ORCID Profile
0000-0002-7765-5182
Current Organisation
UNSW Australia
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In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Life Histories | Behavioural Ecology | Evolutionary Biology | Biological Adaptation | Animal Behaviour | Evolutionary biology | Behavioural ecology | Ecology | Life histories | Evolutionary ecology | Evolutionary Biology not elsewhere classified
Expanding Knowledge in the Biological Sciences | Expanding Knowledge in the Medical and Health Sciences | Expanding Knowledge in Psychology and Cognitive Sciences |
Publisher: Cold Spring Harbor Laboratory
Date: 09-11-2017
DOI: 10.1101/216580
Abstract: Zeta ersity provides the average number of shared species across n sites (or shared operational taxonomic units (OTUs) across n cases). It quantifies the variation in species composition of multiple assemblages in space and time to capture the contribution of the full suite of narrow, intermediate and wide-ranging species to biotic heterogeneity. Zeta ersity was proposed for measuring compositional turnover in plant and animal assemblages, but is equally relevant for application to any biological system that can be characterised by a row by column incidence matrix. Here we illustrate the application of zeta ersity to explore compositional change in empirical data, and how observed patterns may be interpreted. We use 10 datasets from a broad range of scales and levels of biological organisation – from DNA molecules to microbes, plants and birds – including one of the original data sets used by R.H. Whittaker in the 1960’s to express compositional change and distance decay using beta ersity. The applications show (i) how different s ling schemes used during the calculation of zeta ersity may be appropriate for different data types and ecological questions, (ii) how higher orders of zeta may in some cases better detect shifts, transitions or periodicity, and importantly (iii) the relative roles of rare versus common species in driving patterns of compositional change. By exploring the application of zeta ersity across this broad range of contexts, our goal is to demonstrate its value as a tool for understanding continuous bio ersity turnover and as a metric for filling the empirical gap that exists on spatial or temporal change in compositional ersity.
Publisher: Elsevier BV
Date: 2011
DOI: 10.1016/J.NEUBIOREV.2010.06.003
Abstract: Neuroscience is one of the most heavily experimental fields of biological and medical research. As such, statistical approaches have traditionally focused on testing specific predictions based upon well-focused hypotheses. However, neuroscience data are often derived from repeated measurements and stimulus type presentations with a limited number of subjects, some of which may have incomplete data per subject. Here we provide an introduction to a group of erse and powerful statistical approaches, which we term the '5 Ms', which have been successfully used in other fields of biological research facing similar constraints. Specifically, we detail how M1: meta-analysis can combine, reconcile, and analyse between- and within-study results, M2: mixed-effects modelling is beneficial through replacing statistical tests involving pseudoreplication, M3: multiple imputation may be used to account for the biases caused by missing data arising from incomplete experimental protocols, and M4: model averaging from information-theoretic approaches allows to discriminate among alternative functional hypotheses. We also provide a brief introduction to Bayesian statistics using M5: Markov chain Monte Carlo (MCMC). Taken together, these approaches provide neuroscientists with a robust statistical toolbox containing elements that alleviate some of the analytical constraints generated by limited s le sizes, repeated subject use, and incomplete replicates of experimental manipulation.
Publisher: Elsevier BV
Date: 12-2017
DOI: 10.1016/J.DEVCEL.2017.11.010
Abstract: The attenuation of ancestral pro-regenerative pathways may explain why humans do not efficiently regenerate damaged organs. Vertebrate lineages that exhibit robust regeneration, including the teleost zebrafish, provide insights into the maintenance of adult regenerative capacity. Using established models of spinal cord, heart, and retina regeneration, we discovered that zebrafish T
Publisher: Springer Science and Business Media LLC
Date: 13-07-2012
Publisher: Wiley
Date: 30-05-2017
Publisher: The Royal Society
Date: 03-2017
Abstract: Nutritional environments, particularly those experienced during early life, are hypothesized to affect longevity. A recent cross-taxa meta-analysis found that, depending upon circumstance, average longevity may be increased or decreased by early-life dietary restriction. Unstudied are the effects of diet during development on among-in idual variance in longevity. Here, we address this issue using emerging methods for meta-analysis of variance. We found that, in general, standard deviation (s.d.) in longevity is around 8% higher under early-life dietary restriction than a standard diet. The effects became especially profound when dietary insults were experienced prenatally (s.d. increased by 29%) and/or extended into adulthood (s.d. increased by 36.6%). Early-life dietary restriction may generate variance in longevity as a result of increased variance in resource acquisition or allocation, but the mechanisms underlying these largely overlooked patterns clearly warrant elucidation.
Publisher: Wiley
Date: 23-09-2022
DOI: 10.1111/MEC.16673
Abstract: The insects constitute the majority of animal ersity. Most insects are holometabolous: during complete metamorphosis their bodies are radically reorganized. This reorganization poses a significant challenge to the gut microbiota, as the gut is replaced during pupation, a process that does not occur in hemimetabolous insects. In holometabolous hosts, it offers the opportunity to decouple the gut microbiota between the larval and adult life stages resulting in high beta ersity whilst limiting alpha ersity. Here, we studied 18 different herbivorous insect species from five orders of holometabolous and three orders of hemimetabolous insects. Comparing larval and adult specimens, we find a much higher beta- ersity and hence microbiota turnover in holometabolous insects compared to hemimetabolous insects. Alpha ersity did not differ between holo- and hemimetabolous insects nor between developmental stages within these groups. Our results support the idea that pupation offers the opportunity to change the gut microbiota and hence might facilitate ecological niche shifts. This possible effect of niche shift facilitation could explain a selective advantage of the evolution of complete metamorphosis, which is a defining trait of the most speciose insect taxon, the holometabola.
Publisher: Wiley
Date: 29-11-2022
Abstract: Meta‐analyses in ecology and evolution require special attention due to certain study characteristics in these fields. First, the primary articles in these fields usually report results that are observed from studies conducted with different species, and the phylogeny among the species violates the independence assumption. Second, articles frequently allow the computation of multiple effect sizes which cannot be accounted for by conventional meta‐analytic models. While both issues can be dealt with by utilizing a multilevel model that accounts for phylogeny, the performance of such a model has not been examined extensively. In this article, we investigate the performance of this model in comparison with some simpler models. We conducted an extensive simulation study where data with different hierarchical structures (in terms of study and species levels) were generated and then various models were fitted to examine their performance. The models we used include the conventional random effects and multilevel random‐effects models along with more complex multilevel models that account for species‐level variance with different variance components. Furthermore, we present an illustrative application of these models based on the data from a meta‐analysis on sizeassortative mating and comment on the results in light of the findings from the simulation study. Our simulation results show that, when the phylogenetic relationships among the species are at least moderately strong, only the most complex model that decomposes the species‐level variance into nonphylogenetic and phylogenetic components provides approximately unbiased estimates of the overall mean and variance components and yields confidence intervals with an approximately nominal coverage rate. Contrarily, removing the phylogenetic or non‐phylogenetic component leads to biased variance component estimates and an increased risk for incorrect inferences about the overall mean. These findings are supported by the results derived from the illustrative application. Based on our results, we suggest that meta‐analyses in ecology and evolution should use the model that accounts for both the nonphylogenetic and phylogenetic species‐level variance in addition to the multilevel structure of the data. Any attempts to simplify this model, such as using only the phylogenetic variance component, may lead to erroneous inferences from the data.
Publisher: Oxford University Press (OUP)
Date: 11-2004
Publisher: The Royal Society
Date: 06-2011
Abstract: Life-history theory predicts that in iduals should adjust their reproductive effort according to the expected fitness returns on investment. Because sexually selected male traits should provide honest information about male genetic or phenotypic quality, females may invest more when paired with attractive males. However, there is substantial disagreement in the literature whether such differential allocation is a general pattern. Using a comparative meta-regression approach, we show that female birds generally invest more into reproduction when paired with attractive males, both in terms of egg size and number as well as food provisioning. However, whereas females of species with bi-parental care tend to primarily increase the number of eggs when paired with attractive males, females of species with female-only care produce larger, but not more, eggs. These patterns may reflect adaptive differences in female allocation strategies arising from variation in the signal content of sexually selected male traits between systems of parental care. In contrast to reproductive effort, female allocation of immune-stimulants, anti-oxidants and androgens to the egg yolk was not consistently increased when mated to attractive males, which probably reflects the context-dependent costs and benefits of those yolk compounds to females and offspring.
Publisher: Wiley
Date: 17-12-2014
Abstract: Meta‐analysis has become a standard way of summarizing empirical studies in many fields, including ecology and evolution. In ecology and evolution, meta‐analyses comparing two groups (usually experimental and control groups) have almost exclusively focused on comparing the means, using standardized metrics such as Cohen's / Hedges’ d or the response ratio. However, an experimental treatment may not only affect the mean but also the variance. Investigating differences in the variance between two groups may be informative, especially when a treatment influences the variance in addition to or instead of the mean. In this paper, we propose the effect size statistic ln CVR (the natural logarithm of the ratio between the coefficients of variation, CV, from two groups), which enables us to meta‐analytically compare differences between the variability of two groups. We illustrate the use of lnCVR with ex les from ecology and evolution. Further, as an alternative approach to the use of lnCVR, we propose the combined use of ln s (the log standard deviation) and (the log mean) in a hierarchical (linear mixed) model. The use of ln s with overcomes potential limitations of lnCVR and it provides a more flexible, albeit more complex, way to examine variation beyond two‐group comparisons. Relevantly, we also refer to the potential use of ln s and lnCV (the log CV) in the context of comparative analysis. Our approaches to compare variability could be applied to already published meta‐analytic data sets that compare two‐group means to uncover potentially overlooked effects on the variance. Additionally, our approaches should be applied to future meta‐analyses, especially when one suspects a treatment has an effect not only on the mean, but also on the variance. Notably, the application of the proposed methods extends beyond the fields of ecology and evolution.
Publisher: Wiley
Date: 20-11-2022
Abstract: Organisms use labile traits to respond to different conditions over short time‐scales. When a population experiences the same conditions, we might expect all in iduals to adjust their trait expression to the same, optimal, value, thereby minimising phenotypic variation. Instead, variation abounds. In iduals substantially differ not only from each other, but also from their former selves, with the expression of labile traits varying both predictably and unpredictably over time. A powerful tool for studying the evolution of phenotypic variation in labile traits is the mixed model. Here, we review how mixed models are used to quantify in idual differences in both means and variability, and their between‐in idual correlations. In iduals can differ in their average phenotypes (e.g. behavioural personalities), their variability (known as ‘predictability’ or intra‐in idual variability), and their plastic response to different contexts. We provide detailed descriptions and resources for simultaneously modelling in idual differences in averages, plasticity and predictability. Empiricists can use these methods to quantify how traits covary across in iduals and test theoretical ideas about phenotypic integration. These methods can be extended to incorporate plastic changes in predictability (termed ‘stochastic malleability’). Overall, we showcase the unfulfilled potential of existing statistical tools to test more holistic and nuanced questions about the evolution, function, and maintenance of phenotypic variation, for any trait that is repeatedly expressed.
Publisher: Oxford University Press (OUP)
Date: 2015
Publisher: Wiley
Date: 12-05-2022
DOI: 10.1111/ELE.14025
Abstract: Ecological restoration projects often have variable and unpredictable outcomes, and these can limit the overall impact on bio ersity. Previous syntheses have investigated restoration effectiveness by comparing average restored conditions to average conditions in unrestored or reference systems. Here, we provide the first quantification of the extent to which restoration affects both the mean and variability of bio ersity outcomes, through a global meta-analysis of 83 terrestrial restoration studies. We found that, relative to unrestored (degraded) sites, restoration actions increased bio ersity by an average of 20%, while decreasing the variability of bio ersity (quantified by the coefficient of variation) by an average of 14%. As restorations aged, mean bio ersity increased and variability decreased relative to unrestored sites. However, restoration sites remained, on average, 13% below the bio ersity of reference (target) ecosystems, and were characterised by higher (20%) variability. The lower mean and higher variability in bio ersity at restored sites relative to reference sites remained consistent over time, suggesting that sources of variation (e.g. prior land use, restoration practices) have an enduring influence on restoration outcomes. Our results point to the need for new research confronting the causes of variability in restoration outcomes, and close variability and bio ersity gaps between restored and reference conditions.
Publisher: Wiley
Date: 10-2022
Abstract: The health of coral reef ecosystems is declining. As research examining this decline has grown, review articles (secondary literature) have emerged. Secondary literature can include narrative reviews, systematic reviews, and bibliometric analyses. Synthesizing secondary literature can influence research directions, as syntheses visualize both the current state of knowledge and trends in research. Therefore, we propose to use the combination of bibliometric mapping and systematic mapping techniques to synthesize the secondary literature on coral health and coral reef decline. We will examine secondary literature on coral health published in peer‐reviewed journals and indexed in Scopus or Web of Science databases. After screening the title, abstract, and keywords of each paper, we will extract information that encompasses the type and purpose of the review, the identified factors affecting coral health, and the health‐related outcomes on coral reefs. We will also conduct a critical appraisal using the Collaboration for Environmental Evidence Synthesis Assessment Tool (CEESAT) criteria for papers that are self‐reported to be systematic reviews. We will also extract bibliometric data to identify author affiliations, collaboration networks, and journals. We will communicate our results from systematic and bibliometric mapping using visualizations and tabulations. Our systematic map aims to reveal gaps and clusters of topics in review articles on coral health. These findings can guide future research into coral health in both primary and secondary literature. Our critical appraisal will evaluate the robustness of systematic reviews, informing researchers on how to identify and conduct high‐quality reviews. Our bibliometric map will uncover the extent and connectivity of researchers synthesizing evidence on coral health, highlighting the ersity (or lack thereof) of those engaging in coral health research.
Publisher: The Royal Society
Date: 25-01-2017
Abstract: Elaborate ornamental traits are often under directional selection for greater elaboration, which in theory should deplete underlying genetic variation. Despite this, many ornamental traits appear to remain highly variable and how this essential variation is maintained is a key question in evolutionary biology. One way to address this question is to compare differences in intraspecific variability across different types of traits to determine whether high levels of variation are associated with specific trait characteristics. Here we assess intraspecific variation in more than 100 plumage colours across 55 bird species to test whether colour variability is linked to their level of elaboration (indicated by degree of sexual dichromatism and conspicuousness) or their condition dependence (indicated by mechanism of colour production). Conspicuous colours had the highest levels of variation and conspicuousness was the strongest predictor of variability, with high explanatory power. After accounting for this, there were no significant effects of sexual dichromatism or mechanisms of colour production. Conspicuous colours may entail higher production costs or may be more sensitive to disruptions during production. Alternatively, high variability could also be related to increased perceptual difficulties inherent to discriminating highly elaborate colours. Such psychophysical effects may constrain the exaggeration of animal colours.
Publisher: Wiley
Date: 29-11-2013
Publisher: Oxford University Press (OUP)
Date: 31-12-2019
Abstract: Phylogenetic comparative methods (PCMs), especially ones based on linear models, have played a central role in understanding species' trait evolution. These methods, however, usually assume that phylogenetic trees are known without error or uncertainty, but this assumption is most likely incorrect. So far, Markov chain Monte Carlo (MCMC)-based Bayesian methods have mainly been deployed to account for such "phylogenetic uncertainty" in PCMs. Herein, we propose an approach with which phylogenetic uncertainty is incorporated in a simple, readily implementable and reliable manner. Our approach uses Rubin's rules, which are an integral part of a standard multiple imputation procedure, often employed to recover missing data. We see true phylogenetic trees as missing data under this approach. Further, unmeasured species in comparative data (i.e., missing trait data) can be seen as another source of uncertainty in PCMs because arbitrary s ling of species in a given taxon or "species s ling uncertainty" can affect estimation in PCMs. Using two simulation studies, we show our method can account for phylogenetic uncertainty under many different scenarios (e.g., uncertainty in topology and branch lengths) and, at the same time, it can handle missing trait data (i.e., species s ling uncertainty). A unique property of the multiple imputation procedure is that an index, named "relative efficiency," could be used to quantify the number of trees required for incorporating phylogenetic uncertainty. Thus, by using the relative efficiency, we show the required tree number is surprisingly small ($\sim$50 trees). However, the most notable advantage of our method is that it could be combined seamlessly with PCMs that utilize multiple imputation to handle simultaneously phylogenetic uncertainty (i.e., missing true trees) and species s ling uncertainty (i.e., missing trait data) in PCMs.
Publisher: California Digital Library (CDL)
Date: 24-01-2020
Publisher: Wiley
Date: 22-05-2019
DOI: 10.1111/COBI.13342
Publisher: Oxford University Press (OUP)
Date: 11-2016
DOI: 10.1534/GENETICS.115.186536
Abstract: Methods for inference and interpretation of evolutionary quantitative genetic parameters, and for prediction of the response to selection, are best developed for traits with normal distributions. Many traits of evolutionary interest, including many life history and behavioral traits, have inherently nonnormal distributions. The generalized linear mixed model (GLMM) framework has become a widely used tool for estimating quantitative genetic parameters for nonnormal traits. However, whereas GLMMs provide inference on a statistically convenient latent scale, it is often desirable to express quantitative genetic parameters on the scale upon which traits are measured. The parameters of fitted GLMMs, despite being on a latent scale, fully determine all quantities of potential interest on the scale on which traits are expressed. We provide expressions for deriving each of such quantities, including population means, phenotypic (co)variances, variance components including additive genetic (co)variances, and parameters such as heritability. We demonstrate that fixed effects have a strong impact on those parameters and show how to deal with this by averaging or integrating over fixed effects. The expressions require integration of quantities determined by the link function, over distributions of latent values. In general cases, the required integrals must be solved numerically, but efficient methods are available and we provide an implementation in an R package, QGglmm. We show that known formulas for quantities such as heritability of traits with binomial and Poisson distributions are special cases of our expressions. Additionally, we show how fitted GLMM can be incorporated into existing methods for predicting evolutionary trajectories. We demonstrate the accuracy of the resulting method for evolutionary prediction by simulation and apply our approach to data from a wild pedigreed vertebrate population.
Publisher: Frontiers Media SA
Date: 03-05-2019
Publisher: Proceedings of the National Academy of Sciences
Date: 03-2022
Publisher: Wiley
Date: 06-06-2023
DOI: 10.1111/ELE.14266
Abstract: Coral reefs are under threat from disease as climate change alters environmental conditions. Rising temperatures exacerbate coral disease, but this relationship is likely complex as other factors also influence coral disease prevalence. To better understand this relationship, we meta‐analytically examined 108 studies for changes in global coral disease over time alongside temperature, expressed using average summer sea surface temperature (SST) and cumulative heat stress as weekly sea surface temperature anomalies (WSSTAs). We found that both rising average summer SST and WSSTA were associated with global increases in the mean and variability in coral disease prevalence. Global coral disease prevalence tripled, reaching 9.92% in the 25 years examined, and the effect of ‘year’ became more stable (i.e. prevalence has lower variance over time), contrasting the effects of the two temperature stressors. Regional patterns erged over time and differed in response to average summer SST. Our model predicted that, under the same trajectory, 76.8% of corals would be diseased globally by 2100, even assuming moderate average summer SST and WSSTA. These results highlight the need for urgent action to mitigate coral disease. Mitigating the impact of rising ocean temperatures on coral disease is a complex challenge requiring global discussion and further study.
Publisher: Springer Science and Business Media LLC
Date: 06-2002
Publisher: Wiley
Date: 26-12-2023
DOI: 10.1111/ELE.14144
Abstract: The log response ratio, lnRR, is the most frequently used effect size statistic for meta‐analysis in ecology. However, often missing standard deviations (SDs) prevent estimation of the s ling variance of lnRR. We propose new methods to deal with missing SDs via a weighted average coefficient of variation (CV) estimated from studies in the dataset that do report SDs. Across a suite of simulated conditions, we find that using the average CV to estimate s ling variances for all observations, regardless of missingness, performs with minimal bias. Surprisingly, even with missing SDs, this simple method outperforms the conventional approach (basing each effect size on its in idual study‐specific CV) with complete data. This is because the conventional method ultimately yields less precise estimates of the s ling variances than using the pooled CV from multiple studies. Our approach is broadly applicable and can be implemented in all meta‐analyses of lnRR, regardless of ‘missingness’.
Publisher: Wiley
Date: 15-01-2021
Abstract: Biotic pollination can benefit crop production, but its effects are highly variable. To maximise benefits from this ecosystem service, we need a greater understanding of the factors that cause variation so that ecological intensification can be more effectively applied. We focus on understanding the benefits of pollination to faba bean Vicia faba . We use a literature review followed by multi‐level meta‐analysis to estimate overall benefits of pollination to faba bean yield and to quantify variation (heterogeneity) in these benefits associated with different contextual factors (e.g. plant genotype, growing environment). Our overall estimate of pollination benefit to faba bean yield, expressed as the percentage yield reduction without pollination, is 32.9% (confidence interval: 21%–43%). Based on the prediction intervals, which include the heterogeneity in pollination benefit, there is an 80% chance that pollination will increase yield of a faba bean crop. Half of all heterogeneity in pollination dependence was due to differences between plant genotypes. The number of beans per plant showed similar pollination dependence to yield mass per plant while pod number and number of beans per pod underestimated yield benefits. There was weak evidence to suggest pollination benefits vary between pollinator species, with honeybees showing a smaller yield increase. Differences in the experimental method used to assess pollination benefit did not significantly affect the estimate, including the growing environment, measurement scale, or whether the effects of experimental pollinator enclosures were controlled. This suggests that simplified experimental studies comparing yield of open‐pollinated and enclosed plants can provide reliable insights into pollination benefits across a large range of plant genotypes and landscapes. Synthesis and application . We found high variability in pollination benefits both between and within publications in our meta‐analysis. Plant genotype, how yield was measured, and pollinator species affected the level of pollination benefit. Despite variability in pollination benefits due to various contextual factors (both inside and outside of grower control), there is a high likelihood that biotic pollination will increase faba bean yield. Our findings support ecological intensification and specifically the management of pollinators to maximise pollination benefits to faba bean production.
Publisher: Informa UK Limited
Date: 09-2013
DOI: 10.4161/EPI.25797
Publisher: Wiley
Date: 17-10-2016
Publisher: Wiley
Date: 22-05-2013
DOI: 10.1111/EFF.12064
Publisher: California Digital Library (CDL)
Date: 10-11-2018
Publisher: Cold Spring Harbor Laboratory
Date: 03-07-2017
DOI: 10.1101/158816
Abstract: A much-debated issue is whether or not males should reduce parental care when they lose paternity (i.e. the certainty of paternity hypothesis). While there is general support for this relationship across species, within-population evidence is still contentious. Among the main reasons behind such problem is the confusion discerning between-from within-in idual patterns. Here, we tested this hypothesis empirically by investigating the parental care of male dunnocks (Prunella modularis) in relation to paternity. We used a thorough dataset of observations in a wild population, genetic parentage, and a within-subject centring statistical approach to disentangle paternal care adjustment within-male and between males. We found support for the certainty of paternity hypothesis, as there was evidence for within-male adjustment in paternal care when socially monogamous males lost paternity to extra-pair sires. There was little evidence of a between-male effect overall. Our findings show that monogamous males adjust paternal care when paired to the same female partner. We also show that – in monogamous broods – the proportion of provisioning visits made by males yields fitness benefits in terms of fledging success. Our results suggest that socially monogamous females that engage in extra-pair behaviour may suffer fitness costs, as their partners’ reduction in paternal care can negatively affect fledging success.
Publisher: Springer Science and Business Media LLC
Date: 03-11-2022
DOI: 10.1038/S41559-022-01891-Z
Abstract: Synthesis of primary ecological data is often assumed to achieve a notion of 'generality', through the quantification of overall effect sizes and consistency among studies, and has become a dominant research approach in ecology. Unfortunately, ecologists rarely define either the generality of their findings, their estimand (the target of estimation) or the population of interest. Given that generality is fundamental to science, and the urgent need for scientific understanding to curb global scale ecological breakdown, loose usage of the term 'generality' is problematic. In other disciplines, generality is defined as comprising both generalizability-extending an inference about an estimand from the s le to the population-and transferability-the validity of estimand predictions in a different s ling unit or population. We review current practice in ecological synthesis and demonstrate that, when researchers fail to define the assumptions underpinning generalizations and transfers of effect sizes, generality often misses its target. We provide guidance for communicating nuanced inferences and maximizing the impact of syntheses both within and beyond academia. We propose pathways to generality applicable to ecological syntheses, including the development of quantitative and qualitative criteria with which to license the transfer of estimands from both primary and synthetic studies.
Publisher: Wiley
Date: 13-11-2018
DOI: 10.1111/JEB.13197
Abstract: How has evolution led to the variation in behavioural phenotypes (personalities) in a population? Knowledge of whether personality is heritable, and to what degree it is influenced by the social environment, is crucial to understanding its evolutionary significance, yet few estimates are available from natural populations. We tracked three behavioural traits during different life-history stages in a pedigreed population of wild house sparrows. Using a quantitative genetic approach, we demonstrated heritability in adult exploration, and in nestling activity after accounting for fixed effects, but not in adult boldness. We did not detect maternal effects on any traits, but we did detect a social brood effect on nestling activity. Boldness, exploration and nestling activity in this population did not form a behavioural syndrome, suggesting that selection could act independently on these behavioural traits in this species, although we found no consistent support for phenotypic selection on these traits. Our work shows that repeatable behaviours can vary in their heritability and that social context influences personality traits. Future efforts could separate whether personality traits differ in heritability because they have served specific functional roles in the evolution of the phenotype or because our concept of personality and the stability of behaviour needs to be revised.
Publisher: California Digital Library (CDL)
Date: 07-02-2022
Publisher: California Digital Library (CDL)
Date: 10-11-2021
Publisher: Wiley
Date: 26-12-2021
DOI: 10.1111/JEB.13752
Abstract: Sexual selection shapes the adaptive landscape in complex ways that lead to trait integration. Much of our understanding of selection comes from studies of morphological traits. However, few studies attempt to quantify the form and direction of selection on performance even though it is predicted to be a more direct target of selection in nature. We measured sexual selection on performance traits (bite force, sprint speed and endurance) in an Australian lizard, the Eastern water skink ( Eul rus quoyii ). We first staged 123 contests between size‐matched males to investigate whether performance traits were important in determining contest outcome. In a second experiment, we established six breeding populations in large replicate semi‐natural enclosures to estimate whether performance traits predicted reproductive success. Our results show that none of the performance measures were important in predicting contest outcome and were not generally strong predictors of reproductive success. However, our analyses suggest a complex fitness landscape driven by males adopting different alternative reproductive tactics (ARTs). We provide a rare test of the role performance plays in sexual selection and highlight the need to test common assumptions regarding the link between maximal performance and fitness. Our results suggest that performance traits may not necessarily be direct targets of sexual selection, but rather indirect targets through their integration with morphological and/or behavioural traits, highlighting a need for more explicit tests of the predicted links between performance and fitness.
Publisher: California Digital Library (CDL)
Date: 23-11-2020
Publisher: American Association for the Advancement of Science (AAAS)
Date: 20-05-2022
Abstract: Forest restoration is being scaled up globally to deliver critical ecosystem services and bio ersity benefits however, there is a lack of rigorous comparison of cobenefit delivery across different restoration approaches. Through global synthesis, we used 25,950 matched data pairs from 264 studies in 53 countries to assess how delivery of climate, soil, water, and wood production services, in addition to bio ersity, compares across a range of tree plantations and native forests. Benefits of aboveground carbon storage, water provisioning, and especially soil erosion control and bio ersity are better delivered by native forests, with compositionally simpler, younger plantations in drier regions performing particularly poorly. However, plantations exhibit an advantage in wood production. These results underscore important trade-offs among environmental and production goals that policy-makers must navigate in meeting forest restoration commitments.
Publisher: Wiley
Date: 13-04-2022
DOI: 10.1111/CSP2.12687
Abstract: Bio ersity is in crisis, and insects are no exception. To understand insect population and community trends globally, it is necessary to identify and synthesize erse datasets representing different taxa, regions, and habitats. The relevant literature is, however, vast and challenging to aggregate. The Entomological Global Evidence Map (EntoGEM) project is a systematic effort to search for and catalogue studies with long‐term data that can be used to understand changes in insect abundance and ersity. Here, we present the overall EntoGEM framework and results of the first completed subproject of the systematic map, which compiled sources of information about changes in dragonfly and damselfly (Odonata) occurrence, abundance, biomass, distribution, and ersity. We identified 45 multi‐year odonate datasets, including 10 studies with data that span more than 10 years. If data from each study could be gathered or extracted, these studies could contribute to analyses of long‐term population trends of this important group of indicator insects. The methods developed to support the EntoGEM project, and its framework for synthesizing a vast literature, have the potential to be applied not only to other broad topics in ecology and conservation, but also to other areas of research where data are widely distributed.
Publisher: Springer Science and Business Media LLC
Date: 26-09-2015
DOI: 10.1007/S10519-015-9749-Z
Abstract: Octopamine- and dopamine-based neuromodulatory systems play a critical role in learning and learning-related behaviour in insects. To further our understanding of these systems and resulting phenotypes, we quantified DNA sequence variations at six loci coding octopamine-and dopamine-receptors and their association with aversive and appetitive learning traits in a population of honeybees. We identified 79 polymorphic sequence markers (mostly SNPs and a few insertions/deletions) located within or close to six candidate genes. Intriguingly, we found that levels of sequence variation in the protein-coding regions studied were low, indicating that sequence variation in the coding regions of receptor genes critical to learning and memory is strongly selected against. Non-coding and upstream regions of the same genes, however, were less conserved and sequence variations in these regions were weakly associated with between-in idual differences in learning-related traits. While these associations do not directly imply a specific molecular mechanism, they suggest that the cross-talk between dopamine and octopamine signalling pathways may influence olfactory learning and memory in the honeybee.
Publisher: eLife Sciences Publications, Ltd
Date: 28-09-2018
Publisher: Public Library of Science (PLoS)
Date: 19-05-2021
DOI: 10.1371/JOURNAL.PBIO.3001009
Abstract: The replicability of research results has been a cause of increasing concern to the scientific community. The long-held belief that experimental standardization begets replicability has also been recently challenged, with the observation that the reduction of variability within studies can lead to idiosyncratic, lab-specific results that cannot be replicated. An alternative approach is to, instead, deliberately introduce heterogeneity, known as “heterogenization” of experimental design. Here, we explore a novel perspective in the heterogenization program in a meta-analysis of variability in observed phenotypic outcomes in both control and experimental animal models of ischemic stroke. First, by quantifying interin idual variability across control groups, we illustrate that the amount of heterogeneity in disease state (infarct volume) differs according to methodological approach, for ex le, in disease induction methods and disease models. We argue that such methods may improve replicability by creating erse and representative distribution of baseline disease state in the reference group, against which treatment efficacy is assessed. Second, we illustrate how meta-analysis can be used to simultaneously assess efficacy and stability (i.e., mean effect and among-in idual variability). We identify treatments that have efficacy and are generalizable to the population level (i.e., low interin idual variability), as well as those where there is high interin idual variability in response for these, latter treatments translation to a clinical setting may require nuance. We argue that by embracing rather than seeking to minimize variability in phenotypic outcomes, we can motivate the shift toward heterogenization and improve both the replicability and generalizability of preclinical research.
Publisher: BMJ
Date: 22-11-2022
Abstract: To examine changes in completeness of reporting and frequency of sharing data, analytical code, and other review materials in systematic reviews over time and factors associated with these changes. Cross sectional meta-research study. Random s le of 300 systematic reviews with meta-analysis of aggregate data on the effects of a health, social, behavioural, or educational intervention. Reviews were indexed in PubMed, Science Citation Index, Social Sciences Citation Index, Scopus, and Education Collection in November 2020. The extent of complete reporting and the frequency of sharing review materials in the systematic reviews indexed in 2020 were compared with 110 systematic reviews indexed in February 2014. Associations between completeness of reporting and various factors (eg, self-reported use of reporting guidelines, journal policies on data sharing) were examined by calculating risk ratios and 95% confidence intervals. Several items were reported suboptimally among 300 systematic reviews from 2020, such as a registration record for the review (n=113 38%), a full search strategy for at least one database (n=214 71%), methods used to assess risk of bias (n=185 62%), methods used to prepare data for meta-analysis (n=101 34%), and source of funding for the review (n=215 72%). Only a few items not already reported at a high frequency in 2014 were reported more frequently in 2020. No evidence indicated that reviews using a reporting guideline were more completely reported than reviews not using a guideline. Reviews published in 2020 in journals that mandated either data sharing or inclusion of data availability statements were more likely to share their review materials (eg, data, code files) than reviews in journals without such mandates (16/87 (18%) v 4/213 (2%)). Incomplete reporting of several recommended items for systematic reviews persists, even in reviews that claim to have followed a reporting guideline. Journal policies on data sharing might encourage sharing of review materials.
Publisher: California Digital Library (CDL)
Date: 18-11-2020
Publisher: California Digital Library (CDL)
Date: 03-07-2022
Publisher: Wiley
Date: 14-05-2021
DOI: 10.1111/ELE.13757
Abstract: Symbioses exert substantial biological influence, with great evolutionary and ecological relevance for disease, major evolutionary transitions, and the structure and function of ecological communities. Yet, much remains unknown about the patterns and processes that characterise symbioses. A major unanswered question is the extent to which symbiont phylogenies mirror those of their hosts and if patterns differ for parasites and mutualists. Addressing this question offers fundamental insights into evolutionary processes, such as whether symbionts typically co erge with their hosts or if ersity is generated via host switches. Here, we perform a meta‐analysis of host‐symbiont phylogenetic congruence, encompassing 212 host‐symbiont cophylogenetic studies that include ~10,000 species. Our analysis supersedes previous qualitative assessments by utilising a quantitative framework. We show that symbiont phylogeny broadly reflects host phylogeny across bio ersity and life‐history, demonstrating a general pattern of phylogenetic congruence in host‐symbiont interactions. We reveal two key aspects of symbiont life‐history that promote closer ties between hosts and symbionts: vertical transmission and mutualism. Mode of symbiosis and mode of transmission are intimately interlinked, but vertical transmission is the dominant factor. Given the pervasiveness of symbioses, these findings provide important insights into the processes responsible for generating and maintaining the Earth's rich bio ersity.
Publisher: Springer Science and Business Media LLC
Date: 03-04-2023
Publisher: Wiley
Date: 19-06-2019
DOI: 10.1111/BRV.12524
Abstract: Theory predicts that costly sexual traits should be reduced when in iduals are in poor condition (i.e. traits should exhibit condition-dependent expression). It is therefore widely expected that male ejaculate traits, such as sperm and seminal fluid, will exhibit reduced quantity and quality when dietary nutrients are limited. However, reported patterns of ejaculate condition dependence are highly variable, and there has been no comprehensive synthesis of underlying sources of such variation in condition-dependent responses. In particular, it remains unclear whether all ejaculate traits are equally sensitive to nutrient intake, and whether such traits are particularly sensitive to certain dietary nutrients, respond more strongly to nutrients during specific life stages, or respond more strongly in some taxonomic groups. We systematically reviewed these potential sources of variation through a meta-analysis across 50 species of arthropods and vertebrates (from 71 papers and 348 effect sizes). We found that overall, ejaculate traits are moderately reduced when dietary nutrients are limited, but we also detected substantial variation in responses. Seminal fluid quantity was strongly and consistently condition dependent, while sperm quantity was moderately condition dependent. By contrast, aspects of sperm quality (particularly sperm viability and morphology) were less consistently reduced under nutrient limitation. Ejaculate traits tended to respond in a condition-dependent manner to a wide range of dietary manipulations, especially to caloric and protein restriction. Finally, while all major taxa for which sufficient data exist (i.e. arthropods, mammals, fish) showed condition dependence of ejaculate traits, we detected some taxonomic differences in the life stage that is most sensitive to nutrient limitation, and in the degree of condition dependence of specific ejaculate traits. Together, these biologically relevant factors accounted for nearly 20% of the total variance in ejaculate responses to nutrient limitation. Interestingly, body size showed considerably stronger condition-dependent responses compared to ejaculate traits, suggesting that ejaculate trait expression may be strongly canalised to protect important reproductive functions, or that the cost of producing an ejaculate is relatively low. Taken together, our findings show that condition-dependence of ejaculate traits is taxonomically widespread, but there are also many interesting, biologically relevant sources of variation that require further investigation. In particular, further research is needed to understand the differences in selective pressures that result in differential patterns of ejaculate condition dependence across taxa and ejaculate traits.
Publisher: Wiley
Date: 22-06-2009
Publisher: Wiley
Date: 29-04-2021
DOI: 10.1111/OIK.08122
Abstract: Physiological processes vary widely across in iduals and can influence how in iduals respond to environmental change. Repeatability in how metabolic rate changes across temperatures (i.e. metabolic thermal plasticity) can influence mass‐scaling exponents in different thermal environments. Moreover, repeatable plastic responses are necessary for reaction norms to respond to selective forces which is important for populations living in fluctuating environments. Nonetheless, only a small number of studies have explicitly quantified repeatability in metabolic plasticity, and fewer have explored how it can impact mass‐scaling. We repeatedly measured standard metabolic rate of n = 42 delicate skinks L ropholis delicata at six temperatures over the course of four months ( N [observations] = 4952). Using hierarchical statistical techniques, we accounted for multi‐level variation and measurement error in our data in order to obtain more precise estimates of reaction norm repeatability and mass‐scaling exponents at different acute temperatures. Our results show that in idual differences in metabolic thermal plasticity were somewhat consistent over time (R slope = 0.25, 95% CI = 2.48 × 10 −8 – 0.67), however estimates were associated with a large degree of error. After accounting for measurement error, which decreased steadily with temperature, we show that among in idual variance remained consistent across all temperatures. Congruently, temperature specific repeatability of average metabolic rate was stable across temperatures. Cross‐temperature correlations were positive but were not uniform across the reaction norm. After taking into account multiple sources of variation, our estimates for mass‐scaling did not change with temperature and were in line with published values for snakes and lizards. This implies that repeatable plastic responses may promote thermal stability of scaling exponents. Our work contributes to understanding how energy expenditure scales with abiotic and biotic factors and the capacity for reaction norms to respond to selection.
Publisher: Wiley
Date: 13-08-2013
DOI: 10.1111/JEB.12212
Abstract: The evolution of adaptive phenotypic plasticity relies on the presence of cues that enable organisms to adjust their phenotype to match local conditions. Although mostly studied with respect to nonsocial cues, it is also possible that parents transmit information about the environment to their offspring. Such 'anticipatory parental effects' or 'adaptive transgenerational plasticity' can have important consequences for the dynamics and adaptive potential of populations in heterogeneous environments. Yet, it remains unknown how widespread this form of plasticity is. Using a meta-analysis of experimental studies with a fully factorial design, we show that there is only weak evidence for higher offspring performance when parental and offspring environments are matched compared with when they are mismatched. Estimates of heterogeneity among studies suggest that effects, when they occur, are subtle. Study features, environmental context, life stage and trait categories all failed to explain significant amounts of variation in effect sizes. We discuss theoretical and methodological reasons for the limited evidence for anticipatory parental effects and suggest ways to improve our understanding of the prevalence of this form of plasticity in nature.
Publisher: Wiley
Date: 06-07-2020
DOI: 10.1111/JEB.13661
Publisher: Cold Spring Harbor Laboratory
Date: 10-12-2022
DOI: 10.1101/2022.12.08.519666
Abstract: Research institutions and researchers have become increasingly concerned about poor research reproducibility and replicability, and research waste more broadly. Research institutions play an important role and understanding their intervention options is important. This review aims to identify and classify possible interventions to improve research quality, reduce waste, and improve reproducibility and replicability within research-performing institutions. Taxonomy development steps: 1) use of an exemplar paper of journal-level research quality improvement interventions, 2) 2-stage search in PubMed using seed and exemplar articles, and forward and backward citation searching to identify articles evaluating or describing research quality improvement, 3) elicited draft taxonomy feedback from researchers at an open-sciences conference workshop, and 4) cycles of revisions from the research team. The search identified 11 peer-reviewed articles on relevant interventions. Overall, 93 interventions were identified from peer-review literature and researcher reporting. Interventions covered before, during, and after study conduct research stages and whole of institution. Types of intervention included: Tools, Education & Training, Incentives, Modelling & Mentoring, Review & Feedback, Expert involvement, and Policies & Procedures. Identified areas for research institutions to focus on to improve research quality and for further research includes improving incentives to implement quality research practices, evaluating current interventions, encourage no- or low-cost/high-benefit interventions, examine institution research culture, and encourage mentor-mentee relationships.
Publisher: Springer Science and Business Media LLC
Date: 23-10-2004
Publisher: Springer Science and Business Media LLC
Date: 21-08-2015
DOI: 10.1038/IJO.2015.160
Abstract: There is increasing recognition that maternal effects contribute to variation in in idual food intake and metabolism. For ex le, many experimental studies on model animals have reported the effect of a maternal obesogenic diet during pregnancy on the appetite of offspring. However, the consistency of effects and the causes of variation among studies remain poorly understood. After a systematic search for relevant publications, we selected 53 studies on rats and mice for a meta-analysis. We extracted and analysed data on the differences in food intake and body weight between offspring of dams fed obesogenic diets and dams fed standard diets during gestation. We used meta-regression to study predictors of the strength and direction of the effect sizes. We found that experimental offspring tended to eat more than control offspring but this difference was small and not statistically significant (0.198, 95% highest posterior density (HPD)=-0.118-0.627). However, offspring from dams on obesogenic diets were significantly heavier than offspring of control dams (0.591, 95% HPD=0.052-1.056). Meta-regression analysis revealed no significant influences of tested predictor variables (for ex le, use of choice vs no-choice maternal diet, offspring sex) on differences in offspring appetite. Dietary manipulations that extended into lactation had the largest effect on body weight. Subgroup analysis revealed that high protein to non-protein ratio of the maternal diet may promote increased body weight in experimental offspring in comparison with control offspring low protein content in the maternal chow can have opposite effect. Exposure to maternal obesogenic diets in early life is not likely to result in a substantial change in offspring appetite. Nevertheless, we found an effect on offspring body weight, consistent with permanent alterations of offspring metabolism in response to maternal diet. Additionally, it appears that protein content of the obesogenic diet and timing of manipulation modulate the effects on offspring body weight in later life.
Publisher: Wiley
Date: 11-09-2016
DOI: 10.1111/FAF.12096
Publisher: Elsevier BV
Date: 07-2019
Publisher: The Royal Society
Date: 09-2017
Abstract: The coefficient of determination R 2 quantifies the proportion of variance explained by a statistical model and is an important summary statistic of biological interest. However, estimating R 2 for generalized linear mixed models (GLMMs) remains challenging. We have previously introduced a version of R 2 that we called for Poisson and binomial GLMMs, but not for other distributional families. Similarly, we earlier discussed how to estimate intra-class correlation coefficients (ICCs) using Poisson and binomial GLMMs. In this paper, we generalize our methods to all other non-Gaussian distributions, in particular to negative binomial and gamma distributions that are commonly used for modelling biological data. While expanding our approach, we highlight two useful concepts for biologists, Jensen's inequality and the delta method, both of which help us in understanding the properties of GLMMs. Jensen's inequality has important implications for biologically meaningful interpretation of GLMMs, whereas the delta method allows a general derivation of variance associated with non-Gaussian distributions. We also discuss some special considerations for binomial GLMMs with binary or proportion data. We illustrate the implementation of our extension by worked ex les from the field of ecology and evolution in the R environment. However, our method can be used across disciplines and regardless of statistical environments.
Publisher: Elsevier BV
Date: 09-2012
Publisher: Wiley
Date: 11-2022
DOI: 10.1002/ECE3.9511
Abstract: The obesity epidemic, largely driven by the accessibility of ultra‐processed high‐energy foods, is one of the most pressing public health challenges of the 21st century. Consequently, there is increasing concern about the impacts of diet‐induced obesity on behavior and cognition. While research on this matter continues, to date, no study has explicitly investigated the effect of obesogenic diet on variance and covariance (correlation) in behavioral traits. Here, we examined how an obesogenic versus control diet impacts means and (co‐)variances of traits associated with body condition, behavior, and cognition in a laboratory population of ~160 adult zebrafish ( Danio rerio ). Overall, an obesogenic diet increased variation in several zebrafish traits. Zebrafish on an obesogenic diet were significantly heavier and displayed higher body weight variability fasting blood glucose levels were similar between control and treatment zebrafish. During behavioral assays, zebrafish on the obesogenic diet displayed more exploratory behavior and were less reactive to video stimuli with conspecifics during a personality test, but these significant differences were sex‐specific. Zebrafish on an obesogenic diet also displayed repeatable responses in aversive learning tests whereas control zebrafish did not, suggesting an obesogenic diet resulted in more consistent, yet impaired, behavioral responses. Where behavioral syndromes existed (inter‐class correlations between personality traits), they did not differ between obesogenic and control zebrafish groups. By integrating a multifaceted, holistic approach that incorporates components of (co‐)variances, future studies will greatly benefit by quantifying neglected dimensions of obesogenic diets on behavioral changes.
Publisher: Cold Spring Harbor Laboratory
Date: 16-03-2018
DOI: 10.1101/283150
Abstract: The status signalling hypothesis aims to explain conspecific variation in ornamentation by suggesting that some ornaments signal dominance status. Here, we use multilevel meta-analytic models to challenge the textbook ex le of this hypothesis, the black bib of house sparrows ( Passer domesticus ). We conducted a systematic review, and obtained raw data from published and unpublished studies to test whether dominance rank is positively associated with bib size across studies. Contrary to previous studies, our meta-analysis did not support this prediction. Furthermore, we found several biases in the literature that further question the support available for the status signalling hypothesis. First, the overall effect size of unpublished studies was zero, compared to the medium effect size detected in published studies. Second, the effect sizes of published studies decreased over time, and recently published effects were, on average, no longer distinguishable from zero. We discuss several explanations including pleiotropic, population- and context-dependent effects. Our findings call for reconsidering this established textbook ex le in evolutionary and behavioural ecology, raise important concerns about the validity of the current scientific publishing culture, and should stimulate renewed interest in understanding within-species variation in ornamental traits.
Publisher: Springer Science and Business Media LLC
Date: 24-08-2020
Publisher: Wiley
Date: 10-12-2021
DOI: 10.1111/GCB.15972
Abstract: Field studies are essential to reliably quantify ecological responses to global change because they are exposed to realistic climate manipulations. Yet such studies are limited in replicates, resulting in less power and, therefore, potentially unreliable effect estimates. Furthermore, while manipulative field experiments are assumed to be more powerful than non‐manipulative observations, it has rarely been scrutinized using extensive data. Here, using 3847 field experiments that were designed to estimate the effect of environmental stressors on ecosystems, we systematically quantified their statistical power and magnitude (Type M) and sign (Type S) errors. Our investigations focused upon the reliability of field experiments to assess the effect of stressors on both ecosystem's response magnitude and variability. When controlling for publication bias, single experiments were underpowered to detect response magnitude (median power: 18%–38% depending on effect sizes). Single experiments also had much lower power to detect response variability (6%–12% depending on effect sizes) than response magnitude. Such underpowered studies could exaggerate estimates of response magnitude by 2–3 times (Type M errors) and variability by 4–10 times. Type S errors were comparatively rare. These observations indicate that low power, coupled with publication bias, inflates the estimates of anthropogenic impacts. Importantly, we found that meta‐analyses largely mitigated the issues of low power and exaggerated effect size estimates. Rather surprisingly, manipulative experiments and non‐manipulative observations had very similar results in terms of their power, Type M and S errors. Therefore, the previous assumption about the superiority of manipulative experiments in terms of power is overstated. These results call for highly powered field studies to reliably inform theory building and policymaking, via more collaboration and team science, and large‐scale ecosystem facilities. Future studies also require transparent reporting and open science practices to approach reproducible and reliable empirical work and evidence synthesis.
Publisher: Wiley
Date: 30-06-2021
Abstract: Well‐conducted systematic reviews are invaluable for synthesising research findings. The conclusions of a review depend on how the research question was formulated, how relevant studies were found and how studies were selected for synthesis. Here, we present a practical guide for ecologists and evolutionary biologists on formulating a question for a systematic review, and finding a representative s le of research findings. We explain the steps involved using a worked ex le and practical training exercises. Throughout this guide we share tricks of the trade, included rules of thumb and software that we have found useful. We hope our paper helps demystify the systematic search process and encourages more researchers to adopt a systematic and reproducible approach when searching the literature.
Publisher: Wiley
Date: 07-11-2016
Publisher: Wiley
Date: 25-07-2007
DOI: 10.1111/J.1420-9101.2007.01403.X
Abstract: Repeatability of parental care, let alone heritability of care, has been rarely measured, although there has been much research linking sexual selection to male parental care and also examining biparental care in relation to game theory models. We investigated within- and between-year repeatabilities of incubation and nestling provisioning and how these two types of parental care were related in a sexually dimorphic species, the house sparrow, Passer domesticus. We found that between- and within-year repeatabilities of feeding rate were high in males and low to moderate in females, but that between- and within-year repeatabilities of incubation time were low to moderate in both sexes. Interestingly, the amount of time during which neither sex incubated significantly predicted the subsequent male feeding rate but not the female feeding rate. Our results suggest a need for a new theoretical framework that encompasses variation in the predictability and plasticity of parental investment by in iduals.
Publisher: The Royal Society
Date: 14-03-2012
Abstract: The well-established view of the evolution of sex chromosome dimorphism is of a gradual genetic and morphological degeneration of the hemizygous chromosome. Yet, no large-scale comparative analysis exists to support this view. Here, we analysed karyotypes of 200 bird species to test whether the supposed directional changes occur in bird sex chromosomes. We found no support for the view that W chromosomes gradually become smaller over evolutionary time. On the contrary, the length of the W chromosome can fluctuate over short time scales, probably involving both shortening and elongation of non-coding regions. Recent discoveries of near-identical palindromes and neo-sex chromosomes in birds may also contribute to the observed variation. Further studies are now needed to investigate how chromosome morphology relates to its gene content, and whether the changes in size were driven by selection.
Publisher: Wiley
Date: 10-2023
Publisher: University of Chicago Press
Date: 08-2016
DOI: 10.1086/687243
Abstract: One predicted cost of female infidelity in socially monogamous species is that cuckolded males should provide less parental care. This relationship is robust across species, but evidence is ambiguous within species. We do not know whether in idual males reduce their care when paired with cheating females compared with when paired with faithful females (within-male adjustment) or, alternatively, if the males that pair with cheating females are the same males that provide less parental care in general (between-male effect). Our exceptionally extensive long-term data set of repeated observations of a wild passerine allows us to disentangle paternal care adjustment within males-within pairs and between males-while accounting for environmental variables. We found a within-male adjustment of paternal provisioning, but not incubation effort, relative to the cuckoldry in their nest. This effect was mainly driven by females differing consistently in their fidelity. There was no evidence that this within-male adjustment also took place across broods with the same female, and we found no between-male effect. Interestingly, males that gained more extrapair paternity provided less care. Data from a cross-foster experiment suggested that males did not use kin recognition to assess paternity. Our results provide insight into the role of in idual variation in parental care and mating systems.
Publisher: Wiley
Date: 22-05-2017
Publisher: The Royal Society
Date: 09-2020
Abstract: Spider major ullate (MA) silk, with its combination of strength and extensibility, outperforms any synthetic equivalents. There is thus much interest in understanding its underlying materiome. While the expression of the different silk proteins (spidroins) appears an integral component of silk performance, our understanding of the nature of the relationship between the spidroins, their constituent amino acids and MA silk mechanics is ambiguous. To provide clarity on these relationships across spider species, we performed a meta-analysis using phylogenetic comparative methods. These showed that glycine and proline, both of which are indicators of differential spidroin expression, had effects on MA silk mechanics across the phylogeny. We also found serine to correlate with silk mechanics, probably via its presence within the carboxyl and amino-terminal domains of the spidroins. From our analyses, we concluded that the spidroin expression shifts across the phylogeny from predominantly MaSp1 in the MA silks of ancestral spiders to predominantly MaSp2 in the more derived spiders' silks. This trend was accompanied by an enhanced ultimate strain and decreased Young's modulus in the silks. Our meta-analysis enabled us to decipher between real and apparent influences on MA silk properties, providing significant insights into spider silk and web coevolution and enhancing our capacity to create spider silk-like materials.
Publisher: California Digital Library (CDL)
Date: 19-05-2022
Publisher: Wiley
Date: 08-03-2022
DOI: 10.1111/ELE.13981
Abstract: Male mate choice occurs in several animal species, but we know little about the factors that influence the expression of this behaviour. Males vary in their capacity to acquire mates (i.e. male quality), which could be crucial to male mate choice expression but it is often overlooked. Using a meta-analytical approach, we explore interin idual variation in the expression of male mate choice by comparing the mating investment of males of different qualities and phenotypes to high- and low-quality females. We used two datasets that together contained information from 60 empirical studies, comprising 52 species. We found that males of all qualities and phenotypes prefer high-quality females, but differ in the strength of such preference. High- and medium-quality males are choosier than low-quality males. Similarly, males that are larger or in greater body condition are choosier than their counterparts. In contrast, male body mass and age are not associated with changes in male mate choice. We also show that experimental design may influence our understanding of male mating investment patterns, which may limit the generalisation of our findings. Nonetheless, we argue that male quality may be an important feature in the expression of male mate choice.
Publisher: Elsevier BV
Date: 08-2018
Publisher: Cold Spring Harbor Laboratory
Date: 21-12-2016
DOI: 10.1101/095851
Abstract: The coefficient of determination R 2 quantifies the proportion of variance explained by a statistical model and is an important summary statistic of biological interest. However, estimating R 2 for generalized linear mixed models (GLMMs) remains challenging. We have previously introduced a version of R 2 that we called R 2 GLMM for Poisson and binomial GLMMs, but not for other distributional families. Similarly, we earlier discussed how to estimate intra-class correlation coefficients ICC using Poisson and binomial GLMMs. In this article, we expand our methods to all other non-Gaussian distributions, in particular to negative binomial and gamma distributions that are commonly used for modelling biological data. While expanding our approach, we highlight two useful concepts for biologists, Jensen’s inequality and the delta method, both of which help us in understanding the properties of GLMMs. Jensen’s inequality has important implications for biologically meaningful interpretation of GLMMs, while the delta method allows a general derivation of variance associated with non-Gaussian distributions. We also discuss some special considerations for binomial GLMMs with binary or proportion data. We illustrate the implementation of our extension by worked ex les from the field of ecology and evolution in the R environment. However, our method can be used across disciplines and regardless of statistical environments.
Publisher: Wiley
Date: 16-08-2011
DOI: 10.1111/J.1420-9101.2011.02366.X
Abstract: Theory proposes that sexually dimorphic, polygynous species are at particularly high risk of sex-biased predation, because conspicuous males are more often preyed upon compared to females. We tested the effects of predation on population sex ratio in a highly sexually dimorphic insect genus (Hemideina). In addition, introduction of a suite of novel mammalian predators to New Zealand during the last 800 years is likely to have modified selection pressures on native tree weta. We predicted that the balance between natural and sexual selection would be disrupted by the new predator species. We expected to see a sex ratio skew resulting from higher mortality in males with expensive secondary sexual weaponry combat occurs outside refuge cavities between male tree weta. We took a meta-analytic approach using generalized linear mixed models to compare sex ratio variation in 58 populations for six of the seven species in Hemideina. We investigated adult sex ratio across these populations to determine how much variation in sex ratio can be attributed to sex-biased predation in populations with either low or high number of invasive mammalian predators. Surprisingly, we did not detect any significant deviation from 1 : 1 parity for adult sex ratio and found little difference between populations or species. We conclude that there is little evidence of sex-biased predation by either native or mammalian predators and observed sex ratio skew in in idual populations of tree weta is probably an artefact of s ling error. We argue that sex-biased predation may be less prevalent in sexually dimorphic species than previously suspected and emphasize the usefulness of a meta-analytic approach to robustly analyse disparate and heterogeneous data.
Publisher: California Digital Library (CDL)
Date: 02-08-2019
Publisher: Springer Science and Business Media LLC
Date: 04-01-2017
DOI: 10.1038/HDY.2016.116
Publisher: Wiley
Date: 17-07-2013
DOI: 10.1111/IBI.12080
Publisher: American Society of Hematology
Date: 05-11-2020
DOI: 10.1182/BLOOD-2020-142565
Abstract: Introduction: The open-label, international, randomized, phase 3 KEYNOTE-204 (NCT02684292) study showed that in pts with R/R cHL, the PD-1 inhibitor pembro was superior to BV and demonstrated statistically significant, clinically meaningful improvement in PFS, with safety consistent with previous reports. This post hoc exploratory analysis of KEYNOTE-204 evaluated pembro vs BV by number of prior lines of therapy. Methods: Eligible pts were aged ≥18 y, had measurable disease and ECOG PS 0 or 1, and were post−autologous stem cell transplant (auto-SCT) or ineligible for auto-SCT. Pts who were BV-naive or BV-exposed were also eligible. Pts were randomized 1:1 to pembro 200 mg IV Q3W or BV 1.8 mg/kg IV Q3W. Randomization was stratified by status after 1L therapy (primary refractory vs relapsed & mo vs relapsed ≥12 mo after end of 1L therapy) and prior auto-SCT (yes vs no). Pts in this exploratory analysis were evaluated by number of prior therapies before enrollment (1 and ≥2 prior therapies). Primary end points were PFS by blinded independent central review (BICR) per International Working Group (IWG) criteria, including clinical and imaging data after auto-SCT or allogeneic SCT (allo-SCT) and OS. Additional end points were PFS excluding clinical and imaging data after auto-SCT or allo-SCT (secondary PFS analysis), ORR and duration of response (DOR) by BICR per IWG, and safety. Results: Of 304 randomized pts, 55 (pembro, 27 BV, 28) received 1 prior therapy and 249 (pembro, 124 BV, 125) received ≥2 prior therapies. For pts with 1 prior therapy, median (range) age was 49 y (22-84) and 22 pts (40.0%) were aged ≥65 y. No pts received prior auto-SCT and 18 (32.7%) had primary refractory disease. Auto-SCT ineligibility was due to chemorefractory disease for 21 pts (38.2%) and reasons not related to chemorefractory disease (eg, age, comorbidities) for 34 pts (61.8%). 23 pts (85.2%) and 25 pts (92.6%) in the pembro and BV groups, respectively, discontinued treatment the most common reason was progressive disease. Median (range) time from randomization to data cutoff was 24.0 mo (18.7-34.8) for pembro and 23.6 mo (18.2-34.6) for BV. For the primary PFS analysis, median PFS was 16.4 mo for pembro and 8.4 mo for BV (HR 0.70 95% CI 0.031-1.59) 12 mo PFS rates were 58.9% and 37.4%, respectively. For the secondary PFS analysis, median PFS was 11.7 mo for pembro and 8.3 mo for BV (HR 0.62 95% CI 0.28-1.40). ORR was 66.7% for pembro and 53.6% for BV. Median (range) DOR for pembro was 20.7 mo (2.8-20.7) and 14.1 mo (0.0+ to 21.9) for BV. 7 pts (25.9%) and 9 pts (33.3%) in the pembro and BV groups, respectively, received subsequent auto-SCT 1 pt in the BV group received subsequent allo-SCT. 21 pts (77.8%) on pembro and 20 (74.1%) on BV experienced a treatment-related adverse event (TRAE) most common were hyperthyroidism (22.2%) for pembro and peripheral neuropathy (22.2%) for BV. 1 (3.7%) and 8 (29.6%) of pts on pembro and BV, respectively, experienced grade 3-5 TRAEs. For pts with ≥2 prior therapies median (range) age was 34 y (18-83) and 27 (10.8%) pts were aged ≥65 y. 112 pts (45.0%) received prior auto-SCT and 105 (42.2%) had primary refractory disease. Median (range) time from randomization to data cutoff was 27.1 mo (18.8-42.0) for pembro and 27.6 (18.2-42.3) for BV. 87 (71.9%) and 121 (96.8%) in the pembro and BV groups discontinued most common reason was progressive disease. For the primary PFS analysis, median PFS was 12.6 mo for pembro and 8.2 mo for BV (HR 0.66 95% CI 0.47-0.92) 12-mo PFS rates were 52.8% and 35.3%, respectively. For the secondary PFS analysis, median PFS was 12.6 mo for pembro and 8.2 mo for BV (HR 0.63 95% CI 0.45-0.88). ORR for pembro was 65.3% and 54.4% for BV. Median (range) DOR for pembro was 20.5 mo (0.0+ to 33.2+) and 11.2 mo (0.0+ to 33.9+) for BV. 23 (19.0%) and 25 (20.0%) pts in the pembro and BV groups, respectively, received subsequent auto-SCT 14 (11.6 %) and 12 (9.6%) received subsequent allo-SCT. 89 pts (73.6%) on pembro and 97 (77.6%) on BV experienced a TRAE most common were hypothyroidism (14.9%) for pembro and peripheral neuropathy (17.6%) for BV. 23.1% and 24.0% of pts on pembro and BV, respectively, experienced grade 3-5 TRAEs. Conclusion: In pts with R/R cHL, pembro monotherapy resulted in an improvement in PFS and ORR vs BV in pts regardless of number of prior therapies. In particular, these data suggest that pembro monotherapy may be a promising option as 2L+ therapy for pts with R/R cHL ineligible for auto-SCT. Kuruvilla: Bristol-Myers Squibb Company: Consultancy TG Therapeutics: Honoraria Pfizer: Honoraria Gilead: Consultancy, Honoraria AbbVie: Consultancy Karyopharm: Consultancy, Honoraria AstraZeneca Pharmaceuticals LP: Honoraria, Research Funding Novartis: Honoraria Antengene: Honoraria Merck: Consultancy, Honoraria Celgene Corporation: Honoraria Amgen: Honoraria Roche: Consultancy, Honoraria, Research Funding Janssen: Honoraria, Research Funding Seattle Genetics: Consultancy, Honoraria. Ramchandren:Seattle Genetics, Sandoz-Novartis, Pharmacyclics, an AbbVie Company, Janssen, Bristol-Myers Squibb: Consultancy Merck, Seattle Genetics, Janssen, Genentech: Research Funding. Santoro:Arqule, Sanofi: Consultancy Bristol-Myers Squibb, SERVIER, Gilead Sciences, Pfizer, Eisai, Bayer, MSD, Sanofi, ArQule: Consultancy, Speakers Bureau Bristol Myers Squibb, Servier, Gilead, Pfizer, Eisai, Bayer, MSD: Membership on an entity's Board of Directors or advisory committees Bristol-Myers Squibb, SERVIER, Gilead Sciences, Pfizer, Eisai, Bayer, MSD, Sanofi, ArQule: Consultancy Takeda, Roche, Abbvie, Amgen, Celgene, AstraZeneca, ArQule, Lilly, Sandoz, Novartis, Bristol-Myers Squibb, Servier, Gilead Sciences, Pfizer, Eisai, Bayer, MSD: Speakers Bureau Bristol-Myers Squibb, SERVIER, Gilead Sciences, Pfizer, Eisai, Bayer, MSD, Sanofi, ArQule: Consultancy Takeda, Roche, Abbvie, Amgen, Celgene, AstraZeneca, ArQule, Lilly, Sandoz, Novartis, Bristol-Myers Squibb, Servier, Gilead Sciences, Pfizer, Eisai, Bayer, MSD: Speakers Bureau. Paszkiewicz-Kozik:Roche, Takeda, Celgene: Other: Travel, accommodations, expenses. Gasiorowski:MSD, Takeda, Novartis, AbbVie: Honoraria. Johnson:Roche/Genentech, Merck: Honoraria Roche/Genentech, Merck, Bristol-Myers Squibb, AbbVie: Consultancy AbbVie: Research Funding. Goncalves:Janssen, Takeda, Amgen, Bayer, Novartis, Merck, Bayer, Celgene, GSK, BMS: Research Funding Janssen: Consultancy, Speakers Bureau. Perini:Janssen, Takeda: Honoraria AbbVie, Janssen: Speakers Bureau. Goldschmidt:Abbvie Inc: Consultancy, Research Funding. Kryachok:Janssen, Bayer, Karyopharm, MSD, AbbVie, Acerta, Debiopharm: Research Funding Takeda, Janssen: Consultancy Takeda, MSD, AbbVie, Roche: Other: Travel, accommodations, expenses. Sekiguchi:Ono, A2 Healthcare, Astellas, Janssen, Merck Sharp & Dohme, Otsuka, Pfizer, PPD-SNBL, Sumitomo Dainippon, Daiichi Sankyo, and Bristol-Myers Squibb: Research Funding. Lin:Merck & Co., Inc.: Current Employment. Nahar:Merck Sharp & Dohme, Corp., a subsididary of Merck & Co., Inc., Kenlworth, NJ, USA: Current Employment. Marinello:Merck & Co., Inc.: Other: Travel, accommodations, expenses Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA: Current Employment Merck & Co., Inc., Kenilworth, NJ, USA: Other: Stock ownership. Zinzani:Merck: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau BMS: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau Gilead: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau AbbVie: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau Incyte: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau Roche: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau TG Therapeutics, Inc.: Honoraria, Speakers Bureau Servier: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau Janssen: Consultancy, Honoraria, Speakers Bureau EUSA Pharma: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau Kirin Kyowa: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau ADC Therapeutics: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau Sanofi: Consultancy, Membership on an entity's Board of Directors or advisory committees MSD: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau Verastem: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau Celltrion: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau Janssen-Cilag: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau Sandoz: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau Immune Design: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau Portola: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau Eusapharma: Consultancy, Speakers Bureau Kyowa Kirin: Consultancy, Speakers Bureau Immune Design: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau.
Publisher: California Digital Library (CDL)
Date: 15-10-2020
Publisher: Wiley
Date: 21-06-2020
DOI: 10.1111/JEB.13655
Publisher: Elsevier BV
Date: 09-2022
Publisher: California Digital Library (CDL)
Date: 29-12-2019
Publisher: Wiley
Date: 03-12-2013
Publisher: Springer Science and Business Media LLC
Date: 11-02-2021
Publisher: Oxford University Press (OUP)
Date: 28-02-2018
DOI: 10.1093/JAS/SKY072
Publisher: Wiley
Date: 09-02-2012
DOI: 10.1111/J.1755-0998.2012.03115.X
Abstract: We identified microsatellite sequences of potential utility in the house sparrow (Passer domesticus) and assigned their predicted genome locations. These sequences included newly isolated house sparrow loci, which we fully characterized. Many of the newly isolated loci were polymorphic in two other species of Passeridae: Berthelot's pipit Anthus berthelotii and zebra finch Taeniopygia guttata. In total, we identified 179 microsatellite markers that were either isolated directly from, or are of known utility in, the house sparrow. Sixty-seven of these markers were designed from unique sequences that we isolated from a house sparrow genomic library. These new markers were combined with 36 house sparrow markers isolated by other studies and 76 markers isolated from other passerine species but known to be polymorphic in the house sparrow. We utilized sequence homology to assign chromosomal locations for these loci in the assembled zebra finch genome. One hundred and thirty-four loci were assigned to 25 different autosomes and eight loci to the Z chromosome. Examination of the genotypes of known-sex house sparrows for 37 of the new loci revealed a W-linked locus and an additional Z-linked locus. Locus Pdoμ2, previously reported as autosomal, was found to be Z-linked. These loci enable the creation of powerful and cost-effective house sparrow multiplex primer sets for population and parentage studies. They can be used to create a house sparrow linkage map and will aid the identification of quantitative trait loci in passerine species.
Publisher: Wiley
Date: 19-01-2012
Publisher: Wiley
Date: 15-09-2011
Publisher: Springer Science and Business Media LLC
Date: 04-10-2022
DOI: 10.1038/S41597-022-01704-9
Abstract: Rising temperatures represent a significant threat to the survival of ectothermic animals. As such, upper thermal limits represent an important trait to assess the vulnerability of ectotherms to changing temperatures. For instance, one may use upper thermal limits to estimate current and future thermal safety margins (i.e., the proximity of upper thermal limits to experienced temperatures), use this trait together with other physiological traits in species distribution models, or investigate the plasticity and evolvability of these limits for buffering the impacts of changing temperatures. While datasets on thermal tolerance limits have been previously compiled, they sometimes report single estimates for a given species, do not present measures of data dispersion, and are biased towards certain parts of the globe. To overcome these limitations, we systematically searched the literature in seven languages to produce the most comprehensive dataset to date on hibian upper thermal limits, spanning 3,095 estimates across 616 species. This resource will represent a useful tool to evaluate the vulnerability of hibians, and ectotherms more generally, to changing temperatures.
Publisher: California Digital Library (CDL)
Date: 28-02-2021
Publisher: Springer Science and Business Media LLC
Date: 17-02-2012
Publisher: Wiley
Date: 25-09-2015
DOI: 10.1111/BRV.12220
Abstract: Females can benefit from mate choice for male traits (e.g. sexual ornaments or body condition) that reliably signal the effect that mating will have on mean offspring fitness. These male-derived benefits can be due to material and/or genetic effects. The latter include an increase in the attractiveness, hence likely mating success, of sons. Females can potentially enhance any sex-biased benefits of mating with certain males by adjusting the offspring sex ratio depending on their mate's phenotype. One hypothesis is that females should produce mainly sons when mating with more attractive or higher quality males. Here we perform a meta-analysis of the empirical literature that has accumulated to test this hypothesis. The mean effect size was small (r = 0.064-0.095 i.e. explaining <1% of variation in offspring sex ratios) but statistically significant in the predicted direction. It was, however, not robust to correction for an apparent publication bias towards significantly positive results. We also examined the strength of the relationship using different indices of male attractiveness/quality that have been invoked by researchers (ornaments, behavioural displays, female preference scores, body condition, male age, body size, and whether a male is a within-pair or extra-pair mate). Only ornamentation and body size significantly predicted the proportion of sons produced. We obtained similar results regardless of whether we ran a standard random-effects meta-analysis, or a multi-level, Bayesian model that included a correction for phylogenetic non-independence. A moderate proportion of the variance in effect sizes (51.6-56.2%) was due to variation that was not attributable to s ling error (i.e. s le size). Much of this non-s ling error variance was not attributable to phylogenetic effects or high repeatability of effect sizes among species. It was approximately equally attributable to differences (occurring for unknown reasons) in effect sizes among and within studies (25.3, 22.9% of the total variance). There were no significant effects of year of publication or two aspects of study design (experimental/observational or field/laboratory) on reported effect sizes. We discuss various practical reasons and theoretical arguments as to why small effect sizes should be expected, and why there might be relatively high variation among studies. Currently, there are no species where replicated, experimental studies show that mothers adjust the offspring sex ratio in response to a generally preferred male phenotype. Ultimately, we need more experimental studies that test directly whether females produce more sons when mated to relatively more attractive males, and that provide the requisite evidence that their sons have higher mean fitness than their daughters.
Publisher: Wiley
Date: 25-07-2012
DOI: 10.1111/J.1420-9101.2012.02569.X
Abstract: A fundamental premise of life-history theory is that organisms that increase current reproductive investment suffer increased mortality. Possibly the most studied life-history phenotypic relationship is the trade-off between parental effort and survival. However, evidence supporting this trade-off is equivocal. Here, we conducted a meta-analysis to test the generality of this tenet. Using experimental studies that manipulated parental effort in birds, we show that (i) the effect of parental effort on survival was similar across species regardless of phylogeny (ii) in iduals that experienced reduced parental effort had similar survival probabilities than control in iduals, regardless of sex and (iii) males that experienced increased parental effort were less likely to survive than control males, whereas females that experienced increased effort were just as likely to survive as control females. Our results suggest that the trade-off between parental effort and survival is more complex than previously assumed. Finally, our study provides recommendations of unexplored avenues of future research into life-history trade-offs.
Publisher: The Royal Society
Date: 05-2019
Abstract: Protein and calorie restrictions extend median lifespan in many organisms. However, studies suggest that among-in idual variation in the age at death is also affected. Ultimately, both of these outcomes must be caused by effects of nutrition on underlying patterns of age-specific mortality (ASM). Using model life tables , we tested for effects of dietary macronutrients on ASM in mice ( Mus musculus ). High concentrations of protein and fat relative to carbohydrates were associated with low life expectancy and high variation in the age at death, a result caused predominantly by high mortality prior to middle age. A lifelong diet comprising the ratio of macronutrients self-selected by mouse (in early adulthood) was associated with low mortality up until middle age, but higher late-life mortality. This pattern results in reasonably high life expectancy, but very low variation in the age at death. Our analyses also indicate that it may be possible to minimize ASM across life by altering the ratio of dietary protein to carbohydrate in the approach to old age. Mortality in early and middle life was minimized at around one-part protein to two-parts carbohydrate, whereas in later life slightly greater than equal parts protein to carbohydrate reduced mortality.
Publisher: Wiley
Date: 14-08-2019
DOI: 10.1002/ECY.2832
Abstract: Incidence, or compositional, matrices are generated for a broad range of research applications in biology. Zeta ersity provides a common currency and conceptual framework that links incidence-based metrics with multiple patterns of interest in biology, ecology, and bio ersity science. It quantifies the variation in species (or OTU) composition of multiple assemblages (or cases) in space or time, to capture the contribution of the full suite of narrow, intermediate, and wide-ranging species to biotic heterogeneity. Here we provide a conceptual framework for the application and interpretation of patterns of continuous change in compositional ersity using zeta ersity. This includes consideration of the survey design context, and the multiple ways in which zeta ersity decline and decay can be used to examine and test turnover in the identity of elements across space and time. We introduce the zeta ratio-based retention rate curve to quantify rates of compositional change. We illustrate these applications using 11 empirical data sets from a broad range of taxa, scales, and levels of biological organization-from DNA molecules and microbes to communities and interaction networks-including one of the original data sets used to express compositional change and distance decay in ecology. We show (1) how different s le selection schemes used during the calculation of compositional change are appropriate for different data types and questions, (2) how higher orders of zeta may in some cases better detect shifts and transitions, and (3) the relative roles of rare vs. common species in driving patterns of compositional change. By exploring the application of zeta ersity decline and decay, including the retention rate, across this broad range of contexts, we demonstrate its application for understanding continuous turnover in biological systems.
Publisher: Wiley
Date: 24-01-2018
DOI: 10.1111/MAM.12115
Publisher: Oxford University Press (OUP)
Date: 2009
Publisher: Wiley
Date: 20-10-2021
DOI: 10.1002/ECY.3490
Publisher: Wiley
Date: 10-10-2011
Publisher: Wiley
Date: 11-06-2020
DOI: 10.1002/JRSM.1424
Publisher: California Digital Library (CDL)
Date: 13-01-2019
Publisher: Wiley
Date: 15-06-2020
DOI: 10.1002/JRSM.1423
Publisher: California Digital Library (CDL)
Date: 09-12-2018
Publisher: Public Library of Science (PLoS)
Date: 16-07-2018
Publisher: Springer Science and Business Media LLC
Date: 07-10-2022
DOI: 10.1038/S41467-022-33548-7
Abstract: Female ornaments are often reduced, male-like traits. Although these were long perceived as non-functional, it is now broadly accepted that female ornaments can be adaptive. However, it is unclear whether this is as common in females as it is in males, and whether ornaments fulfil similar signalling roles. Here, we apply a bivariate meta-analysis to a large dataset of ornaments in mutually ornamented birds. As expected, female ornament expression tends to be reduced compared to males. However, ornaments are equally strongly associated with indicators of condition and aspects of reproductive success in both sexes, regardless of the degree of sexual dimorphism. Thus, we show here in a paired comparison within-and-across species, that ornaments in birds provide similar information in both sexes: more ornamented in iduals are in better condition and achieve higher reproductive success. Although limited by their correlational nature, these outcomes imply that female ornaments could widely function in a similar manner as male ornaments.
Publisher: Wiley
Date: 16-07-2020
Publisher: Oxford University Press (OUP)
Date: 27-04-2016
DOI: 10.1111/BIJ.12813
Publisher: Elsevier BV
Date: 11-2004
DOI: 10.1016/J.BEPROC.2004.07.005
Abstract: A delayed-matching-to-s le (DMTS) task was used to investigate remembering with domestic hens. In Conditions 1 and 3 of Experiment 1, six hens responded under a mixed-delay procedure with delays of 0.25, 2, and 8 s. In Condition 2, the reinforcer for correct responding was delayed for 6 s after each correct matching response on 2-s delay trials. In Condition 1, discrimination performance decreased monotonically over the three delays. With the delay to the reinforcer, the decreases were non-monotonic as a result of the considerable drop in the accuracy of discrimination on the 2-s delay trials. Performance at the 2-s delay did not recover completely in Condition 3. In Conditions 1 and 3 of Experiment 2, five hens responded under a mixed-delay procedure with delays of 0, 4, and 16 s. In Condition 2 no reinforcers were provided for correct responding on 0- and 16-s delay trials. When reinforcers were available on all trials discrimination performance decreased monotonically with delay. There were non-monotonic changes in discrimination with delay when there was extinction at two delays resulting mainly from a large drop in discrimination performance at 0 s. In addition, response latencies increased markedly at the two delays associated with extinction. Performance recovered completely in Condition 3. The data support the ideas that remembering involves a temporal discrimination that the effects of delaying reinforcement and removing reinforcement may differ, and that the measurement of response latencies may be a useful tool in DMTS procedures.
Publisher: Oxford University Press (OUP)
Date: 10-2016
DOI: 10.1642/AUK-16-122.1
Publisher: Springer Science and Business Media LLC
Date: 30-11-2018
Publisher: Wiley
Date: 15-07-2015
DOI: 10.1111/BRV.12210
Abstract: Maternal nutrition can have long-term effects on offspring morphology, physiology and behaviours. However, it is unclear whether mothers 'program' offspring behavioural coping strategy (proactive/reactive) according to the predicted nutritional quality of their future environment. We conducted a systematic review on this topic and meta-analytically synthesized relevant experimental data on mice and rats (46 studies). We included data from experiments where dams were subjected to caloric restriction, protein restriction or overfeeding around gestation and subsequently measured offspring activity, exploration, or anxiety. Overall, little evidence existed for effects of maternal nutrition on the three investigated behavioural traits. The high heterogeneity observed in the data set suggests that maternal programming may sometimes occur. However, because offspring had access to a balanced diet before testing, behaviours may have been reprogrammed. Our results may indicate that reprogrammed behaviours could ameliorate negative effects associated with sub-optimal nutrition in early life. Further, our systematic review revealed clear knowledge gaps and fruitful future research avenues.
Publisher: Wiley
Date: 04-12-2020
Abstract: The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long‐term studies of in idually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Furthermore, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad‐scale global issues (e.g. climate change). To solve data integration issues and enable a new scale of ecological and evolutionary research based on long‐term studies of birds, we have created the SPI‐Birds Network and Database ( www.spibirds.org )—a large‐scale initiative that connects data from, and researchers working on, studies of wild populations of in idually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI‐Birds has recruited over 120 members, and currently hosts data on almost 1.5 million in idual birds collected in 80 populations over 2,000 cumulative years, and counting. SPI‐Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration and thus facilitates collaboration and synthesis. We provide community‐derived data and meta‐data standards and improve data integrity guided by the principles of Findable, Accessible, Interoperable and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta‐data language). The encouraging community involvement stems from SPI‐Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI‐Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community‐specific hubs (such as ours, COMADRE for animal demography, etc.) will aid much‐needed large‐scale ecological data integration.
Publisher: Elsevier BV
Date: 11-2020
DOI: 10.1016/J.NEUBIOREV.2020.07.012
Abstract: Just as happy people see the proverbial glass as half-full, 'optimistic' or 'pessimistic' responses to ambiguity might also reflect affective states in animals. Judgement bias tests, designed to measure these responses, are an increasingly popular way of assessing animal affect and there is now a substantial, but heterogeneous, literature on their use across different species, affect manipulations, and study designs. By conducting a systematic review and meta-analysis of 459 effect sizes from 71 studies of non-pharmacological affect manipulations on 22 non-human species, we show that animals in relatively better conditions, assumed to generate more positive affect, show more 'optimistic' judgements of ambiguity than those in relatively worse conditions. Overall effects are small when considering responses to all cues, but become more pronounced when non-ambiguous training cues are excluded from analyses or when focusing only on the most ergent responses between treatment groups. Task type (go/no-go go/go active choice), training cue reinforcement (reward-punishment reward-null reward-reward) and sex of animals emerge as potential moderators of effect sizes in judgement bias tests.
Publisher: Wiley
Date: 22-02-2021
DOI: 10.1111/IBI.12939
Abstract: The nestlings of many bird species have ornaments in their mouths, yet the within‐species function of these ornaments remains relatively little studied compared with adult ornaments. Here, we describe the pattern of variation in the tongue spots of Dunnock Prunella modularis nestlings and evaluate their potential influence on parental allocation. We observed that some nestlings hatch with a third tongue spot at the tip of the tongue, which then fades as nestlings age. The number of tongue spots present is inversely related to nestling weight, but the number of tongue spots present does not appear consistently to influence parental allocation. This suggests the need for further investigations into within‐species variation of mouth marks in nestling birds to pave the way to a better understanding of these intriguing ornaments.
Publisher: University of Chicago Press
Date: 11-2015
DOI: 10.1086/683182
Abstract: The determinants of diet breadth are of interest to nutritionists, ecologists, and evolutionary biologists. A recent synthesis addressing this issue found conflicting evidence for the relationship between diet breadth and mean in idual fitness. Specifically, it found that while, on average, a mixed diet does increase mean fitness, in some instances, a single food provides equal (or higher) fitness than a mixed diet. Critical to ecological and evolutionary considerations of diet, however, is not only mean fitness but also variance in fitness. We combine contemporary meta-analytic methods with models of nutritional geometry to evaluate how diet affects between-in idual variance in fitness within generalist consumers from a range of trophic levels. As predicted by nutritional geometry, we found that between-in idual variance in fitness-related traits is higher on single-food than mixed diets. The effect was strong for longevity traits (57% higher) and reproductive traits (37%) and present but weaker for size-related traits (10%). Further, the effect became stronger as the number of available foods increased. The availability of multiple foods likely allows in iduals with differing nutritional optima to customize intake, each maximizing their own fitness. Importantly, these findings may suggest that selection on traits correlated with nutritional requirements is weak in heterogeneous nutritional environments.
Publisher: Proceedings of the National Academy of Sciences
Date: 16-11-2020
Abstract: We compiled the most extensive dataset to date of corresponding national macronutrient supplies, survival statistics, and economic data. We show that the national macronutrient supply is a strong predictor of the pattern of mortality in different age classes. Our analyses can show how the optimum macronutrient supply that is predicted to maximize survival changes with age. In early life, equal amounts of fat and carbohydrate are predicted to improve survival. However, as we age, reducing fat in exchange for carbohydrates is associated with the lowest rates of mortality. Our results accord with published experimental and epidemiological data and can help define the mechanisms by which food supply and intake affect public health and demographic processes.
Publisher: Springer Science and Business Media LLC
Date: 22-05-2018
DOI: 10.1038/S41559-018-0545-Z
Abstract: Peer review is widely considered fundamental to maintaining the rigour of science, but it often fails to ensure transparency and reduce bias in published papers, and this systematically weakens the quality of published inferences. In part, this is because many reviewers are unaware of important questions to ask with respect to the soundness of the design and analyses, and the presentation of the methods and results also some reviewers may expect others to be responsible for these tasks. We therefore present a reviewers' checklist of ten questions that address these critical components. Checklists are commonly used by practitioners of other complex tasks, and we see great potential for the wider adoption of checklists for peer review, especially to reduce bias and facilitate transparency in published papers. We expect that such checklists will be well received by many reviewers.
Publisher: California Digital Library (CDL)
Date: 23-08-2020
Publisher: Wiley
Date: 11-08-2023
DOI: 10.1002/JRSM.1663
Abstract: Extracting data from studies is the norm in meta‐analyses, enabling researchers to generate effect sizes when raw data are otherwise not available. While there has been a general push for increased reproducibility in meta‐analysis, the transparency and reproducibility of the data extraction phase is still lagging behind. Unfortunately, there is little guidance of how to make this process more transparent and shareable. To address this, we provide several steps to help increase the reproducibility of data extraction in meta‐analysis. We also provide suggestions of R software that can further help with reproducible data policies: the shinyDigitise and juicr packages. Adopting the guiding principles listed here and using the appropriate software will provide a more transparent form of data extraction in meta‐analyses.
Publisher: Springer Science and Business Media LLC
Date: 16-04-2021
DOI: 10.1186/S13643-021-01670-0
Abstract: Investigations of transparency, reproducibility and replicability in science have been directed largely at in idual studies. It is just as critical to explore these issues in syntheses of studies, such as systematic reviews, given their influence on decision-making and future research. We aim to explore various aspects relating to the transparency, reproducibility and replicability of several components of systematic reviews with meta-analysis of the effects of health, social, behavioural and educational interventions. The REPRISE (REProducibility and Replicability In Syntheses of Evidence) project consists of four studies. We will evaluate the completeness of reporting and sharing of review data, analytic code and other materials in a random s le of 300 systematic reviews of interventions published in 2020 (Study 1). We will survey authors of systematic reviews to explore their views on sharing review data, analytic code and other materials and their understanding of and opinions about replication of systematic reviews (Study 2). We will then evaluate the extent of variation in results when we (a) independently reproduce meta-analyses using the same computational steps and analytic code (if available) as used in the original review (Study 3), and (b) crowdsource teams of systematic reviewers to independently replicate a subset of methods (searches for studies, selection of studies for inclusion, collection of outcome data, and synthesis of results) in a s le of the original reviews 30 reviews will be replicated by 1 team each and 2 reviews will be replicated by 15 teams (Study 4). The REPRISE project takes a systematic approach to determine how reliable systematic reviews of interventions are. We anticipate that results of the REPRISE project will inform strategies to improve the conduct and reporting of future systematic reviews.
Publisher: Public Library of Science (PLoS)
Date: 23-10-2019
Publisher: Elsevier BV
Date: 07-2011
Publisher: Springer Science and Business Media LLC
Date: 03-07-2012
Publisher: Elsevier BV
Date: 12-2014
Publisher: The Royal Society
Date: 12-08-2008
Abstract: The maintenance of honesty in a badge-of-status system is not fully understood, despite numerous empirical and theoretical studies. Our experiment examined the relationship between a status signal and winter survival, and the long-term costs of cheating, by manipulating badge size in male house sparrows, Passer domesticus . The effect of badge-size manipulation on survival was complex owing to the significant interactions between the treatments and original (natural) badge size, and between the treatments and age classes (yearlings and older birds). Nevertheless, in the experimental (badge-enlargement) group, males with originally large badges had increased winter survival, while males with originally small badges had decreased survival. This indicates that differential selection can act on a trait according to the degree of cheating.
Publisher: Wiley
Date: 06-08-2022
DOI: 10.1111/JEB.13906
Abstract: Although consistent between-in idual differences in behaviour (i.e. animal personality) are ubiquitous in natural populations, relatively few studies have examined how personalities influence the formation of social relationships. Yet, behavioural characteristics of both sexes might be key when it comes to pair-bond formation, and cooperation with partners to successfully rear offspring. We here use a wild population of dunnocks (Prunella modularis) to first investigate whether in iduals mate nonrandomly (i.e. assortative mating) with regard to four behavioural traits-flight-initiation distance (FID), provisioning, activity and vigilance-that differ in repeatability and have previously been associated with mating patterns and fitness in other species. Second, we test whether an in idual's FID is associated with variability in the dunnocks' mating system (i.e. monogamous pairs vs. polygamous groups). Finally, we determine whether FID and provisioning of males and females associate with their reproductive success. We found no statistical support for assortative mating in FID between males and females. Interestingly, in polygamous groups, co-breeding males differed in their FIDs with dominant alpha males having significantly shorter FIDs compared with subordinate beta-males. Moreover, there was evidence for assortative mating in provisioning for alpha males and females in polygamous groups. We also found that male provisioning influenced reproductive success of both sexes, whereas female provisioning rates only positively correlated with her own but not their partner(s) reproductive output. Our results suggest that personality differences may have important implications for social relationships, the emergence of different mating patterns and ultimately reproductive success within populations.
Publisher: Wiley
Date: 02-2004
DOI: 10.1017/S1464793103006249
Abstract: Avian literature on sibling recognition is rare compared to that developed by mammalian researchers. We compare avian and mammalian research on sibling recognition to identify why avian work is rare, how approaches differ and what avian and mammalian researchers can learn from each other. Three factors: (1) biological differences between birds and mammals, (2) conceptual biases and (3) practical constraints, appear to influence our current understanding. Avian research focuses on colonial species because sibling recognition is considered adaptive where 'mixing potential' of dependent young is high research on a wider range of species, breeding systems and ecological conditions is now needed. Studies of acoustic recognition cues dominate avian literature other types of cues (e.g. visual, olfactory) deserve further attention. The effect of gender on avian sibling recognition has yet to be investigated mammalian work shows that gender can have important influences. Most importantly, many researchers assume that birds recognise siblings through 'direct familiarisation' (commonly known as associative learning or familiarity) future experiments should also incorporate tests for 'indirect familiarisation' (commonly known as phenotype matching). If direct familiarisation proves crucial, avian research should investigate how periods of separation influence sibling discrimination. Mammalian researchers typically interpret sibling recognition in broad functional terms (nepotism, optimal outbreeding) some avian researchers more successfully identify specific and testable adaptive explanations, with greater relevance to natural contexts. We end by reporting exciting discoveries from recent studies of avian sibling recognition that inspire further interest in this topic.
Publisher: Proceedings of the National Academy of Sciences
Date: 22-02-2021
Publisher: Springer Science and Business Media LLC
Date: 23-03-2020
Publisher: The Royal Society
Date: 20-06-2012
Abstract: Resveratrol has shown evidence of decreasing cancer incidence, heart disease, metabolic syndrome and neural degeneration in animal studies. However, the effects on longevity are mixed. We aimed to quantify the current knowledge of life extension from resveratrol. We used meta-analytic techniques to assess the effect resveratrol has on survival, using data from 19 published papers, including six species: yeast, nematodes, mice, fruitflies, Mexican fruitflies and turquoise killifish. Overall, our results indicate that resveratrol acts as a life-extending agent. The effect is most potent in yeast and nematodes, with diminished reliability in most higher-order species. Turquoise killifish were especially sensitive to life-extending effects of resveratrol but showed much variation. Much of the considerable heterogeneity in our analysis was owing to unexplained variation between studies. In summary, we can report that few species conclusively show life extension in response to resveratrol. As such, we question the practice of the substance being marketed as a life-extending health supplement for humans.
Publisher: Springer Science and Business Media LLC
Date: 16-11-2015
DOI: 10.1038/NCOMMS9877
Abstract: Human disturbance drives the decline of many species, both directly and indirectly. Nonetheless, some species do particularly well around humans. One mechanism that may explain coexistence is the degree to which a species tolerates human disturbance. Here we provide a comprehensive meta-analysis of birds, mammals and lizards to investigate species tolerance of human disturbance and explore the drivers of this tolerance in birds. We find that, overall, disturbed populations of the three major taxa are more tolerant of human disturbance than less disturbed populations. The best predictors of the direction and magnitude of bird tolerance of human disturbance are the type of disturbed area (urbanized birds are more tolerant than rural or suburban populations) and body mass (large birds are more tolerant than small birds). By identifying specific features associated with tolerance, these results guide evidence-based conservation strategies to predict and manage the impacts of increasing human disturbance on birds.
Publisher: Frontiers Media SA
Date: 30-10-2019
Publisher: Brill
Date: 2010
Publisher: Springer Science and Business Media LLC
Date: 13-12-2014
Publisher: Wiley
Date: 08-10-2014
DOI: 10.1111/MEC.12934
Abstract: Sexual selection hypotheses stipulate that the major histocompatibility complex genes (MHC) constitute a key molecular underpinning for mate choice in vertebrates. The last four decades saw growing empirical literature on the role of MHC ersity and dissimilarity in mate choice for a wide range of vertebrate animals, but with mixed support for its significance in natural populations. Using formal phylogenetic meta-analysis and meta-regression techniques, we quantitatively review the existing literature on MHC-dependent mating preferences in nonhuman vertebrates with a focus on the role of MHC ersity and dissimilarity. Overall, we found small, statistically nonsignificant, average effect sizes for both ersity- and dissimilarity-based mate choice (r = 0.113 and 0.064, respectively). Importantly, however, meta-regression models revealed statistically significant support regarding female choice for ersity, and choice for dissimilarity (regardless of choosy sex) only when dissimilarity is characterized across multiple loci. Little difference was found among vertebrate taxa however, the lack of statistical power meant statistically significant effects were limited to some taxa. We found little sign of publication bias thus, our results are likely to be robust. In light of our quantitative assessment, methodological improvements and fruitful future avenues of research are highlighted.
Publisher: CSIRO Publishing
Date: 2012
DOI: 10.1071/ZO12014
Abstract: In many species, male animals produce costly signals to attract females. Intersexual indicator theories propose that these signals are indicative of male quality, whereas in idual recognition models are based on the idea that male signals are used primarily to allow for in idual discrimination. These two types of models make differing predictions about the nature of male signals. In particular, these models’ predictions differ in the information about a male’s quality that will be included in his signal, the frequency distributions of male signals in a population, and the ways in which the different traits that make up a signal will covary. Calls from the Australian frog Litoria chloris were tested for consistency with the predictions of intersexual indicator models and in idual recognition models. The calls were found to contain minimal information on male quality, and the covariance between different signal traits was consistent with the in idual recognition models. However, the frequency distributions of male signal traits agreed with intersexual indicator models. In addition, this study found evidence that the information content of calls may instead mediate intrasexual interactions, although more research is required to determine if this is the case.
Publisher: Wiley
Date: 09-01-2008
Publisher: eLife Sciences Publications, Ltd
Date: 29-10-2020
Publisher: Springer Science and Business Media LLC
Date: 07-08-2004
Publisher: The Royal Society
Date: 16-11-2011
Abstract: Potential mechanistic mediators of Darwinian fitness, such as stress hormones or sex hormones, have been the focus of many studies. An inverse relationship between fitness and stress or sex hormone concentrations has been widely assumed, although empirical evidence is scarce. Feathers gradually accumulate hormones during their growth and provide a novel way to measure hormone concentrations integrated over time. Using liquid chromatography–tandem mass spectrometry, we measured testosterone, corticosterone and cortisol in the feathers of house sparrows ( Passer domesticus ) in a wild population which is the subject of a long-term study. Although corticosterone is considered the dominant avian glucocorticoid, we unambiguously identified cortisol in feathers. In addition, we found that feathers grown during the post-nuptial moult in autumn contained testosterone, corticosterone and cortisol levels that were significantly higher in birds that subsequently died over the following winter than in birds that survived. Thus, feather steroids are candidate prospective biomarkers to predict the future survival of in iduals in the wild.
Publisher: Oxford University Press (OUP)
Date: 03-2011
Publisher: Elsevier BV
Date: 09-2016
DOI: 10.1016/J.TREE.2016.07.002
Abstract: To make progress scientists need to know what other researchers have found and how they found it. However, transparency is often insufficient across much of ecology and evolution. Researchers often fail to report results and methods in detail sufficient to permit interpretation and meta-analysis, and many results go entirely unreported. Further, these unreported results are often a biased subset. Thus the conclusions we can draw from the published literature are themselves often biased and sometimes might be entirely incorrect. Fortunately there is a movement across empirical disciplines, and now within ecology and evolution, to shape editorial policies to better promote transparency. This can be done by either requiring more disclosure by scientists or by developing incentives to encourage disclosure.
Publisher: Cold Spring Harbor Laboratory
Date: 04-07-2017
DOI: 10.1101/159210
Abstract: Linear mixed effects models are frequently used for estimating quantitative genetic parameters, including the heritability, of traits of interest. Heritability is an important metric, because it acts as a filter that determines how efficiently phenotypic selection translates into evolutionary change. As a quantity of biological interest, it is important that the denominator, the phenotypic variance, actually reflects the amount of phenotypic variance in the relevant ecological stetting. The current practice of quantifying heritability from mixed effects models frequently deprives the heritability of variance explained by fixed effects (often leading to upward-bias) and it has been suggested to omit fixed effects when estimating heritabilities. We advocate an alternative option of fitting complex models incorporating all relevant effects, while including the variance explained by fixed effects into the estimation of heritabilities. The approach is easily implemented (an ex le is provided) and allows corrections for the estimation of heritability, such as the exclusion of variance arising from experimental design effects while still including all biologically relevant sources of variation. We explore the complications arising depending on the nature of the covariates included as fixed effects (e.g. biological or experimental origin, characteristics of biological covariates). Furthermore, we discuss fixed effects in non-linear and generalized linear models when fixed effects. In these cases, the variance parameters depend on the location of the intercept and hence on the scaling of the fixed effects. Integration over the biologically relevant range of fixed effects offers a preferred solution in those situations.
Publisher: Cold Spring Harbor Laboratory
Date: 09-12-2020
DOI: 10.1101/2020.12.09.416727
Abstract: In a time of rapid environmental change, understanding how the challenges experienced by one generation can influence the fitness of future generations is critically needed. Using tolerance assays, transcriptomic and methylome approaches, we use zebrafish as a model to investigate transgenerational acclimation to hypoxia. We show that short-term paternal exposure to hypoxia endows offspring with greater tolerance to acute hypoxia. We detected two hemoglobin genes that are significantly upregulated by more than 7-fold in the offspring of hypoxia exposed males. Moreover, the offspring which maintained equilibrium the longest showed greatest upregulation in hemoglobin expression. We did not detect differential methylation at any of the differentially expressed genes, suggesting that another epigenetic mechanism is responsible for alterations in gene expression. Overall, our findings suggest that a ‘memory’ of past hypoxia exposure is maintained and that this environmentally induced information is transferred to subsequent generations, pre-acclimating progeny to cope with hypoxic conditions.
Publisher: Wiley
Date: 15-10-2013
Publisher: The Royal Society
Date: 24-01-2018
Abstract: Models of ageing predict that sperm function and fertility should decline with age as sperm are exposed to free radical damage and mutation accumulation. However, theory also suggests that mating with older males should be beneficial for females because survival to old age is a demonstration of a male's high genetic and/or phenotypic quality. Consequently, declines in sperm fitness may be offset by indirect fitness benefits exhibited in offspring. While numerous studies have investigated age-based declines in male fertility, none has taken the integrated approach of studying age-based effects on both male fertility and offspring fitness. Here, using a cohort-based longitudinal study of zebrafish ( Danio rerio ), we report a decline in male mating success and fertility with male age but also compensating indirect benefits. Using in vitro fertilization, we show that offspring from older males exhibit superior early survival compared to those from their youngest counterparts. These findings suggest that the high offspring fitness observed for the subset of males that survive to an old age (approx. 51% in this study) may represent compensating benefits for declining fertility with age, thus challenging widely held views about the fitness costs of mating with older males.
Publisher: Wiley
Date: 06-2014
DOI: 10.1111/EVO.12446
Abstract: Interspecifically, a reasonable body of evidence supports a trade-off between offspring size and number. However, at the intraspecific level, a whole manner of phenotypic correlations between offspring size and number are observed. These correlations may be predicted when heterogeneity in resource availability, or quality, is considered. Making the assumption that maternal size is a proxy for resource availability, we meta-analytically quantified four phenotypic reproductive correlations within numerous species: (1) maternal size and offspring size, (2) maternal size and offspring number, (3) offspring number and offspring size, and (4) offspring number and offspring size after controlling for maternal size. Within species, maternal size showed a positive correlation with both offspring size and number. Despite this consistency, no correlation between offspring size and number was found. After controlling for maternal size, however, offspring size and number showed a significant negative correlation. A phylogenetic component of our analysis accounted for little heterogeneity in the data, suggesting that our findings show remarkable consistency across taxa. Overall, our results support an observable phenotypic trade-off between offspring size and number. However, this analysis also highlights the importance of considering quality when examining trade-offs, a task that is not always straightforward as quality is context dependant.
Publisher: Cold Spring Harbor Laboratory
Date: 27-10-2020
DOI: 10.1101/2020.10.26.354274
Abstract: The reproducibility of research results has been a cause of increasing concern to the scientific community. The long-held belief that experimental standardization begets reproducibility has also been recently challenged, with the observation that the reduction of variability within studies can lead to idiosyncratic, lab-specific results that are irreproducible. An alternative approach is to, instead, deliberately introduce heterogeneity known as “heterogenization” of experimental design. Here, we explore a novel perspective in the heterogenization program in a meta-analysis of variability in observed phenotypic outcomes in both control and experimental animal models of ischaemic stroke. First, by quantifying inter-in idual variability across control groups we illustrate that the samount of heterogeneity in disease-state (infarct volume) differs according to methodological approach, for ex le, in disease-induction methods and disease models. We argue that such methods may improve reproducibility by creating erse and representative distribution of baseline disease-state in the reference group, against which treatment efficacy is assessed. Second, we illustrate how meta-analysis can be used to simultaneously assess efficacy and stability (i.e., mean effect and among-in idual variability). We identify treatments that have efficacy and are generalizable to the population level (i.e. low inter-in idual variability), as well as those where there is high inter-in idual variability in response for these latter treatments translation to a clinical setting may require nuance. We argue that by embracing rather than seeking to minimise variability in phenotypic outcomes, we can motivate the shift towards heterogenization and improve both the reproducibility and generalizability of preclinical research.
Publisher: Elsevier BV
Date: 2020
Publisher: Research Square Platform LLC
Date: 15-12-2021
DOI: 10.21203/RS.3.RS-1141520/V1
Abstract: Female ornaments are often reduced, male-like traits. Although these were long perceived as nonadaptive, it is now broadly accepted that female ornaments can be functional. However, it is unclear whether this is as common in females as it is in males, and whether ornaments fulfil similar signalling roles. To test this, we conduct a systematic review and apply a phylogenetically controlled bivariate meta-analysis to a large dataset of ornaments in mutually ornamented birds. As expected, female ornament expression tends to be reduced compared to males. However, ornaments are equally strongly associated with indicators of body condition and aspects of reproductive success in both sexes, regardless of the degree of sexual dimorphism. Thus, ornaments in birds provide similar information in both sexes: more ornamented in iduals are in better condition and achieve higher reproductive success. Although limited by their correlational nature, these outcomes imply that female ornaments could widely function in a similar manner as male ornaments.
Publisher: Wiley
Date: 12-11-2020
Publisher: Public Library of Science (PLoS)
Date: 11-07-2012
Publisher: University of Chicago Press
Date: 07-2015
DOI: 10.1086/681572
Abstract: In seasonal environments, the timing of reproduction has important fitness consequences. Our current understanding of the determinants of reproductive phenology in natural systems is limited because studies often ignore the spatial scale on which animals interact with their environment. When animals use a restricted amount of space and the phenology of resources is spatially variable, selection may favor sensitivity to small-scale environmental variation. Population-level studies of how songbirds track the changing phenology of their food source have been influential in explaining how populations adjust to changing climates but have largely ignored the spatial scale at which phenology varies. We explored whether in idual great tits (Parus major) synchronize their breeding with phenological events in their local environment and investigated the spatial scale at which this occurs. We demonstrate marked variation in the timing of food availability, at a spatial scale relevant to in idual birds, and that such local variation predicts the breeding phenology of in iduals. Using a 45-year data set, we show that measures of vegetation phenology at very local scales are the most important predictors of timing of breeding within years, suggesting that birds can fine-tune their phenology to that of other trophic levels. Knowledge of the determinants of variation in reproductive behavior at different spatial scales is likely to be critical in understanding how selection operates on breeding phenology in natural populations.
Publisher: Springer Science and Business Media LLC
Date: 03-04-2023
Publisher: California Digital Library (CDL)
Date: 12-05-2021
Publisher: Wiley
Date: 10-06-2016
DOI: 10.1111/ELE.12610
Publisher: Public Library of Science (PLoS)
Date: 07-03-2014
Publisher: Springer Science and Business Media LLC
Date: 27-11-2020
DOI: 10.1186/S12915-020-00892-3
Abstract: Although in all sexually reproducing organisms an in idual has a mother and a father, non-genetic inheritance has been predominantly studied in mothers. Paternal effects have been far less frequently studied, until recently. In the last 5 years, research on environmentally induced paternal effects has grown rapidly in the number of publications and ersity of topics. Here, we provide an overview of this field using synthesis of evidence (systematic map) and influence (bibliometric analyses). We find that motivations for studies into paternal effects are erse. For ex le, from the ecological and evolutionary perspective, paternal effects are of interest as facilitators of response to environmental change and mediators of extended heredity. Medical researchers track how paternal pre-fertilization exposures to factors, such as diet or trauma, influence offspring health. Toxicologists look at the effects of toxins. We compare how these three research guilds design experiments in relation to objects of their studies: fathers, mothers and offspring. We highlight ex les of research gaps, which, in turn, lead to future avenues of research. The literature on paternal effects is large and disparate. Our study helps in fostering connections between areas of knowledge that develop in parallel, but which could benefit from the lateral transfer of concepts and methods.
Publisher: Wiley
Date: 21-06-2010
Publisher: Wiley
Date: 22-02-2012
DOI: 10.1111/J.1474-9726.2012.00798.X
Abstract: Dietary restriction (DR) extends the lifespan of a wide range of species, although the universality of this effect has never been quantitatively examined. Here, we report the first comprehensive comparative meta-analysis of DR across studies and species. Overall, DR significantly increased lifespan, but this effect is modulated by several factors. In general, DR has less effect in extending lifespan in males and also in non-model organisms. Surprisingly, the proportion of protein intake was more important for life extension via DR than the degree of caloric restriction. Furthermore, we show that reduction in both age-dependent and age-independent mortality rates drives life extension by DR among the well-studied laboratory model species (yeast, nematode worms, fruit flies and rodents). Our results suggest that convergent adaptation to laboratory conditions better explains the observed DR-longevity relationship than evolutionary conservation although alternative explanations are possible.
Publisher: Elsevier BV
Date: 2015
DOI: 10.1016/J.ARR.2014.10.007
Abstract: Reduced fertility typically occurs among women in their late 30s, but increasing evidence indicates that advanced paternal age is associated with changes in reproduction as well. Numerous studies have investigated age-based declines in semen traits, but the impact of paternal age on semen parameter values remains inconclusive. Using data from 90 studies (93,839 subjects), we conducted a systematic review and meta-analysis to quantify the effect of male age on seven ejaculate traits (semen volume, sperm concentration, total sperm count, morphology, total motility, progressive motility and DNA fragmentation). Age-associated declines in semen volume, percentage motility, progressive motility, normal morphology and unfragmented cells were statistically significant and results generally seemed to be robust against confounding factors. Unexpectedly, sperm concentration did not decline with increasing male age, even though we found that sperm concentration declined over time. Our findings indicate that male age needs more recognition as a potential contributor to the negative pregnancy outcomes and reduced offspring health associated with delayed first reproduction. We suggest that greater focus on collection of DNA fragmentation and progressive motility in a clinical setting may lead to better patient outcomes during fertility treatments of aging couples.
Publisher: John Wiley & Sons, Ltd
Date: 09-01-2014
Publisher: Springer Science and Business Media LLC
Date: 07-2001
Publisher: Wiley
Date: 12-08-2004
Publisher: Wiley
Date: 27-04-2012
Publisher: Wiley
Date: 15-06-2016
DOI: 10.1111/COBI.12760
Publisher: Springer Science and Business Media LLC
Date: 07-10-2016
Publisher: Cold Spring Harbor Laboratory
Date: 03-10-2023
Publisher: Proceedings of the National Academy of Sciences
Date: 09-03-2015
Abstract: As parents age, gamete quality declines. If this decline affects the next generation, it could influence the evolution of longevity. Older parents often produce offspring of low fitness in the laboratory. Our long-term data from a natural bird population shows, for the first time to our knowledge, a transgenerational reduction in fitness of the next generation associated with parental age. We use a 10-year cross-fostering experiment to exclude environmental explanations. Our results challenge the currently favored hypothesis in evolutionary biology and behavioral ecology that old age signals high quality in mating partners. Our results imply a substantial cost of reproducing with older, rather than younger, partners. The results inform increasing concern about delayed reproduction in medicine, sociology, and conservation biology.
Publisher: Springer Science and Business Media LLC
Date: 22-06-2007
DOI: 10.1007/S00442-007-0765-4
Abstract: Theory predicts that traits which signal parental quality might evolve in males of species with biparental care. In avian species, male ornaments may be the most likely candidates for such signals. Male house sparrows (Passer domesticus) possess a black throat patch often referred to as a "badge" or a "badge of status". By assuming a trade-off between male attractiveness (reflected in male ornaments) and parental care under the differential allocation hypothesis, we predicted that badge size would be negatively correlated with male parental investment. An experiment in which the badge was enlarged in one group and unchanged in a control group was conducted. Our manipulation was predicted to affect female as well as male parental investment. However, we found that eight variables associated with parental investment-the start date for breeding, clutch size, male and female incubation time, male and female food provisioning rate, and average chick weight and the number of fledglings-barely differed between treatments. Also, little evidence for correlations between natural variation in badge size and any of these eight variables was found. Instead, the start date for breeding and the number of fledglings were significantly correlated with both male and female age, while clutch size increased with female age. Female condition was a positive predictor of clutch size and number of fledglings. Female tarsus length, unexpectedly, is related to both male and female incubation time. Badge size was also positively correlated with male age. However, parental age (male or female) was not related to parental care. We conclude that badge size does not signal parental quality, but that the ages of both sexes and the condition of the female play significant roles in the reproductive performance of this species.
Publisher: Elsevier BV
Date: 07-2022
DOI: 10.1016/J.ENVPOL.2022.119081
Abstract: Per- and polyfluoroalkyl substances (PFAS) are ubiquitous in the environment and often ingested with food. PFAS exposure in people can have detrimental health consequences. Therefore, reducing PFAS burdens in food items is of great importance to public health. Here, we investigated whether cooking reduces PFAS concentrations in animal-derived food products by synthesizing experimental studies. Further, we examined the moderating effects of the following five variables: cooking time, liquid/animal tissue ratio, cooking temperature, carbon chain length of PFAS and the cooking category (oil-based, water-based & no-liquid cooking). In our systematic review searches, we obtained 512 effect sizes (relative differences in PFAS concentration between raw and cooked s les) from 10 relevant studies. These studies exclusively explored changes in PFAS concentrations in cooked seafood and freshwater fish. Our multilevel-meta-analysis has revealed that, on average, cooking reduced PFAS concentrations by 29%, although heterogeneity among effect sizes was very high (I
Publisher: Wiley
Date: 30-12-2016
DOI: 10.1111/CCH.12437
Abstract: Systematic reviews and meta-analyses are considered to be the 'gold standards' for synthesizing research evidence in particular areas of enquiry. However, such reviews are only useful if they themselves are conducted to a sufficiently high standard. The aim of this study was to conduct a narrative meta-review of existing analyses of the effectiveness of interventions designed for children with developmental co-ordination disorder (DCD). A narrative meta-review of systematic and meta-analytic reviews aimed at evaluating the effectiveness of intervention for children with DCD was conducted on studies published between 1950 and 2014. We identified suitable reviews, using a modification of the Population, Intervention, Comparison, Outcome (PICO) system and evaluated their methodological quality using the Assessment of Multiple Systematic Reviews (AMSTAR). In addition, the consistency of the quality of evidence and classification of intervention approaches was assessed independently by two assessors. The literature search yielded a total of four appropriate reviews published in the selected time span. The Assessment of Multiple Systematic Reviews percentage quality scores assigned to each review ranged from 0% (low quality) to 55% (medium quality). Evaluation of the quality of evidence and classification of intervention approaches yielded a discrepancy rate of 25%. All reviews concluded that some kind of intervention was better than none at all. Although the quality of the reviews progressively improved over the years, the shortcomings identified need to be addressed before concrete evidence regarding the best approach to intervention for children with DCD can be specified.
Publisher: Oxford University Press (OUP)
Date: 2012
DOI: 10.1093/EHJCI/JER316
Publisher: Wiley
Date: 11-11-2010
DOI: 10.1111/J.1523-1739.2010.01549.X
Abstract: Studies evaluating the impact of inbreeding depression on population viability of threatened species tend to focus on the effects of inbreeding at a single life-history stage (e.g., juvenile survival). We examined the effects of inbreeding across the full life-history continuum, from survival up to adulthood, to subsequent reproductive success, and to the recruitment of second-generation offspring, in wild Takahe ( Porphyrio hochstetteri ) by analyzing pedigree and fitness data collected over 21 breeding seasons. Although the effect size of inbreeding at in idual life-history stages was small, inbreeding depression accumulated across multiple life-history stages and ultimately reduced long-term fitness (i.e., successful recruitment of second-generation offspring). The estimated total lethal equivalents (2B) summed across all life-history stages were substantial (16.05, 95% CI 0.08-90.8) and equivalent to an 88% reduction in recruitment of second-generation offspring for closely related pairs (e.g., sib-sib pairings) relative to unrelated pairs (according to the pedigree). A history of small population size in the Takahe could have contributed to partial purging of the genetic load and the low level of inbreeding depression detected at each single life-history stage. Nevertheless, our results indicate that such "purged" populations can still exhibit substantial inbreeding depression, especially when small but negative fitness effects accumulate across the species' life history. Because inbreeding depression can ultimately affect population viability of small, isolated populations, our results illustrate the importance of measuring the effects of inbreeding across the full life-history continuum.
Publisher: California Digital Library (CDL)
Date: 12-10-2019
Publisher: California Digital Library (CDL)
Date: 03-08-2021
Publisher: AIP Publishing LLCMelville, New York
Date: 22-12-2021
DOI: 10.1063/9780735423664_006
Abstract: Tissue mechanical properties determine the relationship between an applied mechanical load and the resulting deformation of the s le. In optical coherence elastography (OCE), the objective is to spatially resolve tissue mechanical properties from often incomplete and noisy measurements of the load and deformation. This is achieved by solving an inverse problem, using a model of elasticity that reasonably describes the behavior of tissue. Incorporating more parameters into the model (such as heterogeneity, anisotropy, nonlinearity, or viscoelasticity) than are needed in a given application can unnecessarily complicate the inverse problem. Also, how the load is applied can enhance certain tissue responses, and the validity of an elasticity model, and, thus, allow for the characterization of tissue in different regimes. A successful OCE technique offers a good match between the load application method, and the tissue mechanical properties of interest, and employs a reasonably complete but simplified mechanical model that provides a noise-robust inversion. OCE techniques can be classified into two broad categories: those inducing and subsequently tracking propagating mechanical waves, and those applying and assuming a uniaxial load, and tracking the deformation in response. With a brief introduction to the former, this chapter focuses on the latter group, describes the most prominent of these techniques, and presents an overview of studies that have successfully extracted mechanical properties in tissue-like media.
Publisher: California Digital Library (CDL)
Date: 15-05-2020
Publisher: Springer Science and Business Media LLC
Date: 12-2018
Publisher: Springer Science and Business Media LLC
Date: 04-10-2013
Publisher: Wiley
Date: 26-11-2019
Publisher: Springer Science and Business Media LLC
Date: 03-04-2023
DOI: 10.1186/S12915-022-01485-Y
Abstract: 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 s le 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.
Publisher: Wiley
Date: 25-01-2010
DOI: 10.1111/J.1420-9101.2009.01915.X
Abstract: Although many of the statistical techniques used in comparative biology were originally developed in quantitative genetics, subsequent development of comparative techniques has progressed in relative isolation. Consequently, many of the new and planned developments in comparative analysis already have well-tested solutions in quantitative genetics. In this paper, we take three recent publications that develop phylogenetic meta-analysis, either implicitly or explicitly, and show how they can be considered as quantitative genetic models. We highlight some of the difficulties with the proposed solutions, and demonstrate that standard quantitative genetic theory and software offer solutions. We also show how results from Bayesian quantitative genetics can be used to create efficient Markov chain Monte Carlo algorithms for phylogenetic mixed models, thereby extending their generality to non-Gaussian data. Of particular utility is the development of multinomial models for analysing the evolution of discrete traits, and the development of multi-trait models in which traits can follow different distributions. Meta-analyses often include a nonrandom collection of species for which the full phylogenetic tree has only been partly resolved. Using missing data theory, we show how the presented models can be used to correct for nonrandom s ling and show how taxonomies and phylogenies can be combined to give a flexible framework with which to model dependence.
Publisher: Wiley
Date: 23-01-2014
Publisher: Public Library of Science (PLoS)
Date: 21-07-2014
Publisher: Elsevier BV
Date: 08-2013
Publisher: California Digital Library (CDL)
Date: 17-11-2021
Publisher: Springer Berlin Heidelberg
Date: 2014
Publisher: Wiley
Date: 10-2016
DOI: 10.1111/JEB.12945
Publisher: Wiley
Date: 23-01-2012
DOI: 10.1111/J.1365-2656.2011.01942.X
Abstract: 1. 'Compensatory growth' and 'catch-up growth' are often used interchangeably to describe the faster than optimal growth that occurs following a period of dietary restriction in the development of many animals. Concerns about the statistical analysis of these studies have drawn attention to the risk of false detection in reports of compensatory and catch-up growth. 2. This study aims to quantify the degree to which these compensatory responses occur across the animal kingdom. In addition, this study distinguishes the two terms, 'compensatory growth' and 'catch-up growth', to clarify the fitness consequences of rapid growth. Compensatory growth refers to a faster than usual growth rate, while catch-up growth implies attainment of control size. 3. Eight meta-analyses and meta-regression analyses were conducted on data extracted from 88 papers, including 11 taxonomic classes. The results confirmed that both growth tactics (i.e. compensatory and catch-up growth) occur across a wide range of taxa and result in decreased direct fitness components. 4. Importantly, the meta-analytic methods used made it possible to identify the specific experimental techniques that most successfully promoted rapid growth after restriction and key differences in the responses of the four major groups (mammals, birds, fish and arthropods) to dietary restriction. Endotherms are more likely to show a compensatory growth response because of their determinate growth in contrast, the indeterminate and saltatory growth tactics of fish and arthropods reduce the pressure to rapidly achieve a large size. 5. Among the first meta-analyses to be conducted in this field, this study provides valuable support for the premises of compensatory and catch-up growth and also discusses weaknesses in experimental design, and possible solutions, in compensatory growth research. For ex le, we recommend conducting the experiment within the most linear phase of an animal's growth to avoid analytical complications arising from size-dependent growth, and our results indicate that dietary dilution more closely resembles quantitative restriction than clutch size and intermittent feeding restriction methods when normal quantitative restriction is not possible.
Publisher: Wiley
Date: 30-09-2022
DOI: 10.1111/OBR.13342
Abstract: Obesity is a major health condition that affects millions worldwide. There is an increased interest in understanding the adverse outcomes associated with obesogenic diets. A multitude of studies have investigated the transgenerational impacts of maternal and parental obesogenic diets on subsequent generations of offspring, but results have largely been mixed. We conducted a systematic review and meta‐analysis on rodent studies to elucidate how obesogenic diets impact the mean and variance of grand‐offspring traits. Our study focused on transgenerational effects (i.e., F2 and F3 generations) in one‐off and multigenerational exposure studies. From 33 included articles, we obtained 407 effect sizes representing pairwise comparisons of control and treatment grand‐offspring groups pertaining to measures of body weight, adiposity, glucose, insulin, leptin, and triglycerides. We found evidence that male and female grand‐offspring descended from grandparents exposed to an obesogenic diet displayed phenotypes consistent with metabolic syndrome, especially in cases where the obesogenic diet was continued across generations. Further, we found stronger evidence for the effects of grand‐maternal than grand‐paternal exposure on grand‐offspring traits. A high‐fat diet in one‐off exposure studies did not seem to impact phenotypic variation, whereas in multigenerational exposure studies it reduced variation in several traits.
Publisher: Wiley
Date: 03-04-2021
Abstract: The use of bio‐logging devices to track animal movement continues to grow as technological advances and device miniaturisation allow researchers to study animal behaviour in unprecedented detail. Balanced against the remarkable data that bio‐loggers can provide is a need to understand the impact of devices on animal behaviour and welfare. Recent meta‐analyses have demonstrated the impacts of device attachment on animal behaviour, but there is a concern about the frequency and clarity with which device effects are reported. One aspect lacking in many studies is assessment of the statistical power of tests of device effects, yet such information would assist the interpretation of results. We address this issue by providing an overview of the statistical power, as well as the Type M (magnitude) and Type S (sign) error rate, of tests of device effects within the avian tracking literature across a range of assumed effect sizes. The median power of statistical tests ranged from 9% to 65% across a range of assumed effect sizes corresponding to benchmark values for small, moderate and large effects ( d = 0.2, 0.5, 0.8, respectively). Moreover, when using effect sizes derived from previous a meta‐analysis ( d = 0.1), median power was only 6%. When assuming smaller effect sizes, statistical tests were characterised by high Type M and Type S error rates, suggesting that statistically significant results of device effects will tend to exaggerate the size of such effects and may estimate the sign of an effect in the wrong direction. Well‐designed tracking studies will reduce device effects to low levels and consequently issues associated with low power will be commonplace. Nevertheless, assessment of device effects remains important, particularly when embarking on novel tracking studies. We recommend that statistical tests of device effects are reported clearly and are routinely accompanied by assessment of statistical power, including Type M and Type S errors, based upon realistic external estimates of effect size. Reporting the statistical power can help avoid the pitfalls of overstating results from in idual studies, shift the emphasis to accurate reporting of effect sizes and guide decisions about the ethical impacts of device attachment.
Publisher: California Digital Library (CDL)
Date: 12-09-2019
Publisher: Springer Science and Business Media LLC
Date: 03-2018
DOI: 10.1038/NATURE25753
Abstract: Meta-analysis is the quantitative, scientific synthesis of research results. Since the term and modern approaches to research synthesis were first introduced in the 1970s, meta-analysis has had a revolutionary effect in many scientific fields, helping to establish evidence-based practice and to resolve seemingly contradictory research outcomes. At the same time, its implementation has engendered criticism and controversy, in some cases general and others specific to particular disciplines. Here we take the opportunity provided by the recent fortieth anniversary of meta-analysis to reflect on the accomplishments, limitations, recent advances and directions for future developments in the field of research synthesis.
Publisher: Springer Science and Business Media LLC
Date: 03-06-2014
Publisher: Wiley
Date: 10-2021
Abstract: Per‐ and polyfluoroalkyl substances (PFAS) are a large group of manufactured chemicals. Since the beginning of their commercial production in the 1950s, PFAS have not only found their way into numerous industrial and commercial applications, but also into the bloodstream of much of the human population, the natural environment and wildlife. Exposure to high levels of PFAS poses a health risk for humans and animals, and may exacerbate the effects of other anthropogenic impacts faced by wildlife species. To gain a comprehensive overview of the abundance and distribution of PFAS research on wildlife species, and to better understand the drivers of this research, we will collate the available literature into a systematic evidence map and perform bibliometric analyses. The systematic mapping will present the distribution of research evidence that exists on PFAS in wildlife. The bibliometric analysis will provide an insight into the historical trends, interdisciplinarity, connectedness and the impact of the in idual papers. We will conduct a systematic literature search on Scopus, Web of Science and 10 other databases using predefined search strings. We will screen title, abstract and keywords first. We will then screen full‐text papers. Two reviewers will be involved in the screening process. We will only consider publications in English, peer‐reviewed articles, preprints and theses. We will include papers reporting concentrations of any of 34 main PFAS types (based on a previous study) in wild animals. We will assess all publications included in the systematic map for predetermined indicators of quality and potential study‐level biases. In addition, we will use bibliometric records from Scopus to perform impact and network analyses. We will present the results using a narrative summary, tables and colour‐coded maps, bar and network plots. Results and associated database will be available on a dedicated freely accessible website. This study will provide critical insight into the gaps and clusters of the literature with regard to the PFAS concentrations in wildlife. Our study will inform and direct future research efforts to fill the gaps revealed.
Publisher: Public Library of Science (PLoS)
Date: 12-11-2014
Publisher: Wiley
Date: 03-2023
DOI: 10.1111/BRV.12939
Abstract: Ecologists routinely use statistical models to detect and explain interactions among ecological drivers, with a goal to evaluate whether an effect of interest changes in sign or magnitude in different contexts. Two fundamental properties of interactions are often overlooked during the process of hypothesising, visualising and interpreting interactions between drivers: the measurement scale – whether a response is analysed on an additive or multiplicative scale, such as a ratio or logarithmic scale and the symmetry – whether dependencies are considered in both directions. Overlooking these properties can lead to one or more of three inferential errors: misinterpretation of ( i ) the detection and magnitude (Type‐D error), and ( ii ) the sign of effect modification (Type‐S error) and ( iii ) misidentification of the underlying processes (Type‐A error). We illustrate each of these errors with a broad range of ecological questions applied to empirical and simulated data sets. We demonstrate how meta‐analysis, a widely used approach that seeks explicitly to characterise context dependence, is especially prone to all three errors. Based on these insights, we propose guidelines to improve hypothesis generation, testing, visualisation and interpretation of interactions in ecology.
Publisher: Wiley
Date: 02-12-2021
DOI: 10.1111/BRV.12819
Abstract: Within populations, in iduals often show repeatable variation in behaviour, called ‘animal personality’. In the last few decades, numerous empirical studies have attempted to elucidate the mechanisms maintaining this variation, such as life‐history trade‐offs. Theory predicts that among‐in idual variation in behavioural traits could be maintained if traits that are positively associated with reproduction are simultaneously associated with decreased survival, such that different levels of behavioural expression lead to the same net fitness outcome. However, variation in resource acquisition may also be important in mediating the relationship between in idual behaviour and fitness components (survival and reproduction). For ex le, if certain phenotypes (e.g. dominance or aggressiveness) are associated with higher resource acquisition, those in iduals may have both higher reproduction and higher survival, relative to others in the population. When in iduals differ in their ability to acquire resources, trade‐offs are only expected to be observed at the within‐in idual level (i.e. for a given amount of resource, if an in idual increases its allocation to reproduction, it comes at the cost of allocation to survival, and vice versa ), while among in iduals traits that are associated with increased survival may also be associated with increased reproduction. We performed a systematic review and meta‐analysis, asking: ( i ) do among‐in idual differences in behaviour reflect among‐in idual differences in resource acquisition and/or allocation, and ( ii ) is the relationship between behaviour and fitness affected by the type of behaviour and the testing environment? Our meta‐analysis consisted of 759 estimates from 193 studies. Our meta‐analysis revealed a positive correlation between pairs of estimates using both survival and reproduction as fitness proxies. That is, for a given study, behaviours that were associated with increased reproduction were also associated with increased survival, suggesting that variation in behaviour at the among‐in idual level largely reflects differences among in iduals in resource acquisition. Furthermore, we found the same positive correlation between pairs of estimates using both survival and reproduction as fitness proxies at the phenotypic level. This is significant because we also demonstrated that these phenotypic correlations primarily reflect within‐in idual correlations. Thus, even when accounting for among‐in idual differences in resource acquisition, we did not find evidence of trade‐offs at the within‐in idual level. Overall, the relationship between behaviour and fitness proxies was not statistically different from zero at the among‐in idual, phenotypic, and within‐in idual levels this relationship was not affected by behavioural category nor by the testing condition. Our meta‐analysis highlights that variation in resource acquisition may be more important in driving the relationship between behaviour and fitness than previously thought, including at the within‐in idual level. We suggest that this may come about via heterogeneity in resource availability or age‐related effects, with higher resource availability and/or age leading to state‐dependent shifts in behaviour that simultaneously increase both survival and reproduction. We emphasize that future studies examining the mechanisms maintaining behavioural variation in populations should test the link between behavioural expression and resource acquisition – both within and among in iduals. Such work will allow the field of animal personality to develop specific predictions regarding the mediating effect of resource acquisition on the fitness consequences of in idual behaviour.
Publisher: Wiley
Date: 06-01-2014
DOI: 10.1111/OBR.12138
Abstract: Maternal undernutrition can result in significant alterations to the post-natal offspring phenotype, including body size and behaviour. For ex le, maternal food restriction has been implicated in offspring hyperphagia, potentially causing increased weight gain and fat accumulation. This could result in obesity and other adverse long-term health effects in offspring. We investigated the link between maternal caloric restriction during gestation and offspring appetite by conducting the first meta-analysis on this topic using experimental data from mammalian laboratory models (i.e. rats and mice). We collected 89 effect sizes from 35 studies, together with relevant moderators. Our analysis revealed weak and statistically non-significant overall effect on offspring's appetite. However, we found that lower protein content of restricted diets is associated with higher food intake in female offspring. Importantly, we show that a main source of variation among studies arises from whether, and how, food intake was adjusted for body mass. This probably explains many of the contradictory results in the field. Based on our results, we recommend using allometric scaling of food intake to body mass in future studies.
Publisher: Oxford University Press (OUP)
Date: 04-2018
DOI: 10.1642/AUK-17-129.1
Publisher: Cold Spring Harbor Laboratory
Date: 12-03-2012
Abstract: Dopamine and octopamine released in the mushroom bodies of the insect brain play a critical role in the formation of aversive and appetitive memories, respectively. As recent evidence suggests a complex relationship between the effects of these two amines on the output of mushroom body circuits, we compared the expression of dopamine- and octopamine-receptor genes in three major subpopulations of mushroom body intrinsic neurons (Kenyon cells). Using the brain of the honeybee, Apis mellifera , we found that expression of amine-receptor genes differs markedly across Kenyon cell subpopulations. We found, in addition, that levels of expression of these genes change dramatically during the lifetime of the bee and that shifts in expression are cell population-specific. Differential expression of amine-receptor genes in mushroom body neurons and the plasticity that exists at this level are features largely ignored in current models of mushroom body function. However, our results are consistent with the growing body of evidence that short- and long-term olfactory memories form in different regions of the mushroom bodies of the brain and that there is functional compartmentalization of the modulatory inputs to this multifunctional brain center.
Publisher: Springer Science and Business Media LLC
Date: 09-04-2021
DOI: 10.1186/S12915-021-01006-3
Abstract: Unreliable research programmes waste funds, time, and even the lives of the organisms we seek to help and understand. Reducing this waste and increasing the value of scientific evidence require changing the actions of both in idual researchers and the institutions they depend on for employment and promotion. While ecologists and evolutionary biologists have somewhat improved research transparency over the past decade (e.g. more data sharing), major obstacles remain. In this commentary, we lift our gaze to the horizon to imagine how researchers and institutions can clear the path towards more credible and effective research programmes.
Publisher: Wiley
Date: 18-10-2007
Publisher: Springer Science and Business Media LLC
Date: 10-2016
DOI: 10.1038/538459D
Publisher: No publisher found
Date: 2012
Publisher: Wiley
Date: 26-12-2019
DOI: 10.1111/BRV.12491
Abstract: Energy metabolism has received much attention as a potential driver of repeatable among-in idual differences in behaviour (animal personality). Several factors have been hypothesized to mediate this relationship. We performed a systematic review with a meta-analysis of >70 studies comprised of >8000 in iduals reporting relationships between measures of maintenance metabolic rates (i.e. basal metabolic rate, resting metabolic rate, and standard metabolic rate) and behaviour. We evaluated support for three hypothesized mediators: (i) type of behaviour, (ii) opportunities for energy re-allocation, and (iii) magnitude of energetic constraints. Relationships between measures of maintenance metabolic rate (MR) and behaviour are predicted to be strongest for behaviours with strong consequences for energy turnover (acquisition or expenditure). Consistent with this, we found that behaviours with known consequences for energy gain (e.g. foraging, dominance, boldness) or expenditure (e.g. maximum sprint speed, sustained running speed, maximum distance travelled, etc.) had strong positive correlations with MR, while behaviours with putatively weak and/or inconsistent associations with net energy gain or loss (e.g. exploration, activity, sociability) were not correlated with MR. Greater opportunities for energy reallocation are predicted to weaken relationships between MR and behaviour by creating alternative pathways to balance energy budgets. We tested this by contrasting relationships between MR and behaviour in ectotherms versus endotherms, as thermoregulation in endotherms creates additional opportunities for energy reallocation compared with ectotherms. As predicted, the relationship between behaviour and MR was stronger in ectotherms compared with endotherms. However, statistical analyses of heterogeneity among effect sizes from different species did not support energy re-allocation as the main driver of these differences. Finally, we tested whether conditions where animals face greater constraints in meeting their energy budgets (e.g. field versus laboratory, breeding versus non-breeding) increased the strength of the relationship between MR and behaviour. We found that the relationship between MR and behaviour was unaffected by either of these modifiers. This meta-analysis provides two key insights. First, we observed positive relationships of similar magnitude between MR and behaviours that bring in net energy, and behaviours that cost net energy. This result is only consistent with a performance energy-management model. Given that the studies included in our meta-analysis represent a wide range of taxa, this suggests that the performance model may be the most common model in general. Second, we found that behaviours with putatively weak or inconsistent consequences for net energy gain or expenditure (exploration, activity, sociability) show no relationship with MR. The lack of relationship between MR and behavioural traits with weak and/or inconsistent consequences for energy turnover provides the first systematic demonstration of the central importance of the ecological function of traits in mediating relationships between MR and behaviour.
Publisher: Wiley
Date: 15-02-2018
DOI: 10.1111/JEB.13232
Abstract: Linear mixed-effects models are frequently used for estimating quantitative genetic parameters, including the heritability, as well as the repeatability, of traits. Heritability acts as a filter that determines how efficiently phenotypic selection translates into evolutionary change, whereas repeatability informs us about the in idual consistency of phenotypic traits. As quantities of biological interest, it is important that the denominator, the phenotypic variance in both cases, reflects the amount of phenotypic variance in the relevant ecological setting. The current practice of quantifying heritabilities and repeatabilities from mixed-effects models frequently deprives their denominator of variance explained by fixed effects (often leading to upward bias of heritabilities and repeatabilities), and it has been suggested to omit fixed effects when estimating heritabilities in particular. We advocate an alternative option of fitting models incorporating all relevant effects, while including the variance explained by fixed effects into the estimation of the phenotypic variance. The approach is easily implemented and allows optimizing the estimation of phenotypic variance, for ex le by the exclusion of variance arising from experimental design effects while still including all biologically relevant sources of variation. We address the estimation and interpretation of heritabilities in situations in which potential covariates are themselves heritable traits of the organism. Furthermore, we discuss complications that arise in generalized and nonlinear mixed models with fixed effects. In these cases, the variance parameters on the data scale depend on the location of the intercept and hence on the scaling of the fixed effects. Integration over the biologically relevant range of fixed effects offers a preferred solution in those situations.
Publisher: Wiley
Date: 27-01-2011
DOI: 10.1111/J.1420-9101.2010.02210.X
Abstract: Information theoretic approaches and model averaging are increasing in popularity, but this approach can be difficult to apply to the realistic, complex models that typify many ecological and evolutionary analyses. This is especially true for those researchers without a formal background in information theory. Here, we highlight a number of practical obstacles to model averaging complex models. Although not meant to be an exhaustive review, we identify several important issues with tentative solutions where they exist (e.g. dealing with collinearity amongst predictors how to compute model-averaged parameters) and highlight areas for future research where solutions are not clear (e.g. when to use random intercepts or slopes which information criteria to use when random factors are involved). We also provide a worked ex le of a mixed model analysis of inbreeding depression in a wild population. By providing an overview of these issues, we hope that this approach will become more accessible to those investigating any process where multiple variables impact an evolutionary or ecological response.
Publisher: Elsevier BV
Date: 12-2016
Publisher: Oxford University Press (OUP)
Date: 07-09-2022
Abstract: There exists growing evidence that animal personality (consistent between in idual differences in behavior) can influence an in idual’s fitness. Furthermore, limitations in behavioral plasticity may cause personality-mediated tradeoffs to occur, for ex le, between speed and accuracy in decision making. We explored whether various measures of personality could predict speed-accuracy tradeoffs in mate selection using Pharaoh cicadas (Magicicada septendecim) and examined the phenotypic traits predicting male mating performance and advertisement rates. We assessed whether male exploration behavior, boldness, and weight could predict a male’s overall copulation attempt rate (the number of attempted copulations with conspecifics of either sex), the number of errors a male made when selecting a mate (the number of same-sex copulation attempts), and male reproductive performance (whether a male successfully copulated with a female). We also assessed whether personality-dependent variation in male advertisement rate (the number of calling song bouts) might underpin the correlation between exploration behavior and mating performance. Although male exploration behavior did not predict male advertisement rate, we found that faster-exploring males exhibited higher overall rates of attempted copulations while also attempting more same-sex copulations, compared to slower-exploring males, suggesting a personality-mediated speed-accuracy tradeoff. Despite making more mate choice errors, however, faster explorers were more likely to successfully copulate with females, compared to slower explorers, indicating that speed may be favored over accuracy in systems where heavily male-biased sex ratios lead to scramble competition. Overall, this work highlights the role of personality in sexual selection and demonstrates that personality can influence speed-accuracy trade-offs in mating.
Publisher: Oxford University Press (OUP)
Date: 09-07-2007
Publisher: Springer Science and Business Media LLC
Date: 28-09-2012
Publisher: PeerJ
Date: 17-01-2018
DOI: 10.7717/PEERJ.4292
Abstract: Zebrafish are increasingly used as a vertebrate model organism for various traits including swimming performance, obesity and metabolism, necessitating high-throughput protocols to generate standardized phenotypic information. Here, we propose a novel and cost-effective method for exercising zebrafish, using a coffee plunger and magnetic stirrer. To demonstrate the use of this method, we conducted a pilot experiment to show that this simple system provides repeatable estimates of maximal swim performance (intra-class correlation [ICC] = 0.34–0.41) and observe that exercise training of zebrafish on this system significantly increases their maximum swimming speed. We propose this high-throughput and reproducible system as an alternative to traditional linear chamber systems for exercising zebrafish and similarly sized fishes.
Publisher: Springer Science and Business Media LLC
Date: 03-03-2017
Publisher: California Digital Library (CDL)
Date: 06-06-2022
Publisher: Wiley
Date: 22-01-2017
DOI: 10.1111/BRV.12243
Abstract: The effects of sex hormones on immune function have received much attention, especially following the proposal of the immunocompetence handicap hypothesis. Many studies, both experimental and correlational, have been conducted to test the relationship between immune function and the sex hormones testosterone in males and oestrogen in females. However, the results are mixed. We conducted four cross-species meta-analyses to investigate the relationship between sex hormones and immune function: (i) the effect of testosterone manipulation on immune function in males, (ii) the correlation between circulating testosterone level and immune function in males, (iii) the effect of oestrogen manipulation on immune function in females, and (iv) the correlation between circulating oestrogen level and immune function in females. The results from the experimental studies showed that testosterone had a medium-sized immunosuppressive effect on immune function. The effect of oestrogen, on the other hand, depended on the immune measure used. Oestrogen suppressed cell-mediated immune function while reducing parasite loads. The overall correlation (meta-analytic relationship) between circulating sex hormone level and immune function was not statistically significant for either testosterone or oestrogen despite the power of meta-analysis. These results suggest that correlational studies have limited value for testing the effects of sex hormones on immune function. We found little evidence of publication bias in the four data sets using indirect tests. There was a weak and positive relationship between year of publication and effect size for experimental studies of testosterone that became non-significant after we controlled for castration and immune measure, suggesting that the temporal trend was due to changes in these moderators over time. Graphical analyses suggest that the temporal trend was due to an increased use of cytokine measures across time. We found substantial heterogeneity in effect sizes, except in correlational studies of testosterone, even after we accounted for the relevant random and fixed factors. In conclusion, our results provide good evidence that testosterone suppresses immune function and that the effect of oestrogen varies depending on the immune measure used.
Publisher: Wiley
Date: 18-04-2022
Abstract: Changes in phenology and distribution are being widely reported for many migratory species in response to shifting environmental conditions. Understanding these changes and the situations in which they occur can be aided by understanding consistent in idual differences in phenology and distribution and the situations in which consistency varies in strength or detectability. Studies tracking the same in iduals over consecutive years are increasingly reporting migratory timings to be a repeatable trait, suggesting that flexible in idual responses to environmental conditions may contribute little to population-level changes in phenology and distribution. However, how this varies across species and sexes, across the annual cycle and in relation to study (tracking method, study design) and/or ecosystem characteristics is not yet clear. Here, we take advantage of the growing number of publications in movement ecology to perform a phylogenetic multilevel meta-analysis of repeatability estimates for avian migratory timings to investigate these questions. Of 2,433 reviewed studies, 54 contained suitable information for meta-analysis, resulting in 177 effect sizes from 47 species. In idual repeatability of avian migratory timings averaged 0.414 (95% confidence interval: 0.3-0.5) across landbirds, waterbirds and seabirds, suggesting consistent in idual differences in migratory timings is a common feature of migratory systems. Timing of departure from the non-breeding grounds was more repeatable than timings of arrival at or departure from breeding grounds, suggesting that conditions encountered on migratory journeys and outcome of breeding attempts can influence in idual variation. Population-level shifts in phenology could arise through in idual timings changing with environmental conditions and/or through shifts in the numbers of in iduals with different timings. Our findings suggest that, in addition to identifying the conditions associated with in idual variation in phenology, exploring the causes of between-in idual variation will be key in predicting future rates and directions of changes in migratory timings. We therefore encourage researchers to report the within- and between- in idual variance components underpinning the reported repeatability estimates to aid interpretation of migration behaviour. In addition, the lack of studies in the tropics means that levels of repeatability in less strongly seasonal environments are not yet clear.
Publisher: Wiley
Date: 12-03-2021
Publisher: Wiley
Date: 26-08-2020
DOI: 10.1111/ELE.13479
Publisher: Elsevier BV
Date: 10-2015
DOI: 10.1016/J.TREE.2015.07.006
Abstract: The recent trend for journals to require open access to primary data included in publications has been embraced by many biologists, but has caused apprehension amongst researchers engaged in long-term ecological and evolutionary studies. A worldwide survey of 73 principal investigators (Pls) with long-term studies revealed positive attitudes towards sharing data with the agreement or involvement of the PI, and 93% of PIs have historically shared data. Only 8% were in favor of uncontrolled, open access to primary data while 63% expressed serious concern. We present here their viewpoint on an issue that can have non-trivial scientific consequences. We discuss potential costs of public data archiving and provide possible solutions to meet the needs of journals and researchers.
Publisher: California Digital Library (CDL)
Date: 03-04-2021
Publisher: Public Library of Science (PLoS)
Date: 09-07-2013
Publisher: Elsevier BV
Date: 03-2013
DOI: 10.1016/J.ARR.2013.03.005
Abstract: Hormesis is the response of organisms to a mild stressor resulting in improved health and longevity. Mild heat shocks have been thought to induce hormetic response because they promote increased activity of heat shock proteins (HSPs), which may extend lifespan. Using data from 27 studies on 12 animal species, we performed a comparative meta-analysis to quantify the effect of heat shock exposure on longevity. Contrary to our expectations, heat shock did not measurably increase longevity in the overall meta-analysis, although we observed much heterogeneity among studies. Thus, we explored the relative contributions of different experimental variables (i.e. moderators). Higher temperatures, longer durations of heat shock exposure, increased shock repeat and less time between repeat shocks, all decreased the likelihood of a life-extending effect, as would be expected when a hormetic response crosses the threshold to being a damaging exposure. We conclude that there is limited evidence that mild heat stress is a universal way of promoting longevity at the whole-organism level. Life extension via heat-induced hormesis is likely to be constrained to a narrow parameter window of experimental conditions.
Publisher: Wiley
Date: 05-2011
Publisher: Springer Science and Business Media LLC
Date: 19-11-2011
Publisher: Oxford University Press (OUP)
Date: 03-11-2018
Publisher: Elsevier BV
Date: 05-2017
DOI: 10.1016/J.CUB.2017.03.049
Abstract: Phylogenetic comparative methods (PCMs) enable us to study the history of organismal evolution and ersification. PCMs comprise a collection of statistical methods for inferring history from piecemeal information, primarily combining two types of data: first, an estimate of species relatedness, usually based on their genes, and second, contemporary trait values of extant organisms. Some PCMs also incorporate information from geological records, especially fossils, but also other gradual and episodic events in the Earth's history (for ex le, trait data from fossils or the global oxygen concentration as an independent variable). It is important to note at the outset that PCMs are not concerned with reconstructing the evolutionary relationships among species this has to do with estimating the phylogeny from genetic, fossil and other data, and a separate set of methods for this process makes up the field of phylogenetics. PCMs as a set of methods are distinct from, but are not completely independent of, phylogenetics. PCMs are used to address the questions: how did the characteristics of organisms evolve through time and what factors influenced speciation and extinction?
Publisher: Springer Science and Business Media LLC
Date: 11-10-2011
Publisher: Wiley
Date: 05-11-2015
Publisher: Springer Science and Business Media LLC
Date: 18-10-2021
DOI: 10.1186/S13750-021-00241-Z
Abstract: Globally, there is growing concern over the impacts of pharmaceuticals and drug manufacturing on aquatic animals, and pharmaceuticals are now recognized as contaminants of emerging environmental concern. In recent years, scientists, environmental managers, and policymakers have been interested in using behavioural endpoints for chemical regulation, given their importance for fitness and survival. The body of research on whether and how pharmaceutical exposure alters the behaviour of aquatic animals has grown exponentially, making it difficult to get an overview of the results. With an international spotlight on the management of these environmental threats, synthesizing the currently available data is vital to inform managers and policymakers, as well as highlighting areas where more research is needed. This is a protocol for a systematic evidence map (SEM) and serves as an a priori record of our objectives and methodological decisions. Our objectives are to identify, catalogue, and present primary research articles on the effects of human and veterinary pharmaceuticals on aquatic animal behaviour. The literature search will be conducted using two electronic databases: Web of Science and Scopus, and we will supplement these searches with additional sources. The search string has been developed using a Population–Exposure–Comparison–Outcome (PECO) framework, to capture articles that used an aquatic organism (P, population) to test the effects of a pharmaceutical (E, exposure) on behaviour (O, outcome). Eligible articles must also have a control group (C, comparison). Articles will be screened in two stages, title and abstract, followed by full-text screening before data extraction. Decision trees have been designed a priori to appraise articles for eligibility at both stages of screening. At both stages, screening each article will be completed by two independent reviewers. Study validity will be appraised but not used as a basis for article inclusion. The information extracted from the eligible articles, along with bibliometric data, will be mapped and displayed. All data associated with this SEM will be publicly available through the Open Science Framework (OSF) and a future project webpage.
Publisher: Oxford University Press (OUP)
Date: 2022
DOI: 10.1093/GIGASCIENCE/GIAC074
Abstract: Taxonomic bias is a known issue within the field of biology, causing scientific knowledge to be unevenly distributed across species. However, a systematic quantification of the research interest that the scientific community has allocated to in idual species remains a big data problem. Scalable approaches are needed to integrate bio ersity data sets and bibliometric methods across large numbers of species. The outputs of these analyses are important for identifying understudied species and directing future research to fill these gaps. In this study, we used the species h-index to quantity the research interest in 7,521 species of mammals. We tested factors potentially driving species h-index, by using a Bayesian phylogenetic generalized linear mixed model (GLMM). We found that a third of the mammals had a species h-index of zero, while a select few had inflated research interest. Further, mammals with higher species h-index had larger body masses were found in temperate latitudes had their humans uses documented, including domestication and were in lower-risk International Union for Conservation of Nature Red List categories. These results surprisingly suggested that critically endangered mammals are understudied. A higher interest in domesticated species suggested that human use is a major driver and focus in mammalian scientific literature. Our study has demonstrated a scalable workflow and systematically identified understudied species of mammals, as well as identified the likely drivers of this taxonomic bias in the literature. This case study can become a benchmark for future research that asks similar biological and meta-research questions for other taxa.
Publisher: Cold Spring Harbor Laboratory
Date: 20-11-2019
DOI: 10.1101/846287
Abstract: Transgenerational plasticity (TGP) occurs when the environment experienced by parents induces changes in traits of offspring and/or subsequent generations. Such effects can be adaptive or non-adaptive and are increasingly recognised as key determinants of health, cognition, development and performance across a wide range of taxa, including humans. While the conditions that favour maternal TGP are well understood, rapidly accumulating evidence indicates that TGP can be maternal or paternal, and offspring responses can be sex-specific. However, the evolutionary mechanisms that drive this ersity are unknown. We used an in idual-based model to investigate the evolution of TGP when the sexes experience different ecologies. We find that adaptive TGP rarely evolves when alleles at loci that determine offspring responses to environmental information originating from the mother and father are subject to sexually antagonistic selection. By contrast, duplication and sex-limitation of such loci can allow for the evolution of a variety of sex-specific responses, including non-adaptive sex-specific TGP when sexual selection is strong. Sexual conflict could therefore help to explain why adaptive TGP evolves in some species but not others, why sons and daughters respond to parental signals in different ways, and why complex patterns of sex-specific TGP may often be non-adaptive.
Publisher: California Digital Library (CDL)
Date: 05-07-2021
Publisher: Oxford University Press (OUP)
Date: 03-2017
Publisher: California Digital Library (CDL)
Date: 02-2019
Publisher: Wiley
Date: 25-04-2014
DOI: 10.1111/ECOG.00929
Publisher: California Digital Library (CDL)
Date: 06-01-2019
Publisher: Wiley
Date: 17-12-2012
Publisher: Elsevier BV
Date: 08-2014
DOI: 10.1016/J.TREE.2014.05.005
Abstract: Why do females of so many socially monogamous species regularly engage in matings outside the pair bond? This question has puzzled behavioural ecologists for more than two decades. Until recently, an adaptionist's point of view prevailed: if females actively seek extra-pair copulations, as has been observed in several species, they must somehow benefit from this behaviour. However, do they? In this review, we argue that adaptive scenarios have received disproportionate research attention, whereas nonadaptive phenomena, such as pathological polyspermy, de novo mutations, and genetic constraints, have been neglected by empiricists and theoreticians alike. We suggest that these topics deserve to be taken seriously and that future work would benefit from combining classical behavioural ecology with reproductive physiology and evolutionary genetics.
Publisher: Wiley
Date: 07-12-2014
DOI: 10.1111/JEB.12282
Abstract: Sex-biased resource allocation in avian eggs has gained increasing interest. The adaptive explanations of such allocation are often related to life-history strategies of the studied species. In some species, egg sexual size dimorphism (SSD) was suggested to promote future size differences between adults of each sex. In other species, egg SSD was invoked as an adaptive means by which a mother balances sex-specific nestling mortality. According to the first scenario, mothers should produce bigger eggs for the bigger sex, thus across species, adult SSD should be a significant positive predictor of egg SSD. Under the second scenario, mothers should produce bigger eggs for the smaller sex. If different species use contrasting strategies, then a universal expectation is that there should be a significant relationship between the magnitude of adult SSD and the magnitude of egg SSD, irrespective of the direction of those differences. Our aim was to examine whether the direction of egg SSD is predicted by the direction of adult SSD or whether degree of egg SSD is related to degree of adult SSD. To answer that question, we performed meta-analysis of 63 studies, which included information on egg SSD of 65 effect sizes from 51 avian species. We found that across species, adult SSD does not predict egg SSD. More importantly, the observed variation in effect sizes in our data set was largely explained by s ling error (variance). Although adult SSD is undoubtedly a prominent feature of birds, there is little evidence for egg SSD across avian species.
Publisher: Wiley
Date: 19-07-2019
DOI: 10.1111/ELE.13343
Abstract: Immunosenescence, the decline in immune defense with age, is an important mortality source in elderly humans but little is known of immunosenescence in wild animals. We systematically reviewed and meta-analysed evidence for age-related changes in immunity in captive and free-living populations of wild species (321 effect sizes in 62 studies across 44 species of mammals, birds and reptiles). As in humans, senescence was more evident in adaptive (acquired) than innate immune functions. Declines were evident for cell function (antibody response), the relative abundance of naïve immune cells and an in vivo measure of overall immune responsiveness (local response to phytohaemagglutinin injection). Inflammatory markers increased with age, similar to chronic inflammation associated with human immunosenescence. Comparisons across taxa and captive vs free-living animals were difficult due to lack of overlap in parameters and species measured. Most studies are cross-sectional, which yields biased estimates of age-effects when immune function co-varies with survival. We therefore suggest longitudinal s ling approaches, and highlight techniques from human cohort studies that can be incorporated into ecological research. We also identify avenues to address predictions from evolutionary theory and the contribution of immunosenescence to age-related increases in disease susceptibility and mortality.
Publisher: Wiley
Date: 16-05-2012
DOI: 10.1111/J.1420-9101.2012.02533.X
Abstract: Numerous models have attempted to explain the evolution of extravagant male ornaments found in many species. Inter-sexual indicator models postulate that male ornaments evolved as signals of quality, and that females use these signals to select the highest quality males. These models involve three traits--male quality, male signals and female preferences--and have specific expectations about the relative strengths of the phenotypic relationships between these traits. Using data from anuran species, we assessed the relative strengths of the phenotypic relationships using meta-analysis. The relative strengths of these phenotypic correlations were as expected by indicator models, providing support for indicator models of inter-sexual selection. We also found much variation in our data, suggesting that additional, untested factors may mediate inter-sexual interactions in this taxon, such as differences in the importance of quality signalling between species. These factors require investigation, in order to improve our understanding of inter-sexual selection.
Publisher: California Digital Library (CDL)
Date: 07-05-2020
Publisher: Wiley
Date: 30-03-2020
DOI: 10.1111/CCH.12763
Publisher: Springer Science and Business Media LLC
Date: 31-07-2012
Publisher: Wiley
Date: 19-02-2016
DOI: 10.1111/JFB.12912
Abstract: An investigation of intraspecific habitat-related patterns of variation in oculoscapular lateral-line superficial neuromasts (SN) identified a decrease in the ratio of total SNs to pores, and a trend towards decreased asymmetry in SNs in the habitat-generalist common bully Gobiomorphus cotidianus from fluvial habitats compared to lacustrine habitats, suggesting habitat-related phenotypic variability. A greater ratio of pores to SNs, as well as less variation in the total number and asymmetry of SNs observed in the fluvial habitat-specialist redfin bully Gobiomorphus huttoni may provide further evidence of variations in the oculoscapular lateral-line morphology of fluvial habitat G. cotidianus in iduals serving as adaptations to more turbulent environments.
Publisher: California Digital Library (CDL)
Date: 21-03-2018
Publisher: The Royal Society
Date: 13-08-2018
Abstract: Behavioural and cognitive processes play important roles in mediating an in idual's interactions with its environment. Yet, while there is a vast literature on repeatable in idual differences in behaviour, relatively little is known about the repeatability of cognitive performance. To further our understanding of the evolution of cognition, we gathered 44 studies on in idual performance of 25 species across six animal classes and used meta-analysis to assess whether cognitive performance is repeatable. We compared repeatability ( R ) in performance (1) on the same task presented at different times (temporal repeatability), and (2) on different tasks that measured the same putative cognitive ability (contextual repeatability). We also addressed whether R estimates were influenced by seven extrinsic factors (moderators): type of cognitive performance measurement, type of cognitive task, delay between tests, origin of the subjects, experimental context, taxonomic class and publication status. We found support for both temporal and contextual repeatability of cognitive performance, with mean R estimates ranging between 0.15 and 0.28. Repeatability estimates were mostly influenced by the type of cognitive performance measures and publication status. Our findings highlight the widespread occurrence of consistent inter-in idual variation in cognition across a range of taxa which, like behaviour, may be associated with fitness outcomes. This article is part of the theme issue ‘Causes and consequences of in idual differences in cognitive abilities’.
Publisher: Springer Science and Business Media LLC
Date: 06-11-2021
DOI: 10.1186/S13750-021-00245-9
Abstract: Over the last few decades, we increasingly see ex les of parental environmental experiences influencing offspring health and fitness. More recently, it has become clear that some non-genetic effects can be conferred across multiple generations. This topic has attracted research from a ersity of disciplines such as toxicology, biomedical sciences, and ecology, due to its importance for environmental and health issues, as well as ecological and evolutionary processes, with implications for environmental policies. The rapid accumulation of primary research has enabled researchers to perform systematic reviews (SRs), including meta-analyses, to investigate the generality of and sources of variation in non-genetic effects. However, different disciplines ask different questions and SRs can vary substantially in scope, quality, and terminology usage. This ersity in SRs makes it difficult to assess broad patterns of non-genetic effects across disciplines as well as determine common areas of interest and gaps in the literature. To clarify research patterns within the SR literature on non-genetic inheritance, we plan to create a map of systematic reviews as well as conduct bibliometric mapping (referred to as ‘research weaving’). We will address four key questions: first, what are the broad research patterns unifying the SR literature on non-genetic inheritance across disciplines? Second, are there discipline-specific research patterns, including terminology use, between disciplines? Third, how are authors of the SR literature connected? Fourth, what is the reliability of the SR literature? We will systematically collect reviews within the SR ‘family’ that examine non-genetic inheritance arising from parental and ancestral environment by searching databases for journal articles and grey literature, as well as conducting backwards and forwards searching. Search hits will be double screened using ‘decision trees’ that represent the inclusion criteria. All relevant data elements on the review’s topic, as well as a critical appraisal of the review’s approach and reporting, will be extracted into Excel flat sheets. Bibliometric data will be directly extracted from Scopus. We will then query all relevant data elements to address our objectives and present outcomes in easily interpretable tables and figures, accompanied by a narrative description of results.
Publisher: Springer Science and Business Media LLC
Date: 30-09-2017
Publisher: Elsevier BV
Date: 09-2016
DOI: 10.1016/J.GENE.2016.05.042
Abstract: The sex drive hypothesis predicts that stronger selection on male traits has resulted in masculinization of the genome. Here we test whether such masculinizing effects can be detected at the level of the transcriptome and methylome in the adult zebrafish brain. Although methylation is globally similar, we identified 914 specific differentially methylated CpGs (DMCs) between males and females (435 were hypermethylated and 479 were hypomethylated in males compared to females). These DMCs were prevalent in gene body, intergenic regions and CpG island shores. We also discovered 15 distinct CpG clusters with striking sex-specific DNA methylation differences. In contrast, at transcriptome level, more female-biased genes than male-biased genes were expressed, giving little support for the male sex drive hypothesis. Our study provides genome-wide methylome and transcriptome assessment and sheds light on sex-specific epigenetic patterns and in zebrafish for the first time.
Publisher: Wiley
Date: 27-08-2021
Abstract: Climate change is putting the fate of ectothermic animals at stake because their body temperature closely tracks environmental temperatures. The ability to adjust thermal limits and preference through acclimation (i.e. acclimation capacity) may compensate for temperature changes. However, although necessary for forecasting the future of ectotherms in a changing climate, knowledge on the factors modulating these plastic responses is fragmentary. For instance, the influence of an animal's sex in driving acclimation capacity has been underappreciated. Here, we present the first systematic review and meta‐analysis on sex differences in thermal acclimation capacity. Using 239 effect sizes from 37 studies and 44 species, we revealed that males and females did not differ significantly in their overall capacity to acclimate their thermal limits and preference. However, in some instances, females expressed significantly greater plastic responses than males. In wild animals, females had a greater heat tolerance plasticity than males. In addition, females had a greater cold tolerance plasticity in terrestrial habitats, but the strength and direction of this sexual dimorphism was associated with the duration of acclimation. We also found a negative correlation between body mass and plasticity. Finally, we demonstrated that the capacity for each sex to adjust their thermal tolerance and preference was remarkably limited. It is important to acknowledge that the above effects were weak and heterogeneous. Hence, in the species we investigated, minor differences in acclimation capacity may not translate into major ecological mismatch between sexes with climate change. Our systematic review also revealed that over 75% of the studies we identified either did not report or confounded the sex of the animals. This under‐reporting may cause to overlook ecologically relevant sex differences in plasticity in ectothermic taxa. We stress the need for further research on sex‐based responses to temperatures. Our synthesis provides additional evidence that the capacity for ectotherms to acclimate to temperatures is limited, and likely insufficient to compensate for the impacts of climate change. A free Plain Language Summary can be found within the Supporting Information of this article.
Publisher: Springer Science and Business Media LLC
Date: 18-07-2015
DOI: 10.1007/S10695-015-0095-0
Abstract: In order to develop biomarkers that may help predict the egg quality of captive hapuku (Polyprion oxygeneios) and provide potential avenues for its manipulation, the present study (1) sequenced the proteome of early-stage embryos using isobaric tag for relative and absolute quantification analysis, and (2) aimed to establish the predictive value of the abundance of identified proteins with regard to egg quality through regression analysis. Egg quality was determined for eight different egg batches by blastomere symmetry scores. In total, 121 proteins were identified and assigned to one of nine major groups according to their function athway. A mixed-effects model analysis revealed a decrease in relative protein abundance that correlated with (decreasing) egg quality in one major group (heat-shock proteins). No differences were found in the other protein groups. Linear regression analysis, performed for each identified protein separately, revealed seven proteins that showed a significant decrease in relative abundance with reduced blastomere symmetry: two correlates that have been named in other studies (vitellogenin, heat-shock protein-70) and a further five new candidate proteins (78 kDa glucose-regulated protein, elongation factor-2, GTP-binding nuclear protein Ran, iduronate 2-sulfatase and 6-phosphogluconate dehydrogenase). Notwithstanding issues associated with multiple statistical testing, we conclude that these proteins, and especially iduronate 2-sulfatase and the generic heat-shock protein group, could serve as biomarkers of egg quality in hapuku.
Publisher: The Royal Society
Date: 04-10-2017
Abstract: An emerging hypothesis of animal personality posits that animals choose the habitat that best fits their personality, and that the match between habitat and personality can facilitate population differentiation, and eventually speciation. However, behavioural plasticity and the adjustment of behaviours to new environments have been a classical explanation for such matching patterns. Using a population of dunnocks ( Prunella modularis ), we empirically tested whether personality or behavioural plasticity is responsible for the non-random distribution of shy and bold in iduals in a heterogeneous environment. We found evidence for bold in iduals settling in areas with high human disturbance, but also that birds became bolder with increasing age. Importantly, personality primarily determines the distribution of in iduals, and behavioural adjustment over time contributes very little to the observed patterns. We cannot, however, exclude a possibility of very early behavioural plasticity (a type of developmental plasticity) shaping what we refer to as ‘personality’. Nonetheless, our findings highlight the role personality plays in shaping population structure, lending support to the theory of personality-mediated speciation. Moreover, personality-matching habitat choice has important implications for population management and conservation.
Publisher: Wiley
Date: 08-08-2012
Publisher: Wilson Ornithological Society
Date: 09-2017
DOI: 10.1676/16-059.1
Publisher: The Company of Biologists
Date: 08-03-2022
DOI: 10.1242/JEB.243225
Abstract: Meta-analysis is a powerful tool used to generate quantitatively informed answers to pressing global challenges. By distilling data from broad sets of research designs and study systems into standardised effect sizes, meta-analyses provide physiologists with opportunities to estimate overall effect sizes and understand the drivers of effect variability. Despite this ambition, research designs in the field of comparative physiology can appear, at the outset, as being vastly different to each other because of ‘nuisance heterogeneity’ (e.g. different temperatures or treatment dosages used across studies). Methodological differences across studies have led many to believe that meta-analysis is an exercise in comparing ‘apples with oranges’. Here, we dispel this myth by showing how standardised effect sizes can be used in conjunction with multilevel meta-regression models to both account for the factors driving differences across studies and make them more comparable. We assess the prevalence of nuisance heterogeneity in the comparative physiology literature – showing it is common and often not accounted for in analyses. We then formalise effect size measures (e.g. the temperature coefficient, Q10) that provide comparative physiologists with a means to remove nuisance heterogeneity without the need to resort to more complex statistical models that may be harder to interpret. We also describe more general approaches that can be applied to a variety of different contexts to derive new effect sizes and s ling variances, opening up new possibilities for quantitative synthesis. By using effect sizes that account for components of effect heterogeneity, in combination with existing meta-analytic models, comparative physiologists can explore exciting new questions while making results from large-scale data sets more accessible, comparable and widely interpretable.
Publisher: Wiley
Date: 17-07-2022
DOI: 10.1111/ELE.14069
Abstract: The benefits of animal pollination to crop yield are well known. In contrast, the effects of animal pollination on the spatial or temporal stability (the opposite of variability) of crop yield remain poorly understood. We use meta‐analysis to combine variability information from 215 experimental comparisons between animal‐pollinated and wind‐ or self‐pollinated control plants in apple, oilseed rape and faba bean. Animal pollination increased yield stability (by an average of 32% per unit of yield) at between‐flower, ‐plant, ‐plot and ‐field scales. Evidence suggests this occurs because yield benefits of animal pollination become progressively constrained closer to the maximum potential yield in a given context, causing clustering. The increase in yield stability with animal pollination is greatest when yield benefits of animal pollination are greatest, indicating that managing crop pollination to increase yield also increases yield stability. These additional pollination benefits have not yet been included in economic assessments but provide further justification for policies to protect pollinators.
Publisher: University of Chicago Press
Date: 02-2014
DOI: 10.1086/674445
Abstract: The evolution of traits involved in ecological interactions such as predator-prey, host-parasite, and plant-pollinator interactions, are likely to be shaped by the phylogenetic history of both parties. We develop generalized linear mixed-effects models (GLMM) that estimate the effect of both parties' phylogenetic history on trait evolution, both in isolation but also in terms of how the two histories interact. Using data on the incidence and abundance of 206 flea species on 121 mammal species, we illustrate our method and compare it to previously used methods for detecting host-parasite coevolution. At large spatial scales we find that the phylogenetic interaction effect was substantial, indicating that related parasite species were more likely to be found on related host species. At smaller spatial scales, and when s ling effort was not controlled for, phylogenetic effects on the number and types of parasite species harbored by hosts were found to dominate. We go on to show that in situations where these additional phylogenetic effects exist, then previous methods have very high Type I error rates when testing for the phylogenetic interaction. Our GLMM method represents a robust and reliable approach to quantify the phylogenetic effects of traits determined by, or defined by, ecological interactions and has the advantage that it can easily be extended and interpreted in a broader context than existing permutation tests.
Publisher: Springer Science and Business Media LLC
Date: 15-02-2022
Publisher: Springer Science and Business Media LLC
Date: 28-10-2015
Publisher: California Digital Library (CDL)
Date: 16-09-2022
Publisher: Elsevier BV
Date: 03-2018
DOI: 10.1016/J.TREE.2018.11.007
Abstract: We propose a new framework for research synthesis of both evidence and influence, named research weaving. It summarizes and visualizes information content, history, and networks among a collection of documents on any given topic. Research weaving achieves this feat by combining the power of two methods: systematic mapping and bibliometrics. Systematic mapping provides a snapshot of the current state of knowledge, identifying areas needing more research attention and those ready for full synthesis. Bibliometrics enables researchers to see how pieces of evidence are connected, revealing the structure and development of a field. We explain how researchers can use some or all of these tools to gain a deeper, more nuanced understanding of the scientific literature.
Publisher: Springer Science and Business Media LLC
Date: 21-10-2011
Publisher: Wiley
Date: 29-07-2019
DOI: 10.1111/FAF.12394
Publisher: eLife Sciences Publications, Ltd
Date: 13-11-2018
DOI: 10.7554/ELIFE.37385
Abstract: 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 ex le 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 ex le in evolutionary and behavioural ecology, and should stimulate renewed interest in understanding within-species variation in ornamental traits.
Publisher: Springer Science and Business Media LLC
Date: 25-09-2018
DOI: 10.1038/S41467-018-06292-0
Abstract: Fewer women than men pursue careers in science, technology, engineering and mathematics (STEM), despite girls outperforming boys at school in the relevant subjects. According to the ‘variability hypothesis’, this over-representation of males is driven by gender differences in variance greater male variability leads to greater numbers of men who exceed the performance threshold. Here, we use recent meta-analytic advances to compare gender differences in academic grades from over 1.6 million students. In line with previous studies we find strong evidence for lower variation among girls than boys, and of higher average grades for girls. However, the gender differences in both mean and variance of grades are smaller in STEM than non-STEM subjects, suggesting that greater variability is insufficient to explain male over-representation in STEM. Simulations of these differences suggest the top 10% of a class contains equal numbers of girls and boys in STEM, but more girls in non-STEM subjects.
Publisher: Springer Science and Business Media LLC
Date: 04-09-2011
Publisher: Wiley
Date: 19-05-2010
DOI: 10.1111/J.1420-9101.2010.02025.X
Abstract: Although recent models for the evolution of personality, using game theory and life-history theory, predict that in iduals should differ consistently in their cooperative behaviour, consistent in idual differences in cooperative behaviour have rarely been documented. In this study, we used a long-term data set on wild meerkats to quantify the repeatability of two types of cooperative care (babysitting and provisioning) within in iduals and examined how repeatability varied across age, sex and status categories. Contributions to babysitting and provisioning were significantly repeatable and positively correlated within in iduals, with provisioning more repeatable than babysitting. While repeatability of provisioning was relatively invariant across categories of in iduals, repeatability of babysitting increased with age and was higher for subordinates than dominants. These results provide support for theoretical predictions that life-history trade-offs favour the evolution of consistent in idual differences in cooperative behaviour and raise questions about why some in iduals consistently help more than others across a suite of cooperative behaviours.
Publisher: Wiley
Date: 12-2016
DOI: 10.1002/ECY.1591
Abstract: Meta-analysis is the gold standard for synthesis in ecology and evolution. Together with estimating overall effect magnitudes, meta-analyses estimate differences between effect sizes via heterogeneity statistics. It is widely hypothesized that heterogeneity will be present in ecological/evolutionary meta-analyses due to the system-specific nature of biological phenomena. Despite driving recommended best practices, the generality of heterogeneity in ecological data has never been systematically reviewed. We reviewed 700 studies, finding 325 that used formal meta-analysis, of which total heterogeneity was reported in fewer than 40%. We used second-order meta-analysis to collate heterogeneity statistics from 86 studies. Our analysis revealed that the median and mean heterogeneity, expressed as I
Publisher: University of Chicago Press
Date: 07-2009
DOI: 10.1086/599299
Abstract: Studies of animals often report a greater sensitivity of one sex to poor rearing environments. However, it is unclear whether size differences associated with sex, sex itself, or other factors are responsible for differences in performance. While the greater nutritional requirement of the larger sex is a plausible explanation for increased sensitivity (i.e., size-dependent vulnerability), other hypotheses suggest that size-independent traits may have effects on the fitness of offspring (i.e., sex-dependent vulnerability). For ex le, the heterogametic sex may be more vulnerable to expression of sex-linked recessives in poor environments, or sex-specific phenotypes may have negative effects (e.g., increased testosterone in males). We examined support for these hypotheses through the use of meta-analytic techniques based on the published literature on avian species. Our results revealed small, nonsignificant effects for hypotheses of size- and sex-dependent susceptibilities alone. Application of a multivariate meta-analytic technique (meta-regression) suggests a joint influence of sexual size dimorphism and clutch size in explaining sex-specific patterns of vulnerability. These findings suggest that none of the proposed hypotheses tested here on their own can sufficiently explain the observed patterns and that additional factors must be considered in order to explain the ersity of patterns of sex-specific sensitivity observed in the literature.
Publisher: University of Chicago Press
Date: 09-2011
DOI: 10.1086/661244
Abstract: The way females utilize the gametes of different males has important consequences for sexual selection, sexual conflict, and intersexual coevolution in natural populations. However, patterns of sperm utilization by females are difficult to demonstrate, and their functional significance remains unclear. Here, we experimentally study sperm ejection in the fowl Gallus gallus domesticus, where females eject preferentially the sperm of socially subordinate males. We study two measures of sperm ejection, (i) the probability that an ejaculate is ejected ("risk") and (ii) the proportion of semen ejected ("intensity"), and show that both measures are strongly nonrandom with respect to characteristics of the ejaculate, the male, and the female. Sperm ejection neutralized on average 80% of an ejaculate, and while larger ejaculates suffered a higher ejection risk, smaller ejaculates suffered more intense ejection. After controlling for ejaculate volume, we found socially subdominant males suffered higher ejection intensity. After controlling for male and ejaculate effects, we found ejection risk increased and intensity declined as females mated with successive males. Collectively, these results reveal that sperm ejection risk and intensity are at least partly actively caused by female behavior and generate independent selective pressures on male and ejaculate phenotypes.
Publisher: Springer Science and Business Media LLC
Date: 03-2022
DOI: 10.1007/S10682-022-10160-1
Abstract: Phenotypic plasticity is an important mechanism that allows populations to adjust to changing environments. Early life experiences can have lasting impacts on how in iduals respond to environmental variation later in life (i.e., in idual reaction norms), altering the capacity for populations to respond to selection. Here, we incubated lizard embryos ( L ropholis delicata ) at two fluctuating developmental temperatures (cold = 23 ºC + / − 3 ºC, hot = 29 ºC + / − 3 ºC, n cold = 26, n hot = 25) to understand how it affected metabolic plasticity to temperature later in life. We repeatedly measured in idual reaction norms across six temperatures 10 times over ~ 3.5 months (n obs = 3,818) to estimate the repeatability of average metabolic rate (intercept) and thermal plasticity (slope). The intercept and the slope of the population-level reaction norm was not affected by developmental temperature. Repeatability of average metabolic rate was, on average, 10% lower in hot incubated lizards but stable across all temperatures. The slope of the thermal reaction norm was overall moderately repeatable ( R = 0.44, 95% CI = 0.035 – 0.93) suggesting that in idual metabolic rate changed consistently with short-term changes in temperature, although credible intervals were quite broad. Importantly, reaction norm repeatability did not depend on early developmental temperature. Identifying factors affecting among-in idual variation in thermal plasticity will be increasingly more important for terrestrial ectotherms living in changing climate. Our work implies that thermal metabolic plasticity is robust to early developmental temperatures and has the capacity to evolve, despite there being less consistent variation in metabolic rate under hot environments.
Publisher: Proceedings of the National Academy of Sciences
Date: 17-05-2021
Abstract: For the fields of ecology, evolutionary biology, and conservation, abundance estimates of organisms are essential. Quantifying abundance, however, is difficult and time consuming. Using a data integration approach integrating expert-derived abundance estimates and global citizen science data, we estimate the global population of 9,700 bird species (∼92% of all extant bird species). We conclude that there are many rare species, highlighting the need to continue to refine global population estimates for all taxa and the role that global citizen science data can play in this effort.
Publisher: Springer Science and Business Media LLC
Date: 09-2017
Publisher: Springer Science and Business Media LLC
Date: 24-01-2013
Publisher: Wiley
Date: 02-2016
DOI: 10.1111/MEC.13514
Abstract: Quantifying the variation in behaviour-related genes within and between populations provides insight into how evolutionary processes shape consistent behavioural traits (i.e. personality). Deliberate introductions of non-native species offer opportunities to investigate how such genes differ between native and introduced populations and how polymorphisms in the genes are related to variation in behaviour. Here, we compared the genetic variation of the two 'personality' genes, DRD4 and SERT, between a native (United Kingdom, UK) and an introduced (New Zealand, NZ) population of dunnocks, Prunella modularis. The NZ population showed a significantly lower number of single nucleotide polymorphisms (SNPs) compared to the UK population. Standardized F'st estimates of the personality genes and neutral microsatellites indicate that selection (anthropogenic and natural) probably occurred during and post the introduction event. Notably, the largest genetic differentiation was found in the intronic regions of the genes. In the NZ population, we also examined the association between polymorphisms in DRD4 and SERT and two highly repeatable behavioural traits: flight-initiation distance and mating status (promiscuous females and cobreeding males). We found 38 significant associations (for different allele effect models) between the two behavioural traits and the studied genes. Further, 22 of the tested associations showed antagonistic allele effects for males and females. Our findings illustrate how introduction events and accompanying ecological changes could influence the genetic ersity of behaviour-related genes.
Publisher: Wiley
Date: 24-05-2021
DOI: 10.1111/BRV.12734
Abstract: Sustaining multiple ecosystem services across a landscape requires an understanding of how consistently services are shaped by different categories of land uses. Yet, this understanding is generally constrained by the availability of fine‐resolution data for multiple services across large areas and the spatial variability of land‐use effects on services. We systematically surveyed published literature for New Zealand (1970–2015) to quantify the supply of 17 non‐production services across 25 land covers (as a proxy for land use). We found a consistent trade‐off in the services supplied by anthropogenic land covers with a high production intensity (e.g. cropping) versus those with extensive or no production. By contrast, forest cover was not associated with any distinct patterns of service supply. By drawing on existing research findings, we reveal complementarity and redundancy (potentially influencing resilience) in service supply from different land covers. This will guide practitioners in shaping land systems that sustainably support human well‐being.
Publisher: Elsevier BV
Date: 05-2021
Publisher: Wiley
Date: 08-06-2023
DOI: 10.1002/ECY.4069
Publisher: Springer Science and Business Media LLC
Date: 09-11-2017
Publisher: Wiley
Date: 03-01-2013
DOI: 10.1111/JEB.12068
Abstract: There exists remarkable interspecific variation in mitochondrial sequence evolution rates and in mitochondrial genome sizes. A number of hypotheses based on the forces of mutation and selection have been proposed to explain this variation. Among such hypotheses, we test three: 1) the 'longevity-dependent selection', 2) the 'functional constraints' and 3) the 'race for replication' hypotheses, using published mtDNA genomic sequences of 47 Nematoda species. We did not find any relationship between body size (used as a proxy for longevity) and genome size or the substitution rate of protein sequences, providing little evidence for the first hypothesis. Parasitic species from different thermal habitats, as determined by their definitive host type (ectothermal vs. endothermal), did not differ in their rates of protein evolution. Therefore, little support was obtained for the second hypothesis. However, we revealed that mitogenomes of parasites of endotherms were significantly smaller than those of parasites of ectotherms, supporting the race for replication hypothesis. As mitochondrial genomes of endothermal animals are usually more compact than those of ectothermal animals, intriguingly, nematode parasites of endotherms and ectotherms exhibit similar patterns of mtDNA length variation to their hosts.
Publisher: Frontiers Media SA
Date: 25-11-2014
Publisher: Wiley
Date: 10-2022
DOI: 10.1002/ECE3.9423
Abstract: The obesity epidemic is concerning as obesity appears to negatively impact cognition and behavior. Furthermore, some studies suggest that this negative effect could be carried across generations from both mothers and fathers although evidence is not consistent. Here, we attempt to address how obesogenic diets in the parental generation (F0) can impact offspring's cognition and anxiety intergenerationally (F1) in a zebrafish model. We compare both mean trait values and their variances. Using a multifactorial design, we created a total of four groups: F1T (treatment mothers × treatment fathers) F1M (treatment mothers × control fathers) F1P (treatment fathers × control mothers) and F1C (control mothers × control fathers, F1C) and subjected them to anxiety tank tests and aversive learning assays. When both parents were exposed, offspring (F1T) displayed the poorest aversive learning, while offspring that only had one parent exposed (F1P and F1M) learnt the aversive learning task the best. Zebrafish in all groups displayed no statistically significant differences in anxiety‐associated behaviors. Males and females also performed similarly in both anxiety and aversive learning assays. While all F1 groups had similar levels of fasting blood glucose, variance in glucose levels were reduced in F1P and F1T indicating the importance of investigating heteroskedasticity between groups. Furthermore, anxiety behaviors of these two groups appeared to be less repeatable. To our knowledge, this is the first study to test the intergenerational effects of an obesogenic diet on zebrafish cognition. Our multifactorial design as well as repeated tests also allowed us to disentangle maternal and paternal effects (as well as combined effects) and accurately detect subtle information such as between‐in idual variation.
Publisher: Wiley
Date: 06-06-2023
Abstract: Although meta‐analysis has become an essential tool in ecology and evolution, reporting of meta‐analytic results can still be much improved. To aid this, we have introduced the orchard plot, which presents not only overall estimates and their confidence intervals, but also shows corresponding heterogeneity (as prediction intervals) and in idual effect sizes. Here, we have added significant enhancements by integrating many new functionalities into orchaRd 2.0 . This updated version allows the visualisation of heteroscedasticity (different variances across levels of a categorical moderator), marginal estimates (e.g. marginalising out effects other than the one visualised), conditional estimates (i.e. estimates of different groups conditioned upon specific values of a continuous variable) and visualisations of all types of interactions between two categorical/continuous moderators. orchaRd 2.0 has additional functions which calculate key statistics from multilevel meta‐analytic models such as I 2 and R 2 . Importantly, orchaRd 2.0 contributes to better reporting by complying with PRISMA‐EcoEvo (preferred reporting items for systematic reviews and meta‐analyses in ecology and evolution). Taken together, orchaRd 2.0 can improve the presentation of meta‐analytic results and facilitate the exploration of previously neglected patterns. In addition, as a part of a literature survey, we found that graphical packages are rarely cited (~3%). We plea that researchers credit developers and maintainers of graphical packages, for ex le, by citations in a figure legend, acknowledging the use of relevant packages.
Publisher: The Royal Society
Date: 05-2023
Abstract: On a global scale, organisms face significant challenges due to climate change and anthropogenic disturbance. In many ectotherms, developmental and physiological processes are sensitive to changes in temperature and resources. Developmental plasticity in thermal physiology may provide adaptive advantages to environmental extremes if early environmental conditions are predictive of late-life environments. Here, we conducted a laboratory experiment to test how developmental temperature and maternal resource investment influence thermal physiological traits (critical thermal maximum: CT max and thermal preference: T pref ) in a common skink ( L ropholis delicata ). We then compared our experimental findings more broadly across reptiles (snakes, lizards and turtles) using meta-analysis. In both our experimental study and meta-analysis, we did not find evidence that developmental environments influence CT max or T pref . Furthermore, the effects of developmental environments on thermal physiology did not vary by age, taxon or climate zone (temperate/tropical). Overall, the magnitude of developmental plasticity on thermal physiology appears to be limited across reptile taxa suggesting that behavioural or evolutionary processes may be more important. However, there is a paucity of information across most reptile taxa, and a broader focus on thermal performance curves themselves will be critical in understanding the impacts of changing thermal conditions on reptiles in the future.
Publisher: Oxford University Press (OUP)
Date: 19-10-2010
Publisher: Wiley
Date: 13-03-0009
Publisher: Wiley
Date: 03-12-2013
DOI: 10.1111/FWB.12067
Publisher: Frontiers Media SA
Date: 11-04-2017
Publisher: Wiley
Date: 18-01-2019
DOI: 10.1111/GEB.12877
Publisher: Public Library of Science (PLoS)
Date: 23-02-2015
Publisher: California Digital Library (CDL)
Date: 19-11-2021
Publisher: Wiley
Date: 09-03-2017
DOI: 10.1111/MEC.14031
Abstract: Meta-analysis is an important tool for synthesizing research on a variety of topics in ecology and evolution, including molecular ecology, but can be susceptible to nonindependence. Nonindependence can affect two major interrelated components of a meta-analysis: (i) the calculation of effect size statistics and (ii) the estimation of overall meta-analytic estimates and their uncertainty. While some solutions to nonindependence exist at the statistical analysis stages, there is little advice on what to do when complex analyses are not possible, or when studies with nonindependent experimental designs exist in the data. Here we argue that exploring the effects of procedural decisions in a meta-analysis (e.g. inclusion of different quality data, choice of effect size) and statistical assumptions (e.g. assuming no phylogenetic covariance) using sensitivity analyses are extremely important in assessing the impact of nonindependence. Sensitivity analyses can provide greater confidence in results and highlight important limitations of empirical work (e.g. impact of study design on overall effects). Despite their importance, sensitivity analyses are seldom applied to problems of nonindependence. To encourage better practice for dealing with nonindependence in meta-analytic studies, we present accessible ex les demonstrating the impact that ignoring nonindependence can have on meta-analytic estimates. We also provide pragmatic solutions for dealing with nonindependent study designs, and for analysing dependent effect sizes. Additionally, we offer reporting guidelines that will facilitate disclosure of the sources of nonindependence in meta-analyses, leading to greater transparency and more robust conclusions.
Publisher: Oxford University Press (OUP)
Date: 16-02-2017
Publisher: Wiley
Date: 28-02-2019
DOI: 10.1111/EFF.12474
Publisher: Elsevier BV
Date: 07-2011
Publisher: Wiley
Date: 20-06-2013
DOI: 10.1111/BRV.12046
Abstract: Although a small set of external factors account for much of the spatial variation in plant and animal ersity, the search continues for general drivers of variation in parasite species richness among host species. Qualitative reviews of existing evidence suggest idiosyncrasies and inconsistent predictive power for all proposed determinants of parasite richness. Here, we provide the first quantitative synthesis of the evidence using a meta-analysis of 62 original studies testing the relationship between parasite richness across animal, plant and fungal hosts, and each of its four most widely used presumed predictors: host body size, host geographical range size, host population density, and latitude. We uncover three universal predictors of parasite richness across host species, namely host body size, geographical range size and population density, applicable regardless of the taxa considered and independently of most aspects of study design. A proper match in the primary studies between the focal predictor and both the spatial scale of study and the level at which parasite species richness was quantified (i.e. within host populations or tallied across a host species' entire range) also affected the magnitude of effect sizes. By contrast, except for a couple of indicative trends in subsets of the full dataset, there was no strong evidence for an effect of latitude on parasite species richness where found, this effect ran counter to the general latitude gradient in ersity, with parasite species richness tending to be higher further from the equator. Finally, the meta-analysis also revealed a negative relationship between the magnitude of effect sizes and the year of publication of original studies (i.e. a time-lag bias). This temporal bias may be due to the increasing use of phylogenetic correction in comparative analyses of parasite richness over time, as this correction yields more conservative effect sizes. Overall, these findings point to common underlying processes of parasite ersification fundamentally different from those controlling the ersity of free-living organisms.
Publisher: Cold Spring Harbor Laboratory
Date: 26-05-2020
DOI: 10.1101/2020.05.23.106146
Abstract: Biomedical and clinical sciences are experiencing a renewed interest in the fact that males and females differ in many anatomic, physiological, and behavioral traits. Sex differences in trait variability, however, are yet to receive similar recognition. In medical science, mammalian females are assumed to have higher trait variability due to estrous cycles (the ‘estrus-mediated variability hypothesis’) historically in biomedical research, females have been excluded for this reason. Contrastingly, evolutionary theory and associated data support the ‘greater male variability hypothesis’. Here, we test these competing hypotheses in 218 traits measured in ,900 mice, using meta-analysis methods. Neither hypothesis could universally explain patterns in trait variability. Sex-bias in variability was trait-dependent. While greater male variability was found in morphological traits, females were much more variable in immunological traits. Sex-specific variability has eco-evolutionary ramifications including sex-dependent responses to climate change, as well as statistical implications including power analysis considering sex difference in variance.
Publisher: Wiley
Date: 14-11-2011
DOI: 10.1111/J.1420-9101.2011.02412.X
Abstract: Within-in idual consistency and among-in idual heterogeneity in fitness are prerequisites for selection to take place. Within-in idual variation in productivity between years, however, can vary considerably, especially when organisms become older and more experienced. We examine in idual consistency in annual productivity, the covariation between survival and annual productivity, and the sources of variation in annual productivity, while accounting for advancing age, to test the in idual-quality and resource-allocation life-history theory hypotheses. We use long-term data from a pedigreed, wild population of house sparrows. Within-in idual annual productivity first increased and later decreased with age, but there were no selective mortality due to in idual quality and no correlation between lifespan and productivity. In iduals were consistent in their annual productivity (C = 0.49). Narrow-sense heritability was low (h(2) = 0.09), but maternal effects explained much of the variation (M = 0.33). Such effects can influence evolutionary processes and are of major importance for our understanding of how variation in fitness can be maintained.
Publisher: Wiley
Date: 03-2022
DOI: 10.1111/BRV.12844
Abstract: Animal behaviour is remarkably sensitive to disruption by chemical pollution, with widespread implications for ecological and evolutionary processes in contaminated wildlife populations. However, conventional approaches applied to study the impacts of chemical pollutants on wildlife behaviour seldom address the complexity of natural environments in which contamination occurs. The aim of this review is to guide the rapidly developing field of behavioural ecotoxicology towards increased environmental realism, ecological complexity, and mechanistic understanding. We identify research areas in ecology that to date have been largely overlooked within behavioural ecotoxicology but which promise to yield valuable insights, including within‐ and among‐in idual variation, social networks and collective behaviour, and multi‐stressor interactions. Further, we feature methodological and technological innovations that enable the collection of data on pollutant‐induced behavioural changes at an unprecedented resolution and scale in the laboratory and the field. In an era of rapid environmental change, there is an urgent need to advance our understanding of the real‐world impacts of chemical pollution on wildlife behaviour. This review therefore provides a roadmap of the major outstanding questions in behavioural ecotoxicology and highlights the need for increased cross‐talk with other disciplines in order to find the answers.
Publisher: eLife Sciences Publications, Ltd
Date: 17-11-2020
DOI: 10.7554/ELIFE.63170
Abstract: Biomedical and clinical sciences are experiencing a renewed interest in the fact that males and females differ in many anatomic, physiological, and behavioural traits. Sex differences in trait variability, however, are yet to receive similar recognition. In medical science, mammalian females are assumed to have higher trait variability due to estrous cycles (the ‘estrus-mediated variability hypothesis’) historically in biomedical research, females have been excluded for this reason. Contrastingly, evolutionary theory and associated data support the ‘greater male variability hypothesis’. Here, we test these competing hypotheses in 218 traits measured in ,900 mice, using meta-analysis methods. Neither hypothesis could universally explain patterns in trait variability. Sex bias in variability was trait-dependent. While greater male variability was found in morphological traits, females were much more variable in immunological traits. Sex-specific variability has eco-evolutionary ramifications, including sex-dependent responses to climate change, as well as statistical implications including power analysis considering sex difference in variance.
Publisher: Wiley
Date: 07-05-2021
DOI: 10.1111/BRV.12721
Abstract: 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 ex les 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.
Publisher: Springer Science and Business Media LLC
Date: 17-07-2018
Publisher: Wiley
Date: 31-07-2017
Publisher: Wiley
Date: 24-04-2022
Abstract: In iduals differ in average phenotypes and in sensitivity to environmental variation. Such context sensitivity can be modelled as random slope variation. Random slope variation implies that the proportion of between‐in idual variation varies across the range of a covariate (environment/context/time/age) and has thus been called ‘conditional’ repeatability. We propose to put conditional repeatabilities in perspective of the total phenotypic variance and suggest a way of standardization using the random slope coefficient of determination . Furthermore, we illustrate that the marginalized repeatability averaged across an environmental gradient offers a biologically relevant description of between‐in idual variation. We provide simple equations for calculating key descriptors of conditional repeatabilities, clarify the difference between random intercept variation and average between‐in idual variation and make recommendations for comprehensive reporting. While we introduce the concept with in idual variation in mind, the framework is equally applicable to other type of between‐group/cluster variation that varies across some (environmental) gradient.
Publisher: California Digital Library (CDL)
Date: 29-10-2021
Publisher: American Society of Plant Taxonomists
Date: 09-2016
Publisher: Springer Science and Business Media LLC
Date: 04-07-2014
Publisher: Wiley
Date: 10-10-2014
DOI: 10.1111/JAV.00413
Publisher: Wiley
Date: 21-04-2021
DOI: 10.1111/EVO.14224
Publisher: Springer Science and Business Media LLC
Date: 12-12-2022
DOI: 10.1038/S41467-022-35266-6
Abstract: Sex differences in the lifetime risk and expression of disease are well-known. Preclinical research targeted at improving treatment, increasing health span, and reducing the financial burden of health care, has mostly been conducted on male animals and cells. The extent to which sex differences in phenotypic traits are explained by sex differences in body weight remains unclear. We quantify sex differences in the allometric relationship between trait value and body weight for 363 phenotypic traits in male and female mice, recorded in million measurements from the International Mouse Phenotyping Consortium. We find sex differences in allometric parameters (slope, intercept, residual SD) are common (73% traits). Body weight differences do not explain all sex differences in trait values but scaling by weight may be useful for some traits. Our results show sex differences in phenotypic traits are trait-specific, promoting case-specific approaches to drug dosage scaled by body weight in mice.
Publisher: California Digital Library (CDL)
Date: 15-07-2020
Publisher: Oxford University Press (OUP)
Date: 11-11-2020
Abstract: Citizen science is fundamentally shifting the future of bio ersity research. But although citizen science observations are contributing an increasingly large proportion of bio ersity data, they only feature in a relatively small percentage of research papers on bio ersity. We provide our perspective on three frontiers of citizen science research, areas that we feel to date have had minimal scientific exploration but that we believe deserve greater attention as they present substantial opportunities for the future of bio ersity research: s ling the unders led, capitalizing on citizen science's unique ability to s le poorly s led taxa and regions of the world, reducing taxonomic and spatial biases in global bio ersity data sets estimating abundance and density in space and time, develop techniques to derive taxon-specific densities from presence or absence and presence-only data and capitalizing on secondary data collection, moving beyond data on the occurrence of single species and gain further understanding of ecological interactions among species or habitats. The contribution of citizen science to understanding the important bio ersity questions of our time should be more fully realized.
Publisher: The Company of Biologists
Date: 06-2021
DOI: 10.1242/JEB.240846
Abstract: Aversive learning – avoiding certain situations based on negative experiences – can profoundly increase fitness in animal species, yet no studies have systematically quantified its repeatability. Therefore, we assessed the repeatability of aversive learning by conditioning approximately 100 zebrafish (Danio rerio) to avoid a colour cue associated with a mild electric shock. Across eight different colour conditions, zebrafish did not show consistent in idual differences in aversive learning (R=0.04). Within conditions, when zebrafish were conditioned to the same colour, blue conditioning was more repeatable than green conditioning (R=0.15 and R=0.02). Overall, aversive learning responses of zebrafish were weak and variable. We speculate that the effect of aversive learning might have been too weak to quantify consistent in idual differences, or directional selection might have eroded additive genetic variance. We also discuss how confounded repeatability assays and publication bias could have inflated estimates of repeatability in the literature.
Publisher: Wiley
Date: 22-07-2021
DOI: 10.1111/EVA.13273
Abstract: Ecological and evolutionary research questions are increasingly requiring the integration of research fields along with larger data sets to address fundamental local‐ and global‐scale problems. Unfortunately, these agendas are often in conflict with limited funding and a need to balance animal welfare concerns. Planned missing data design (PMDD), where data are randomly and deliberately missed during data collection, combined with missing data procedures, can be useful tools when working under greater research constraints. Here, we review how PMDD can be incorporated into existing experimental designs by discussing alternative design approaches and demonstrate with simulated data sets how missing data procedures work with incomplete data. PMDDs can provide researchers with a unique toolkit that can be applied during the experimental design stage. Planning and thinking about missing data early can (1) reduce research costs by allowing for the collection of less expensive measurement variables (2) provide opportunities to distinguish predictions from alternative hypotheses by allowing more measurement variables to be collected and (3) minimize distress caused by experimentation by reducing the reliance on invasive procedures or allowing data to be collected on fewer subjects (or less often on a given subject). PMDDs and missing data methods can even provide statistical benefits under certain situations by improving statistical power relative to a complete case design. The impacts of unplanned missing data, which can cause biases in parameter estimates and their uncertainty, can also be ameliorated using missing data procedures. PMDDs are still in their infancy. We discuss some of the difficulties in their implementation and provide tentative solutions. While PMDDs may not always be the best option, missing data procedures are becoming more sophisticated and more easily implemented and it is likely that PMDDs will be effective tools for a wide range of experimental designs, data types and problems in ecology and evolution.
Publisher: Springer Science and Business Media LLC
Date: 23-05-2023
DOI: 10.1186/S12915-023-01567-5
Abstract: Canadian policymakers are interested in determining whether farmed Atlantic salmon, frequently infected with Piscine orthoreovirus (PRV), may threaten wild salmon populations in the Pacific Northwest. A relevant work has been published in BMC Biology by Polinksi and colleagues, but their conclusion that PRV has a negligible impact on the energy expenditure and respiratory performance of sockeye salmon is disputed by Mordecai and colleagues, whose re-analysis is presented in a correspondence article. So, what is the true effect and what should follow this unresolved dispute? We suggest a ‘registered multi-lab replication with adversaries’.
Publisher: Elsevier BV
Date: 04-2022
DOI: 10.1016/J.JENVMAN.2022.114549
Abstract: Urbanisation of coastal areas and growth in the blue economy drive the proliferation of artificial structures in marine environments. These structures support distinct ecological communities compared to natural hard substrates, potentially reflecting differences in the materials from which they are constructed. We undertook a meta-analysis of 46 studies to compare the effects of different material types (natural or eco-friendly vs. artificial) on the colonising biota on built structures. Neither the abundance nor richness of colonists displayed consistent patterns of difference between artificial and natural substrates or between eco-friendly and standard concrete. Instead, there were differences in the abundance of organisms (but not richness) between artificial and natural materials, that varied according to material type and by functional group. When compared to biogenic materials and rock, polymer and metal supported significantly lower abundances of total benthic species (in studies assessing sessile and mobile species together), sessile invertebrates and corals (in studies assessing these groups in idually). In contrast, non-indigenous species were significantly more abundant on wood than metal. Concrete supported greater abundances of the general community, including habitat-forming species, compared to wood. Our results suggest that the ecological requirements of the biological community, alongside economic, logistic and engineering factors should be considered in material selection for multifunctional marine structures that deliver both engineering and ecological (enhanced abundance and ersity) benefits.
Publisher: Springer Science and Business Media LLC
Date: 04-10-2013
DOI: 10.1007/S10522-013-9471-2
Abstract: Telomere length and the rate of telomere attrition vary between in iduals and have been interpreted as the rate at which in iduals have aged. The biology of telomeres dictates shortening with age, although telomere elongation with age has repeatedly been observed within a minority of in iduals in several populations. These findings have been attributed to error, rather than actual telomere elongation, restricting our understanding of its possible biological significance. Here we present a method to distinguish between error and telomere elongation in longitudinal datasets, which is easy to apply and has few assumptions. Using simulations, we show that the method has considerable statistical power (>80 %) to detect even a small proportion (6.7 %) of TL increases in the population, within a relatively small s le (N = 200), while maintaining the standard level of Type I error rate (α ≤ 0.05).
Publisher: California Digital Library (CDL)
Date: 12-09-2022
Publisher: Elsevier BV
Date: 11-2008
DOI: 10.1016/J.TREE.2008.06.014
Abstract: The most common approach to dealing with missing data is to delete cases containing missing observations. However, this approach reduces statistical power and increases estimation bias. A recent study shows how estimates of heritability and selection can be biased when the 'invisible fraction' (missing data due to mortality) is ignored, thus demonstrating the dangers of neglecting missing data in ecology and evolution. We highlight recent advances in the procedures of handling missing data and their relevance and applicability.
Publisher: Springer Science and Business Media LLC
Date: 21-07-2021
Publisher: PeerJ
Date: 14-08-2018
DOI: 10.7287/PEERJ.PREPRINTS.1216V2
Abstract: Phylogenetic comparative methods (PCMs), especially ones based on linear models, have played a central role in understanding species’ trait evolution. These methods, however, usually assume that phylogenetic trees are known without error or uncertainty, but this assumption is most likely incorrect. So far, Markov chain Monte Carlo, MCMC-based Bayesian methods have mainly been deployed to account for such ‘phylogenetic uncertainty’ in PCMs. Here, we propose an approach with which phylogenetic uncertainty is incorporated in a simple, readily implementable and reliable manner. Our approach uses Rubin’s rules, which are an integral part of a standard multiple imputation procedure, often employed to recover missing data. We see true phylogenetic trees as missing data under this approach. Further, unmeasured species in comparative data (i.e. missing trait data) can be seen as another source of uncertainty in PCMs because arbitrary s ling of species in a given taxon or ‘species s ling uncertainty’ can affect estimation in PCMs. Using two simulation studies, we show our method can account for phylogenetic uncertainty under many different scenarios (e.g. uncertainty in branching and branch lengths) and, at the same time, it can handle missing trait data (i.e., species s ling uncertainty). A unique property of the multiple imputation procedure is that an index, named ‘relative efficiency’, could be used to quantify the number of trees required for incorporating phylogenetic uncertainty. Thus, by using the relative efficiency, we show the required tree number is surprisingly small (~50 trees). However, the most notable advantage of our method is that it could be combined seamlessly with PCMs that utilize multiple imputation to handle simultaneously phylogenetic uncertainty (i.e. missing true trees) and species s ling uncertainty (i.e., missing trait data) in PCMs.
Publisher: Mary Ann Liebert Inc
Date: 04-2018
Abstract: An emergent field of animal personality necessitates a method for repeated high-throughput quantification of behavioral traits across contexts. In this study, we have developed an automated video stimulus approach to sequentially present different contexts relevant to five "personality" traits (exploration, boldness, neophobia, aggression, and sociability), successfully quantifying repeatable trait measurements in multiple in iduals simultaneously. Although our method is designed to quantify personality traits in zebrafish, our approach can accommodate the quantification of other behaviors, and could be customized for other species. All digital materials and detailed protocols are publicly available online for researchers to freely use and modify.
Publisher: Wiley
Date: 25-08-2022
DOI: 10.1111/ELE.14083
Abstract: Understanding the factors affecting thermal tolerance is crucial for predicting the impact climate change will have on ectotherms. However, the role developmental plasticity plays in allowing populations to cope with thermal extremes is poorly understood. Here, we meta-analyse how thermal tolerance is initially and persistently impacted by early (embryonic and juvenile) thermal environments by using data from 150 experimental studies on 138 ectothermic species. Thermal tolerance only increased by 0.13°C per 1°C change in developmental temperature and substantial variation in plasticity (~36%) was the result of shared evolutionary history and species ecology. Aquatic ectotherms were more than three times as plastic as terrestrial ectotherms. Notably, embryos expressed weaker but more heterogenous plasticity than older life stages, with numerous responses appearing as non-adaptive. While developmental temperatures did not have persistent effects on thermal tolerance overall, persistent effects were vastly under-studied, and their direction and magnitude varied with ontogeny. Embryonic stages may represent a critical window of vulnerability to changing environments and we urge researchers to consider early life stages when assessing the climate vulnerability of ectotherms. Overall, our synthesis suggests that developmental changes in thermal tolerance rarely reach levels of perfect compensation and may provide limited benefit in changing environments.
Publisher: California Digital Library (CDL)
Date: 10-11-2018
Publisher: Springer Science and Business Media LLC
Date: 05-03-2020
DOI: 10.1186/S12915-020-0755-0
Abstract: Research synthesis is the process of bringing together findings and attributes from different publications, for ex le, to give a more complete description of phenomena than is usually possible in a single work. We bring the Research Synthesis Series to BMC Biology to promote meta-analyses, other research syntheses including meta-research studies, and research synthesis methodologies in biology, facilitating their dissemination to broader communities.
Publisher: Wiley
Date: 10-2015
Abstract: Conflict and cooperation within and between the sexes are among the driving forces that lead to the evolution of mating systems. Among mating strategies, female genetic polyandry and male reproductive cooperation pose challenging evolutionary questions regarding the maintenance of systems where one sex suffers from reduced fitness. Here, we investigate the consequences of social and genetic polyandry for reproductive success of females and males in a population of the dunnock, Prunella modularis. We show that female multiple mating ameliorates the negative effects of inbreeding. We, however, found little evidence that females engage in extra-group (pair) mating with less related or more heterozygous males. Breeding in socially polyandrous groups reduced the amount of paternity lost to extra-group males, such that, on average, cobreeding and monogamous males fledged a similar number of young. Importantly, c. 30% of cobreeding male dyads were related, suggesting they could gain indirect fitness benefits. Taken together, cobreeding males achieve equivalent reproductive success to monogamous counterparts under most circumstances. Our study has revealed unexpected complexities in the variable mating system of dunnocks in New Zealand. Our results differ from the well-known Cambridge dunnock study and can help our understanding of the evolution and maintenance of various breeding systems in the animal kingdom.
Publisher: Elsevier BV
Date: 11-2016
DOI: 10.1016/J.CUB.2016.07.047
Abstract: Shinichi Nakagawa and Joel Pick introduce what we can learn from house sparrows.
Publisher: Wiley
Date: 18-05-2015
DOI: 10.1111/ELE.12454
Abstract: Estimates of molecular genetic variation are often used as a cheap and simple surrogate for a population's adaptive potential, yet empirical evidence suggests they are unlikely to be a valid proxy. However, this evidence is based on molecular genetic variation poorly predicting estimates of adaptive potential rather than how well it predicts true values. As a consequence, the relationship has been systematically underestimated and the precision with which it could be measured severely overstated. By collating a large database, and using suitable statistical methods, we obtain a 95% upper bound of 0.26 for the proportion of variance in quantitative genetic variation explained by molecular ersity. The relationship is probably too weak to be useful, but this conclusion must be taken as provisional: less noisy estimates of quantitative genetic variation are required. In contrast, and perhaps surprisingly, current s ling strategies appear sufficient for characterising a population's molecular genetic variation at comparable markers.
Publisher: Wiley
Date: 07-2021
Abstract: Research weaving is an approach that combines systematic mapping methods with bibliometric and scientometric analyses, shedding light on how research in a systematic map is connected or disconnected. Given its novelty, few ex les exist that demonstrate methods for research weaving or highlight its value in the evidence synthesis context. Here, we seek to fill this gap by applying a research weaving analysis to a previously published systematic map on the roles of buffer strips in agricultural fields. This work identified a lack of studies addressing multifunctional roles of buffer strips and a remarkable array of terminology used by researchers to describe buffer strips. Using network visualization, such as co‐authorship and bibliographic coupling networks, as well as content and text analyses, we aim to build on these findings addressing questions related to collaboration, disciplinary contributions and citation and term usage patterns. As a result of this work, we aim to provide workflows, tools, and recommendations for the application of research weaving across a wide range of evidence maps in any domain. We will discuss the unique challenges of conducting bibliometric analysis in an evidence synthesis context and will propose solutions to address these challenges.
Publisher: Wiley
Date: 03-2011
DOI: 10.1002/DEV.20538
Abstract: In iduals are often consistent in their behavior but vary from each other in the level of behavior shown. Despite burgeoning interest in such animal personality variation, studies on invertebrates are scarce, and studies on clonal invertebrates nonexistent. This is surprising given the obvious advantages of using invertebrates/clones to tackle the crucial question why such consistent behavioral differences exist. Here we show that in iduals of clonal pea aphids exhibit consistent behavioral differences in their escape responses to a predator attack (dropping vs. nondropping off a plant). However, behavior was not repeatable at the clonal level. Genetically identical clones expressed various phenotypes but different clones produced different proportions of each phenotype (dropper, nondropper, and inconsistent). Manipulations of early environmental conditions had little qualitative impact on such patterns. We discuss the importance of our findings for future studies of the evolutionary and ecological consequences of personality variation.
Publisher: Wiley
Date: 29-03-2021
DOI: 10.1111/BRV.12712
Abstract: Physical exercise not only helps to improve physical health but can also enhance brain development and cognition. Recent reports on parental (both maternal and paternal) effects raise the possibility that parental exercise may provide benefits to offspring through intergenerational inheritance. However, the general magnitude and consistency of parental exercise effects on offspring is still controversial. Additionally, empirical research has long overlooked an important aspect of exercise: its effects on variability in neurodevelopmental and cognitive traits. Here, we compiled data from 52 studies involving 4786 rodents (412 effect sizes) to quantify the intergenerational transmission of exercise effects on brain and cognition. Using a multilevel meta‐analytic approach, we found that, overall, parental exercise showed a tendency for increasing their offspring's brain structure by 12.7% (albeit statistically non‐significant) probably via significantly facilitating neurogenesis (16.5%). Such changes in neural anatomy go in hand with a significant 20.8% improvement in neurobehaviour (improved learning and memory, and reduced anxiety). Moreover, we found parental exercise significantly reduces inter‐in idual differences (i.e. reduced variance in the treatment group) in progeny's neurobehaviour by 10.2% (coefficient of variation ratio, lnCVR), suggesting the existence of an in idual by intervention interaction. The positive effects of exercise are modulated by several covariates (i.e. moderators), such as the exercised parent's sex, offspring's sex, and age, mode of exercise, and exercise timing. In particular, parental forced exercise is more efficient than voluntary exercise at significantly improving offspring neurobehaviour (26.0%) and reducing its variability (14.2%). We observed larger effects when parental exercise started before pregnancy. However, exercising only during pregnancy also had positive effects. Mechanistically, exercise significantly upregulated brain‐derived neurotrophic factor (BDNF) by 28.9%, vascular endothelial growth factor (VEGF) by 35.8%, and significantly decreased hippoc al DNA methylation by 3.5%, suggesting that brain growth factor cascades and epigenetic modifications can moderate the transmission of parental exercise effects. Collectively, by coupling mean with variance effects, our analyses draw a more integrated picture of the benefits that parental exercise has on offspring: not only does it improve offspring brain development and cognitive performance, but it also reduces inter‐in idual differences in cognition‐related traits. We advocate that meta‐analysis of variation together with the mean of a trait provides novel insights for old controversies as well as emerging new questions, opening up a new era for generating variance‐based hypotheses.
Publisher: Public Library of Science (PLoS)
Date: 21-06-2017
Publisher: Wiley
Date: 10-11-2022
Abstract: Publication bias threatens the validity of quantitative evidence from meta‐analyses as it results in some findings being overrepresented in meta‐analytic datasets because they are published more frequently or sooner (e.g. ‘positive’ results). Unfortunately, methods to test for the presence of publication bias, or assess its impact on meta‐analytic results, are unsuitable for datasets with high heterogeneity and non‐independence, as is common in ecology and evolutionary biology. We first review both classic and emerging publication bias tests (e.g. funnel plots, Egger's regression, cumulative meta‐analysis, fail‐safe N , trim‐and‐fill tests, p ‐curve and selection models), showing that some tests cannot handle heterogeneity, and, more importantly, none of the methods can deal with non‐independence. For each method, we estimate current usage in ecology and evolutionary biology, based on a representative s le of 102 meta‐analyses published in the last 10 years. Then, we propose a new method using multilevel meta‐regression, which can model both heterogeneity and non‐independence, by extending existing regression‐based methods (i.e. Egger's regression). We describe how our multilevel meta‐regression can test not only publication bias, but also time‐lag bias, and how it can be supplemented by residual funnel plots. Overall, we provide ecologists and evolutionary biologists with practical recommendations on which methods are appropriate to employ given independent and non‐independent effect sizes. No method is ideal, and more simulation studies are required to understand how Type 1 and Type 2 error rates are impacted by complex data structures. Still, the limitations of these methods do not justify ignoring publication bias in ecological and evolutionary meta‐analyses.
Publisher: Wiley
Date: 03-04-2017
DOI: 10.1111/JEB.13058
Abstract: Reproductive success is associated with age in many taxa, increasing in early life followed by reproductive senescence. In socially monogamous but genetically polygamous species, this generates the interesting possibility of differential trajectories of within-pair and extra-pair siring success with age in males. We investigate these relationships simultaneously using within-in idual analyses with 13 years of data from an insular house sparrow (Passer domesticus) population. As expected, we found that both within- and extra-pair paternity success increased with age, followed by a senescence-like decline. However, the age trajectories of within- and extra-pair paternity successes differed significantly, with the extra-pair paternity success increasing faster, although not significantly, in early life, and showing a delayed decline by 1.5 years on average later in life compared to within-pair paternity success. These different trajectories indicate that the two alternative mating tactics should have age-dependent pay-offs. Males may partition their reproductive effort between within- and extra-pair matings depending on their current age to reap the maximal combined benefit from both strategies. The interplay between these mating strategies and age-specific mortality may explain the variation in rates of extra-pair paternity observed within and between species.
Publisher: Elsevier BV
Date: 10-2004
Publisher: Springer Science and Business Media LLC
Date: 24-04-2023
DOI: 10.1186/S13750-023-00301-6
Abstract: Meta-analysis is a quantitative way of synthesizing results from multiple studies to obtain reliable evidence of an intervention or phenomenon. Indeed, an increasing number of meta-analyses are conducted in environmental sciences, and resulting meta-analytic evidence is often used in environmental policies and decision-making. We conducted a survey of recent meta-analyses in environmental sciences and found poor standards of current meta-analytic practice and reporting. For ex le, only ~ 40% of the 73 reviewed meta-analyses reported heterogeneity (variation among effect sizes beyond s ling error), and publication bias was assessed in fewer than half. Furthermore, although almost all the meta-analyses had multiple effect sizes originating from the same studies, non-independence among effect sizes was considered in only half of the meta-analyses. To improve the implementation of meta-analysis in environmental sciences, we here outline practical guidance for conducting a meta-analysis in environmental sciences. We describe the key concepts of effect size and meta-analysis and detail procedures for fitting multilevel meta-analysis and meta-regression models and performing associated publication bias tests. We demonstrate a clear need for environmental scientists to embrace multilevel meta-analytic models, which explicitly model dependence among effect sizes, rather than the commonly used random-effects models. Further, we discuss how reporting and visual presentations of meta-analytic results can be much improved by following reporting guidelines such as PRISMA-EcoEvo (Preferred Reporting Items for Systematic Reviews and Meta-Analyses for Ecology and Evolutionary Biology). This paper, along with the accompanying online tutorial, serves as a practical guide on conducting a complete set of meta-analytic procedures (i.e., meta-analysis, heterogeneity quantification, meta-regression, publication bias tests and sensitivity analysis) and also as a gateway to more advanced, yet appropriate, methods.
Publisher: Elsevier BV
Date: 2022
Location: United Kingdom of Great Britain and Northern Ireland
Start Date: 2016
End Date: 2019
Funder: Marsden Fund
View Funded ActivityStart Date: 2017
End Date: 2020
Funder: Marsden Fund
View Funded ActivityStart Date: 2013
End Date: 2018
Funder: Rutherford Discovery Fellowship
View Funded ActivityStart Date: 07-2023
End Date: 06-2026
Amount: $420,909.00
Funder: Australian Research Council
View Funded ActivityStart Date: 02-2015
End Date: 10-2019
Amount: $872,240.00
Funder: Australian Research Council
View Funded ActivityStart Date: 06-2021
End Date: 05-2025
Amount: $421,510.00
Funder: Australian Research Council
View Funded ActivityStart Date: 03-2018
End Date: 05-2021
Amount: $298,409.00
Funder: Australian Research Council
View Funded ActivityStart Date: 2020
End Date: 06-2023
Amount: $473,782.00
Funder: Australian Research Council
View Funded Activity