Confirmation bias in studies of nestmate recognition: a cautionary note for research into the behaviour of animals

Highly diverse cuticular hydrocarbon profiles but no evidence for aggression towards non-kin in the ambrosia beetle Xyleborinus saxesenii

Animal societies use nestmate recognition to protect against social cheaters and parasites. In most social insect societies, individuals recognize and exclude any non-nestmates and the roles of cuticular hydrocarbons as recognition cues are well documented. Some ambrosia beetles live in cooperatively breeding societies with farmed fungus cultures that are challenging to establish, but of very high value once established. Hence, social cheaters that sneak into a nest without paying the costs of nest foundation may be selected. Therefore, nestmate recognition is also expected to exist in ambrosia beetles, but so far nobody has investigated this behavior and its underlying mechanisms. Here we studied the ability for nestmate recognition in the cooperatively breeding ambrosia beetle Xyleborinus saxesenii, combining behavioural observations and cuticular hydrocarbon analyses. Laboratory nests of X. saxesenii were exposed to foreign adult females from the same population, another population and another species. Survival as well as the behaviours of the foreign female were observed. The behaviours of the receiving individuals were also observed. We expected that increasing genetic distance would cause increasing distance in chemical profiles and increasing levels of behavioural exclusion and possibly mortality. Chemical profiles differed between populations and appeared as variable as in other highly social insects. However, we found only very little evidence for the behavioural exclusion of foreign individuals. Interpopulation donors left nests at a higher rate than control donors, but neither their behaviours nor the behaviours of receiver individuals within the nest showed any response to the foreign individual in either of the treatments. These results suggest that cuticular hydrocarbon profiles might be used for communication and nestmate recognition, but that behavioural exclusion of non-nestmates is either absent in X. saxesenii or that agonistic encounters are so rare or subtle that they could not be detected by our method. Additional studies are needed to investigate this further.

Human interventions in a behavioural experiment for Asian Elephants (Elephas maximus)

Experiments are widely used to investigate the behaviour and cognition of animals. While the automation of experiments to avoid potential experimenter bias is sometimes possible, not all experiments can be conducted without human presence. This is particularly true for large animals in captivity, which are often managed by professional handlers. For the safety of the animals and experimenters, a handler must be present during behavioural studies with certain species. It is not always clear to what extent cues provided by handlers affect the animals, and therefore the experimental results. In this study, we investigate handler interventions during the training process for a behavioural experiment with Asian elephants (Elephas maximus) in Nepal. We show that elephant handlers (mahouts) intervened to guide elephants in performing the learning task using vocal and behavioural cues, despite experimenters requesting minimal intervention. We found that although the frequency of mahout interventions did not decrease as the training progressed, the nature of their interventions changed. We also found more non-verbal than verbal cues across the training. Our results suggest that guidance from handlers may be common in behavioural studies, and continued consideration should be put into experimental design to reduce or account for cues that animals may receive from humans. This study also emphasises the need to take into account the presence of humans in interpreting the results of animal behavioural experiments, which not only presents challenges to behavioural research, but also represents opportunities for further study.

A qualitative study of the barriers to using blinding in in vivo experiments and suggestions for improvement

In animal experiments, blinding (also known as masking) is a methodological strategy to reduce the risk that scientists, animal care staff, or other staff involved in the research may consciously or subconsciously influence the outcome. Lack of masking has been shown to correlate with an overestimation of treatment efficacy and false positive findings. We conducted exploratory interviews across academic and a commercial setting to discuss the implementation of masking at four stages of the experiment: during allocation and intervention, during the conduct of the experiment, during the outcome assessment, and during the data analysis. The objective was to explore the awareness, engagement, perceptions, and the barriers to implementing masking in animal experiments. We conducted multiple interviews, to explore 30 different experiments, and found examples of excellent practice but also areas where masking was rarely implemented. Significant barriers arose from the operational and informatic systems implemented. These systems have prioritised the management of welfare without considering how to allow researchers to use masking in their experiments. For some experiments, there was a conflict between the management of welfare for an individual animal versus delivering a robust experiment where all animals are treated in the same manner. We identified other challenges related to the level of knowledge on the purpose of masking or the implementation and the work culture. The exploration of these issues provides insight into how we, as a community, can identify the most significant barriers in a given research environment. Here, we offer practical solutions to enable researchers to implement masking as standard. To move forward, we need both the individual scientists to embrace the use of masking and the facility managers and institutes to engage and provide a framework that supports the scientists.

Quantifying research waste in ecology

Research inefficiencies can generate huge waste: evidence from biomedical research has shown that most research is avoidably wasted and steps have been taken to tackle this costly problem. Although other scientific fields could also benefit from identifying and quantifying waste and acting to reduce it, no other estimates of research waste are available. Given that ecological issues interweave most of the United Nations Sustainable Development Goals, we argue that tackling research waste in ecology should be prioritized. Our study leads the way. We estimate components of waste in ecological research based on a literature review and a meta-analysis. Shockingly, our results suggest only 11-18% of conducted ecological research reaches its full informative value. All actors within the research system-including academic institutions, policymakers, funders and publishers-have a duty towards science, the environment, study organisms and the public, to urgently act and reduce this considerable yet preventable loss. We discuss potential ways forward and call for two major actions: (1) further research into waste in ecology (and beyond); (2) focused development and implementation of solutions to reduce unused potential of ecological research.

Intraspecific Relationships and Nest Mound Shape Are Affected by Habitat Features in Introduced Populations of the Red Wood Ant Formica paralugubris

Simple Summary

Red wood ants (Formica rufa goup) are dominant ant species widespread in the Eurasian continent. These species have a strong ecological impact on the habitats they dwell in, being top-ranked predators. One of the most striking features of these ants is represented by the large nest mounds they build. In this study, we investigated how nest mound shape and colony organization of imported populations of Formica paralugubris varied in three different habitat types. We found that nest mounds differed in size, number and shape in the three habitats. In all the three sites, nests were connected by trails of workers, but the size of these nest-networks differed. We also investigated the pattern of intraspecific aggression among ants from different nests, and we showed that aggressiveness was higher within each population than between separate populations, a finding in line with a ‘nasty neighbor’ behavior.

Abstract

Ants belonging to the Formica rufa group build large nest mounds, which aid their survival during severe winters. We investigated whether different environmental features of the habitats affected the nest mound shape and the population structure. We assessed the shape of all the nest mounds and mapped inter-nest trails connecting mounds for three imported populations of Formica paralugubris in three forest habitats: fir-dominated, beech-dominated, and a mixture of fir and beech. Single-nest mounds were averagely smaller and flatter in the beech-dominated forest, probably because of lighter building materials. Nonetheless, by summing the volumes of all interconnected nests, the size was similar among all three sites. In fir- and beech-dominated forests, large nests were also central in the networks, suggesting a central place foraging model with these nests as reference. We finally performed aggression tests, and found that aggressiveness was significantly higher among nests belonging to the same population than between populations. The results highlight the plasticity of the species to adapt nest and colony structure to different environments. Additionally, it appears that none of these populations is unicolonial, as observed in various alpine sites, there and the observed patterns of aggression are coherent with the ‘nasty neighbor’ effect.

Preferred reporting items for systematic reviews and meta-analyses in ecology and evolutionary biology: a PRISMA extension

Since the early 1990s, ecologists and evolutionary biologists have aggregated primary research using meta-analytic methods to understand ecological and evolutionary phenomena. Meta-analyses can resolve long-standing disputes, dispel spurious claims, and generate new research questions. At their worst, however, meta-analysis publications are wolves in sheep's clothing: subjective with biased conclusions, hidden under coats of objective authority. Conclusions can be rendered unreliable by inappropriate statistical methods, problems with the methods used to select primary research, or problems within the primary research itself. Because of these risks, meta-analyses are increasingly conducted as part of systematic reviews, which use structured, transparent, and reproducible methods to collate and summarise evidence. For readers to determine whether the conclusions from a systematic review or meta-analysis should be trusted - and to be able to build upon the review - authors need to report what they did, why they did it, and what they found. Complete, transparent, and reproducible reporting is measured by 'reporting quality'. To assess perceptions and standards of reporting quality of systematic reviews and meta-analyses published in ecology and evolutionary biology, we surveyed 208 researchers with relevant experience (as authors, reviewers, or editors), and conducted detailed evaluations of 102 systematic review and meta-analysis papers published between 2010 and 2019. Reporting quality was far below optimal and approximately normally distributed. Measured reporting quality was lower than what the community perceived, particularly for the systematic review methods required to measure trustworthiness. The minority of assessed papers that referenced a guideline (~16%) showed substantially higher reporting quality than average, and surveyed researchers showed interest in using a reporting guideline to improve reporting quality. The leading guideline for improving reporting quality of systematic reviews is the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) statement. Here we unveil an extension of PRISMA to serve the meta-analysis community in ecology and evolutionary biology: PRISMA-EcoEvo (version 1.0). PRISMA-EcoEvo is a checklist of 27 main items that, when applicable, should be reported in systematic review and meta-analysis publications summarising primary research in ecology and evolutionary biology. In this explanation and elaboration document, we provide guidance for authors, reviewers, and editors, with explanations for each item on the checklist, including supplementary examples from published papers. Authors can consult this PRISMA-EcoEvo guideline both in the planning and writing stages of a systematic review and meta-analysis, to increase reporting quality of submitted manuscripts. Reviewers and editors can use the checklist to assess reporting quality in the manuscripts they review. Overall, PRISMA-EcoEvo is a resource for the ecology and evolutionary biology community to facilitate transparent and comprehensively reported systematic reviews and meta-analyses.

Replications, Comparisons, Sampling and the Problem of Representativeness in Animal Cognition Research

Animal cognition research often involves small and idiosyncratic samples. This can constrain the generalizability and replicability of a study's results and prevent meaningful comparisons between samples. However, there is little consensus about what makes a strong replication or comparison in animal research. We apply a resampling definition of replication to answer these questions in Part 1 of this article, and, in Part 2, we focus on the problem of representativeness in animal research. Through a case study and a simulation study, we highlight how and when representativeness may be an issue in animal behavior and cognition research and show how the representativeness problems can be viewed through the lenses of, i) replicability, ii) generalizability and external validity, iii) pseudoreplication and, iv) theory testing. Next, we discuss when and how researchers can improve their ability to learn from small sample research through, i) increasing heterogeneity in experimental design, ii) increasing homogeneity in experimental design, and, iii) statistically modeling variation. Finally, we describe how the strongest solutions will vary depending on the goals and resources of individual research programs and discuss some barriers towards implementing them.

Biases in ecological research: attitudes of scientists and ways of control

The properties of the human mind affect the quality of scientific knowledge through the insertion of unconscious biases during the research process. These biases frequently cause overestimation of the effects under study, thereby violating the reproducibility of the research and potentially leading to incorrect conclusions in subsequent research syntheses. We explored the level of knowledge about biases and attitudes to this problem by analysing 308 responses of ecology scientists to a specifically developed survey. We show that knowledge about biases and attitude towards biases depend on the scientist’s career stage, gender and affiliation country. Early career scientists are more concerned about biases, know more about measures to avoid biases, and twice more frequently have learned about biases from their university courses when compared with senior scientists. The respondents believe that their own studies are less prone to biases than are studies by other scientists, which hampers the control of biases in one’s own research. We conclude that education about biases is necessary, but not yet sufficient, to avoid biases because the unconscious origin of biases necessitates external intervention to combat them. Obligatory reporting of measures taken against biases in all relevant manuscripts will likely enhance the reproducibility of scientific results.

M. tuberculosis infection of human iPSC-derived macrophages reveals complex membrane dynamics during xenophagy evasion

Xenophagy is an important cellular defence mechanism against cytosol-invading pathogens, such as Mycobacterium tuberculosis (Mtb). Activation of xenophagy in macrophages targets Mtb to autophagosomes; however, how Mtb is targeted to autophagosomes in human macrophages at a high spatial and temporal resolution is unknown. Here, we use human induced pluripotent stem cell-derived macrophages (iPSDMs) to study the human macrophage response to Mtb infection and the role of the ESX-1 type VII secretion system. Using RNA-seq, we identify ESX-1-dependent transcriptional responses in iPSDMs after infection with Mtb. This analysis revealed differential inflammatory responses and dysregulated pathways such as eukaryotic initiation factor 2 (eIF2) signalling and protein ubiquitylation. Moreover, live-cell imaging revealed that Mtb infection in human macrophages induces dynamic ESX-1-dependent, LC3B-positive tubulovesicular autophagosomes (LC3-TVS). Through a correlative live-cell and focused ion beam scanning electron microscopy (FIB SEM) approach, we show that upon phagosomal rupture, Mtb induces the formation of LC3-TVS, from which the bacterium is able to escape to reside in the cytosol. Thus, iPSDMs represent a valuable model for studying spatiotemporal dynamics of human macrophage-Mtb interactions, and Mtb is able to evade capture by autophagic compartments.

Perceived and actual fighting ability: determinants of success by decision, knockout or submission in human combat sports

Animal contest theory assumes individuals to possess accurate information about their own fighting ability or resource-holding potential (RHP) and, under some models, that of their opponent. However, owing to the difficulty of disentangling perceived and actual RHP in animals, how accurately individuals are able to assess RHP remains relatively unknown. Furthermore, it is not just individuals within a fight that evaluate RHP. Third-party observers evaluate the fight performance of conspecifics in order to make behavioural decisions. In human combat sports, when fights remain unresolved at the end of the allotted time, bystanders take a more active role, with judges assigning victory based on their assessment of each fighter's performance. Here, we use fight data from mixed martial arts in order to investigate whether perceived fighting performance (judges' decisions) and actual fighting success (fights ending in knockout or submission) are based on the same performance traits, specifically striking skill and vigour. Our results indicate that both performance traits are important for victory, but that vigour is more important for fights resolved via decision, even though the effect of vigour is enhanced by skill. These results suggest that while similar traits are important for fighting success across the board, vigour is overvalued in judges' perceptions of RHP.

Confirmation Bias as a Factor in Pharmacy Student Assessment of Research Study Quality

Objective. To determine whether pharmacy students' prior beliefs and attitudes about drug products and dietary supplements affected their ability to analyze the quality of research study abstracts and use them in making drug recommendations to patients. Methods. Fifty-nine Doctor of Pharmacy (PharmD) students in a drug literature course were randomly assigned to receive one of two forms to evaluate four drug literature abstracts of varying quality and study design. On each form, there were two abstracts that had been taken directly from published research studies and two abstracts in which a different product had been substituted for the actual product studied. Pharmacy students completed a questionnaire about the studies to determine whether their evaluation of quality was affected by their prior opinions about the products. Results. Students correctly recognized the relative quality of the studies. However, after reading abstracts of research articles that were identical except for the product named, students were still more likely to recommend drugs approved by the Food and Drug Administration than dietary supplements. Conclusion. Pharmacy students' evaluation of clinical research studies was mildly influenced by confirmation bias but more so by the quality of the research.

Insect Antennal Morphology: The Evolution of Diverse Solutions to Odorant Perception

Chemical communication involves the production, transmission, and perception of odors. Most adult insects rely on chemical signals and cues to locate food resources, oviposition sites or reproductive partners and, consequently, numerous odors provide a vital source of information. Insects detect these odors with receptors mostly located on the antennae, and the diverse shapes and sizes of these antennae (and sensilla) are both astonishing and puzzling: what selective pressures are responsible for these different solutions to the same problem - to perceive signals and cues? This review describes the selection pressures derived from chemical communication that are responsible for shaping the diversity of insect antennal morphology. In particular, we highlight new technologies and techniques that offer exciting opportunities for addressing this surprisingly neglected and yet crucial component of chemical communication.

Reanalysis of an oft-cited paper on honeybee magnetoreception reveals random behavior

While mounting evidence indicates that a phylogenetically diverse group of animals detect Earth-strength magnetic fields, a magnetoreceptor has not been identified in any animal. One possible reason that identifying a magnetoreceptor has proven challenging is that, like many research fields, magnetoreception research lacks extensive independent replication. Independent replication is important because a subset of studies undoubtedly contain false positive results and without replication it is difficult to determine whether the outcome of an experiment is a false positive. However, we report here a reanalysis of a well-cited paper on honeybee magnetoreception demonstrating that the original paper represented a false positive finding caused by incorrect estimates of probability. We also point out how good experimental design practices could have revealed the error prior to publication. Hopefully, this reanalysis will serve as a reminder of the importance of good experimental design in order to reduce the likelihood of publishing false positive results.

Improving the ACGIH threshold limit value (TLV) process

The intent of this manuscript is to elucidate needed improvements in American Conference of Governmental Industrial Hygienists (ACGIH) threshold limit value (TLV) deliberations. More broadly, irreproducibility and bias adversely impact the collection, interpretation, statistical analysis, presentation, and reporting of results in many fields. In 2012, Begley and Ellis reported that scientists at Amgen had attempted to confirm published findings related to research topics of possible interest to Amgen. Fifty-three papers were deemed “landmark” studies. The authors were “shocked” when scientific findings were confirmed in only 6 (11%) cases. Many studies have confirmed that the peer-reviewed literature in biomedicine is in the midst of an irreproducibility crisis. Compounding the irreproducibility crisis is the existence of a significant bias against the publication of negative results. In the toxicology setting, negative toxicity test results are infrequently published as compared with reports that a chemical possesses a particular toxicity in a given test. Despite these deficiencies, the ACGIH states that “…the TLV®-CS Committee preferably relies on published, peer reviewed literature available in the public domain.” The primarily academic studies published in the peer-reviewed literature upon which ACGIH relies to determine TLVs rarely report raw data not already statistically transformed that are thus incalculable. In contrast, consideration of unpublished studies funded by industry, the vast majority of which are good laboratory practice-conducted contract lab studies, is only acceptable to ACGIH if the data owner provides the raw data to third parties upon request. This asymmetry in both the source of data emphasized, and inability to independently statistically analyze findings reported in the published academic literature, introduces a strong skew toward reliance on unverifiable although published measurements in the TLV process. Since Occupational Safety and Health Administration (OSHA) recommends that workplaces rely on ACGIH TLVs and National Institute for Occupational Safety and Health recommended exposure limits rather than older OSHA permissible exposure limit values to optimize worker safety, ACGIH should adopt a more transparent and science-based process.

GCalignR: An R package for aligning gas-chromatography data for ecological and evolutionary studies

Chemical cues are arguably the most fundamental means of animal communication and play an important role in mate choice and kin recognition. Consequently, there is growing interest in the use of gas chromatography (GC) to investigate the chemical basis of eco-evolutionary interactions. Both GC-MS (mass spectrometry) and FID (flame ionization detection) are commonly used to characterise the chemical composition of biological samples such as skin swabs. The resulting chromatograms comprise peaks that are separated according to their retention times and which represent different substances. Across chromatograms of different samples, homologous substances are expected to elute at similar retention times. However, random and often unavoidable experimental variation introduces noise, making the alignment of homologous peaks challenging, particularly with GC-FID data where mass spectral data are lacking. Here we present GCalignR, a user-friendly R package for aligning GC-FID data based on retention times. The package was developed specifically for ecological and evolutionary studies that seek to investigate similarity patterns across multiple and often highly variable biological samples, for example representing different sexes, age classes or reproductive stages. The package also implements dynamic visualisations to facilitate inspection and fine-tuning of the resulting alignments and can be integrated within a broader workflow in R to facilitate downstream multivariate analyses. We demonstrate an example workflow using empirical data from Antarctic fur seals and explore the impact of user-defined parameter values by calculating alignment error rates for multiple datasets. The resulting alignments had low error rates for most of the explored parameter space and we could also show that GCalignR performed equally well or better than other available software. We hope that GCalignR will help to simplify the processing of chemical datasets and improve the standardization and reproducibility of chemical analyses in studies of animal chemical communication and related fields.

A systematic review of context bias in invasion biology

The language that scientists use to frame biological invasions may reveal inherent bias—including how data are interpreted. A frequent critique of invasion biology is the use of value-laden language that may indicate context bias. Here we use a systematic study of language and interpretation in papers drawn from invasion biology to evaluate whether there is a link between the framing of papers and the interpretation of results. We also examine any trends in context bias in biological invasion research. We examined 651 peer-reviewed invasive species competition studies and implemented a rigorous systematic review to examine bias in the presentation and interpretation of native and invasive competition in invasion biology. We predicted that bias in the presentation of invasive species is increasing, as suggested by several authors, and that bias against invasive species would result in misinterpreting their competitive dominance in correlational observational studies compared to causative experimental studies. We indeed found evidence of bias in the presentation and interpretation of invasive species research; authors often introduced research with invasive species in a negative context and study results were interpreted against invasive species more in correlational studies. However, we also found a distinct decrease in those biases since the mid-2000s. Given that there have been several waves of criticism from scientists both inside and outside invasion biology, our evidence suggests that the subdiscipline has somewhat self-corrected apparent biases.

Serpentine soils affect heavy metal tolerance but not genetic diversity in a common Mediterranean ant

Natural habitats with serpentine soils are rich in heavy metal ions, which may significantly affect ecological communities. Exposure to metal pollutants results, for instance, in a reduction of population genetic diversity and a diffused higher tolerance towards heavy metals. In this study, we investigated whether chronic exposure to metals in serpentine soils affect accumulation patterns, tolerance towards metal pollutants, and genetic diversity in ants. In particular, we studied colonies of the common Mediterranean ant, Crematogaster scutellaris, along a contamination gradient consisting of two differently contaminated forests and a reference soil with no geogenic contamination. We first evaluated the metal content in both soil and ants' body. Then, we tested for tolerance towards metal pollutants by evaluating the mortality of ants fed with nickel (Ni) solutions of increasing concentrations. Finally, differences in genetic diversity among ants from different areas were assessed using eight microsatellite loci. Interestingly, a higher tolerance to nickel solutions was found in ants sampled in sites with intermediate levels of heavy metals. This may occur, because ants inhabiting strongly contaminated areas tend to accumulate higher amounts of contaminants. Additional ingestion of toxicants beyond the saturation threshold would lead to death. There was no difference in the genetic diversity among ant colonies sampled in different sites. This was probably the result of queen mediated gene flow during nuptial flights across uncontaminated and contaminated areas of limited geographical extent.

An Alpine ant's behavioural polymorphism: monogyny with and without internest aggression in Tetramorium alpestre

Social structure influences animal societies on various levels (e.g., relatedness, behaviour). In ants, both the number of matings per queen and the number of queens per colony can vary strongly. While workers from both monogynous and polygynous colonies often fight fiercely, in supercolonies (an extreme form of polygyny comprising thousands of queens in spatially separated but interconnected nests), non-nestmates interact peacefully. Studies on social and behavioural polymorphism within ant species can help elucidate their influence on genetic diversity and behaviour and the factors triggering variation in social structure and behaviour. Here, we reveal a behavioural and social polymorphism comprising monogyny with and without internest aggression in Tetramorium alpestre sampled in Tyrol, Austria. The social polymorphism is based on genetic and behavioural evidence and contrasts with the supercolonial organisation known from another location in Austria (Carinthia), 150 km away. Microsatellite genotyping using eight polymorphic loci revealed monogyny-monandry and high intranest pairwise relatedness. Interestingly, various experimental one-on-one worker encounters revealed only occasional aggressive behaviour between monogynous colonies, and thus a behavioural polymorphism. Mantel tests revealed a significant negative correlation between spatial distance and relatedness, while worker behaviour was not correlated with relatedness or spatial distance. These results indicate that behaviour might be influenced by other factors - for example, the experience of workers, ecological, chemical, and/or genetic factors not characterised in this study. However, workers distinguished nestmates from non-nestmates also when aggression was lacking. We hypothesise an adaptive value of reduced aggression. We speculate that the non-aggressive and partly aggressive encounters observed represent different options in the social structure of T. alpestre, the non-aggressiveness possibly also promoting supercolony development. The social and behavioural polymorphisms observed offer opportunities to identify the factors triggering these changes and thus further explore the behavioural and social polymorphism of this ant species.

Logical fallacies in animal model research

Background

Animal models of human behavioural deficits involve conducting experiments on animals with the hope of gaining new knowledge that can be applied to humans. This paper aims to address risks, biases, and fallacies associated with drawing conclusions when conducting experiments on animals, with focus on animal models of mental illness.

Conclusions

Researchers using animal models are susceptible to a fallacy known as false analogy, where inferences based on assumptions of similarities between animals and humans can potentially lead to an incorrect conclusion. There is also a risk of false positive results when evaluating the validity of a putative animal model, particularly if the experiment is not conducted double-blind. It is further argued that animal model experiments are reconstructions of human experiments, and not replications per se, because the animals cannot follow instructions. This leads to an experimental setup that is altered to accommodate the animals, and typically involves a smaller sample size than a human experiment. Researchers on animal models of human behaviour should increase focus on mechanistic validity in order to ensure that the underlying causal mechanisms driving the behaviour are the same, as relying on face validity makes the model susceptible to logical fallacies and a higher risk of Type 1 errors. We discuss measures to reduce bias and risk of making logical fallacies in animal research, and provide a guideline that researchers can follow to increase the rigour of their experiments.

Inferring polydomy: a review of functional, spatial and genetic methods for identifying colony boundaries

Identifying the boundaries of a social insect colony is vital for properly understanding its ecological function and evolution. Many species of ants are polydomous: colonies inhabit multiple, spatially separated, nests. Ascertaining which nests are parts of the same colony is an important consideration when studying polydomous populations. In this paper, we review the methods that are used to identify which nests are parts of the same polydomous colony and to determine the boundaries of colonies. Specifically, we define and discuss three broad categories of approach: identifying nests sharing resources, identifying nests sharing space, and identifying nests sharing genes. For each of these approaches, we review the theoretical basis, the limitations of the approach and the methods that can be used to implement it. We argue that all three broad approaches have merits and weaknesses, and provide a methodological comparison to help researchers select the tool appropriate for the biological question they are investigating.

Transparency in Ecology and Evolution: Real Problems, Real Solutions

To make progress scientists need to know what other researchers have found and how they found it. However, transparency is often insufficient across much of ecology and evolution. Researchers often fail to report results and methods in detail sufficient to permit interpretation and meta-analysis, and many results go entirely unreported. Further, these unreported results are often a biased subset. Thus the conclusions we can draw from the published literature are themselves often biased and sometimes might be entirely incorrect. Fortunately there is a movement across empirical disciplines, and now within ecology and evolution, to shape editorial policies to better promote transparency. This can be done by either requiring more disclosure by scientists or by developing incentives to encourage disclosure.

The Rules of Aggression: How Genetic, Chemical and Spatial Factors Affect Intercolony Fights in a Dominant Species, the Mediterranean Acrobat Ant Crematogaster scutellaris

Nest-mate recognition plays a key role in the biology of ants. Although individuals coming from a foreign nest are, in most cases, promptly rejected, the degree of aggressiveness towards non nest-mates may be highly variable among species and relies on genetic, chemical and environmental factors. We analyzed intraspecific relationships among neighboring colonies of the dominant Mediterranean acrobat ant Crematogaster scutellaris integrating genetic, chemical and behavioral analyses. Colony structure, parental relationships between nests, cuticular hydrocarbons profiles (CHCs) and aggressive behavior against non nest-mates were studied in 34 nests located in olive tree trunks. Bayesian clustering analysis of allelic variation at nine species-specific microsatellite DNA markers pooled nests into 14 distinct clusters, each representing a single colony, confirming a polydomous arrangement of nests in this species. A marked genetic separation among colonies was also detected, probably due to long distance dispersion of queens and males during nuptial flights. CHCs profiles varied significantly among colonies and between nests of the same colony. No relationship between CHCs profiles and genetic distances was detected. The level of aggressiveness between colonies was inversely related to chemical and spatial distance, suggesting a ‘nasty neighbor’ effect. Our findings also suggest that CHCs profiles in C. scutellaris may be linked to external environmental factors rather than genetic relationships.

Evidence of Experimental Bias in the Life Sciences: Why We Need Blind Data Recording

Observer bias and other "experimenter effects" occur when researchers' expectations influence study outcome. These biases are strongest when researchers expect a particular result, are measuring subjective variables, and have an incentive to produce data that confirm predictions. To minimize bias, it is good practice to work "blind," meaning that experimenters are unaware of the identity or treatment group of their subjects while conducting research. Here, using text mining and a literature review, we find evidence that blind protocols are uncommon in the life sciences and that nonblind studies tend to report higher effect sizes and more significant p-values. We discuss methods to minimize bias and urge researchers, editors, and peer reviewers to keep blind protocols in mind.

Distributed nestmate recognition in ants

We propose a distributed model of nestmate recognition, analogous to the one used by the vertebrate immune system, in which colony response results from the diverse reactions of many ants. The model describes how individual behaviour produces colony response to non-nestmates. No single ant knows the odour identity of the colony. Instead, colony identity is defined collectively by all the ants in the colony. Each ant responds to the odour of other ants by reference to its own unique decision boundary, which is a result of its experience of encounters with other ants. Each ant thus recognizes a particular set of chemical profiles as being those of non-nestmates. This model predicts, as experimental results have shown, that the outcome of behavioural assays is likely to be variable, that it depends on the number of ants tested, that response to non-nestmates changes over time and that it changes in response to the experience of individual ants. A distributed system allows a colony to identify non-nestmates without requiring that all individuals have the same complete information and helps to facilitate the tracking of changes in cuticular hydrocarbon profiles, because only a subset of ants must respond to provide an adequate response.

Confirmation bias leads to overestimation of losses of woody plant foliage to insect herbivores in tropical regions

Confirmation bias, i.e., the tendency of humans to seek out evidence in a manner that confirms their hypotheses, is almost overlooked in ecological studies. For decades, insect herbivory was commonly accepted to be highest in tropical regions. By comparing the data collected blindly (when the observer was not aware of the research hypothesis being tested) with the results of non-blind studies (when the observer knew what results could be expected), we tested the hypothesis that the records made in the tropics could have overestimated community-wide losses of plant foliage to insects due to the confirmation bias. The average loss of leaf area of woody plants to defoliating insects in Brazil, when measured by a blind method (1.11%), was significantly lower than the loss measured in non-blind studies, both original (5.14%) and published (6.37%). We attribute the overestimation of the community-wide losses of plant foliage to insects in non-blind studies to the unconsciously preconceived selection of study species with higher-than-average levels of herbivory. Based on our findings, we urge for caution in obtaining community-wide characteristics from the results of multiple single-species studies. Our data suggest that we may need to revise the paradigm of the highest level of background insect herbivory in the tropical regions. More generally, we argue that more attention should be paid by ecologists to the problem of biases occurring at the pre-publication phases of the scientific research and, consequently, to the development and the wide application of methods that avoid biases occurring due to unconscious psychological processes.

Bias Neglect: A Blind Spot in the Evaluation of Scientific Results

Experimenter bias occurs when scientists' hypotheses influence their results, even if involuntarily. Meta-analyses have suggested that in some domains, such as psychology, up to a third of the studies could be unreliable due to such biases. A series of experiments demonstrates that while people are aware of the possibility that scientists can be more biased when the conclusions of their experiments fit their initial hypotheses, they robustly fail to appreciate that they should also be more sceptical of such results. This is true even when participants read descriptions of studies that have been shown to be biased. Moreover, participants take other sources of bias—such as financial incentives—into account, showing that this bias neglect may be specific to theory-driven hypothesis testing. In combination with a common style of scientific reporting, bias neglect could lead the public to accept premature conclusions.

US studies may overestimate effect sizes in softer research

Many biases affect scientific research, causing a waste of resources, posing a threat to human health, and hampering scientific progress. These problems are hypothesized to be worsened by lack of consensus on theories and methods, by selective publication processes, and by career systems too heavily oriented toward productivity, such as those adopted in the United States (US). Here, we extracted 1,174 primary outcomes appearing in 82 meta-analyses published in health-related biological and behavioral research sampled from the Web of Science categories Genetics & Heredity and Psychiatry and measured how individual results deviated from the overall summary effect size within their respective meta-analysis. We found that primary studies whose outcome included behavioral parameters were generally more likely to report extreme effects, and those with a corresponding author based in the US were more likely to deviate in the direction predicted by their experimental hypotheses, particularly when their outcome did not include additional biological parameters. Nonbehavioral studies showed no such "US effect" and were subject mainly to sampling variance and small-study effects, which were stronger for non-US countries. Although this latter finding could be interpreted as a publication bias against non-US authors, the US effect observed in behavioral research is unlikely to be generated by editorial biases. Behavioral studies have lower methodological consensus and higher noise, making US researchers potentially more likely to express an underlying propensity to report strong and significant findings.