Estimating maximum oxygen uptake of fishes during swimming and following exhaustive chase - different results, biological bases and applications.

The maximum rate at which animals take up oxygen from their environment (MO2,max) is a crucial aspect of their physiology and ecology. In fishes, MO2,max is commonly quantified by measuring oxygen uptake either during incremental swimming tests or during recovery from an exhaustive chase. In this Commentary, we compile recent studies that apply both techniques to the same fish and show that the two methods typically yield different mean estimates of MO2,max for a group of individuals. Furthermore, within a group of fish, estimates of MO2,max determined during swimming are poorly correlated with estimates determined during recovery from chasing (i.e. an individual's MO2,max is not repeatable across methods). One explanation for the lack of agreement is that these methods measure different physiological states, each with their own behavioural, anatomical and biochemical determinants. We propose that these methods are not directly interchangeable but, rather, each is suited to address different questions in fish biology. We suggest that researchers select the method that reflects the biological contexts of their study, and we advocate for the use of accurate terminology that acknowledges the technique used to elevate MO2 (e.g. peak MO2,swim or peak MO2,recovery). If the study's objective is to estimate the 'true' MO2,max of an individual or species, we recommend that pilot studies compare methods, preferably using repeated-measures designs. We hope that these recommendations contribute new insights into the causes and consequences of variation in MO2,max within and among fish species.

Postdoctoral scientists are mentors, and it is time to recognize their work.

Academia often fails to recognize the important work that supports its functioning, such as mentoring and teaching performed by postdoctoral researchers. This is a particular problem for early-career researchers, but opportunities exist to improve the status quo.

Open science.

The term 'open science' refers to a range of methods, tools, platforms and practices that aim to make scientific research more accessible, transparent, reproducible and reliable. This includes, for example, sharing code, data and research materials, embracing new publishing formats such as registered reports and preprints, pursuing replication studies and reanalyses, optimising statistical approaches to improve evidence assessment and re-evaluating institutional incentives. The ongoing shift towards open science practices is partly due to mounting evidence that studies across disciplines suffer from biases, underpowered designs and irreproducible or non-replicable results. It also stems from a general desire amongst many researchers to reduce hyper-competitivity in science and instead promote collaborative research that benefits science and society.

Kinematics and behaviour in fish escape responses: guidelines for conducting, analysing and reporting experiments.

Work carried out since the late 1970s has provided key insights into the comparative biomechanics, kinematics, behaviour and neurobiology of fish escape responses. An escape response is an ecologically important behaviour used by fishes to evade predation and aggression via rapid swimming movements. With environmental change expected to affect the physiology and biomechanics of aquatic ectotherms, there is a growing interest in understanding how environmental stressors affect the swimming performance and behaviour of fishes during escape responses, particularly in the context of predator-prey interactions. As the study of fish swimming continues to expand, there have been repeated calls to standardise experiments and reporting practices to facilitate integrative and comparative studies. Here, we provide a set of practical guidelines for conducting, analysing and reporting experiments on escape responses in fish, including a reporting checklist to assist authors undertaking these experiments. These resources will facilitate executing and reporting escape response experiments in a rigorous and transparent fashion, helping to advance the study of fish swimming in an era of rapid environmental change.

Early Release Science of the exoplanet WASP-39b with JWST NIRCam.

Measuring the metallicity and carbon-to-oxygen (C/O) ratio in exoplanet atmospheres is a fundamental step towards constraining the dominant chemical processes at work and, if in equilibrium, revealing planet formation histories. Transmission spectroscopy (for example, refs. 1,2) provides the necessary means by constraining the abundances of oxygen- and carbon-bearing species; however, this requires broad wavelength coverage, moderate spectral resolution and high precision, which, together, are not achievable with previous observatories. Now that JWST has commenced science operations, we are able to observe exoplanets at previously uncharted wavelengths and spectral resolutions. Here we report time-series observations of the transiting exoplanet WASP-39b using JWST's Near InfraRed Camera (NIRCam). The long-wavelength spectroscopic and short-wavelength photometric light curves span 2.0-4.0 micrometres, exhibit minimal systematics and reveal well defined molecular absorption features in the planet's spectrum. Specifically, we detect gaseous water in the atmosphere and place an upper limit on the abundance of methane. The otherwise prominent carbon dioxide feature at 2.8 micrometres is largely masked by water. The best-fit chemical equilibrium models favour an atmospheric metallicity of 1-100-times solar (that is, an enrichment of elements heavier than helium relative to the Sun) and a substellar C/O ratio. The inferred high metallicity and low C/O ratio may indicate significant accretion of solid materials during planet formation (for example, refs. 3,4,) or disequilibrium processes in the upper atmosphere (for example, refs. 5,6).

No evidence that mandatory open data policies increase error correction.

Using a database of open data policies for 199 journals in ecology and evolution, we found no detectable link between data sharing requirements and article retractions or corrections. Despite the potential for open data to facilitate error detection, poorly archived datasets, the absence of open code and the stigma associated with correcting or retracting articles probably stymie error correction. Requiring code alongside data and destigmatizing error correction among authors and journal editors could increase the effectiveness of open data policies at helping science self-correct.

Increased parasite load is associated with reduced metabolic rates and escape responsiveness in pumpkinseed sunfish.

Wild animals have parasites that can compromise their physiological and/or behavioural performance. Yet, the extent to which parasite load is related to intraspecific variation in performance traits within wild populations remains relatively unexplored. We used pumpkinseed sunfish (Lepomis gibbosus) and their endoparasites as a model system to explore the effects of infection load on host aerobic metabolism and escape performance. Metabolic traits (standard and maximum metabolic rates, aerobic scope) and fast-start escape responses following a simulated aerial attack by a predator (responsiveness, response latency and escape distance) were measured in fish from across a gradient of visible (i.e. trematodes causing black spot disease counted on fish surfaces) and non-visible (i.e. cestodes in fish abdominal cavity counted post-mortem) endoparasite infection. We found that a higher infection load of non-visible endoparasites was related to lower standard and maximum metabolic rates, but not aerobic scope in fish. Non-visible endoparasite infection load was also related to decreased responsiveness of the host to a simulated aerial attack. Visible endoparasites were not related to changes in metabolic traits or fast-start escape responses. Our results suggest that infection with parasites that are inconspicuous to researchers can result in intraspecific variation in physiological and behavioural performance in wild populations, highlighting the need to more explicitly acknowledge and account for the role played by natural infections in studies of wild animal performance.

Data rescue: saving environmental data from extinction.

Historical and long-term environmental datasets are imperative to understanding how natural systems respond to our changing world. Although immensely valuable, these data are at risk of being lost unless actively curated and archived in data repositories. The practice of data rescue, which we define as identifying, preserving, and sharing valuable data and associated metadata at risk of loss, is an important means of ensuring the long-term viability and accessibility of such datasets. Improvements in policies and best practices around data management will hopefully limit future need for data rescue; these changes, however, do not apply retroactively. While rescuing data is not new, the term lacks formal definition, is often conflated with other terms (i.e. data reuse), and lacks general recommendations. Here, we outline seven key guidelines for effective rescue of historically collected and unmanaged datasets. We discuss prioritization of datasets to rescue, forming effective data rescue teams, preparing the data and associated metadata, and archiving and sharing the rescued materials. In an era of rapid environmental change, the best policy solutions will require evidence from both contemporary and historical sources. It is, therefore, imperative that we identify and preserve valuable, at-risk environmental data before they are lost to science.

Slow improvement to the archiving quality of open datasets shared by researchers in ecology and evolution.

Many leading journals in ecology and evolution now mandate open data upon publication. Yet, there is very little oversight to ensure the completeness and reusability of archived datasets, and we currently have a poor understanding of the factors associated with high-quality data sharing. We assessed 362 open datasets linked to first- or senior-authored papers published by 100 principal investigators (PIs) in the fields of ecology and evolution over a period of 7 years to identify predictors of data completeness and reusability (data archiving quality). Datasets scored low on these metrics: 56.4% were complete and 45.9% were reusable. Data reusability, but not completeness, was slightly higher for more recently archived datasets and PIs with less seniority. Journal open data policy, PI gender and PI corresponding author status were unrelated to data archiving quality. However, PI identity explained a large proportion of the variance in data completeness (27.8%) and reusability (22.0%), indicating consistent inter-individual differences in data sharing practices by PIs across time and contexts. Several PIs consistently shared data of either high or low archiving quality, but most PIs were inconsistent in how well they shared. One explanation for the high intra-individual variation we observed is that PIs often conduct research through students and postdoctoral researchers, who may be responsible for the data collection, curation and archiving. Levels of data literacy vary among trainees and PIs may not regularly perform quality control over archived files. Our findings suggest that research data management training and culture within a PI's group are likely to be more important determinants of data archiving quality than other factors such as a journal's open data policy. Greater incentives and training for individual researchers at all career stages could improve data sharing practices and enhance data transparency and reusability.

Paths towards greater consensus building in experimental biology.

In a recent editorial, the Editors-in-Chief of Journal of Experimental Biology argued that consensus building, data sharing, and better integration across disciplines are needed to address the urgent scientific challenges posed by climate change. We agree and expand on the importance of cross-disciplinary integration and transparency to improve consensus building and advance climate change research in experimental biology. We investigated reproducible research practices in experimental biology through a review of open data and analysis code associated with empirical studies on three debated paradigms and for unrelated studies published in leading journals in comparative physiology and behavioural ecology over the last 10 years. Nineteen per cent of studies on the three paradigms had open data, and 3.2% had open code. Similarly, 12.1% of studies in the journals we examined had open data, and 3.1% had open code. Previous research indicates that only 50% of shared datasets are complete and re-usable, suggesting that fewer than 10% of studies in experimental biology have usable open data. Encouragingly, our results indicate that reproducible research practices are increasing over time, with data sharing rates in some journals reaching 75% in recent years. Rigorous empirical research in experimental biology is key to understanding the mechanisms by which climate change affects organisms, and ultimately promotes evidence-based conservation policy and practice. We argue that a greater adoption of open science practices, with a particular focus on FAIR (Findable, Accessible, Interoperable, Re-usable) data and code, represents a much-needed paradigm shift towards improved transparency, cross-disciplinary integration, and consensus building to maximize the contributions of experimental biologists in addressing the impacts of environmental change on living organisms.

Closing the knowledge-action gap in conservation with open science.

The knowledge-action gap in conservation science and practice occurs when research outputs do not result in actions to protect or restore biodiversity. Among the diverse and complex reasons for this gap, three barriers are fundamental: knowledge is often unavailable to practitioners and challenging to interpret or difficult to use or both. Problems of availability, interpretability, and useability are solvable with open science practices. We considered the benefits and challenges of three open science practices for use by conservation scientists and practitioners. First, open access publishing makes the scientific literature available to all. Second, open materials (detailed methods, data, code, and software) increase the transparency and use of research findings. Third, open education resources allow conservation scientists and practitioners to acquire the skills needed to use research outputs. The long-term adoption of open science practices would help researchers and practitioners achieve conservation goals more quickly and efficiently and reduce inequities in information sharing. However, short-term costs for individual researchers (insufficient institutional incentives to engage in open science and knowledge mobilization) remain a challenge. We caution against a passive approach to sharing that simply involves making information available. We advocate a proactive stance toward transparency, communication, collaboration, and capacity building that involves seeking out and engaging with potential users to maximize the environmental and societal impact of conservation science.

Cierre de la Brecha entre el Conocimiento y la Acción en la Conservación con Ciencia Abierta 21-311 Resumen La brecha entre el conocimiento y la acción en las ciencias de la conservación y en su práctica ocurre cuando los resultados de las investigaciones no derivan en acciones para proteger o restaurar la biodiversidad. Entre las razones complejas y diversas de esta brecha, existen tres barreras que son fundamentales: con frecuencia el conocimiento no está disponible para los practicantes, es difícil de interpretar o difícil de usar, o ambas. Los problemas con la disponibilidad, interpretabilidad y utilidad son solucionables mediante las prácticas de ciencia abierta. Consideramos los beneficios y los obstáculos de tres prácticas de ciencia abierta para su uso por parte de los científicos y practicantes de la conservación. Primero, las publicaciones de acceso abierto hacen que la literatura científica esté disponible para todos. Segundo, los materiales abiertos (métodos detallados, datos, códigos y software) incrementan la transparencia y el uso de los hallazgos de las investigaciones. Tercero, los recursos educativos abiertos permiten que los científicos y practicantes de la conservación adquieran las habilidades necesarias para utilizar los productos de las investigaciones. La adopción a largo plazo de las prácticas de ciencia abierta ayudaría a los investigadores y a los practicantes a lograr los objetivos de conservación mucho más rápido y de manera eficiente y a reducir las desigualdades que existen en la divulgación de información. Sin embargo, los costos a corto plazo para los investigadores individuales (incentivos institucionales insuficientes para participar en la ciencia abierta y en la movilización del conocimiento) todavía son un reto. Advertimos sobre las estrategias pasivas de divulgación que simplemente hacen que la información esté disponible. Abogamos por una postura proactiva hacia la transparencia, la comunicación, la colaboración y la construcción de las capacidades que incluyen la búsqueda de y la interacción con los usuarios potenciales para maximizar el impacto ambiental y social de las ciencias de la conservación.

Towards open, reliable, and transparent ecology and evolutionary biology.

Unreliable research programmes waste funds, time, and even the lives of the organisms we seek to help and understand. Reducing this waste and increasing the value of scientific evidence require changing the actions of both individual researchers and the institutions they depend on for employment and promotion. While ecologists and evolutionary biologists have somewhat improved research transparency over the past decade (e.g. more data sharing), major obstacles remain. In this commentary, we lift our gaze to the horizon to imagine how researchers and institutions can clear the path towards more credible and effective research programmes.

Effects of wave-driven water flow on the fast-start escape response of juvenile coral reef damselfishes.

Fish often evade predators with a fast-start escape response. Studies typically examine this behaviour in still water despite water motion being an inherent feature of aquatic ecosystems. In shallow habitats, waves create complex flows that likely influence escape performance, particularly in small fishes with low absolute swimming speeds relative to environmental flows. I examined how wave-driven water flow affects the behaviour and kinematics of escape responses in juveniles of three coral reef damselfishes (Pomacentridae) with different body morphologies. Tropical damselfishes have similar fin and body shapes during early development, with the exception of body depth, a trait deemed important for postural control and stability. Wave-driven flow increased response latency in two of the three species tested: fish with a fusiform body responded 2.9 times slower in wave-driven flow than in still water, whereas this difference was less pronounced in fish with an intermediate body depth (1.9 times slower response) and absent in fish with a laterally compressed body. The effect of wave-driven flow on swimming performance (cumulative escape distance and turning rate) was variable and depended on the timing and trajectory of escape responses in relation to the wave phase. Given intense predation pressure on juvenile coral reef fishes during settlement, interspecific differences in how wave-driven flow affects their ability to escape predators could influence the distribution and abundance of species across spatial and temporal scales.

Three lessons conservation science can learn from the COVID-19 pandemic.

Article impact statement: COVID-19 has demonstrated the need to optimize research activity, convey the gravity of loss, and reevaluate merit in conservation science.

Ocean acidification does not impair the behaviour of coral reef fishes.

The partial pressure of CO2 in the oceans has increased rapidly over the past century, driving ocean acidification and raising concern for the stability of marine ecosystems1-3. Coral reef fishes are predicted to be especially susceptible to end-of-century ocean acidification on the basis of several high-profile papers4,5 that have reported profound behavioural and sensory impairments-for example, complete attraction to the chemical cues of predators under conditions of ocean acidification. Here, we comprehensively and transparently show that-in contrast to previous studies-end-of-century ocean acidification levels have negligible effects on important behaviours of coral reef fishes, such as the avoidance of chemical cues from predators, fish activity levels and behavioural lateralization (left-right turning preference). Using data simulations, we additionally show that the large effect sizes and small within-group variances that have been reported in several previous studies are highly improbable. Together, our findings indicate that the reported effects of ocean acidification on the behaviour of coral reef fishes are not reproducible, suggesting that behavioural perturbations will not be a major consequence for coral reef fishes in high CO2 oceans.

Brain cooling marginally increases acute upper thermal tolerance in Atlantic cod.

Physiological mechanisms determining thermal limits in fishes are debated but remain elusive. It has been hypothesised that motor function loss, observed as loss of equilibrium during acute warming, is due to direct thermal effects on brain neuronal function. To test this, we mounted cooling plates on the heads of Atlantic cod (Gadus morhua) and quantified whether local brain cooling increased whole-organism acute upper thermal tolerance. Brain cooling reduced brain temperature by 2-6°C below ambient water temperature and increased thermal tolerance by 0.5 and 0.6°C on average relative to instrumented and uninstrumented controls, respectively, suggesting that direct thermal effects on brain neurons may contribute to setting upper thermal limits in fish. However, the improvement in thermal tolerance with brain cooling was small relative to the difference in brain temperature, demonstrating that other mechanisms (e.g. failure of spinal and peripheral neurons, or muscle) may also contribute to controlling acute thermal tolerance.

Environmental sciences benefit from robust evidence irrespective of speed.

Discussions around the "slow science movement" abound in environmental sciences, yet they are generally counterproductive. Researchers must focus on producing robust and transparent knowledge, regardless of speed. Slow versus fast science is irrelevant - what we need is reproducible research to support evidence-based decision making and tackle urgent and costly environmental problems.

MIReAD, a minimum information standard for reporting arthropod abundance data.

Arthropods play a dominant role in natural and human-modified terrestrial ecosystem dynamics. Spatially-explicit arthropod population time-series data are crucial for statistical or mathematical models of these dynamics and assessment of their veterinary, medical, agricultural, and ecological impacts. Such data have been collected world-wide for over a century, but remain scattered and largely inaccessible. In particular, with the ever-present and growing threat of arthropod pests and vectors of infectious diseases, there are numerous historical and ongoing surveillance efforts, but the data are not reported in consistent formats and typically lack sufficient metadata to make reuse and re-analysis possible. Here, we present the first-ever minimum information standard for arthropod abundance, Minimum Information for Reusable Arthropod Abundance Data (MIReAD). Developed with broad stakeholder collaboration, it balances sufficiency for reuse with the practicality of preparing the data for submission. It is designed to optimize data (re)usability from the "FAIR," (Findable, Accessible, Interoperable, and Reusable) principles of public data archiving (PDA). This standard will facilitate data unification across research initiatives and communities dedicated to surveillance for detection and control of vector-borne diseases and pests.