensification and specialisation. In contrast, successful agricultural measures to enhance biodiversity include diversifying cropland and reducing field size, which can multiply biodiversity while sustaining high yields in both conventional and organic systems. Achieving a landscape-level mosaic of natural habitat patches and fine-grained cropland diversification in both conventional and organic agriculture is key for promoting large-scale biodiversity. This needs to be urgently acknowledged by policy makers for an agricultural paradigm shift.

Making the UN Decade on Ecosystem Restoration a Social-Ecological Endeavour.

Abstract: The United Nations (UN) recently declared 2021 to 2030 the Decade on Ecosystem Restoration. Against this background, we review recent social-ecological systems research and summarize key themes that could help to improve ecosystem restoration in dynamic social contexts. The themes relate to resilience and adaptability, ecosystem stewardship and navigation of change, relational values, the coevolution of human and ecological systems, long-range social-ecological connections, and leverage points for transformation. We recommend two cross-cutting new research foci; namely: (i) post hoc cross-sectional assessments of social-ecological restoration projects; and (ii) transdisciplinary social-ecological 'living labs' that accompany new restoration projects as they unfold. With global agendas increasingly taking a social-ecological perspective, the recasting of ecosystem restoration as a social-ecological endeavor offers exciting new opportunities for both research and practice.

Why is Tree Drought Mortality so Hard to Predict

Abstract: Widespread tree mortality following droughts has emerged as an environmentally and economically devastating 'ecological surprise'. It is well established that tree physiology is important in understanding drought-driven mortality; however, the accuracy of predictions based on physiology alone has been limited. We propose that complicating factors at two levels stymie predictions of drought-driven mortality: (i) organismal-level physiological and site factors that obscure understanding of drought exposure and vulnerability and (ii) community-level ecological interactions, particularly with biotic agents whose effects on tree mortality may reverse expectations based on stress physiology. We conclude with a path forward that emphasizes the need for an integrative approach to stress physiology and biotic agent dynamics when assessing forest risk to drought-driven morality in a changing climate.

The Temporal Dynamics of Multiple Stressor Effects: From Individuals to Ecosystems

Abstract: Multiple stressors, such as warming and invasions, often occur together and have nonadditive effects Most studies to date assume that stressors operate in perfect synchrony, but this will rarely be the case in reality Stressor sequence and overlap will have implications for ecological memory – the ability of past stressors to influence future responses Moreover, stressors are usually defined in an anthropocentric context: what we consider a short-term stressor, such as a flood, will span multiple generations of microbes We argue that to predict responses to multiple stressors from individuals to the whole ecosystem, it is necessary to consider metabolic rates, which determine the timescales at which individuals operate and therefore, ultimately, the ecological memory at different levels of ecological organization

Mining museums for historical DNA: advances and challenges in museomics.

Abstract: Historical DNA (hDNA), obtained from museum and herbarium specimens, has yielded spectacular new insights into the history of organisms. This includes documenting historical genetic erosion and extinction, discovering species new to science, resolving evolutionary relationships, investigating epigenetic effects, and determining origins of infectious diseases. However, the development of best-practices in isolating, processing, and analyzing hDNA remain under-explored, due to the substantial diversity of specimen preparation types, tissue sources, archival ages, and collecting histories. Thus, for hDNA to reach its full potential, and justify the destructive sampling of the rarest specimens, more experimental work using time-series collections, and the development of improved methods to correct for data asymmetries and biases due to DNA degradation are required.

Adaptive Evolution in Cities: Progress and Misconceptions.

Abstract: Current narratives suggest that urban adaptation – the adaptive evolution of organisms to cities – is pervasive across taxa and cities. However, in reviewing hundreds of studies, we find only six comprehensive examples of species adaptively evolving to urbanization. We discuss the utility and shortcomings of methods for studying urban adaptation. We then review diverse systems offering preliminary evidence for urban adaptation and outline a research program for advancing its study. Urban environments constitute diverse, interacting selective agents that test the limits of adaptation. Understanding urban adaptation therefore offers unique opportunities for addressing fundamental questions in evolutionary biology and for better conserving biodiversity in cities. However, capitalizing on these opportunities requires appropriate research methods and dissemination of accurate narratives.

Integrating Mitochondrial Aerobic Metabolism into Ecology and Evolution

Abstract: Biologists have long appreciated the critical role that energy turnover plays in understanding variation in performance and fitness among individuals. Whole-organism metabolic studies have provided key insights into fundamental ecological and evolutionary processes. However, constraints operating at subcellular levels, such as those operating within the mitochondria, can also play important roles in optimizing metabolism over different energetic demands and time scales. Herein, we explore how mitochondrial aerobic metabolism influences different aspects of organismal performance, such as through changing adenosine triphosphate (ATP) and reactive oxygen species (ROS) production. We consider how such insights have advanced our understanding of the mechanisms underpinning key ecological and evolutionary processes, from variation in life-history traits to adaptation to changing thermal conditions, and we highlight key areas for future research.

Plant phosphorus-acquisition and -use strategies affect soil carbon cycling

Abstract: Increased anthropogenic nitrogen (N) deposition is driving N-limited ecosystems towards phosphorus (P) limitation. Plants have evolved strategies to respond to P limitation which affect N cycling in plant‐soil systems. A comprehensive understanding of how plants with efficient P‐acquisition or ‐use strategies influence carbon (C) and N cycling remains elusive. We highlight how P‐acquisition/-use strategies, particularly the release of carboxylates into the rhizosphere, accelerate soil organic matter (SOM) decomposition and soil N mineralisation by destabilising aggregates and organic‐mineral associations. We advocate studying the effects of P-acquisition/-use strategies on SOM formation, directly or through microbial turnover.

Addressing context dependence in ecology.

Abstract: Context dependence is widely invoked to explain disparate results in ecology. It arises when the magnitude or sign of a relationship varies due to the conditions under which it is observed. Such variation, especially when unexplained, can lead to spurious or seemingly contradictory conclusions, which can limit understanding and our ability to transfer findings across studies, space, and time. Using examples from biological invasions, we identify two types of context dependence resulting from four sources: mechanistic context dependence arises from interaction effects; and apparent context dependence can arise from the presence of confounding factors, problems of statistical inference, and methodological differences among studies. Addressing context dependence is a critical challenge in ecology, essential for increased understanding and prediction.

Energy Flow Through Marine Ecosystems: Confronting Transfer Efficiency

Abstract: Transfer efficiency is the proportion of energy passed between nodes in food webs. It is an emergent, unitless property that is difficult to measure, and responds dynamically to environmental and ecosystem changes. Because the consequences of changes in transfer efficiency compound through ecosystems, slight variations can have large effects on food availability for top predators. Here, we review the processes controlling transfer efficiency, approaches to estimate it, and known variations across ocean biomes. Both process-level analysis and observed macroscale variations suggest that ecosystem-scale transfer efficiency is highly variable, impacted by fishing, and will decline with climate change. It is important that we more fully resolve the processes controlling transfer efficiency in models to effectively anticipate changes in marine ecosystems and fisheries resources.

Emerging Perspectives on Resource Tracking and Animal Movement Ecology.

Abstract: Resource tracking, where animals increase energy gain by moving to track phenological variation in resources across space, is emerging as a fundamental attribute of animal movement ecology. However, a theoretical framework to understand when and where resource tracking should occur, and how resource tracking should lead to emergent ecological patterns, is lacking. We present a framework that unites concepts from optimal foraging theory and landscape ecology, which can be used to generate and test predictions on how resource dynamics shape animal movement across taxa, systems, and scales. Consideration of the interplay between animal movement and resource dynamics not only advances ecological understanding but can also guide biodiversity conservation in an era of global change.

Plant–Soil Feedbacks and Temporal Dynamics of Plant Diversity–Productivity Relationships

Abstract: Plant–soil feedback (PSF) and diversity–productivity relationships are important research fields to study drivers and consequences of changes in plant biodiversity. While studies suggest that positive plant diversity–productivity relationships can be explained by variation in PSF in diverse plant communities, key questions on their temporal relationships remain. Here, we discuss three processes that change PSF over time in diverse plant communities, and their effects on temporal dynamics of diversity–productivity relationships: spatial redistribution and changes in dominance of plant species; phenotypic shifts in plant traits; and dilution of soil pathogens and increase in soil mutualists. Disentangling these processes in plant diversity experiments will yield new insights into how plant diversity–productivity relationships change over time.

Integrating Behavior in Life-History Theory: Allocation versus Acquisition?

Abstract: Central theories explaining the maintenance of individual differences in behavior build on the assumption that behavior mediates life-history trade-offs between current and future reproduction. However, current empirical evidence does not robustly support this assumption. This mismatch might be because current theory is not clear about the role of behavior in individual allocation versus acquisition of resources, hindering empirical testing. The relative importance of allocation compared to acquisition is a key feature of classic life-history theory, but appears to have been lost in translation in recent developments of life-history theory involving behavior. We argue that determining the relative balance between variation in resource allocation and acquisition, and the role of behavior in this process, will help to build more robust and precise predictions.

Environmental RNA: A Revolution in Ecological Resolution?

Abstract: Current advancements in environmental RNA (eRNA) exploit its relatively fast turnover rate relative to environmental DNA (eDNA) to assess 'metabolically active' or temporally/spatially recent community diversity. However, this focus significantly underutilizes the trove of potential ecological information encrypted in eRNA. Here, we argue for pushing beyond current species-level eDNA detection capabilities by using eRNA to detect any organisms with unique eRNA profiles, potentially including different life-history stages, sexes, or even specific phenotypes within a species. We also discuss the future of eRNA as a means of assessing the physiological status of organisms and the ecological health of populations and communities, reflecting ecosystem-level conditions. We posit that eRNA has the potential to significantly improve the resolution of organism detection, biological monitoring, and biomonitoring applications in ecology.

Unraveling the Zoonotic Origin and Transmission of SARS-CoV-2.

Abstract: The origin and zoonotic transmission route of SARS-CoV-2 remain speculative. We discuss scenarios for the zoonotic emergence of SARS-CoV-2, and also explore the missing evidence and ecological considerations that are necessary to confidently identify the origin and transmission route of SARS-CoV-2 and to prevent future pandemics of zoonotic viruses.

Epigenetic inheritance and reproductive mode in plants and animals.

Abstract: Epigenetic inheritance is another piece of the puzzle of nongenetic inheritance, although the prevalence, sources, persistence, and phenotypic consequences of heritable epigenetic marks across taxa remain unclear. We systematically reviewed over 500 studies from the past 5 years to identify trends in the frequency of epigenetic inheritance due to differences in reproductive mode and germline development. Genetic, intrinsic (e.g., disease), and extrinsic (e.g., environmental) factors were identified as sources of epigenetic inheritance, with impacts on phenotype and adaptation depending on environmental predictability. Our review shows that multigenerational persistence of epigenomic patterns is common in both plants and animals, but also highlights many knowledge gaps that remain to be filled. We provide a framework to guide future studies towards understanding the generational persistence and eco-evolutionary significance of epigenomic patterns.

Evaluating Impact Using Time-Series Data.

Abstract: Humanity's impact on the environment is increasing, as are strategies to conserve biodiversity, but a lack of understanding about how interventions affect ecological and conservation outcomes hampers decision-making. Time series are often used to assess impacts, but ecologists tend to compare average values from before to after an impact; overlooking the potential for the intervention to elicit a change in trend. Without methods that allow for a range of responses, erroneous conclusions can be drawn, especially for large, multi-time-series datasets, which are increasingly available. Drawing on literature in other disciplines and pioneering work in ecology, we present a standardised framework to robustly assesses how interventions, like natural disasters or conservation policies, affect ecological time series.

Making ecology really global.

Abstract: Ecology must flourish globally, especially in a period of unprecedented anthropogenic global change. However, some regions dominate the ecological literature. Multiple barriers prevent global production and exchange of ecological knowledge. The first step towards solutions is acknowledging and diagnosing this inequality and embracing our geographical and cultural diversity.

On the Interpretations of Joint Modeling in Community Ecology.

Abstract: Explaining and modeling species communities is more than ever a central goal of ecology. Recently, joint species distribution models (JSDMs), which extend species distribution models (SDMs) by considering correlations among species, have been proposed to improve species community analyses and rare species predictions while potentially inferring species interactions. Here, we illustrate the mathematical links between SDMs and JSDMs and their ecological implications and demonstrate that JSDMs, just like SDMs, cannot separate environmental effects from biotic interactions. We provide a guide to the conditions under which JSDMs are (or are not) preferable to SDMs for species community modeling. More generally, we call for a better uptake and clarification of novel statistical developments in the field of biodiversity modeling.

Functional trait effects on ecosystem stability: assembling the jigsaw puzzle.

Abstract: Under global change, how biological diversity and ecosystem services are maintained in time is a fundamental question. Ecologists have long argued about multiple mechanisms by which local biodiversity might control the temporal stability of ecosystem properties. Accumulating theories and empirical evidence suggest that, together with different population and community parameters, these mechanisms largely operate through differences in functional traits among organisms. We review potential trait-stability mechanisms together with underlying tests and associated metrics. We identify various trait-based components, each accounting for different stability mechanisms, that contribute to buffering, or propagating, the effect of environmental fluctuations on ecosystem functioning. This comprehensive picture, obtained by combining different puzzle pieces of trait-stability effects, will guide future empirical and modeling investigations.

Urban Biodiversity and the Importance of Scale

Abstract: Many ecological and evolutionary processes are affected by urbanization, but cities vary by orders of magnitude in their human population size and areal extent. To quantify and manage urban biodiversity, one must understand both how biodiversity scales with city size, and how ecological, evolutionary, and socioeconomic drivers of biodiversity scale with city size. We show how environmental abiotic and biotic drivers, as well as human cultural and socioeconomic drivers, may act through ecological and evolutionary processes differently, at different scales, to influence patterns in urban biodiversity. Because relationships likely take linear and nonlinear forms, the need to describe the specific scaling relationships is highlighted, including deviations and potential inflection points, where different management strategies may successfully conserve urban biodiversity.

Towards an Evolutionary Theory of Stress Responses

Abstract: All organisms have a stress response system to cope with environmental threats, yet its precise form varies hugely within and across individuals, populations, and species. While the physiological mechanisms are increasingly understood, how stress responses have evolved remains elusive. Here, we show that important insights can be gained from models that incorporate physiological mechanisms within an evolutionary optimality analysis (the 'evo-mecho' approach). Our approach reveals environmental predictability and physiological constraints as key factors shaping stress response evolution, generating testable predictions about variation across species and contexts. We call for an integrated research programme combining theory, experimental evolution, and comparative analysis to advance scientific understanding of how this core physiological system has evolved.

Winner–loser species replacements in human-modified landscapes

Abstract: Community assembly arguably drives the provision of ecosystem services because they critically depend on which and how species coexist. We examine conspicuous cases of 'winner and loser' replacements (WLRs) in tropical forests to provide a framework integrating drivers, impacts on ecological organization, and reconfiguration of ecosystem service provisioning. Most WLRs involve native species and result from changes in resource availability rather than from altered competition among species. In this context, species dispersal is a powerful force controlling community (re)assembly. Furthermore, replacements imply a nearly complete functional reorganization of assemblages and new 'packages' of ecosystem services and disservices provided by winners. WLRs can thus elucidate the multiple transitions experienced by tropical forests, and have theoretical/applied implications, including the role that human-modified landscapes may play in global-scale sustainability.

Shape-shifting: changing animal morphologies as a response to climatic warming

Abstract: Many animal appendages, such as avian beaks and mammalian ears, can be used to dissipate excess body heat. Allen's rule, wherein animals in warmer climates have larger appendages to facilitate more efficient heat exchange, reflects this. We find that there is widespread evidence of ‘shape-shifting' (changes in appendage size) in endotherms in response to climate change and its associated climatic warming. We re-examine studies of morphological change over time within a thermoregulatory context, finding evidence that temperature can be a strong predictor of morphological change independently of, or combined with, other environmental changes. Last, we discuss how Allen's rule, the degree of temperature change, and other ecological factors facilitate morphological change and make predictions about what animals will show shape-shifting.

Improving Predictions of Climate Change-Land Use Change Interactions.

Abstract: Climate change and land use change often interact, altering biodiversity in unexpected ways. Research into climate change-land use change (CC-LUC) interactions has so far focused on quantifying biodiversity outcomes, rather than identifying the underlying ecological mechanisms, making it difficult to predict interactions and design appropriate conservation responses. We propose a risk-based framework to further our understanding of CC-LUC interactions. By identifying the factors driving the exposure and vulnerability of biodiversity to land use change, and then examining how these factors are altered by climate change (or vice versa), this framework will allow the effects of different interaction mechanisms to be compared across geographic and ecological contexts, supporting efforts to reduce biodiversity loss from interacting stressors.

How useful are thermal vulnerability indices

Abstract: To forecast climate change impacts across habitats or taxa, thermal vulnerability indices (e.g., safety margins and warming tolerances) are growing in popularity. Here, we present their history, context, formulation, and current applications. We highlight discrepancies in terminology and usage, and we draw attention to key assumptions underpinning the main indices and to their ecological and evolutionary relevance. In the process, we flag biases influencing these indices that are not always evaluated. These biases affect both components of index formulations, namely: (i) the characterisation of the thermal environment; and (ii) an organism's physiological and behavioural responses to more frequent and severe warming. Presently, many outstanding questions weaken a thermal vulnerability index approach. We describe ways to validate vulnerability index applications and outline issues to be considered in further developing these indices.

The cold range limit of trees.

Abstract: At high elevation or latitude, trees reach low-temperature range limits. In attempting an explanation, the range limits of individual tree species (set by freezing tolerance) and the general limit of the life-form tree (set by thermal growth constraints) need to be distinguished. The general cold edge of the fundamental niche of trees is termed the treeline, by definition, the lower edge of the alpine belt, a most important bioclimatological reference line. Trees can be absent from the treeline due to disturbances or biotic interactions. The actual local edge of tree distribution, the delineation of the realized niche, is driven by stochastic effects. Therefore, treeline theory and hypothesis testing is inevitably tied to the fundamental niche concept.

Draining the Swamping Hypothesis: Little Evidence that Gene Flow Reduces Fitness at Range Edges.

Abstract: The genetic swamping hypothesis proposes that gene flow from central to peripheral populations inhibits local adaptation and is one of the most widely recognized explanations for range limitation. We evaluated empirical support for this hypothesis in studies quantifying patterns of gene flow to peripheral populations and their resulting fitness outcomes. We found little evidence that gene flow is generally asymmetric from central to peripheral populations and also that gene flow tends to have positive effects on edge population fitness. These findings contravene the long-held assumption that genetic swamping is a common driver of species range limits, and bear important implications for understanding the role of gene flow in range evolution and for predicting and managing eco-evolutionary responses to climate change.

Coral environmental memory: causes, mechanisms, and consequences for future reefs.

Abstract: The apparent ability of corals to acquire and maintain enhanced stress tolerance through a dose-dependent environmental memory, which may persist for multiple years, has critical implications for coral reef conservation research. Such responses are variable across coral species and environmental stressors, with primed corals exhibiting a modified response to secondary stress exposures. While the mechanisms underlying coral memory responses are poorly understood, they likely involve both the coral host and microbiome. With advances in molecular technologies, it is now possible to investigate potential memory mechanisms in non-model organisms, including transcriptional regulation through epigenetic modifications. We integrate evidence of coral environmental memory and suggest future research directions to evaluate the potential for this process to enhance coral resilience under climate change.