Dominique G. Roche

Ocean acidification, caused by rising carbon dioxide (CO ₂ ) in the atmosphere, has been reported to negatively impact a wide variety of behaviours in fishes, including activity, exploration, and predator avoidance. These effects have been documented at the population level, but many animal species naturally show large and repeatable individual‐level differences in behaviour. How environmental stressors, such as ocean acidification, affect behavioural variation at the individual level remains largely unknown but is vital in understanding adaptation given natural selection operates on variation at the individual rather than population level. Using a statistical approach allowing variation in means and variation in variance to be modelled within a single framework, we quantified individual‐level differences across five behaviours in the coral reef Ambon damselfish Pomacentrus amboinensis (emergence time, activity level, time spent sheltering, thigmotaxis and novel object inspection). We measured behaviour in a novel environment assay, twice before (CO ₂ ~450 μatm) and twice following 4–6 days of exposure to predicted end‐of‐century ocean acidification conditions (~1100 μatm). Following behavioural assays, we tested individual survival in a live predation experiment. We used predatory rock cod, Cephalopholis microprion , acclimated to the same CO ₂ treatments as Ambon damsels and examined predictors of survival probability. All behaviours in damselfish were moderately and significantly repeatable, with no marked differences in repeatability estimates between the ambient CO ₂ and elevated CO ₂ treatment groups. Exposure to end‐of‐century ocean acidification conditions had no effect on any of the five behaviours measured, both in terms of group means and residual (within‐individual) variance. The probability of survival in the predation trials was similar for damselfish in the ambient and elevated CO ₂ treatment groups. Smaller damselfish as well as those that spent a greater amount of time inspecting a novel object (i.e. bolder individuals) had a lower probability of survival regardless of their CO ₂ treatment. Our results challenge assumptions about the impacts of ocean acidification on coral reef fish behaviour and susceptibility to predation, both at the population and individual level. They also provide support for a trade‐off between boldness and predation risk in fish.

Data and code are essential for ensuring the credibility of scientific results and facilitating reproducibility, areas in which journal sharing policies play a crucial role. However, in ecology and evolution, we still do not know how widespread data- and code-sharing policies are, how accessible they are, and whether journals support data and code peer review. Here, we first assessed the clarity, strictness and timing of data- and code-sharing policies across 275 journals in ecology and evolution. Second, we assessed initial compliance to journal policies using submissions from two journals: Proceedings of the Royal Society B (Mar 2023–Feb 2024: n = 2340) and Ecology Letters (Jun 2021–Nov 2023: n = 571). Our results indicate the need for improvement: across 275 journals, 22.5% encouraged and 38.2% mandated data-sharing, while 26.6% encouraged and 26.9% mandated code-sharing. Journals that mandated data- or code-sharing typically required it for peer review (59.0% and 77.0%, respectively), which decreased when journals only encouraged sharing (40.3% and 24.7%, respectively). Our evaluation of policy compliance confirmed the important role of journals in increasing data- and code-sharing but also indicated the need for meaningful changes to enhance reproducibility. We provide seven recommendations to help improve data- and code-sharing, and policy compliance.

Although variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in different fields and has found substantial variability among results despite analysts having the same data and research question. Many of these studies have been in the social sciences, but one small “many analyst” study found similar variability in ecology. We expanded the scope of this prior work by implementing a large-scale empirical exploration of the variation in effect sizes and model predictions generated by the analytical decisions of different researchers in ecology and evolutionary biology. We used two unpublished datasets, one from evolutionary ecology (blue tit, Cyanistes caeruleus, to compare sibling number and nestling growth) and one from conservation ecology (Eucalyptus, to compare grass cover and tree seedling recruitment). The project leaders recruited 174 analyst teams, comprising 246 analysts, to investigate the answers to prespecified research questions. Analyses conducted by these teams yielded 141 usable effects (compatible with our meta-analyses and with all necessary information provided) for the blue tit dataset, and 85 usable effects for the Eucalyptus dataset. We found substantial heterogeneity among results for both datasets, although the patterns of variation differed between them. For the blue tit analyses, the average effect was convincingly negative, with less growth for nestlings living with more siblings, but there was near continuous variation in effect size from large negative effects to effects near zero, and even effects crossing the traditional threshold of statistical significance in the opposite direction. In contrast, the average relationship between grass cover and Eucalyptus seedling number was only slightly negative and not convincingly different from zero, and most effects ranged from weakly negative to weakly positive, with about a third of effects crossing the traditional threshold of significance in one direction or the other. However, there were also several striking outliers in the Eucalyptus dataset, with effects far from zero. For both datasets, we found substantial variation in the variable selection and random effects structures among analyses, as well as in the ratings of the analytical methods by peer reviewers, but we found no strong relationship between any of these and deviation from the meta-analytic mean. In other words, analyses with results that were far from the mean were no more or less likely to have dissimilar variable sets, use random effects in their models, or receive poor peer reviews than those analyses that found results that were close to the mean. The existence of substantial variability among analysis outcomes raises important questions about how ecologists and evolutionary biologists should interpret published results, and how they should conduct analyses in the future.

Publishing preprints is quickly becoming commonplace in ecology and evolutionary biology. Preprints can facilitate the rapid sharing of scientific knowledge establishing precedence and enabling feedback from the research community before peer review. Yet, significant barriers to preprint use exist, including language barriers, a lack of understanding about the benefits of preprints and a lack of diversity in the types of research outputs accepted (e.g. reports). Community-driven preprint initiatives can allow a research community to come together to break down these barriers to improve equity and coverage of global knowledge. Here, we explore the first preprints uploaded to EcoEvoRxiv ( n = 1216), a community-driven preprint server for ecologists and evolutionary biologists, to characterize preprint use in ecology, evolution and conservation. Our perspective piece highlights some of the unique initiatives that EcoEvoRxiv has taken to break down barriers to scientific publishing by exploring the composition of articles, how gender and career stage influence preprint use, whether preprints are associated with greater open science practices (e.g. code and data sharing) and tracking preprint publication outcomes. Our analysis identifies areas that we still need to improve upon but highlights how community-driven initiatives, such as EcoEvoRxiv , can play a crucial role in shaping publishing practices in biology.

In March 2021, Canada’s three federal research funding agencies introduced the Tri-Agency Research Data Management (RDM) Policy, with the objective of promoting sound RDM and data stewardship practices at research institutions. Among the requirements of the Policy, each post-secondary institution and research hospital eligible to administer agency funds was required to publish an institutional RDM strategy. This study presents a cross-sectional mapping of published institutional strategies ( n = 211) in response to the Tri-Agency RDM Policy requirement. We extracted information pertaining to institutional characteristics, institutional needs, and support models for data management planning and data deposit. Our analysis of institutional strategies indicates that developing RDM expertise among researchers (84%, n = 177) and research support staff (61%, n = 129) is of high priority. We also found that most institutions did not describe activities to promote behavioural changes and foster a broader culture of RDM among researchers; only 6% of institutional strategies ( n = 12) explored shifting incentives and rewards. A mapping of institutional RDM strategies is an important step to identify potential gaps in responding to the Policy. We find that further efforts are needed to address consultation gaps, resource constraints, and support for data management plans and data deposit to foster a robust and effective RDM culture at Canadian research institutions.

In March 2021 Canada’s three federal research funding agencies introduced the Tri-Agency Research Data Management (RDM) Policy, with the objective of promoting sound RDM and data stewardship practices at research institutions. Among the requirements of the Policy, each post-secondary institution and research hospital eligible to administer agency funds was required to publish an institutional RDM strategy. This study presents a cross-sectional mapping of published institutional strategies (n=211) in response to the Tri-Agency RDM Policy requirement. We extracted information pertaining to institutional characteristics, institutional needs, and support models for data management planning and data deposit. Our analysis of institutional strategies indicates that developing RDM expertise among researchers (84%, n=177) and research support staff (61%, n=129) is of high priority. We also found that institutions did not describe activities, such as shifting incentives and rewards (6%, n=12), to incite behavioural changes and foster a broader culture of RDM among researchers. A mapping of institutional RDM strategies is an important step to identify potential gaps in responding to the Policy. We find that further efforts are needed to address consultation gaps, resource constraints, and support for data management plans and data deposit to foster a robust and effective RDM culture at Canadian research institutions.***En mars 2021, les trois organismes fédéraux de financement de la recherche du Canada ont mis en place la Politique des trois organismes sur la gestion des données de recherche (GDR), en vue de promouvoir de bonnes pratiques de GDR et d’intendance des données dans les établissements de recherche. Entre autres exigences de cette politique, chaque établissement postsecondaire et hôpital de recherche admissible à administrer des fonds attribués par les organismes était tenu de publier une stratégie institutionnelle de GDR. Cette étude présente une schématisation transversale des stratégies institutionnelles publiées (n = 211) en réponse à l’exigence de la Politique des trois organismes sur la GDR. Nous avons extrait des renseignements sur les caractéristiques institutionnelles, les besoins institutionnels et les modèles de soutien pour la planification de la gestion des données et le dépôt des données. Notre analyse des stratégies institutionnelles indique que le développement de l’expertise en GDR chez les chercheurs (84 %, n = 177) et le personnel de soutien à la recherche (61 %, n = 129) est une priorité élevée. Nous avons également constaté que les établissements ne décrivaient pas d’activités, comme la réorientation des mesures incitatives et des récompenses (6 %, n = 12), pour susciter des changements de comportement et favoriser l’élargissement de la culture de la GDR chez les chercheurs. La schématisation des stratégies institutionnelles de GDR est une étape importante pour cerner les lacunes potentielles dans la réponse à la politique. Nous estimons que des efforts supplémentaires sont de mise pour combler les lacunes en matière de consultation, remédier aux contraintes budgétaires et soutenir les plans de gestion des données et le dépôt de données afin de favoriser une culture de GDR solide et efficace dans les établissements de recherche canadiens.

The maximum rate at which animals take up oxygen from their environment (ṀO2,max) is a crucial aspect of their physiology and ecology. In fishes, ṀO2,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 ṀO2,max for a group of individuals. Furthermore, within a group of fish, estimates of ṀO2,max determined during swimming are poorly correlated with estimates determined during recovery from chasing (i.e. an individual's ṀO2,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 ṀO2 (e.g. peak ṀO2,swim or peak ṀO2,recovery). If the study's objective is to estimate the ‘true’ ṀO2,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 ṀO2,max within and among fish species.

While immune responses can be energetically costly, quantifying these costs is challenging. We tested the metabolic costs of immune activation in damselfish ( Pomacentrus amboinensis Bleeker, 1868) following a mass-adjusted injection of lipopolysaccharide (LPS) endotoxin. Fish were divided into eight treatments: two controls (handling and saline injection) and six LPS groups with concentrations ranging from 3 to 100 mg kg⁻¹. We used intermittent flow respirometry to measure differences in oxygen uptake (delta ṀO₂) 20 h before versus 20 h after LPS injection and changes in metabolic traits (lowest, routine, and peak metabolic rates) as proxies of the aerobic costs of metabolism. Spleen somatic index (SSI) and gene expression in spleens were measured to assess immune activation. We found no difference in metabolic traits or SSI but observed different nonlinear patterns of delta ṀO₂ in fish exposed to 50 and 100 mg kg⁻¹ LPS compared to lower doses and controls. Fish exposed to high doses of LPS also had lower residual aerobic scope compared to controls and lower LPS doses. Fish exposed to doses of 3, 50, and 100 mg kg⁻¹ showed altered gene expression compared to the handling control. Overall, our results suggest that immune activation has measurable effects on metabolic traits that are both dose- and time-dependent.

This candid perspective written by scholars from diverse disciplinary backgrounds is intended to advance conversations about the realities of peer review and its inherent limitations. Trust in a process or institution is built slowly and can be destroyed quickly. Trust in the peer review process for scholarly outputs (i.e., journal articles) is being eroded by high-profile scandals, exaggerated news stories, exposés, corrections, retractions, and anecdotes about poor practices. Diminished trust in the peer review process has real-world consequences and threatens the uptake of critical scientific advances. The literature on “crises of trust” tells us that rebuilding diminished trust takes time and requires frank admission and discussion of problems, creative thinking that addresses rather than dismisses criticisms, and planning and enacting short- and long-term reforms to address the root causes of problems. This article takes steps in this direction by presenting eight peer review reality checks and summarizing efforts to address their weaknesses using a harm reduction approach, though we recognize that reforms take time and some problems may never be fully rectified. While some forms of harm reduction will require structural and procedural changes, we emphasize the vital role that training editors, reviewers, and authors has in harm reduction. Additionally, consumers of science need training about how the peer review process works and how to critically evaluate research findings. No amount of self-policing, transparency, or reform to peer review will eliminate all bad actors, unscrupulous publishers, perverse incentives that reward cutting corners, intentional deception, or bias. However, the scientific community can act to minimize the harms from these activities, while simultaneously (re)building the peer review process. A peer review system is needed, even if it is imperfect.