Replicating research in ecology and evolution: feasibility, incentives, and the cost-benefit conundrum

Poor hypotheses and research waste in biology: learning from a theory crisis in psychology

While psychologists have extensively discussed the notion of a "theory crisis" arising from vague and incorrect hypotheses, there has been no debate about such a crisis in biology. However, biologists have long discussed communication failures between theoreticians and empiricists. We argue such failure is one aspect of a theory crisis because misapplied and misunderstood theories lead to poor hypotheses and research waste. We review its solutions and compare them with methodology-focused solutions proposed for replication crises. We conclude by discussing how promoting inclusion, diversity, equity, and accessibility (IDEA) in theoretical biology could contribute to ameliorating breakdowns in the theory-empirical cycle.

Synthesis of sexual selection: a systematic map of meta-analyses with bibliometric analysis

Sexual selection has been a popular subject within evolutionary biology because of its central role in explaining odd and counterintuitive traits observed in nature. Consequently, the literature associated with this field of study became vast. Meta-analytical studies attempting to draw inferences from this literature have now accumulated, varying in scope and quality, thus calling for a synthesis of these syntheses. We conducted a systematic literature search to create a systematic map with a report appraisal of meta-analyses on topics associated with sexual selection, aiming to identify the conceptual and methodological gaps in this secondary literature. We also conducted bibliometric analyses to explore whether these gaps are associated with the gender and origin of the authors of these meta-analyses. We included 152 meta-analytical studies in our systematic map. We found that most meta-analyses focused on males and on certain animal groups (e.g. birds), indicating severe sex and taxonomic biases. The topics in these studies varied greatly, from proximate (e.g. relationship of ornaments with other traits) to ultimate questions (e.g. formal estimates of sexual selection strength), although the former were more common. We also observed several common methodological issues in these studies, such as lack of detailed information regarding searches, screening, and analyses, which ultimately impairs the reliability of many of these meta-analyses. In addition, most of the meta-analyses' authors were men affiliated to institutions from developed countries, pointing to both gender and geographical authorship biases. Most importantly, we found that certain authorship aspects were associated with conceptual and methodological issues in meta-analytical studies. Many of our findings might simply reflect patterns in the current state of the primary literature and academia, suggesting that our study can serve as an indicator of issues within the field of sexual selection at large. Based on our findings, we provide both conceptual and analytical recommendations to improve future studies in the field of sexual selection.

A systematic review and meta-analysis of unimodal and multimodal predation risk assessment in birds

Despite a wealth of studies documenting prey responses to perceived predation risk, researchers have only recently begun to consider how prey integrate information from multiple cues in their assessment of risk. We conduct a systematic review and meta-analysis of studies that experimentally manipulated perceived predation risk in birds and evaluate support for three alternative models of cue integration: redundancy/equivalence, enhancement, and antagonism. One key insight from our analysis is that the current theory, generally applied to study cue integration in animals, is incomplete. These theories specify the effects of increasing information level on mean, but not variance, in responses. In contrast, we show that providing multiple complementary cues of predation risk simultaneously does not affect mean response. Instead, as information richness increases, populations appear to assess risk more accurately, resulting in lower among-population variance in response to manipulations of perceived predation risk. We show that this may arise via a statistical process called maximum-likelihood estimation (MLE) integration. Our meta-analysis illustrates how explicit consideration of variance in responses can yield important biological insights.

Bats, Bacteria, and Bat Smell V.2.0: Repeatable Sex-Specific Differences in Scent Organ Microbiota

Reproducibility is a fundamental principle in science, ensuring reliable and valid findings. However, replication studies are scarce, particularly in ecology, due to the emphasis on novelty for publication. We explored the possibility of replicating original findings in the field of microbial and chemical ecology by conducting a conceptual replication of a previous study analysing the sex-specific differences in the microbial communities inhabiting the wing sacs, a scent organ with crucial functions in olfactory communication, of greater sac-winged bat (Saccopteryx bilineata). In the original study, the skin swabs from the antebrachial wing sacs of the males and wing sac rudiments of the females were analysed using culture-dependent methods to test sex-specific differences. The authors demonstrated that males have lower microbial richness and different microbial composition than females. We attempted to reproduce these findings using 16S rRNA sequencing, which offers improved accuracy in pinpointing microbial members than culture-dependent methods because of advanced statistical methods. Our study validated the original study's findings: Males had a lower microbial richness, and the community composition differed between the sexes. Furthermore, in the current study, males had an increased abundance of bacteria that might potentially be involved in odour production and degradation of malodorous substances and antimicrobial production. Our conceptual replication study corroborated that microbes can play a role in shaping their host's olfactory phenotype and consequently influence sexual selection. Furthermore, the current study emphasises the importance of replication efforts and hopefully encourages a culture that values replication studies in scientific practice.

Compromise or choose: shared movement decisions in wild vulturine guineafowl

Shared-decision making is beneficial for the maintenance of group-living. However, little is known about whether consensus decision-making follows similar processes across different species. Addressing this question requires robust quantification of how individuals move relative to each other. Here we use high-resolution GPS-tracking of two vulturine guineafowl (Acryllium vulturinum) groups to test the predictions from a classic theoretical model of collective motion. We show that, in both groups, all individuals can successfully initiate directional movements, although males are more likely to be followed than females. When multiple group members initiate simultaneously, follower decisions depend on directional agreement, with followers compromising directions if the difference between them is small or choosing the majority direction if the difference is large. By aligning with model predictions and replicating the findings of a previous field study on olive baboons (Papio anubis), our results suggest that a common process governs collective decision-making in moving animal groups.

The 2-week systematic review (2weekSR) method was successfully blind-replicated by another team: a case study

OBJECTIVE

To assess the replicability of a 2-week systematic review (index 2weekSR) created with the assistance of automation tools using the fidelity method.

METHODS

A Preferred Reporting Items for Systematic reviews and Meta-Analyses compliant SR protocol was developed based on the published information of the index 2weekSR study. The replication team consisted of three reviewers. Two reviewers blocked off time during the replication. The total time to complete tasks and the meta-analysis results were compared with the index 2weekSR study. Review process fidelity scores (FSs) were calculated for review methods and outcomes. Barriers to completing the replication were identified.

RESULTS

The review was completed over 63 person-hours (11 workdays/15 calendar days). A FS of 0.95 was achieved for the methods, with 3 (of 8) tasks only partially replicated, and an FS of 0.63 for the outcomes, with 6 (of 7) only partially replicated and one task was not replicated. Nonreplication was mainly caused by missing information in the index 2weekSR study that was not required in standard reporting guidelines. The replication arrived at the same conclusions as the original study.

CONCLUSION

A 2weekSR study was replicated by a small team of three reviewers supported by automation tools. Including additional information when reporting SRs should improve their replicability.

Host body mass, not sex, affects ectoparasite loads in yellow-necked mouse Apodemus flavicollis

We investigated the presence and potential causes of sex bias in ectoparasite infestations in the yellow-necked mouse Apodemus flavicollis. We compared the natural tick and flea burdens of male and female mice in a temperate beech forest and assessed whether the observed differences were driven by host sex or body mass. We found that males were more heavily infested by ticks compared to female mice. However, this difference was driven by host body mass, and not sex itself. Host body mass positively correlated with flea loads, but there was no evidence of sex bias in flea abundance. In addition, the abundance of both ticks and fleas infesting yellow-necked mice changed over time, both seasonally (month to month) and annually (year to year). Our results underscore the importance of the sexual size dimorphism and the parasite taxon as the primary factors that influence the occurrence of sex-biased parasitism in small mammals.

Empirical evidence of widespread exaggeration bias and selective reporting in ecology

In many scientific disciplines, common research practices have led to unreliable and exaggerated evidence about scientific phenomena. Here we describe some of these practices and quantify their pervasiveness in recent ecology publications in five popular journals. In an analysis of over 350 studies published between 2018 and 2020, we detect empirical evidence of exaggeration bias and selective reporting of statistically significant results. This evidence implies that the published effect sizes in ecology journals exaggerate the importance of the ecological relationships that they aim to quantify. An exaggerated evidence base hinders the ability of empirical ecology to reliably contribute to science, policy, and management. To increase the credibility of ecology research, we describe a set of actions that ecologists should take, including changes to scientific norms about what high-quality ecology looks like and expectations about what high-quality studies can deliver.

Next steps after airing disagreement on a scientific issue with policy implications: a meta-analysis, multi-lab replication and adversarial collaboration

Canadian policymakers are interested in determining whether farmed Atlantic salmon, frequently infected with Piscine orthoreovirus (PRV), may threaten wild salmon populations in the Pacific Northwest. A relevant work has been published in BMC Biology by Polinksi and colleagues, but their conclusion that PRV has a negligible impact on the energy expenditure and respiratory performance of sockeye salmon is disputed by Mordecai and colleagues, whose re-analysis is presented in a correspondence article. So, what is the true effect and what should follow this unresolved dispute? We suggest a 'registered multi-lab replication with adversaries'.

Climatic forcing and individual heterogeneity in a resident mountain bird: legacy data reveal effects on reproductive strategies

Optimization of clutch size and timing of reproduction have substantial effects on lifetime reproductive success in vertebrates, and both individual quality and environmental variation may impact life history strategies. We tested hypotheses related to maternal investment and timing of reproduction, using 17 years (1978-1994) of individual-based life history data on willow ptarmigan (Lagopus l. lagopus, n = 290 breeding females with n = 319 breeding attempts) in central Norway. We analysed whether climatic variation and individual state variables (age and body mass) affected the number of offspring and timing of reproduction, and individual repeatability in strategies. The results suggest that willow ptarmigan share a common optimal clutch size that is largely independent of measured individual states. While we found no clear direct weather effects on clutch size, higher spring temperatures advanced onset of breeding, and early breeding was followed by an increased number of offspring. Warmer springs were positively related to maternal mass, and mass interacted with clutch size in production of hatchlings. Finally, clutch size and timing of reproduction were highly repeatable within individuals, indicating that individual quality guided trade-offs in reproductive effort. Our results demonstrate how climatic forcing and individual heterogeneity in combination influenced life history traits in a resident montane keystone species.

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.

Ten simple rules for designing and conducting undergraduate replication projects

Conducting a replication study is a valuable way for undergraduate students to learn about the scientific process and gain research experience. By promoting the evaluation of existing studies to confirm their reliability, replications play a unique, though often underappreciated, role in the scientific enterprise. Involving students early in this process can help make replication mainstream among the new generation of scientists. Beyond their benefit to science, replications also provide an invaluable learning ground for students, from encouraging the development of critical thinking to emphasizing the importance of details and honing research skills. In this piece, we outline 10 simple rules for designing and conducting undergraduate replication projects, from conceptualization to implementation and dissemination. We hope that these guidelines can help educators provide students with a meaningful and constructive pedagogical experience, without compromising the scientific value of the replication project, therefore ensuring robust, valuable contributions to our understanding of the world.

Revisiting and interpreting the role of female dominance in male mate choice: the importance of replication in ecology and evolution

In many species females prefer to mate with socially dominant males, often because it elevates their fecundity by providing greater access to material resources or lowers offspring mortality due to superior male defence. Far fewer studies have tested whether males prefer socially dominant females. Intriguingly, an earlier study showed that when the sexes freely interact, male mosquitofish (Gambusia holbrooki) preferentially attempt to mate with dominant females. Here we replicate this study using a slightly modified experimental design to test the generality of its finding. In addition, we conducted standard, two-choice male mate choice trials to test directly whether males prefer dominant over subordinate females. Corroborating the previous study, we found that when a male and two females freely interact, males more often attempt to mate with the dominant female. However, males did not prefer to associate with (i.e., choose) dominant females in two-choice trials where females could not interact. We discuss whether greater access to males is a benefit of female social dominance, or an epiphenomenon of other benefits of dominance.

Environmental patterns of adaptation after range expansion in Leontodon longirostris: The effect of phenological events on fitness-related traits

PREMISE

Because of expected range shifts associated with climate change, there is a renewed interest in the evolutionary factors constraining adaptation, among which are genetic bottlenecks, drift, and increased mutational load after range expansion. Here we study adaptation in the short-lived species Leontodon longirostris showing reduced genetic diversity and increased genetic load along an expansion route.

METHODS

We assessed the phenological patterns of variation, and their effect on fitness-related traits, on 42 L. longirostris populations and six populations of the sister taxa L. saxatilis in a common garden located within the current range of both species. The comparison among L. longirostris populations allowed us to test for genetic clines consistent with local adaptation, whereas the comparison between taxa provided evidence for common adaptive features at the species level.

RESULTS

We found significant within-species variability for most traits, as well as differences with its close relative L. saxatilis. In general, seeds from drier, warmer, and unpredictable habitats showed overall lower and more restricted conditions for germination, seedlings emerged later and plants flowered earlier. Consequently, genotypes from arid and unpredictable environments attained smaller reproductive sizes and allocated more biomass to reproduction. Flowering time had the strongest direct effect on total plant size, but seedling emergence also showed an important indirect effect.

CONCLUSIONS

Our results show the crucial role of phenological patterns in shaping adaptive clines for major life-history stage transitions. Furthermore, the genetic load observed in L. longirostris does not seem to preclude adaptation to the climatic variability encountered along the expansion route.

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.

The Role of Intra-Clutch Variation of Magpie Clutches in Foreign Egg Rejection Depends on the Egg Trait Considered

The existence of a coevolutionary process between avian brood parasites and their hosts predicts a lower intra-clutch variation in egg appearance of host eggs among rejecters as this would favor egg discrimination of parasite eggs by hosts once parasitic egg mimicry had evolved. So far empirical tests of this prediction have ignored the fact that different aspects of host egg phenotypes may differ in the relative role of environmental vs. genetic determination, and hence that the role of intra-clutch variation in egg rejection within a population cannot be invariant. Here, we estimated whether the intra-clutch variation in several aspects of host eggshell features is consistently associated to rejection of parasitic foreign eggs across years in a magpie host population parasitized by great spotted cuckoos. We innovatively estimated spottiness by means of the fractal dimension of eggs, which considers the homogeneity of spot pattern complexity in eggshells. Our results show that low intra-clutch variation in the blue-green coloration at the middle area of the eggs associated with a high chance of rejection, but only in one of the 3 years we conducted the study. In addition, females that rejected foreign eggs presented more homogenous spot patterns in their clutches as estimated by their fractal dimension than females that accepted experimental eggs, independently of the year of study. Finally, intra-clutch variation in egg volume of host eggs was not associated to rejection. Analyses at the individual level revealed that the relative role of genetic vs. environmental factors that determine egg phenotype would be feature-specific in magpies, females having a characteristic spottiness, but not color or volume, pattern. Our work stresses the importance of considering a holistic approach including several aspects of variation in host egg phenotype (size, color, and homogeneity of spot pattern), as some aspects might be more susceptible to selection through egg rejection than others, presumably because they are less influenced by variation in the environmental conditions. Moreover, our study highlights the importance of replication in studies on the adaptive value of host traits in egg rejection.

How social relationships shape moral wrongness judgments

Judgments of whether an action is morally wrong depend on who is involved and the nature of their relationship. But how, when, and why social relationships shape moral judgments is not well understood. We provide evidence to address these questions, measuring cooperative expectations and moral wrongness judgments in the context of common social relationships such as romantic partners, housemates, and siblings. In a pre-registered study of 423 U.S. participants nationally representative for age, race, and gender, we show that people normatively expect different relationships to serve cooperative functions of care, hierarchy, reciprocity, and mating to varying degrees. In a second pre-registered study of 1,320 U.S. participants, these relationship-specific cooperative expectations (i.e., relational norms) enable highly precise out-of-sample predictions about the perceived moral wrongness of actions in the context of particular relationships. In this work, we show that this 'relational norms' model better predicts patterns of moral wrongness judgments across relationships than alternative models based on genetic relatedness, social closeness, or interdependence, demonstrating how the perceived morality of actions depends not only on the actions themselves, but also on the relational context in which those actions occur.

Melanic pigmentation and light preference within and between two Drosophila species

Environmental adaptation and species divergence often involve suites of co-evolving traits. Pigmentation in insects presents a variable, adaptive, and well-characterized class of phenotypes for which correlations with multiple other traits have been demonstrated. In Drosophila, the pigmentation genes ebony and tan have pleiotropic effects on flies' response to light, creating the potential for correlated evolution of pigmentation and vision. Here, we investigate differences in light preference within and between two sister species, Drosophila americana and D. novamexicana, which differ in pigmentation in part because of evolution at ebony and tan and occupy environments that differ in many variables including solar radiation. We hypothesized that lighter pigmentation would be correlated with a greater preference for environmental light and tested this hypothesis using a habitat choice experiment. In a first set of experiments, using males of D. novamexicana line N14 and D. americana line A00, the light-bodied D. novamexicana was found slightly but significantly more often than D. americana in the light habitat. A second experiment, which included additional lines and females as well as males, failed to find any significant difference between D. novamexicana-N14 and D. americana-A00. Additionally, the other dark line of D. americana (A04) was found in the light habitat more often than the light-bodied D. novamexicana-N14, in contrast to our predictions. However, the lightest line of D. americana, A01, was found substantially and significantly more often in the light habitat than the two darker lines of D. americana, thus providing partial support for our hypothesis. Finally, across all four lines, females were found more often in the light habitat than their more darkly pigmented male counterparts. Additional replication is needed to corroborate these findings and evaluate conflicting results, with the consistent effect of sex within and between species providing an especially intriguing avenue for further research.

Replication studies in the clinical decision support literature-frequency, fidelity, and impact

OBJECTIVE

To assess the frequency, fidelity, and impact of replication studies in the clinical decision support system (CDSS) literature.

MATERIALS AND METHODS

A PRISMA-compliant review identified CDSS replications across 28 health and biomedical informatics journals. Included articles were assessed for fidelity to the original study using 5 categories: Identical, Substitutable, In-class, Augmented, and Out-of-class; and 7 IMPISCO domains: Investigators (I), Method (M), Population (P), Intervention (I), Setting (S), Comparator (C), and Outcome (O). A fidelity score and heat map were generated using the ratings.

RESULTS

From 4063 publications matching search criteria for CDSS research, only 12/4063 (0.3%) were ultimately identified as replications. Six articles replicated but could not reproduce the results of the Han et al (2005) CPOE study showing mortality increase and, over time, changed from truth testing to generalizing this result. Other replications successfully tested variants of CDSS technology (2/12) or validated measurement instruments (4/12).

DISCUSSION

A replication rate of 3 in a thousand studies is low even by the low rates in other disciplines. Several new reporting methods were developed for this study, including the IMPISCO framework, fidelity scores, and fidelity heat maps. A reporting structure for clearly identifying replication research is also proposed.

CONCLUSION

There is an urgent need to better characterize which core CDSS principles require replication, identify past replication data, and conduct missing replication studies. Attention to replication should improve the efficiency and effectiveness of CDSS research and avoiding potentially harmful trial and error technology deployment.

Life-history trade-offs, density, lay date—not personality—explain multibroodedness in great tits

In various taxa, multibroodedness is a common breeding strategy. Life-history theory predicts that individuals can increase fitness by producing multiple broods within a season. Despite the apparent increase in the number of offspring parents might produce per season, not all individuals are multibrooded, suggesting a trade-off. We studied ecological and behavioral factors influencing the initiation of second clutches in great tits (Parus major), an optionally multibrooded bird species, by distinguishing two types of clutches: replacement versus true second clutches, produced after failure versus successful first breeding attempts, respectively. We predicted which lay date, density, and investment in first clutches would decrease the probability of initiating a second clutch, but which faster exploring behavioral types with a faster pace-of-life would be more likely to be multibrooded. The probability of initiating true second clutches varied negatively within-individuals with lay date and breeding density. The initiation of replacement clutches instead varied negatively among-individuals with lay date and density, suggesting nonrandom settlement of behavioral types across environments. Individuals were less likely to be multibrooded when producing many offspring from their first clutch, suggesting within-year reproductive trade-offs, similar to previous studies. No previous research has linked personality to multibroodedness; here we show which neither the repeatable nor the plastic part of an individual’s exploratory behavior predicted multibroodedness. We confirmed our prediction which the resolution of trade-offs may occur either at the within- or among-individual level. Our research contributes to the understanding of life-history evolution in the wild by studying the mechanisms shaping multibroodedness within seasons.

Circumstances of overdose among suburban women who use opioids: Extending an urban analysis informed by drug, set, and setting

BACKGROUND

Opioid overdoses are primarily discussed by the pharmacological properties of the drugs used. Research shows that other factors such as the social/physical environment and the mental/emotional states can have an impact on overdose events. Ataiants and colleagues (2020) used Zinberg's "drug, set, and setting" framework to identify circumstances surrounding overdose experiences of street-involved women in Philadelphia. The aim of this paper is to extend their analysis to a diverse sample of suburban women who experienced overdoses.

METHODS

The mixed-methods design consisted of ethnographic fieldwork, in-depth interviews, and brief surveys with 32 suburban women who use opioids. Inductive theoretical reasoning and constant comparative analysis facilitated themes emerging within the "drug, set, and setting" framework.

RESULTS

Eighteen out of 32 women identified "drug" as the primary factor involved in their overdose events. Major themes were an inability to identify the synthetic opioid fentanyl, lack of knowledge or control over how much to use, poly-substance use, and an insufficient understanding of risks. Eleven out of 32 women linked "set" to their overdose experiences. Themes included emotional trauma, such as death of a child, child custody issues, and mental health conditions, such as depression. Six out of 32 women associated "setting" with one of their overdose experiences. Themes were related to being with friends or partners that used, and having recently been released from treatment or incarceration.

CONCLUSION

Findings show similar themes found among an urban sample, adding insight on the need for effective overdose interventions targeted for suburban populations. The opioid crisis is not confined to the cities, and neither should services aimed at addressing opioid overdose. The knowledge provided here can help policy makers support female-centered harm reduction services not only in urban areas but also in the suburbs.

Repeatable differences in exploratory behaviour predict tick infestation probability in wild great tits

Abstract

Ecological factors and individual-specific traits affect parasite infestation in wild animals. Ixodid ticks are important ectoparasites of various vertebrate hosts, which include passerine bird species such as the great tit (Parus major). We studied various key ecological variables (breeding density, human disturbance) and phenotypic traits (exploratory behaviour, body condition) proposed to predict tick infestation probability and burden in great tits. Our study spanned 3 years and 12 nest box plots located in southern Germany. Breeding, adult great tits were assessed for exploration behaviour, body condition, and tick burden. Plots were open to human recreation; human disturbance was quantified in each plot as a recreation pressure index from biweekly nest box inspections. Infested individuals were repeatable in tick burden across years. These repeatable among-individual differences in tick burden were not attributable to exploration behaviour. However, faster explorers did have a higher infestation probability. Furthermore, body condition was negatively correlated to tick burden. Recreation pressure was correlated to increased infestation probability, although this relationship was just above the threshold of statistical significance. Our study implies that avian infestation probability and tick burden are each determined by distinct phenotypic traits and ecological factors. Our findings highlight the importance of animal behaviour and human disturbance in understanding variation in tick burden among avian hosts.

Significance statement

Various abiotic and biotic factors, including personality type, influence tick parasitism in birds, but exactly how all these factors interplay remains unclear. We studied a wild population of great tits over a 3-year period and assessed birds for their exploration behaviour and tick infestation. We found that more explorative great tits were more likely to be infested with ticks. By contrast, faster explorers did not have higher tick burdens. Tick burden was nevertheless moderately repeatable among individuals. Our results imply that animal personality influences the probability of parasite infestation, and that infestation likelihood versus intensity are determined by distinct mechanisms. Our work highlights the importance of animal behaviour to understand parasite infestation in wild populations.

Hemipteran defensive odors trigger predictable color biases in jumping spider predators

Multimodal warning displays often pair one signal modality (odor) with a second modality (color) to avoid predation. Experiments with bird predators suggest these signal components interact synergistically, with aversive odors triggering otherwise hidden aversions to particular prey colors. In a recent study, this phenomenon was found in a jumping spider (Habronattus trimaculatus), with the defensive odor from a coreid bug (Acanthocephala femorata) triggering an aversion to red. Here, we explore how generalizable this phenomenon is by giving H. trimaculatus the choice between red or black prey in the presence or absence of defensive odors secreted from (1) eastern leaf-footed bugs (Leptoglossus phyllopus, Hemiptera), (2) grass stinkbugs (Mormidea pama, Hemiptera), (3) Asian ladybird beetles (Harmonia axyridis, Coleoptera), and (4) eastern lubber grasshoppers (Romalea microptera, Orthoptera). As expected, in the presence of the hemipteran odors, spiders were less likely to attack red prey (compared to no odor). Unexpectedly, the beetle and grasshopper odors did not bias spiders away from red. Our results with the hemipteran odors were unique to red; follow-up experiments indicated that these odors did not affect biases for/against green prey. We discuss our findings in the context of generalized predator foraging behavior and the functions of multimodal warning displays.

Chemical patterns of colony membership and mother-offspring similarity in Antarctic fur seals are reproducible

Replication studies are essential for evaluating the validity of previous research findings. However, it has proven challenging to reproduce the results of ecological and evolutionary studies, partly because of the complexity and lability of many of the phenomena being investigated, but also due to small sample sizes, low statistical power and publication bias. Additionally, replication is often considered too difficult in field settings where many factors are beyond the investigator’s control and where spatial and temporal dependencies may be strong. We investigated the feasibility of reproducing original research findings in the field of chemical ecology by performing an exact replication of a previous study of Antarctic fur seals (Arctocephalus gazella). In the original study, skin swabs from 41 mother-offspring pairs from two adjacent breeding colonies on Bird Island, South Georgia, were analyzed using gas chromatography-mass spectrometry. Seals from the two colonies differed significantly in their chemical fingerprints, suggesting that colony membership may be chemically encoded, and mothers were also chemically similar to their pups, hinting at the possible involvement of phenotype matching in mother-offspring recognition. In the current study, we generated and analyzed chemical data from a non-overlapping sample of 50 mother-offspring pairs from the same two colonies 5 years later. The original results were corroborated in both hypothesis testing and estimation contexts, with p-values remaining highly significant and effect sizes, standardized between studies by bootstrapping the chemical data over individuals, being of comparable magnitude. However, exact replication studies are only capable of showing whether a given effect can be replicated in a specific setting. We therefore investigated whether chemical signatures are colony-specific in general by expanding the geographic coverage of our study to include pups from a total of six colonies around Bird Island. We detected significant chemical differences in all but a handful of pairwise comparisons between colonies. This finding adds weight to our original conclusion that colony membership is chemically encoded, and suggests that chemical patterns of colony membership not only persist over time but can also be generalized over space. Our study systematically confirms and extends our previous findings, while also implying more broadly that spatial and temporal heterogeneity need not necessarily negate the reproduction and generalization of ecological research findings.

Nutrition as an etiological factor causing diseases in endangered huemul deer

OBJECTIVES

Distinct diseases prevent endangered huemul deer (Hippocamelus bisulcus) recovery. Fundamental etiological factors include nutriments, a mayor component of habitat quality. Undernutrition affects growth, skeletal development, osteopathology, reproduction and immunocompetence: this paper amplifies data corroborating micro-nutrient deficiencies among huemul.

RESULTS

In Argentina, 57% huemul cadavers exhibited osteopathology, with new cases reported here. Recently, 86% live huemul had osteopathology: cranial lesions involved antemortem tooth loss, reducing feeding efficiency and body condition, with starvation deaths. This population had tissues well deficient compared to other cervids, averaging 0.28 ppm selenium, 4.98 ppm copper, whereas for manganese 55% were deficient (2.52 ppm) and 45% adequate (42.79 ppm). Recently, lesions in one Chilean huemul were interpreted to stem from parapoxvirus. That population also has cases with cranial osteopathologies, high disease susceptibility (parapoxvirus, parasitism, foot lesions), crippled antlers, and low density, indicative of marginal habitat and primary etiological factors like undernutrition and immunosuppression. The reported atypical symptoms attributed to parapoxvirus may relate to probable diagnostic limitations, but does support presence of nutritional deficiencies. Patagonia has selenium deficient plants and livestock, including severe muscular dystrophy, and soil levels in extant huemul areas considered very deficient. Moreover, 73% of Chilean huemul were selenium deficient and 64% severely deficient with concomitant cranial osteopathology.

The role of replication studies in ecology

Recent large-scale projects in other disciplines have shown that results often fail to replicate when studies are repeated. The conditions contributing to this problem are also present in ecology, but there have not been any equivalent replication projects. Here, we survey ecologists' understanding of and opinions about replication studies. The majority of ecologists in our sample considered replication studies to be important (97%), not prevalent enough (91%), worth funding even given limited resources (61%), and suitable for publication in all journals (62%). However, there is a disconnect between this enthusiasm and the prevalence of direct replication studies in the literature which is much lower (0.023%: Kelly 2019) than our participants' median estimate of 10%. This may be explained by the obstacles our participants identified including the difficulty of conducting replication studies and of funding and publishing them. We conclude by offering suggestions for how replications could be better integrated into ecological research.

A Guide and Toolbox to Replicability and Open Science in Entomology

The ability to replicate scientific experiments is a cornerstone of the scientific method. Sharing ideas, workflows, data, and protocols facilitates testing the generalizability of results, increases the speed that science progresses, and enhances quality control of published work. Fields of science such as medicine, the social sciences, and the physical sciences have embraced practices designed to increase replicability. Granting agencies, for example, may require data management plans and journals may require data and code availability statements along with the deposition of data and code in publicly available repositories. While many tools commonly used in replicable workflows such as distributed version control systems (e.g., 'git') or script programming languages for data cleaning and analysis may have a steep learning curve, their adoption can increase individual efficiency and facilitate collaborations both within entomology and across disciplines. The open science movement is developing within the discipline of entomology, but practitioners of these concepts or those desiring to work more collaboratively across disciplines may be unsure where or how to embrace these initiatives. This article is meant to introduce some of the tools entomologists can incorporate into their workflows to increase the replicability and openness of their work. We describe these tools and others, recommend additional resources for learning more about these tools, and discuss the benefits to both individuals and the scientific community and potential drawbacks associated with implementing a replicable workflow.

Stress hypothesis overload: 131 hypotheses exploring the role of stress in tradeoffs, transitions, and health

Stress is ubiquitous and thus, not surprisingly, many hypotheses and models have been created to better study the role stress plays in life. Stress spans fields and is found in the literature of biology, psychology, psychophysiology, sociology, economics, and medicine, just to name a few. Stress, and the hypothalamic-pituitaryadrenal/interrenal (HPA/I) axis and sympathetic nervous system (SNS), are involved in a multitude of behaviors and physiological processes, including life-history and ecological tradeoffs, developmental transitions, health, and survival. The goal of this review is to highlight and summarize the large number of available hypotheses and models, to aid in comparative and interdisciplinary thinking, and to increase reproducibility by a) discouraging hypothesizing after results are known (HARKing) and b) encouraging a priori hypothesis testing. For this review I collected 214 published hypotheses or models dealing broadly with stress. In the main paper, I summarized and categorized 131 of those hypotheses and models which made direct connections among stress and/or HPA/I and SNS, tradeoffs, transitions, and health. Of those 131, the majority made predictions about reproduction (n = 43), the transition from health to disease (n = 38), development (n = 23), and stress coping (n = 18). Additional hypotheses were classified as stage-spanning or models (n = 37). The additional 83 hypotheses found during searches were tangentially related, or pertained to immune function or oxidative stress, and these are listed separately. Many of the hypotheses share underlying rationale and suggest similar, if not identical, predictions, and are thus not mutually exclusive; some hypotheses spanned classification categories. Some of the hypotheses have been tested multiple times, whereas others have only been examined a few times. It is the hope that multi-disciplinary stress researchers will begin to harmonize their naming of hypotheses in the literature so as to build a clearer picture of how stress impacts various outcomes across fields. The paper concludes with some considerations and recommendations for robust testing of stress hypotheses.

Does health informatics have a replication crisis?

Objective

Many research fields, including psychology and basic medical sciences, struggle with poor reproducibility of reported studies. Biomedical and health informatics is unlikely to be immune to these challenges. This paper explores replication in informatics and the unique challenges the discipline faces.

Methods

Narrative review of recent literature on research replication challenges.

Results

While there is growing interest in re-analysis of existing data, experimental replication studies appear uncommon in informatics. Context effects are a particular challenge as they make ensuring replication fidelity difficult, and the same intervention will never quite reproduce the same result in different settings. Replication studies take many forms, trading-off testing validity of past findings against testing generalizability. Exact and partial replication designs emphasize testing validity while quasi and conceptual studies test generalizability of an underlying model or hypothesis with different methods or in a different setting.

Conclusions

The cost of poor replication is a weakening in the quality of published research and the evidence-based foundation of health informatics. The benefits of replication include increased rigor in research, and the development of evaluation methods that distinguish the impact of context and the nonreproducibility of research. Taking replication seriously is essential if biomedical and health informatics is to be an evidence-based discipline.

Correlative climatic niche models predict real and virtual species distributions equally well

Climate is one of the main factors driving species distributions and global biodiversity patterns. Obtaining accurate predictions of species' range shifts in response to ongoing climate change has thus become a key issue in ecology and conservation. Correlative species distribution models (cSDMs) have become a prominent tool to this aim in the last decade and have demonstrated good predictive abilities with current conditions, irrespective of the studied taxon. However, cSDMs rely on statistical association between species' presence and environmental conditions and have rarely been challenged on their actual capacity to reflect causal relationships between species and climate. In this study, we question whether cSDMs can accurately identify if climate and species distributions are causally linked, a prerequisite for accurate prediction of range shift in relation to climate change. We compared the performance of cSDMs in predicting the distributions of 132 European terrestrial species, chosen randomly within five taxonomic groups (three vertebrate groups and two plant groups), and of 1,320 virtual species whose distribution is causally fully independent from climate. We found that (1) for real species, the performance of cSDMs varied principally with range size, rather than with taxonomic groups and (2) cSDMs did not predict the distributions of real species with a greater accuracy than the virtual ones. Our results unambiguously show that the high predictive power of cSDMs can be driven by spatial autocorrelation in climatic and distributional data and does not necessarily reflect causal relationships between climate and species distributions. Thus, high predictive performance of cSDMs does not ensure that they accurately depict the role of climate in shaping species distributions. Our findings therefore call for strong caution when using cSDMs to provide predictions on future range shifts in response to climate change.

Non-consumptive effects of predation: does perceived risk strengthen the genetic integration of behaviour and morphology in stickleback?

Predators can shape genetic correlations in prey by altering prey perception of risk. We manipulated perceived risk to test whether such non-consumptive effects tightened behavioural trait correlations in wild-caught stickleback from high- compared to low-risk environments due to genetic variation in plasticity. We expected tighter genetic correlations within perceived risk treatments than across them, and tighter genetic correlations in high-risk than in low-risk treatments. We identified genetic variation in plasticity, with genetic correlations between boldness, sociality, and antipredator morphology, as expected, being tighter within treatments than across them, for both of two populations. By contrast, genetic correlations did not tighten with exposure to risk. Tighter phenotypic correlations in wild stickleback may thus arise because predators induce correlational selection on environmental components of these traits, or because predators tighten residual correlations by causing environmental heterogeneity that is controlled in the laboratory. Our study places phenotypic integration firmly into an ecological context.

Rate and success of study replication in ecology and evolution

The recent replication crisis has caused several scientific disciplines to self-reflect on the frequency with which they replicate previously published studies and to assess their success in such endeavours. The rate of replication, however, has yet to be assessed for ecology and evolution. Here, I survey the open-access ecology and evolution literature to determine how often ecologists and evolutionary biologists replicate, or at least claim to replicate, previously published studies. I found that approximately 0.023% of ecology and evolution studies are described by their authors as replications. Two of the 11 original-replication study pairs provided sufficient statistical detail for three effects so as to permit a formal analysis of replication success. Replicating authors correctly concluded that they replicated an original effect in two cases; in the third case, my analysis suggests that the finding by the replicating authors was consistent with the original finding, contrary the conclusion of “replication failure” by the authors.

Ecological Data Should Not Be So Hard to Find and Reuse

Drawing upon the data deposited in publicly shared archives has the potential to transform the way we conduct ecological research. For this transformation to happen, we argue that data need to be more interoperable and easier to discover. One way to achieve these goals is to adopt domain-specific data representations.

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.

Meta-analysis challenges a textbook example of status signalling and demonstrates publication bias

The status signalling hypothesis aims to explain within-species variation in ornamentation by suggesting that some ornaments signal dominance status. Here, we use multilevel meta-analytic models to challenge the textbook example of this hypothesis, the black bib of male house sparrows (Passer domesticus). We conducted a systematic review, and obtained primary data from published and unpublished studies to test whether dominance rank is positively associated with bib size across studies. Contrary to previous studies, the overall effect size (i.e. meta-analytic mean) was small and uncertain. Furthermore, we found several biases in the literature that further question the support available for the status signalling hypothesis. We discuss several explanations including pleiotropic, population- and context-dependent effects. Our findings call for reconsidering this established textbook example in evolutionary and behavioural ecology, and should stimulate renewed interest in understanding within-species variation in ornamental traits.

Questionable research practices in ecology and evolution

We surveyed 807 researchers (494 ecologists and 313 evolutionary biologists) about their use of Questionable Research Practices (QRPs), including cherry picking statistically significant results, p hacking, and hypothesising after the results are known (HARKing). We also asked them to estimate the proportion of their colleagues that use each of these QRPs. Several of the QRPs were prevalent within the ecology and evolution research community. Across the two groups, we found 64% of surveyed researchers reported they had at least once failed to report results because they were not statistically significant (cherry picking); 42% had collected more data after inspecting whether results were statistically significant (a form of p hacking) and 51% had reported an unexpected finding as though it had been hypothesised from the start (HARKing). Such practices have been directly implicated in the low rates of reproducible results uncovered by recent large scale replication studies in psychology and other disciplines. The rates of QRPs found in this study are comparable with the rates seen in psychology, indicating that the reproducibility problems discovered in psychology are also likely to be present in ecology and evolution.

Evaluating the Efficiency and Safety of Speech Recognition within a Commercial Electronic Health Record System: A Replication Study

OBJECTIVE

To conduct a replication study to validate previously identified significant risks and inefficiencies associated with the use of speech recognition (SR) for documentation within an electronic health record (EHR) system.

METHODS

Thirty-five emergency department clinicians undertook randomly allocated clinical documentation tasks using keyboard and mouse (KBM) or SR using a commercial EHR system. The experiment design, setting, and tasks (E2) replicated an earlier study (E1), while technical integration issues that may have led to poorer SR performance were addressed.

RESULTS

Complex tasks were significantly slower to complete using SR (16.94%) than KBM (KBM: 191.9 s, SR: 224.4 s; p = 0.009; CI, 11.9-48.3), replicating task completion times observed in the earlier experiment. Errors (non-typographical) were significantly higher with SR compared with KBM for both simple (KBM: 3, SR: 84; p < 0.001; CI, 1.5-2.5) and complex tasks (KBM: 23, SR: 53; p = 0.001; CI, 0.5-1.0), again replicating earlier results (E1: 170, E2: 163; p = 0.660; CI, 0.0-0.0). Typographical errors were reduced significantly in the new study (E1: 465, E2: 150; p < 0.001; CI, 2.0-3.0).

DISCUSSION

The results of this study replicate those reported earlier. The use of SR for clinical documentation within an EHR system appears to be consistently associated with decreased time efficiencies and increased errors. Modifications implemented to optimize SR integration in the EHR seem to have resulted in minor improvements that did not fundamentally change overall results.

CONCLUSION

This replication study adds further evidence for the poor performance of SR-assisted clinical documentation within an EHR. Replication studies remain rare in informatics literature, especially where study results are unexpected or have significant implication; such studies are clearly needed to avoid overdependence on the results of a single study.

Which egg features predict egg rejection responses in American robins? Replicating Rothstein's (1982) study

Rothstein (Behavioral Ecology and Sociobiology, 11, 1982, 229) was one of the first comprehensive studies to examine how different egg features influence egg rejection behaviors of avian brood parasite-hosts. The methods and conclusions of Rothstein (1982) laid the foundation for subsequent experimental brood parasitism studies over the past thirty years, but its results have never been evaluated with replication. Here, we partially replicated Rothstein's (1982) experiments using parallel artificial model egg treatments to simulate cowbird (Molothrus ater) parasitism in American robin (Turdus migratorius) nests. We compared our data with those of Rothstein (1982) and confirmed most of its original findings: (1) robins reject model eggs that differ from the appearance of a natural robin egg toward that of a natural cowbird egg in background color, size, and maculation; (2) rejection responses were best predicted by model egg background color; and (3) model eggs differing by two or more features from natural robin eggs were more likely to be rejected than model eggs differing by one feature alone. In contrast with Rothstein's (1982) conclusion that American robin egg recognition is not specifically tuned toward rejection of brown-headed cowbird eggs, we argue that our results and those of other recent studies of robin egg rejection suggest a discrimination bias toward rejection of cowbird eggs. Future work on egg recognition will benefit from utilizing a range of model eggs varying continuously in background color, maculation patterning, and size in combination with avian visual modeling, rather than using model eggs which vary only discretely.