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

Relationships between ambient temperature and diurnal variation in physiological responses to acute handling and restraint stress in the house sparrow, Passer domesticus

Climate change is altering the frequency and intensity of environmental extremes, and the diurnal rates of environmental change. The daily reaction norms of wild animals show spatial and temporal plasticity to allow appropriate physiological responses to predictable environmental challenges, but these responses have rarely been quantified in wild birds. We addressed this by determining whether physiological stress indices (corticosterone [CORT], glucose [GLU], and circulating heat shock proteins [Hsp]) vary with ambient temperature (Ta) or time of day across a 60 latitudinal gradient (320-380 S). We sampled house sparrows, Passer domesticus, at three locations with varying daily rates of Ta increases in 2015 and in 2019-2020 to determine whether physiological responses to capture and handling stress change diurnally. As predicted, plasma CORT and GLU increased during stress. Baseline CORT and GLU levels did not change during the day, but the amplitude of plasma CORT increase (delta CORT) in response to capture decreased as Ta increased, as was the case for GLU, in birds with initially high baseline CORT. Neither baseline nor stress-related plasma CORT or GLU differed consistently across sampling locations. Heat-shock cognate 70 (Hsc70) and heat-shock protein 90α (Hsp90) showed clear temporal dynamics across the day. Thus, the reaction norms of heat shock proteins are temporally plastic during the day and in response to daily Ta changes, as are the reaction norms of CORT and GLU in response to acute stress. However, the study provides little evidence for such plasticity in reaction norms as a function of average local thermal conditions.

Parrot politics: social decision-making in wild parrots relies on both individual recognition and intrinsic markers

Dominance hierarchies are generally thought to form over time via memory of repeated interactions. Yet dominance hierarchies are also occasionally reported in species with fission-fusion social dynamics, where individuals may encounter large numbers of individuals, leading to incomplete social information. In these cases, three potential mechanisms have been proposed. First, the complex decision-making required could increase selection for social cognition. Second, so-called 'badge-of-status' could evolve as shortcuts. Third, mixed strategies could evolve that rely on memory for interactions with familiars and status signals for strangers. Here, we test these hypotheses in wild sulphur-crested cockatoos (Cacatua galerita), recording social associations and aggressive interactions of 411 individuals across three neighbouring roosts. We find cockatoos use a twofold social strategy when initiating or reacting to aggression. For familiar individuals, aggressions were initiated or responded to based on differences in dominance rank. However, when facing less familiar individuals, decisions to interact-or respond-were based on body weight, with interactions directed towards, and more likely to respond to, individuals of similar weight. Our results suggest that social knowledge remains an important determinant of aggressive interactions in fission-fusion systems, but that individuals can dynamically incorporate other cues of competitive ability when knowledge is lacking.

Reliability of meta-analyses in ecology and evolution: (mostly) good news from a case study on sexual signals

Meta-analyses are powerful synthesis tools that are popular in ecology and evolution owing to the rapidly growing literature of this field. Although the usefulness of meta-analyses depends on their reliability, such as the precision of individual and mean effect sizes, attempts to reproduce meta-analyses' results remain rare in ecology and evolution. Here, we assess the reliability of 41 meta-analyses on sexual signals by evaluating the reproducibility and replicability of their results. We attempted to: (i) reproduce meta-analyses' mean effect sizes using the datasets they provided; (ii) reproduce meta-analyses' effect sizes by re-extracting 5703 effect sizes from 246 primary studies they used as sources; (iii) assess the extent of relevant data missed by original meta-analyses; and (iv) replicate meta-analyses' mean effect sizes after incorporating re-extracted and relevant missing data. We found many discrepancies between meta-analyses' reported results and those generated by our analyses for all reproducibility and replicability attempts. Nonetheless, we argue that the meta-analyses we evaluated are largely reproducible and replicable because the differences we found were small in magnitude, leaving the original interpretation of these meta-analyses' results unchanged. Still, we highlight issues we observed in these meta-analyses that affected their reliability, providing recommendations to ameliorate them.

Do Egg Hormones Have Fitness Consequences in Wild Birds? A Systematic Review and Meta-Analysis

Egg-laying species are key models for understanding the adaptive significance of maternal effects, with egg hormones proposed as an important underlying mechanism. However, even thirty years after their discovery, the evolutionary consequences of hormone-mediated maternal effects remain unclear. Using evidence synthesis, we tested the extent to which increased prenatal maternal hormone deposition in eggs relates to fitness in wild birds (19 species, 438 effect sizes and 57 studies). Egg androgens, glucocorticoids, and thyroid hormones showed an overall near-zero mean effect for both maternal and offspring fitness proxies. However, heterogeneity was high, suggesting that egg hormone effects on fitness are context-dependent. Hormone type and age did not explain much of the observed variance, nor did methodological factors such as the type of study or experimental design. Heterogeneity decomposition showed that differences in effect sizes were mostly driven by within-study variability and phylogenetic relationships. Our study provides the most comprehensive investigation to date of the relationship between egg hormones and fitness in vertebrates. By synthesising current knowledge, we aim to overcome theoretical shortcomings in the field of maternal effects via egg hormone deposition and inspire new research into its many intriguing aspects.

Indirect genetic effects increase the heritable variation available to selection and are largest for behaviors: a meta-analysis

The evolutionary potential of traits is governed by the amount of heritable variation available to selection. While this is typically quantified based on genetic variation in a focal individual for its own traits (direct genetic effects, DGEs), when social interactions occur, genetic variation in interacting partners can influence a focal individual's traits (indirect genetic effects, IGEs). Theory and studies on domesticated species have suggested IGEs can greatly impact evolutionary trajectories, but whether this is true more broadly remains unclear. Here, we perform a systematic review and meta-analysis to quantify the amount of trait variance explained by IGEs and the contribution of IGEs to predictions of adaptive potential. We identified 180 effect sizes from 47 studies across 21 species and found that, on average, IGEs of a single social partner account for a small but statistically significant amount of phenotypic variation (0.03). As IGEs affect the trait values of each interacting group member and due to a typically positive-although statistically nonsignificant-correlation with DGEs (r DGE-IGE = 0.26), IGEs ultimately increase trait heritability substantially from 0.27 (narrow-sense heritability) to 0.45 (total heritable variance). This 66% average increase in heritability suggests IGEs can increase the amount of genetic variation available to selection. Furthermore, whilst showing considerable variation across studies, IGEs were most prominent for behaviors and, to a lesser extent, for reproduction and survival, in contrast to morphological, metabolic, physiological, and development traits. Our meta-analysis, therefore, shows that IGEs tend to enhance the evolutionary potential of traits, especially for those tightly related to interactions with other individuals, such as behavior and reproduction.

Not so social in old age: demography as one driver of decreasing sociality

Humans become more selective with whom they spend their time, and as a result, the social networks of older humans are smaller than those of younger ones. In non-human animals, processes such as competition and opportunity can result in patterns of declining sociality with age. While there is support for declining sociality with age in mammals, evidence from wild bird populations is lacking. Here, we test whether sociality declines with age in a wild, insular bird population, where we know the exact ages of individuals. Using 6 years of sociality data, we find that as birds aged, their degree and betweenness decreased. The number of same-age birds still alive also decreased with age. Our results suggest that a longitudinal change in sociality with age may be, in part, an emergent effect of natural changes in demography. This highlights the need to investigate the changing costs and benefits of sociality across a lifetime.This article is part of the discussion meeting issue 'Understanding age and society using natural populations'.

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

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

Assessing the Association Between Animal Color and Behavior: A Meta-Analysis of Experimental Studies

Color varies in pattern and degree across the tree of life. In animals, genetic variation in color is hypothesized to have pleiotropic effects on a variety of behaviors due to shared dependence on underlying biochemical pathways. Such pleiotropy can constrain the independent evolution of color and behavior. Although associations between color and behavior have been reported, this relationship has not yet been addressed across a broad taxonomic scale with a formal meta-analysis. We used a phylogenetic meta-analytic approach to examine the relationship between individual variation in aggressive behavior and variation in multiple colors. Seventy-four studies met our inclusion criteria (vertebrates = 70; invertebrates = 4). After accounting for phylogeny and correcting for publication bias, there was a positive association between measures of aggression and degree or area of coloration (mean = 0.248, 95% CI = (0.044, 0.477)). Because this positive association was not restricted to melanin-based coloration, we conclude that this pattern does not strongly support the melanin pleiotropy hypothesis. Because the association was also not affected by moderators accounting for individual condition, social rank, or age, the results do not strongly support hypotheses that condition dependence accounts for relationships between color and aggressive behavior. The badge of status hypothesis predicts that arbitrary traits can evolve to signal aggression or social dominance. We propose that this is the most parsimonious explanation for the patterns we observe. Because of the lack of evidence for condition dependence in the association between color and aggression, we further propose that the genetic covariation between traits contributes to the evolution of the badges of status.

Opposite-sex associations are linked with annual fitness, but sociality is stable over lifetime

Animal sociality, an individual's propensity to associate with others, has fitness consequences through mate choice, for example, directly, by increasing the pool of prospective partners, and indirectly through increased survival, and individuals benefit from both. Annually, fitness consequences are realized through increased mating success and subsequent fecundity. However, it remains unknown whether these consequences translate to lifetime fitness. Here, we quantified social associations and their link to fitness annually and over lifetime, using a multi-generational, genetic pedigree. We used social network analysis to calculate variables representing different aspects of an individual's sociality. Sociality showed high within-individual repeatability. We found that birds with more opposite-sex associates had higher annual fitness than those with fewer, but this did not translate to lifetime fitness. Instead, for lifetime fitness, we found evidence for stabilizing selection on opposite-sex sociality, and sociality in general, suggesting that reported benefits are only short-lived in a wild population, and that selection favors an average sociality.

Publication bias impacts on effect size, statistical power, and magnitude (Type M) and sign (Type S) errors in ecology and evolutionary biology

Collaborative efforts to directly replicate empirical studies in the medical and social sciences have revealed alarmingly low rates of replicability, a phenomenon dubbed the 'replication crisis'. Poor replicability has spurred cultural changes targeted at improving reliability in these disciplines. Given the absence of equivalent replication projects in ecology and evolutionary biology, two inter-related indicators offer the opportunity to retrospectively assess replicability: publication bias and statistical power. This registered report assesses the prevalence and severity of small-study (i.e., smaller studies reporting larger effect sizes) and decline effects (i.e., effect sizes decreasing over time) across ecology and evolutionary biology using 87 meta-analyses comprising 4,250 primary studies and 17,638 effect sizes. Further, we estimate how publication bias might distort the estimation of effect sizes, statistical power, and errors in magnitude (Type M or exaggeration ratio) and sign (Type S). We show strong evidence for the pervasiveness of both small-study and decline effects in ecology and evolution. There was widespread prevalence of publication bias that resulted in meta-analytic means being over-estimated by (at least) 0.12 standard deviations. The prevalence of publication bias distorted confidence in meta-analytic results, with 66% of initially statistically significant meta-analytic means becoming non-significant after correcting for publication bias. Ecological and evolutionary studies consistently had low statistical power (15%) with a 4-fold exaggeration of effects on average (Type M error rates = 4.4). Notably, publication bias reduced power from 23% to 15% and increased type M error rates from 2.7 to 4.4 because it creates a non-random sample of effect size evidence. The sign errors of effect sizes (Type S error) increased from 5% to 8% because of publication bias. Our research provides clear evidence that many published ecological and evolutionary findings are inflated. Our results highlight the importance of designing high-power empirical studies (e.g., via collaborative team science), promoting and encouraging replication studies, testing and correcting for publication bias in meta-analyses, and adopting open and transparent research practices, such as (pre)registration, data- and code-sharing, and transparent reporting.

Stoichiometric stability of aquatic organisms increases with trophic level under warming and eutrophication

The balance of stoichiometric traits of organisms is crucial for nutrient cycling and energy flow in ecosystems. However, the impacts of different drivers on stoichiometric (carbon, C; nitrogen, N; and phosphorus, P) variations of organisms have not been well addressed. In order to understand how stoichiometric traits vary across trophic levels under different environmental stressors, we performed a mesocosm experiment to explore the impacts of warming (including +3 °C consistent warming above ambient and heat waves ranging from 0 to 6 °C), eutrophication, herbicide and their interactions on stoichiometric traits of organisms at different trophic levels, which was quantified by stable nitrogen isotopes. Results showed that herbicide treatment had no significant impacts on all stochiometric traits, while warming and eutrophication significantly affected the stoichiometric traits of organisms at lower trophic levels. Eutrophication increased nutrient contents and decreased C: nutrient ratios in primary producers, while the response of N:P ratios depended on the taxonomic group. The contribution of temperature treatments to stoichiometric variation was less than that of eutrophication. Heat waves counteracted the impacts of eutrophication, which was different from the effects of continuous warming, indicating that eutrophication impacts on organism stoichiometric traits depended on climate scenarios. Compared to environmental drivers, taxonomic group was the dominant driver that determined the variations of stoichiometric traits. Furthermore, the stoichiometric stability of organisms was strongly positively correlated with their trophic levels. Our results demonstrate that warming and eutrophication might substantially alter the stoichiometric traits of lower trophic levels, thus impairing the nutrient transfer to higher trophic level, which might further change the structure of food webs and functions of the ecosystems.

House sparrows do not exhibit a preference for the scent of potential partners with different MHC-I diversity and genetic distances

MHC genes play a fundamental role in immune recognition of pathogens and parasites. Therefore, females may increase offspring heterozygosity and genetic diversity by selecting males with genetically compatible or heterozygous MHC. In birds, several studies suggest that MHC genes play a role in mate choice, and recent evidence suggests that olfaction may play a role in the MHC-II discrimination. However, whether olfaction is involved in MHC-I discrimination in birds remains unknown. Previous studies indicate that house sparrow females with low allelic diversity prefer males with higher diversity in MHC-I alleles. Here, we directly explored whether female and male house sparrows (Passer domesticus) could estimate by scent MHC-I diversity and/or dissimilarity of potential partners. Our results show that neither females nor males exhibit a preference related to MHC-I diversity or dissimilarity of potential partners, suggesting that MHC-I is not detected through olfaction. Further studies are needed to understand the mechanisms responsible for mate discrimination based on MHC-I in birds.

Canalised and plastic components of melanin-based colouration: a diet-manipulation experiment in house sparrows

Whether melanin-based plumage colouration accurately reflects a bird's quality is still controversial. To better understand potential mechanisms behind the observed variation in plumage colouration, we shifted our attention from a high-level expression of colour to low-level physiological phenomena by targeting the microstructure and pigment content of the feather. In a well-studied model system, the house sparrow (Passer domesticus), we combined an experimental manipulation of birds' physiological condition and availability of resources that are key to the production of the studied colouration (phenylalanine and tyrosine (PT). We found that feathers from sparrows fed with the control diet had noticeably lower values of brightness, suggesting a higher quality of the ornamental "blackness" in comparison to those sampled from birds fed with a PT-reduced diet. Electron paramagnetic resonance (EPR) spectroscopy detected higher melanin concentrations in samples from the control than the PT-reduced group. Our multi-level analysis excluded mechanisms such as barbule density and melanosomes' distribution, clearly pointing to the finest-level proxy of colour: the concentration of melanin in melanosomes themselves. Despite melanins being manufactured by birds endogenously, the efficiency of melanogenesis can be noticeably limited by diet. As a result, the birds' plumage colouration is affected, which may entail consequences in social signalling.

A meta-analysis on the evolution of the Lombard effect reveals that amplitude adjustments are a widespread vertebrate mechanism

Animal communication is central to many animal societies, and effective signal transmission is crucial for individuals to survive and reproduce successfully. One environmental factor that exerts selection pressure on acoustic signals is ambient noise. To maintain signal efficiency, species can adjust signals through phenotypic plasticity or microevolutionary response to natural selection. One of these signal adjustments is the increase in signal amplitude, called the Lombard effect, which has been frequently found in birds and mammals. However, the evolutionary origin of the Lombard effect is largely unresolved. Using a phylogenetically controlled meta-analysis, we show that the Lombard effect is also present in fish and amphibians, and contradictory results in the literature can be explained by differences in signal-to-noise ratios among studies. Our analysis also demonstrates that subcortical processes are sufficient to elicit the Lombard effect and that amplitude adjustments do not require vocal learning. We conclude that the Lombard effect is a widespread mechanism based on phenotypic plasticity in vertebrates for coping with changes in ambient noise levels.

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.

Decline effects are rare in ecology

The scientific evidence base on any given topic changes over time as more studies are published. Currently, there is widespread concern about non-random, directional changes over time in the scientific evidence base associated with many topics. In particular, if studies finding large effects (e.g., large differences between treatment and control means) tend to get published quickly, while small effects tend to get published slowly, the net result will be a decrease over time in the estimated magnitude of the mean effect size, known as a "decline effect". If decline effects are common, then the published scientific literature will provide a biased and misleading guide to management decisions, and to the allocation of future research effort. We compiled data from 466 meta-analyses in ecology to look for evidence of decline effects. We found that decline effects are rare. Only ~5% of ecological meta-analyses truly exhibit a directional change in mean effect size over time arising for some reason other than random chance, usually but not always in the direction of decline. Most apparent directional changes in mean effect size over time are attributable to regression to the mean, consistent with primary studies being published in random order with respect to the effect sizes they report. Our results are good news: decline effects are the exception to the rule in ecology. Identifying and rectifying rare cases of true decline effects remains an important task, but ecologists should not overgeneralize from anecdotal reports of decline effects.

Meta-analysis reveals an extreme "decline effect" in the impacts of ocean acidification on fish behavior

Ocean acidification-decreasing oceanic pH resulting from the uptake of excess atmospheric CO2-has the potential to affect marine life in the future. Among the possible consequences, a series of studies on coral reef fish suggested that the direct effects of acidification on fish behavior may be extreme and have broad ecological ramifications. Recent studies documenting a lack of effect of experimental ocean acidification on fish behavior, however, call this prediction into question. Indeed, the phenomenon of decreasing effect sizes over time is not uncommon and is typically referred to as the "decline effect." Here, we explore the consistency and robustness of scientific evidence over the past decade regarding direct effects of ocean acidification on fish behavior. Using a systematic review and meta-analysis of 91 studies empirically testing effects of ocean acidification on fish behavior, we provide quantitative evidence that the research to date on this topic is characterized by a decline effect, where large effects in initial studies have all but disappeared in subsequent studies over a decade. The decline effect in this field cannot be explained by 3 likely biological explanations, including increasing proportions of studies examining (1) cold-water species; (2) nonolfactory-associated behaviors; and (3) nonlarval life stages. Furthermore, the vast majority of studies with large effect sizes in this field tend to be characterized by low sample sizes, yet are published in high-impact journals and have a disproportionate influence on the field in terms of citations. We contend that ocean acidification has a negligible direct impact on fish behavior, and we advocate for improved approaches to minimize the potential for a decline effect in future avenues of research.

Meta-analysis reveals an extreme "decline effect" in the impacts of ocean acidification on fish behavior

Ocean acidification-decreasing oceanic pH resulting from the uptake of excess atmospheric CO2-has the potential to affect marine life in the future. Among the possible consequences, a series of studies on coral reef fish suggested that the direct effects of acidification on fish behavior may be extreme and have broad ecological ramifications. Recent studies documenting a lack of effect of experimental ocean acidification on fish behavior, however, call this prediction into question. Indeed, the phenomenon of decreasing effect sizes over time is not uncommon and is typically referred to as the "decline effect." Here, we explore the consistency and robustness of scientific evidence over the past decade regarding direct effects of ocean acidification on fish behavior. Using a systematic review and meta-analysis of 91 studies empirically testing effects of ocean acidification on fish behavior, we provide quantitative evidence that the research to date on this topic is characterized by a decline effect, where large effects in initial studies have all but disappeared in subsequent studies over a decade. The decline effect in this field cannot be explained by 3 likely biological explanations, including increasing proportions of studies examining (1) cold-water species; (2) nonolfactory-associated behaviors; and (3) nonlarval life stages. Furthermore, the vast majority of studies with large effect sizes in this field tend to be characterized by low sample sizes, yet are published in high-impact journals and have a disproportionate influence on the field in terms of citations. We contend that ocean acidification has a negligible direct impact on fish behavior, and we advocate for improved approaches to minimize the potential for a decline effect in future avenues of research.

Sensitive periods during the development and expression of vertebrate sexual signals: A systematic review

Many sexually selected traits exhibit phenotypic plasticity. Despite a growing appreciation for the ecological context in which sexual selection occurs, and for the role of plasticity in shaping traits associated with local adaptation and divergence, there is an important gap in knowledge about the onset and duration of plasticity in sexual trait expression. Integrating this temporal dimension of plasticity into models of sexual selection informs our understanding of the information conveyed by sexual traits and our predictions related to trait evolution, and is critical in this time of unprecedented and rapid environmental change. We conducted a systematic review of 869 studies to ask how trait modalities (e.g., visual and chemical) relate to the onset and duration of plasticity in vertebrate sexual signals. We show that this literature is dominated by studies of coloration in birds and fish, and most studies take place during the breeding season. Where possible, we integrate results across studies to link physiology of specific trait modalities with the life stage (e.g., juvenile, breeding, or nonbreeding) during which plasticity occurs in well-studied traits. Limitations of our review included a lack of replication in our dataset, which precluded formal analysis. We argue that the timing of trait plasticity, in addition to environmental context, is critical for determining whether and how various communication signals are associated with ecological context, because plasticity may be ongoing or occur at only one point in an individual's lifetime, and determining a fixed trajectory of trait expression. We advocate for careful consideration of the onset and duration of plasticity when analyzing how environmental variation affects sexual trait expression and associated evolutionary outcomes.

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.

Cumulative meta-analysis: What works

To present time-varying evidence, cumulative meta-analysis (CMA) updates results of previous meta-analyses to incorporate new study results. We investigate the properties of CMA, suggest possible improvements and provide the first in-depth simulation study of the use of CMA and CUSUM methods for detection of temporal trends in random-effects meta-analysis. We use the standardized mean difference (SMD) as an effect measure of interest. For CMA, we compare the standard inverse-variance-weighted estimation of the overall effect using REML-based estimation of between-study variance τ 2 with the sample-size-weighted estimation of the effect accompanied by Kulinskaya-Dollinger-Bjørkestøl (Biometrics. 2011; 67:203-212) (KDB) estimation of τ 2 . For all methods, we consider Type 1 error under no shift and power under a shift in the mean in the random-effects model. To ameliorate the lack of power in CMA, we introduce two-stage CMA, in which τ 2 is estimated at Stage 1 (from the first 5-10 studies), and further CMA monitors a target value of effect, keeping the τ 2 value fixed. We recommend this two-stage CMA combined with cumulative testing for positive shift in τ 2 . In practice, use of CMA requires at least 15-20 studies.

Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing

BACKGROUND

Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS.

RESULTS

In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA.

CONCLUSIONS

Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.

Why don't all animals avoid inbreeding?

Individuals are expected to avoid mating with relatives as inbreeding can reduce offspring fitness, a phenomenon known as inbreeding depression. This has led to the widespread assumption that selection will favour individuals that avoid mating with relatives. However, the strength of inbreeding avoidance is variable across species and there are numerous cases where related mates are not avoided. Here we test if the frequency that related males and females encounter each other explains variation in inbreeding avoidance using phylogenetic meta-analysis of 41 different species from six classes across the animal kingdom. In species reported to mate randomly with respect to relatedness, individuals were either unlikely to encounter relatives, or inbreeding had negligible effects on offspring fitness. Mechanisms for avoiding inbreeding, including active mate choice, post-copulatory processes and sex-biased dispersal, were only found in species with inbreeding depression. These results help explain why some species seem to care more about inbreeding than others: inbreeding avoidance through mate choice only evolves when there is both a risk of inbreeding depression and related sexual partners frequently encounter each other.

Male size and reproductive performance in three species of livebearing fishes (Gambusia spp.): A systematic review and meta-analysis

The genus Gambusia represents approximately 45 species of polyandrous livebearing fishes with reversed sexual size dimorphism (i.e. males smaller than females) and with copulation predominantly via male coercion. Male body size has been suggested as an important sexually selected trait, but despite abundant research, evidence for sexual selection on male body size in this genus is mixed. Studies have found that large males have an advantage in both male-male competition and female choice, but that small males perform sneaky copulations better and at higher frequency and thus may sire more offspring in this coercive mating system. Here, we synthesized this inconsistent body of evidence using pre-registered methods and hypotheses. We performed a systematic review and meta-analysis of summary and primary (raw) data combining both published (n = 19 studies, k = 106 effect sizes) and unpublished effect sizes (n = 17, k = 242) to test whether there is overall selection on male body size across studies in Gambusia. We also tested several specific hypotheses to understand the sources of heterogeneity across effects. Meta-analysis revealed an overall positive correlation between male size and reproductive performance (r = 0.23, 95% confidence interval: 0.10-0.35, n = 36, k = 348, 4,514 males, three Gambusia species). Despite high heterogeneity, the large-male advantage appeared robust across all measures studied (i.e. female choice, mating success, paternity, sperm quantity and quality), and was considerably larger for female choice (r = 0.43, 95% confidence interval: 0.28-0.59, n = 14, k = 43). Meta-regressions found several important factors explaining heterogeneity across effects, including type of sperm characteristic, male-to-female ratio, female reproductive status and environmental conditions. We found evidence of publication bias; however, its influence on our estimates was attenuated by including a substantial amount of unpublished effects, highlighting the importance of open primary data for more accurate meta-analytic estimates. In addition to positive selection on male size, our study suggests that we need to rethink the role and form of sexual selection in Gambusia and, more broadly, to consider the ecological factors that affect reproductive behaviour in livebearing fishes.

Species sensitivities to a global pollutant: A meta-analysis on acoustic signals in response to anthropogenic noise

Anthropogenically driven environmental changes affect our planet at an unprecedented rate. Among these changes are those in the acoustic environment caused by anthropogenic noise, which can affect both animals and humans. In many species, acoustic communication plays a crucial role to maintain social relationships by exchanging information via acoustic signals. However, how species relying on acoustic communication differ in their adjustments to anthropogenic noise is little understood. Yet, this is crucial because protecting species effectively depends on our capability to predict how species differ in their response to human-induced environmental changes. Using a phylogenetically controlled meta-analysis, we quantified differences in adjustments of acoustic signals to anthropogenic noise among species. The effect sizes included in the analysis were obtained from noise exposure experiments, as only carefully controlled experiments allow to establish cause-and-effect relationships. We found that animals changed acoustic signals when exposed to noise, but the magnitude and the direction of adjustments differed among species. Given the importance of communication in the animal kingdom, these adjustments can affect social relationships in many species. The diversity of responses among species highlights the necessity to assess the effect of environmental stressors not only for a few species, because an effect may be positive in one species but negative in another depending on the species' biology. Thus, an effective conservation approach to protect different species is to preserve natural soundscapes of ecosystems to which species have adapted to by reducing or mitigating the emission of anthropogenic noise into the environment.

Adaptive coloration in pied flycatchers (Ficedula hypoleuca)-The devil is in the detail

Understanding the origin and persistence of phenotypic variation within and among populations is a major goal in evolutionary biology. However, the eagerness to find unadulterated explanatory models in combination with difficulties in publishing replicated studies may lead to severe underestimations of the complexity of selection patterns acting in nature. One striking example is variation in plumage coloration in birds, where the default adaptive explanation often is that brightly colored individuals signal superior quality across environmental conditions and therefore always should be favored by directional mate choice. Here, we review studies on the proximate determination and adaptive function of coloration traits in male pied flycatchers (Ficedula hypoleuca). From numerous studies, we can conclude that the dark male color phenotype is adapted to a typical northern climate and functions as a dominance signal in male-male competition over nesting sites, and that the browner phenotypes are favored by relaxed intraspecific competition with more dominant male collared flycatchers (Ficedula albicollis) in areas where the two species co-occur. However, the role of avoidance of hybridization in driving character displacement in plumage between these two species may not be as important as initially thought. The direction of female choice on male coloration in pied flycatchers is not simply as opposite in direction in sympatry and allopatry as traditionally expected, but varies also in relation to additional contexts such as climate variation. While some of the heterogeneity in the observed relationships between coloration and fitness probably indicate type 1 errors, we strongly argue that environmental heterogeneity and context-dependent selection play important roles in explaining plumage color variation in this species, which probably also is the case in many other species studied in less detail.

Illustrating the importance of meta-analysing variances alongside means in ecology and evolution

Meta-analysis is increasingly used in biology to both quantitatively summarize available evidence for specific questions and generate new hypotheses. Although this powerful tool has mostly been deployed to study mean effects, there is untapped potential to study effects on (trait) variance. Here, we use a recently published data set as a case study to demonstrate how meta-analysis of variance can be used to provide insights into biological processes. This data set included 704 effect sizes from 89 studies, covering 56 animal species, and was originally used to test developmental stress effects on a range of traits. We found that developmental stress not only negatively affects mean trait values, but also increases trait variance, mostly in reproduction, showcasing how meta-analysis of variance can reveal previously overlooked effects. Furthermore, we show how meta-analysis of variance can be used as a tool to help meta-analysts make informed methodological decisions, even when the primary focus is on mean effects. We provide all data and comprehensive R scripts with detailed explanations to make it easier for researchers to conduct this type of analysis. We encourage meta-analysts in all disciplines to move beyond the world of means and start unravelling secrets of the world of variance.

The role of replication studies in ecology

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

The house sparrow in the service of basic and applied biology

From the northernmost tip of Scandinavia to the southernmost corner of Patagonia, and across six continents, house sparrows (Passer domesticus) inhabit most human-modified habitats of the globe. With over 7,000 articles published, the species has become a workhorse for not only the study of self-urbanized wildlife, but also for understanding life history and body size evolution, sexual selection and many other biological phenomena. Traditionally, house sparrows were studied for their adaptations to local biotic and climatic conditions, but more recently, the species has come to serve as a focus for studies seeking to reveal the genomic, epigenetic and physiological underpinnings of success among invasive vertebrate species. Here, we review the natural history of house sparrows, highlight what the study of these birds has meant to bioscience generally, and describe the many resources available for future work on this species.

Dynamic phenotypic correlates of social status and mating effort in male and female red junglefowl, Gallus gallus

Despite widespread evidence that mating and intrasexual competition are costly, relatively little is known about how these costs dynamically change male and female phenotypes. Here, we test multiple hypotheses addressing this question in replicate flocks of red junglefowl (Gallus gallus). First, we test the interrelationships between social status, comb size (a fleshy ornament) and body mass at the onset of a mating trial. While comb size covaried positively with body mass across individuals of both sexes, comb size was positively related to social status in females but not in males. Second, we test for changes within individuals in body mass and comb size throughout the mating trial. Both body mass and comb size declined at the end of a trial in both sexes, suggesting that mating effort and exposure to the opposite sex are generally costly. Males lost more body mass if they (a) were socially subordinate, (b) were chased by other males or (c) mated frequently, indicating that subordinate status and mating are independently costly. Conversely, females lost more body mass if they were exposed to a higher frequency of coerced matings, suggesting costs associated with male sexual harassment and female resistance, although costs of mating per se could not be completely ruled out. Neither competitive nor mating interactions predicted comb size change in either sex. Collectively, these results support the notion that sex‐specific costs associated with social status and mating effort result in differential, sex‐specific dynamics of phenotypic change.

Mature sperm small-RNA profile in the sparrow: implications for transgenerational effects of age on fitness

Mammalian sperm RNA has recently received a lot of interest due to its involvement in epigenetic germline inheritance. Studies of epigenetic germline inheritance have shown that environmental exposures can induce effects in the offspring without altering the DNA sequence of germ cells. Most mechanistic studies were conducted in laboratory rodents and C.elegans while observational studies confirm the phenotypic phenomenon in wild populations of humans and other species including birds. Prominently, paternal age in house sparrows affects offspring fitness, yet the mechanism is unknown. This study provides a first reference of house sparrow sperm small RNA as an attempt to uncover their role in the transmission of the effects of paternal age on the offspring. In this small-scale pilot, we found no statistically significant differences between miRNA and tRNA fragments in aged and prime sparrow sperm. These results indicate a role of other epigenetic information carriers, such as distinct RNA classes, RNA modifications, DNA methylation and retained histones, and a clear necessity of future studies in wild populations.

Weak effects of geolocators on small birds: A meta-analysis controlled for phylogeny and publication bias

Currently, the deployment of tracking devices is one of the most frequently used approaches to study movement ecology of birds. Recent miniaturization of light-level geolocators enabled studying small bird species whose migratory patterns were widely unknown. However, geolocators may reduce vital rates in tagged birds and may bias obtained movement data. There is a need for a thorough assessment of the potential tag effects on small birds, as previous meta-analyses did not evaluate unpublished data and impact of multiple life-history traits, focused mainly on large species and the number of published studies tagging small birds has increased substantially. We quantitatively reviewed 549 records extracted from 74 published and 48 unpublished studies on over 7,800 tagged and 17,800 control individuals to examine the effects of geolocator tagging on small bird species (body mass <100 g). We calculated the effect of tagging on apparent survival, condition, phenology and breeding performance and identified the most important predictors of the magnitude of effect sizes. Even though the effects were not statistically significant in phylogenetically controlled models, we found a weak negative impact of geolocators on apparent survival. The negative effect on apparent survival was stronger with increasing relative load of the device and with geolocators attached using elastic harnesses. Moreover, tagging effects were stronger in smaller species. In conclusion, we found a weak effect on apparent survival of tagged birds and managed to pinpoint key aspects and drivers of tagging effects. We provide recommendations for establishing matched control group for proper effect size assessment in future studies and outline various aspects of tagging that need further investigation. Finally, our results encourage further use of geolocators on small bird species but the ethical aspects and scientific benefits should always be considered.

Personality and social foraging tactic use in free-living Eurasian tree sparrows (Passer montanus)

Group-foraging individuals often use alternative behavioral tactics to acquire food: some individuals, the producers, actively search for food, whereas others, the scroungers, look for opportunities to exploit the finders’ discoveries. Although the use of social foraging tactics is partly flexible, yet some individuals tend to produce more, whereas others largely prefer to scrounge. This between-individual variation in tactic use closely resembles the phenomenon of animal personality; however, the connection between personality and social foraging tactic use has rarely been investigated in wild animals. Here, we studied this relationship in free-living Eurasian tree sparrows (Passer montanus) during 2 winters. We found that in females, but not in males, social foraging tactic use was predicted by personality: more exploratory (i.e., more active in a novel environment) females scrounged more. Regardless of sex, the probability of scrounging increased with the density of individuals foraging on feeders and the time of feeding within a foraging bout, that is, the later the individual foraged within a foraging bout the higher the probability of scrounging was. Our results demonstrate that consistent individual behavioral differences are linked, in a sex-dependent manner, to group-level processes in the context of social foraging in free-living tree sparrows, suggesting that individual behavioral traits have implications for social evolution.

Scrutinizing assortative mating in birds

It is often claimed that pair bonds preferentially form between individuals that resemble one another. Such assortative mating appears to be widespread throughout the animal kingdom. Yet it is unclear whether the apparent ubiquity of assortative mating arises primarily from mate choice (“like attracts like”), which can be constrained by same-sex competition for mates; from spatial or temporal separation; or from observer, reporting, publication, or search bias. Here, based on a conventional literature search, we find compelling meta-analytical evidence for size-assortative mating in birds (r = 0.178, 95% CI 0.142–0.215, 83 species, 35,591 pairs). However, our analyses reveal that this effect vanishes gradually with increased control of confounding factors. Specifically, the effect size decreased by 42% when we used previously unpublished data from nine long-term field studies, i.e., data free of reporting and publication bias (r = 0.103, 95% CI 0.074–0.132, eight species, 16,611 pairs). Moreover, in those data, assortative mating effectively disappeared when both partners were measured by independent observers or separately in space and time (mean r = 0.018, 95% CI −0.016–0.057). Likewise, we also found no evidence for assortative mating in a direct experimental test for mutual mate choice in captive populations of Zebra finches (r = −0.020, 95% CI −0.148–0.107, 1,414 pairs). These results highlight the importance of unpublished data in generating unbiased meta-analytical conclusions and suggest that the apparent ubiquity of assortative mating reported in the literature is overestimated and may not be driven by mate choice or mating competition for preferred mates.

Human mate choice is characterized by assortative mating (‘like attracts like’) and similarity of partners is also often reported for birds. A meta-analysis of published and previously unpublished datasets shows that the reported assortative mating in birds may mostly reflect biases in estimation rather than mate choice.

Research on mate choice in birds has attracted much attention, partly because many birds form monogamous pair bonds like humans do. Human mate choice is characterized by the phenomenon of “like attracts like,” meaning that partners resemble each other in multiple ways (“assortative mating”). Assortative mating is also frequently reported for birds, but it is unclear whether this in turn implies that birds also have preferences for a similar partner. Here, we show that a range of methodological issues may provide a simpler and more accurate explanation for the frequent observation of assortative mating in birds. First, studies that report assortative mating may achieve greater visibility than studies that yield no such finding. Hence, the scientific literature may be biased toward positive results. Second, in field studies, it is logistically impossible to measure all birds accurately and under standardized conditions. Hence, fluctuations in, for instance, environmental conditions may induce a spurious similarity between partners when these are measured together in space or time. After accounting for such methodological issues, we conclude that mate preferences for a similar partner may be less common than previously thought.

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

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