Investigating and preventing scientific misconduct using Benford’s Law

Integrity and trust in that integrity are fundamental to academic research. However, procedures for monitoring the trustworthiness of research, and for investigating cases where concern about possible data fraud have been raised are not well established. Here we suggest a practical approach for the investigation of work suspected of fraudulent data manipulation using Benford’s Law. This should be of value to both individual peer-reviewers and academic institutions and journals. In this, we draw inspiration from well-established practices of financial auditing. We provide synthesis of the literature on tests of adherence to Benford’s Law, culminating in advice of a single initial test for digits in each position of numerical strings within a dataset. We also recommend further tests which may prove useful in the event that specific hypotheses regarding the nature of data manipulation can be justified. Importantly, our advice differs from the most common current implementations of tests of Benford’s Law. Furthermore, we apply the approach to previously-published data, highlighting the efficacy of these tests in detecting known irregularities. Finally, we discuss the results of these tests, with reference to their strengths and limitations.Publisher PDFPeer reviewe

Artificial light at night may decrease predation risk for terrestrial insects

This work was supported by the University of St Andrews.Artificial light at night (ALAN) is thought to be detrimental for terrestrial insect populations. While there exists evidence for lower abundance under ALAN, underlying mechanisms remain unclear. One mechanism by which ALAN may contribute to insect declines may be through facilitating increased predation. We investigated this by experimentally manipulating insect-substitute abundance under differential levels of light. We used insect-containing birdfeed placed at varying distances from streetlights as a proxy for terrestrial insects, inspecting the rate of predation before and after dusk (when streetlights are, respectively, off and on). We found that there was a significantly greater effect of increasing distance on predation after dusk, suggesting that predation was actually reduced by greater levels of artificial light. This may occur because ALAN also increases the vulnerability of insectivores to their own predators. Implications for foraging behaviour and alternative explanations are discussed.Publisher PDFPeer reviewe

Consequences of grouped data for testing for departure from circular uniformity

Limits to the precision of circular data often cause grouping of data points into discrete categories; but the effects of grouping on tests for circular uniformity have been little explored. The Rayleigh test is often applied to grouped circular data, despite it being designed for continuous data and the statistical literature recommending a suite of alternative tests specifically designed for grouped data. Here we investigated the performance of the Rayleigh test relative to four alternatives for testing the null hypothesis of uniformity in grouped circular data. We employed simulations grouping data into a discrete number of same-sized categories, and with samples drawn from a range of different distributions. We found that grouping had little effect on the type I error rate or the power of the Rayleigh test, and that the power of the Rayleigh test was very similar to that of the previously-recommended alternative tests designed specifically for grouped circular data. It may thus be appropriate to apply the Rayleigh test to grouped data, providing the situation is one in which the test has substantial statistical power.Publisher PDFPeer reviewe

Camouflage in predators

Camouflage – adaptations that prevent detection and/or recognition – is a key example of evolution by natural selection, making it a primary focus in evolutionary ecology and animal behaviour. Most work has focused on camouflage as an anti‐predator adaptation. However, predators also display specific colours, patterns and behaviours that reduce visual detection or recognition to facilitate predation. To date, very little attention has been given to predatory camouflage strategies. Although many of the same principles of camouflage studied in prey translate to predators, differences between the two groups (in motility, relative size, and control over the time and place of predation attempts) may alter selection pressures for certain visual and behavioural traits. This makes many predatory camouflage techniques unique and rarely documented. Recently, new technologies have emerged that provide a greater opportunity to carry out research on natural predator–prey interactions. Here we review work on the camouflage strategies used by pursuit and ambush predators to evade detection and recognition by prey, as well as looking at how work on prey camouflage can be applied to predators in order to understand how and why specific predatory camouflage strategies may have evolved. We highlight that a shift is needed in camouflage research focus, as this field has comparatively neglected camouflage in predators, and offer suggestions for future work that would help to improve our understanding of camouflage.Publisher PDFPeer reviewe

Evaluation of disruptive camouflage of avian cup-nests

Parent birds employ various strategies to protect their offspring against nest predators. Two well‐researched anti‐nest‐predation strategies involve visual concealment of the nest by way of parental camouflage and egg camouflage. By contrast, camouflage of nest structures is relatively under‐researched, particularly in the case of cup‐nests in trees and bushes. We explored how birds camouflage cup‐nests in nature. Specifically, we tested Hansell’s hypothesis that birds use externally applied pale and white objects such as spider cocoons and lichens to achieve cup‐nest camouflage. To test Hansell’s hypothesis, three complementary experiments were performed: (1) an in situ nest predation experiment; (2) a photo‐based visual search experiment; and (3) contrast analyses using PAT‐GEOM software in IMAGEJ. White paper and chalk spots were used to mimic white objects used by birds in nature. Whereas predation rates in Experiment 1 were not affected by white spots, location rates in Experiment 2 were lower for natural nests with white spots than without white spots. Experiment 3 demonstrated that white spots significantly increased the contrast between different visual elements of nests. It was concluded that white objects can potentially camouflage nests against some nest predators, and that any improved camouflage was probably achieved via disruptive camouflage.Publisher PDFPeer reviewe

Classical tests, linear models, and their extensions for the analysis of 2x2 contingency tables

Funding: Deutsche Forschungsgemeinschaft - 515410943; Royal Society London - University Research Fellowship.1. Ecologists and evolutionary biologists are regularly tasked with the comparison of binary data across groups. There is, however, some discussion in the biostatistics literature about the best methodology for the analysis of data comprising binary explanatory and response variables forming a 2 × 2 contingency table. 2. We assess several methodologies for the analysis of 2 × 2 contingency tables using a simulation scheme of different sample sizes with outcomes evenly or unevenly distributed between groups. Specifically, we assess the commonly recommended logistic (generalised linear model [GLM]) regression analysis, the classical Pearson chi-squared test and four conventional alternatives (Yates' correction, Fisher's exact, exact unconditional and mid-p), as well as the widely discouraged linear model (LM) regression. 3. We found that both LM and GLM analyses provided unbiased estimates of the difference in proportions between groups. LM and GLM analyses also provided accurate standard errors and confidence intervals when the experimental design was balanced. When the experimental design was unbalanced, sample size was small, and one of the two groups had a probability close to 1 or 0, LM analysis could substantially over- or under-represent statistical uncertainty. For null hypothesis significance testing, the performance of the chi-squared test and LM analysis were almost identical. Across all scenarios, both had high power to detect non-null effects and reject false positives. By contrast, the GLM analysis was underpowered when using z-based p-values, in particular when one of the two groups had a probability near 1 or 0. The GLM using the LRT had better power to detect non-null results. 4. Our simulation results suggest that, wherever a chi-squared test would be recommended, a linear regression is a suitable alternative for the analysis of 2 × 2 contingency table data. When researchers opt for more sophisticated procedures, we provide R functions to calculate the standard error of a difference between two probabilities from a Bernoulli GLM output using the delta method. We also explore approaches to compliment GLM analysis of 2 × 2 contingency tables with credible intervals on the probability scale. These additional operations should support researchers to make valid assessments of both statistical and practical significances.Peer reviewe

Deconstructing collective building in social insects : implications for ecological adaptation and evolution

Funding: John Templeton Foundation as part of the research collaboration grant “Putting the extended evolutionary synthesis to the test” (Grant no. 60501).Nests built by eusocial insect species are often complex structures consisting of multiple effectively integrated and functionally distinct substructures. Stigmergy, self-assembly and self-organisation have been proposed as the mechanisms that translate simple individual behaviour into coordinated collective activity. Here, we consider these processes focusing on their implications for the generation of new structures, nest adaptiveness and the evolution of building rules. We discuss in particular how self-organisation and stigmergy may guide the shift between substructures during building and generate new elements, either as an indirect result of building rule sets evolved for other purposes and under direct selection. The same mechanisms generate local, short-term adaptation through exploration of the phenotype space of the construction. Finally, we introduce the hypothesis that feedback dynamics create evolutionary transition between collective level phenotypes when mutations arise in the worker line, thus facilitating colony survival and affecting the evolution of collective building rules and of nest shape. This smooth transition is possible only when the new and the old rule variant are compatible. We call for new research that investigates self-organisation in collective building from an evolutionary perspective.Publisher PDFPeer reviewe

Post-dropping behavior of potato aphids (Macrosiphum euphorbiae)

Funding: Perry Foundation, University of St Andrews, Scottish Government Rural and Environmental Sciences and Analytical Services Division.Dropping behavior is an effective antipredator defense utilized by many insects including aphids, which drop from plants to lower plant parts or underlying substrates to avoid attack from predatory invertebrates. While research commonly focusses on triggers of dropping, less attention is given to what happens to prey individuals following escape drops. In this study, the duration of tonic immobility, recovery rates, and cases of “instant recovery” (re-clinging to lower plant parts) exhibited by potato aphids (Macrosiphum euphorbiae) that dropped from potted seedlings in response to introduced ladybird (Adalia bipunctata) adults, lacewing (Chrysoperla carnea) larvae, and a standardized tactile stimulus were investigated in relation to a range of environmental factors. Air temperature had a negative correlation with the duration of post-dropping tonic immobility; as temperature increased, time spent motionless decreased. Aphids also showed a pattern of increased recovery rate at higher temperatures. Aphids may be selected to move off the substrate quicker to avoid risks of overheating/desiccation at higher temperatures; and/or higher body temperature facilitates locomotion. Stimulus type also influenced recovery rate back to the original seedling, with aphids generally recovering after the standardized stimulus quicker than after dropping triggered by a real predator. Considering cases of instant recovery onto lower-reaches of the host seedling, seedling height influenced the likelihood of re-clinging, with aphids that managed to instantly recover dropping from, on average, taller seedlings than aphids that dropped to the substrate. Plant architecture could mitigate the costs of dropping for aphids, but further studies quantifying understory foliage cover are needed.Publisher PDFPeer reviewe

Multiple regressions: the meaning of multiple regression and the non-problem of collinearity

Simple regression (regression analysis with a single explanatory variable), and multiple regression (regression models with multiple explanatory variables), typically correspond to very different biological questions. The former use regression lines to describe univariate associations. The latter describe the partial, or direct, effects of multiple variables, conditioned on one another. We suspect that the superficial similarity of simple and multiple regression leads to confusion in their interpretation. A clear understanding of these methods is essential, as they underlie a large range of procedures in common use in biology. Beyond simple and multiple regression in their most basic forms, understanding the key principles of these procedures is critical to understanding, and properly applying, many methods, such as mixed models, generalised models, and causal inference using graphs (including path analysis and its extensions). A simple, but careful, look at the distinction between these two analyses is valuable in its own right, and can also be used to clarify widely-held misconceptions about collinearity (correlations among explanatory variables). There is no general sense in which collinearity is a problem. We suspect that the perception of collinearity as a hindrance to analysis stems from misconceptions about interpretation of multiple regression models, and so we pursue discussions about these misconceptions in this light. In particular, collinearity causes multiple regression coefficients to be less precisely estimated than corresponding simple regression coefficients. This should not be interpreted as a problem, as it is perfectly natural that direct effects should be harder to characterise than univariate associations. Purported solutions to the perceived problems of collinearity are detrimental to most biological analyses.Publisher PDFPeer reviewe

Why war is a man's game

A.J.C.M. is supported by a Ph.D. studentship from the School of Biology, University of St Andrews, and A.G. is supported by a Natural Environment Research Council Independent Research Fellowship (NE/K009524/1) and a European Research Council Consolidator Grant (771387).Interest in the evolutionary origins and drivers of warfare in ancient and contemporary small-scale human societies has greatly increased in the last decade, and has been particularly spurred by exciting archaeological discoveries that suggest our ancestors led more violent lives than previously documented. However, the striking observation that warfare is an almost-exclusively male activity remains unexplained. Three general hypotheses have been proposed, concerning greater male effectiveness in warfare, lower male costs, and patrilocality. But while each of these factors might explain why warfare is more common in men, they do not convincingly explain why women almost never participate. Here, we develop a mathematical model to formally assess these hypotheses. Surprisingly, we find that exclusively male warfare may evolve even in the absence of any such sex differences, though sex biases in these parameters can make this evolutionary outcome more likely. The qualitative observation that participation in warfare is almost exclusive to one sex is ultimately explained by the fundamentally sex-specific nature of Darwinian competition—in fitness terms, men compete with men and women with women. These results reveal a potentially key role for ancestral conditions in shaping our species' patterns of sexual division of labour and violence-related adaptations and behavioural disorders.Publisher PDFPeer reviewe