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Wild raccoons are more innovative but not bolder than another ecological generalist, the Virginia opossum, on a pull-string task

Humans are altering natural environments at unprecedented rates. Ecological generalism is one of the strongest predictors of survival in light of these changes which, in animals, may be shaped by bold and innovative behaviours. Species with greater habitat generalism are proposed to behave more boldly (e.g., touching and ingesting novel food). Species with greater dietary generalism are proposed to behave more innovatively (e.g., novel problem-solving to access food). Support for both hypotheses exists but remains largely restricted to broad comparisons between generalists and specialists. Further comparative data are needed to understand the extent to which these behavioural patterns might shape more nuanced ecological variation between species, such as species with finer-scale niche differences. We compared bold and innovative behaviour in two wild sympatric generalists, the Northern raccoon (Procyon lotor) and Virginia opossum (Didelphis virginiana), using a pull-string task with strings and wires attached to vertical cups containing high-value food. Although both species are broadly classified as generalists, raccoons show relatively greater habitat and dietary flexibility than opossums. Because they live sympatrically, it offers a unique opportunity to test - at the same time and locations - whether these finer-scale niche differences are reflective of differences in their bold and innovative behaviour. We predicted that raccoons would display bolder behaviour (in terms of touching our novel task) and more innovative behaviour (in terms of solving it). We found that both species were equally likely to acknowledge and touch the task, but raccoons were more likely to display innovation to access the food. Raccoons propensity for using innovation to solve novel foraging challenges may contribute to their greater ecological flexibility compared to opossums. More broadly, our findings may help explain differences in how each species adapts to environmental changes. HighlightsO_LIBold and innovative behaviour may help some species adapt to environmental changes C_LIO_LIWe administered a novel pull-string task to wild raccoons and opossums C_LIO_LIRaccoons displayed more innovative, not bolder, behaviour than opossums C_LIO_LIBoth species are generalists, but raccoons are more flexible than opossums C_LIO_LIDifferences in innovation may shape their finer-scale niche differences C_LI

animal behavior and cognition↗

Ecologically Significant Genetic Loci of P. allii: Contributions to Pathogenesis and Competition

Pantoea allii, one of four Pantoea species known to cause onion center rot, is infrequently isolated from onion compared to its closely related onion-pathogenic sister taxa. To better understand the genomic diversity and genetic determinants of pathogenicity in this species, we analyzed a collection of 38 P. allii strains isolated from two primary ecological niches, plants and water, across three continents using comparative genomics and phylogenetic approaches. Core-genome phylogeny, average nucleotide identity (ANI), and gene presence-absence analyses revealed three genetically distinct lineages. All strains harbored conserved biosynthetic gene clusters (BGCs) for quorum sensing, carotenoid production, siderophores, and thiopeptides. In contrast, two phosphonate BGCs, key determinants of onion pathogenicity, exhibited lineage-specific distributions. Onion-associated strains from Lineages 1 and 2 carried the Halophos BGC associated with onion tissue necrosis, and onion isolates encoded the alt gene cluster conferring thiosulfinate tolerance. Lineage 3 strains, isolated from both onion and rainwater, either lacked a phosphonate BGC loci or carried the HiVir phosphonate BGC. In addition, Lineage 3 strains lacked the alt cluster altogether. The localization of these virulence genes in the genome varied, with Halophos integrated in the chromosome, HiVir encoded on the conserved Large Pantoea Plasmid, and alt located on a small, variable plasmids (plasmid B). The Type IV and Type VI secretion systems showed variable genomic architectures, with plasmid-borne T4SSs and two chromosomal T6SS loci differing in conservation and gene content. Additionally, conserved Pantailocin phage islands were detected in most genomes. Overall, this study reveals that while core metabolic and competitive traits are conserved across P. allii, virulence-associated loci display lineage-specific partitioning, reflecting ecological differentiation and evolutionary plasticity within the species. Impact StatementThis study presents a comprehensive comparative genomic analysis of available Pantoea allii genomes, a known onion pathogen. By analyzing 38 strains isolated from plant and water sources across three continents, we uncovered lineage-specific distributions of key virulence genes, alongside conserved genetic traits associated with competition and environmental resilience. These findings clarify the genetic basis of P. allii pathogenesis and highlight its potential as a biocontrol agent, offering broader insights into how ecologically significant loci contribute to the dual roles of plant-associated bacteria as both pathogens and beneficial microbes. Data SummaryPENDING

genomics↗

Evolution of quantitative traits: exploring the ecological, social and genetic bases of adaptive polymorphism

Adaptive polymorphisms in quantitative traits are characterised by the coexistence of distinct genetically encoded phenotypes maintained by selection. Such intraspecific genetic and phenotypic variation make a substantial contribution to biological diversity. Building on established results from invasion analysis, we analyse conditions under which adaptive polymorphism can emerge under long-term gradual evolution. We first note that, in general, fully characterising an adaptive polymorphism, including its number of morphs, trait values and frequencies, is a computationally hard problem. Nevertheless, standard invasion results reveal a unifying necessary condition for the gradual emergence of polymorphism: negative trait-dependent selection (NTDS), whereby the marginal fitness effect of increasing trait expression in a mutant depends negatively on the population-level trait expression, reflecting a negative interaction between mutant and population trait changes. We use NTDS as an organising principle to structure the pathways through which polymorphism can evolve. This is based on a decomposition of fitness that distinguishes production factors, the inputs to survival and reproduction that are endogenous to individuals, from regulating factors, the ecological, social or genetic inputs to fitness that are influenced in part by conspecifics. This decomposition allows us to clarify how NTDS arises across three broad classes of interactions: ecological, social and genetic; and to identify previously unrecognised adaptive polymorphisms in well-studied scenarios, including life-history, social preferences, and class-structured populations. More broadly, by integrating perspectives from population genetics, evolutionary ecology, adaptive dynamics, game theory and inclusive fitness theory, we aim to provide a common thread among the pathways through which selection favours intraspecific variation.

evolutionary biology↗

PCR Bias Impacts Microbiome Ecological Analyses

Polymerase Chain Reaction (PCR) is a critical step in amplicon-based microbial community profiling, allowing the selective amplification of marker genes such as 16S rRNA from environmental or host-associated samples. Despite its widespread use, PCR is known to introduce amplification bias, where some DNA sequences are preferentially amplified over others due to factors such as primer-template mismatches, sequence GC content, and secondary structures. Although these biases are known to affect transcript abundance, their implications for ecological metrics remain poorly understood. In this study, we conduct a comprehensive evaluation of how PCR-bias influences both within-samples (-diversity) and between-sample ({beta}-diversity) analyses. We show that perturbation-invariant diversity measures remain unaffected by PCR bias, but widely used metrics such as Shannon diversity and Weighted-Unifrac are sensitive, with their values varying according to the true community composition. To address this, we provide theoretical and empirical insight into how PCR-induced bias varies across ecological analyses and community structures, and we offer practical guidance on when bias-correction methods should be applied. Our findings highlight the importance of selecting appropriate diversity metrics for PCR-based microbial ecology workflows and offer guidance for improving the reliability of diversity analyses.

microbiology↗

Evolutionary rescue in a consumer-resource system: Adaptation and persistence depend on the affected ecological traits

With evolutionary rescue, a population that is declining due to an environmental change adapts to its environment, avoiding extinction. Previous theoretical work has explored the effects of negative density-dependence on rescue, showing that it may aid or hinder persistence. However, these models typically assume that it is only population intrinsic growth rates, r, or carrying capacity, K, that are negatively affected, and do not model density-dependence explicitly. Here, we analyze evolutionary rescue in a consumer-resource species following an abrupt environmental change, characterizing how rescue is dependent on the ecological effects of the environmental change on the consumer, which differently affect r and K through subsequent interactions with an explicit non-substitutable resource species. We derive approximate analytical predictions for the fixation probabilities of beneficial alleles, mutational supply, and times to extinction, which work well when selection is weak and individual turnover rates are low. We demonstrate that consumer rescue is dependent on the ecological effect of the environmental change, the resident life-history of the population, and the genetic architectures of evolving traits (monogenic versus polygenic). Our model suggests that measurements of intrinsic growth rates alone will be insufficient to predict rescue probabilities. This work extends our understanding of the interplay between ecology and evolution in influencing population persistence.

evolutionary biology↗

Colour and shape evolution reflect ecological specialisation in Pomacentridae

Damselfishes (Pomacentridae) display remarkable diversity in colouration and body form, yet the processes shaping this phenotypic variation remain poorly resolved. Our study aimed to characterise the evolution of these traits, evaluate their associations with ecological factors, and identify convergent patterns linked to ecological specialisation. Using image-based quantification of colour patterns, geometric morphometrics, and phylogenetic comparative methods across 343 species, we show that pomacentrid phenotypes are organised around a small number of dominant axes describing brightness, hue, contrast, body elongation, and cranial morphology. Both colour and morphology exhibit early bursts of evolutionary disparity, followed by recurrent lineage-specific radiations and widespread convergence toward similar adaptive optima across the phylogeny. Dietary ecotypes emerged as the strongest predictor of morphological diversification, whereas symbiotic and social regimes exerted the strongest effects on colour evolution. Despite these distinct ecological correlates, several colour and shape axes form partially integrated trait syndromes that evolve in concert. The pervasive convergence of colour-shape syndromes underscores deterministic components of reef-fish evolution and positions Pomacentridae as a model for understanding integrated phenotypic evolution.

evolutionary biology↗

Foraging behavior and ecology drive the evolution of humeral shape in hummingbirds

Understanding how locomotion-related skeletal elements evolve under biomechanical and ecological constraints is central to animal evolutionary biology. In hummingbirds (Trochilidae), the humerus plays a key role in force transmission during hovering and flapping flight, yet the drivers of its shape evolution have not been examined. We combined geometric morphometrics with phylogenetic comparative analyses to examine humeral shape variation, evolutionary rates, and phenotypic integration in male hummingbirds from 78 species. Our analyses identified humerus allometry as the dominant predictor of shape, revealing a pattern in which larger humeri show broader proximal epiphyses, increased shaft robustness, and reduced curvature. In addition to this scaling pattern, we find that male humerus shape differs subtly among hummingbird species that differ in the use of aggression during nectar foraging. Evolutionary rates of humeral shape were heterogeneous and decoupled from ecological predictors. We also find phenotypic integration between the proximal and distal regions of the humerus, indicating coordinated evolution. Together, these results show that humeral evolution in hummingbirds is governed primarily by biomechanical scaling and internal integration, with foraging ecology introducing secondary, size-dependent modifications. This work highlights the importance of considering scaling and internal integration when interpreting morphological evolution in locomotor systems across vertebrates.

evolutionary biology↗

Trait-dependent diversification and spatio-ecological limits drive angiosperm diversity unevenness across the Canary Islands archipelago

Island biotas often show highly uneven species richness among lineages, influenced by clade age, diversification rates, and/or spatio-ecological limits. However, disentangling these drivers has been challenging due to the lack of comprehensive datasets across multiple lineages in the same geographical arena. The flora of the Canary Islands includes hundreds of plant lineages with contrasting species richness and harbours the highest number of species that evolved their woodiness in-situ ("insular woodiness"). Here, we present a phylogenomic reconstruction for Canary Island angiosperms and show that diversity unevenness in the flora is not driven by lineage age but by trait-dependent diversification and spatio-ecological limits. Our phylogenomic dataset, based on 1,244 newly generated and 501 published DNA sequences for 669 Canary Island species and 771 closely related mainland taxa, allows us to simultaneously study 435 plant lineages ([~]50% of total). Applying dynamic stochastic modelling, we find the flora is shaped by high extinction and colonisation rates, maintaining a macroevolutionary equilibrium. Additionally, insular woody lineages exhibit higher diversification rates than the remaining flora. Our results suggest the uneven diversity of a highly dynamic insular region can be explained by the interaction of trait evolution and ecological constraints, providing insights into island biodiversity dynamics.

evolutionary biology↗

Genome-scale metabolic models predict diet- and lifestyle-driven shifts of ecological interactions in the gut microbiome

1.Microbiomes and their host environments form complex, interconnected ecosystems. The microbial species within a microbiome, on the one hand, compete for resources, while on the other hand, they exchange vital metabolites to support their survival. These interactions are influenced by the microbial genetic repertoire, environmental conditions, and the availability of nutrients. We developed EcoGS (http://www.github.com/KaletaLab/EcoGS), a metabolic modelling tool designed to predict ecological interactions between pairs of microbes. Applying EcoGS to the microbiomes of two distinct human cohorts revealed a shift from collaborative to exploitative ecological interactions associated with higher dietary intake of simple sugars (glucose and fructose), in diabetic individuals and those living in industrialised lifestyles. On the other hand, the consumption of Cobalamin (vitamin B12), phylloquinone (vitamin K1) and biotin (vitamin B7), among other compounds, was associated with increased collaboration in the gut microbiome. We conclude that the abundance of simple sugars as an energy source reduces the necessity for microbes to cooperate, thereby increasing competition and hostility among microbiome members. Moreover, our study proposes multiple compounds, such as urate, deoxyadenosine, deoxyguanosine, and hypoxanthine, for in vitro validation tests as dietary interventions that have the potential to restore the ecological balance amongst the community. EcoGS serves as a valuable tool for exploring microbiome dynamics and their connections to environmental changes and disease.

systems biology↗

Genetic divergence in the absence of strong ecological differences between coexisting white and common Atlantic marine sticklebacks

Identifying taxa in the earliest phases of speciation is critical for understanding how reproductive isolation arises. In Nova Scotia, Canada, "white" threespine sticklebacks co-occur with common marine sticklebacks but differ in nuptial coloration, nesting behavior, and parental care, raising the possibility that they represent a nascent species. We combined population genomics, morphometrics, and stable isotope analysis to test whether white sticklebacks represent a distinct lineage and whether they have diverged along ecological axes as in other stickleback populations. Genotyping-by-sequencing revealed that male and female white sticklebacks form a genetic cluster distinct from sympatric common sticklebacks with evidence of ongoing gene flow yet with very low overall genomic divergence (FST {approx} 0.01). Genetic differences were distributed across many loci rather than localized to a single genomic region. Morphological and isotopic analyses revealed no differences in most classic ecological traits (body shape, armor, gill rakers, or trophic niche). Instead, whites are smaller-bodied, paler, and exhibit shorter spines, reduced testes size, and smaller but more numerous eggs compared to common sticklebacks. These results indicate that white sticklebacks are genetically distinct from the common Atlantic threespine stickleback but have not diverged conspicuously in their ecology, suggesting that their differentiation is driven by reproductive and sexual traits rather than trophic specialization. The white stickleback thus represents a promising new system for investigating the interplay of sexual selection, reproductive strategy, and gene flow in the early stages of speciation.

evolutionary biology↗

Demographic, behavioral, and ecological data from a long-term field study of wild baboons in Amboseli, Kenya

Long-term data sets on individually recognized animals and their environments are critical to understanding animal behavior, evolution, and ecology. However, they are resource- and time-intensive and seldom made publicly available. The Amboseli Baboon Research Project (ABRP) is one of the longest-running studies of a wild mammal population in the world and has collected extensive data on the baboon population of the Amboseli ecosystem in Kenya since 1971. Here, we describe four ABRP data sets newly available to the evolutionary biology, behavioral ecology, and primatology communities: (1) the sizes and demographic compositions of 21 social groups from 1971-2023; (2) the activity budgets of adult females and immatures from 1984-2023; (3) behavioral data on diet for adult females and immatures from 1984-2023; and (4) weather data, including precipitation from 1976-2023 and temperature from 1976-2022. Data are aggregated annually and monthly to enable cross-data set analyses. These data offer a rare longitudinal perspective on behavioral and ecological change in a wild mammal population.

animal behavior and cognition↗

Trade-offs between phage resistance and conjugative ability shape the ecological and evolutionary response of a multidrug resistance plasmid to plasmid-dependent phage

Phage therapy is a promising alternative to antibiotics to treat multidrug resistant infections. Plasmid dependent phages (PDPs) are particularly attractive as therapeutics because they can both kill targeted pathogen cells, whilst also potentially preventing the further spread of antibiotic resistance genes encoded by plasmids. However, we lack experimental studies of the ecological and evolutionary response of multidrug resistance plasmids against plasmid dependent phage treatment under ecologically relevant scenarios allowing plasmid conjugation. We experimentally evolved populations of E. coli carrying the multidrug resistance RP4 plasmid with the PRD1 PDP under conditions where conjugation was associated with either strong or weak benefits. When opportunities for conjugation were rare, PRD1 only transiently suppressed the conjugative plasmid population due to the rapid evolution of PRD1 resistant plasmids that lacked conjugative ability. Increasing the ecological opportunity for conjugation enhanced plasmid suppression and delayed the evolution of PRD1 resistant plasmids. PRD1 resistance was associated with reduced conjugative ability, but this trade-off was complex due to the heterogeneous impacts of resistance mutations on pilus production and conjugative ability. Mutations and IS element insertions in conjugation genes caused a wide range of PRD1 resistance phenotypes, ranging from complete resistance (virB4) to partial resistance (trbB, trbL). Bioinformatic analysis of publicly available IncP plasmid sequences showed that truncated variants of VirB4 protein are common in natural populations, suggesting that plasmid-dependent phages are an important selective pressure in microbial communities. Our results demonstrate an evolutionary trade-off between conjugative ability and phage resistance that cannot be easily circumvented by plasmids. Targeting multidrug resistance plasmids with PDPs is likely to drive loss of conjugation limiting the transfer of antibiotic resistance genes in bacterial communities.

evolutionary biology↗

Species interactions, divergence, and the rapid evolution of ecological sexual dimorphism in threespine sticklebacks

Variation in ecological sexual dimorphism (ESD), defined as differences between the sexes in ecologically-relevant traits, is a common feature of adaptive radiation, yet its causes remain unclear. Competition between the sexes for alternative resources can promote evolution of ESD when interspecific competition is reduced (competition hypothesis). Alternatively, sex-specific selection on ecological traits might weaken under strong directional selection in new environments (divergence hypothesis). We tested these hypotheses via their expected evolutionary outcomes in threespine stickleback populations from southwestern Canada. We found striking among-population variation in magnitude of ESD. Consistent with the divergence hypothesis, dimorphism along the main axis of body shape variation was reduced in recently derived freshwater populations compared to their contemporary marine ancestor. However, dimorphism only weakly declined with increasing phenotypic divergence. Average dimorphism along major freshwater body shape axes was similar between solitary populations and those coexisting with a competing species, contrary to the competition hypothesis. Instead, sympatry with a Benthic ecotype led to increased sexual size dimorphism in Limnetics, and total shape dimorphism was elevated in the sympatric stickleback species compared with solitary populations. In contrast to the mechanisms considered in existing theory, interactions in sympatry might produce elevated ESD by generating novel sex-specific selection pressures.

evolutionary biology↗

Developmental trajectories of cognitive traits in meerkats match socio-ecological demands

Understanding cognitive development is fundamental for explaining variation in adult cognitive phenotypes, and thus the processes driving cognitive evolution. The ontogeny of cognitive traits is likely influenced by both population-wide pressures, such as ecological demands, and individual-specific factors, including early life experiences. To properly investigate cognitive variation, we must therefore identify species-level developmental trajectories and individual variation from normative ontogeny. We studied the ontogeny of three cognitive traits--inhibition control, spatial cognition, and physical problem-solving skills--in 28 wild meerkats (Suricata suricatta) from eight litters (seven groups). Our longitudinal study followed individuals from early life to nutritional independence and into sub-adulthood. We found that rates of development (learning curves) varied among traits, reflecting the timing of socio-ecological pressures in this species. Performance of cognitive traits did not correlate over ontogeny nor at specific time points, suggesting independent processes underlying each measured trait. While the development of inhibitory control appeared conserved, that of spatial cognition and physical problem-solving showed substantive individual differences. Furthermore, only physical problem-solving showed consistency in performances over time, emerging near nutritional independence, reflecting its ecological importance early in life. Future research should determine the drivers of individual developmental variation and how such differences translate into fitness consequences.

animal behavior and cognition↗

Ecological Insights from the Evolutionary History of Microbial Innovations

Bacteria and Archaea represent the base of the evolutionary tree of life and contain the vast majority of phylogenetic and functional diversity. Because these organisms and their traits directly impact ecosystems and human health, a focus on functional traits has become increasingly common in microbial ecology. These trait-based approaches have the potential to link microbial communities and their ecological function. But an open question is how, why, and in what order microorganisms acquired the traits we observe in the present day. To address this, we reconstructed the evolutionary history of microbial traits using genomic data to understand the evolution, selective advantage, and similarity of traits in extant organisms and provide insights into the composition of genomes and communities. We used the geological timeline and physiological expectations to provide independent evidence in support of this evolutionary history. Using this reconstructed evolutionary history, we explored hypotheses related to the composition of genomes. We showed that gene transition rates can be used to make predictions about the size and type of genes in a genome: generalist genomes comprise many evolutionarily labile genes while specialist genomes comprise more highly conserved functional genes. These findings suggest that generalist organisms do not build up and hoard an array of functions, but rather tend to experiment with functions related to environmental sensing, transport, and complex resource degradation. Our results provide a framework for understanding the evolutionary history of extant microorganisms, the origin and maintenanceof traits, and linking evolutionary relatedness and ecological function.

microbiology↗

Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

AO_SCPCAPBSTRACTC_SCPCAPThe coincidence of long distance dispersal and biome shift is assumed to be the result of a multifaceted interplay between geographical distance and ecological suitability of source and sink areas. Here, we test the influence of these factors on the dispersal history of the flowering plant genus Erica (Ericaceae) across the Afrotemperate. We quantify similarity of Erica climate niches per biogeographic area using direct observations of species, and test various colonisation scenarios while estimating ancestral areas for the Erica clade using parametric biogeographic model testing. We infer that the overall dispersal history of Erica across the Afrotemperate is the result of infrequent colonisation limited by geographic proximity and niche similarity. However, the Drakensberg Mountains represent a colonisation sink, rather than acting as a \"stepping stone\" between more distant and ecologically dissimilar Cape and Tropical African regions. Strikingly, the most dramatic examples of species radiations in Erica were the result of single unique dispersals over longer distances between ecologically dissimilar areas, contradicting the rule of phylogenetic biome conservatism. These results highlight the importance of rare biome shifts, in which a unique dispersal event fuels evolutionary radiation.\n\nThis article has been peer-reviewed and recommended by: Peer Community in Evolutionary Biology (DOI: 10.24072/pci.evolbiol.100065)

evolutionary biology↗

Synthetic methanogenic communities reveal differential impact of ecological perturbations on aceto- and hydrogeno-trophic methanogens

Synthetic microbial communities provide reduced microbial ecologies that can be studied under defined conditions. Here, we use this approach to study the interactions underpinning anaerobic digestion communities and involving the key microbial populations of a sulfate reducer (Desulfovibrio vulgaris), and aceto-(Methanosarcina barkeri) and hydrogenotrophic (Methanococcus maripaludis) methanogens. We create all possible mixed culture combinations of these species and analyse the stability and productivity of each system over multiple sub-culturings and under different sulfate levels, mimicking ecological perturbation in the form of strong electron acceptor availability. We find that all three species can co-exist in the absence of sulfate, and that system productivity (in form of methane production from lactate) increases by almost two-fold compared to co-cultures. With increasing sulfate availability, co-existence is perturbed and both methanogenic populations display a diminishing trend. Interestingly, we find that, despite the continued presence of acetate in the system, the acetotrophic methanogens are more readily disrupted by sulfate perturbation. We show that this is due to a shift in M. barkeri metabolism towards increased co-utilisation of hydrogen with acetate, which we verified through experiments on mono cultures and mass balance calculations in co-cultures. We conclude that hydrogen is a key factor for both hydrogeno- and aceto-trophic methanogenesis and can influence these populations differentially under the common ecological perturbation of strong electron acceptor availability. These findings will help engineering of larger synthetic communities for specific applications in biodegradation and understanding complex anaerobic digestion communities found in animal guts, sediments, and bioreactors.

synthetic biology↗

High impact journals in ecology cover proportionally more statistically significant findings

Unbiased scientific reporting is crucial for data and research synthesis. Previous studies suggest that statistically significant results are more likely to be published and more likely to be submitted to high impact journals. However, the most recent research on statistical significance in relation to journal impact factors in ecological research was published more than two decades ago or addressed a small subset of the literature. Here, we extract p-values from all articles published in 11 journals in 2012 and 2014 across a wide range of impact factors with six journals sampled in both years. Our results indicate that the proportion of statistically significant results increases with rising impact factor. Such a trend can have important consequences for syntheses of ecological data and it highlights the importance of covering a wide range of impact factors when identifying published studies for data syntheses. This trend can also lead to a biased understanding of the probability of true effects in ecology and conservation. We caution against the possible downplaying of non-significant results by either journals or authors.

scientific communication and education↗