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opencc-zeroMar 2023View details →

Impacts of ecological restoration on the genetic diversity of plant species: A global meta-analysis

1. In contrast to the depth of knowledge available for the enhancement of plant species diversity and ecosystem services through ecological restoration, our understanding of how ecological restoration impacts genetic diversity (GD) of plant species has not yet been synthesized. 2. We performed a global meta-analysis to examine whether ecological restoration improved GD of plant species in restored populations. First, we compared the GD of restored populations with reference or degraded populations. Second, we explored whether the influence of ecological restoration on plant GD varies between species with different characteristics (life form and threat status), between different restoration strategies (active/passive, seeding/planting, mixture/non-mixture) or between different restoration times (<50 and ≥50 years; with an average of 29.3 years). 3. The GD of restored populations was significantly lower (HE, 1.06%; PPB, 5.10%, and SWI, 4.95%) than in reference populations but was comparable to degraded populations. The inbreeding coefficient (FIS, the proportion by which the heterozygosity of an individual is reduced by inbreeding) was consistently comparable between restored populations and reference or degraded populations. 4. Woody species but not herbs had significantly lower GD in restored populations than in reference populations. Forest but not grassland ecosystem had significantly lower GD in restored populations than in reference populations. Passive but not active restoration, seeding rather than planting, and mixing materials from different sources rather than using a single source, all significantly increased the GD of restored populations. When the restoration time was ≥50 years, in contrast to <50 years, GD was comparable between the restored and reference populations. 5. Synthesis and applications. In general, ecological restoration did not significantly improve the GD of plant species compared to reference or degraded populations. This might be due in part to the relatively short restoration time. Using passive restoration, seeding, and mixed sources could significantly increase the GD of restored populations. We emphasize that GD should not be treated as a minor cobenefit of ecological restoration for other purposes and that the recovery of GD should be listed as a vital goal in future ecological restoration with plant species.

opencc-by-4.0Dec 2022View details →

Meta-analysis of diurnal transcriptomics in mouse liver reveals low repeatability of rhythm analyses

The accumulation of public transcriptomic timeseries data enables robust meta-analyses that were not possible until recently. To assess the consistency of biological rhythms across studies, 57 public mouse liver tissue timeseries totaling 1096 RNA-seq samples were obtained and analyzed. Only the control groups of each study were included, to create comparable data. Technical factors in RNA-seq library preparation were the largest contributors to transcriptome-level differences, beyond biological or experiment-specific factors such as lighting conditions. Core clock genes were remarkably consistent in phase across all studies. Overlap of genes identified as rhythmic across studies was generally low, with no pair of studies having over 60% overlap. Distributions of phases of significant genes were remarkably inconsistent across studies, but the genes that consistently identified as rhythmic had acrophase clustering near ZT0 and ZT12. Despite the discrepancies between single-study analyses, cross-study analyses found substantial consistency. Running compareRhythms on each pair of studies identified a median of only 11% of the identified rhythmic genes as rhythmic in only one of the two studies. Data was integrated across studies in a JIVE analysis, which showed that the top two components of joint within-study variation are determined by time of day. A shape-invariant model with random effects was fit to the genes to identify the underlying shape of the rhythms, consistent across all studies, including identifying 72 genes with consistently multiple peaks. This dataset accumulates the quantified values from the 1096 samples along with the sample and study meta-data, and the results of JTK and BooteJTK methods run on each of the individual studies. It also includes the spline-fit curves results from the Shape Invarient Models (SIM).

opencc-zeroApr 2023View details →

Data from: A meta-analysis of plant tissue O2 dynamics

This dataset includes 1,567 recorded tissue O2 levels from 112 plant species extracted from published literature. The data forms the basis of the publication "A meta-analysis of plant tissue O2 dynamics" with the following abstract: Adequate tissue O2 supply is crucial for plant functioning. We therefore aimed at identifying environmental conditions and plant characteristics affecting plant tissue O2 status. We extracted data and performed meta-analysis on > 1,500 published tissue O2 measurements from 112 species. Tissue O2 status ranged from anoxic conditions in especially roots, to > 53 kPa in submerged, photosynthesizing shoots. Using information-theoretic model selection, we identified 'submergence', 'light', 'tissue type' as well as 'light × submergence' interaction as significant drivers of tissue O2 status. Median O2 status was especially low (< 50% of atmospheric equilibrium) in belowground rhizomes, potato tubers and root nodules. Mean shoot and root O2 was ~25% higher in light than in dark when shoots had atmospheric contact. However, light showed a significant interaction with submergence on plant O2, with a submergence-induced 44% increase in light, compared with a 42% decline in dark, relative to plants with atmospheric contact. During submergence, ambient water column O2 and shoot tissue O2 correlated stronger in darkness than in light conditions. Although miniaturised Clark-type O2 electrodes in particular have resulted in enhanced understanding of plant O2 dynamics, the use of non-invasive methods is still lacking behind its widespread use in mammalian tissues.

opencc-zeroApr 2023View details →

A meta-analysis of how parasites affect host consumption rates

Parasites are known to mediate trophic interactions and can, for example, modify how consumers acquire resources. These modifications of host feeding behaviour can be imposed through three interconnected mechanisms affecting: (1) host food acquisition, (2) host food digestion or (3) host energy budgets. As a result, infected hosts may consume more, less or the same amount of food compared to their uninfected conspecifics. It is commonly assumed that infected hosts have lower consumption rates than uninfected hosts, but a comprehensive quantitative synthesis investigating the effects of parasites on host consumption rate has been lacking thus far. To fill this knowledge gap, we systematically searched for experimental studies that evaluated changes in consumption rate of infected vs uninfected hosts. In total, we extracted 158 effect sizes from 68 studies. We then performed meta-analyses of mean differences in host consumption rates and their variation. The analyses were carried out for all taxonomic groups as well as separately for vertebrate and invertebrate hosts. The main-effects meta-analyses confirmed a generally negative effect of parasites on host consumption rates; infected hosts consumed on average 25% less food than their uninfected conspecifics. In addition, there was a significant increase in the variability in host consumption rate, on average by 25%, indicating that parasites can have variable effects on the foraging behaviour of their hosts. The meta-regression models revealed that several moderator variables related to host and parasite characteristics influence host consumption rate. Experimental infection had a stronger influence on variance effects than natural infection. Parasitic infections reduced consumption rate of vertebrate hosts by 28% and thus more strongly than those of invertebrates, which were reduced by 22%. We conclude with recommendations to facilitate future ecological research syntheses on host-parasite interactions and beyond.

opencc-by-4.0May 2023View details →

The efficacy and safety of meal replacement in patients with type 2 diabetes: a systematic review and meta-analysis

There are supplemental materials for a systematic review and meta-analysis, which studied the efficacy and safety of meal replacement in patients with type 2 diabetes, with a focus on subgroup analysis of variable participant characteristics and MR prescription.

openother-openMay 2023View details →

Data and code for "Brehm et al. (2023) The complexity of micro- and nanoplastic research in the genus Daphnia – A systematic review of study variability and a meta-analysis of immobilization rates"

All data and R code for Brehm, J., Ritschar, S., Laforsch, C. and Mair, M.M. (2023). The complexity of micro- and nanoplastic research in the genus Daphnia – A systematic review of study variability and a meta-analysis of immobilization rates. Journal of Hazardous Materials 458: 131839. (<a href="https://doi.org/10.1016/j.jhazmat.2023.131839">https://doi.org/10.1016/j.jhazmat.2023.131839</a>) Abstract In recent years, the number of publications on nano- and microplastic particles (NMPs) effects on freshwater organisms has increased rapidly. Freshwater crustaceans of the genus Daphnia are widely used in ecotoxicological research as model organisms for assessing the impact of NMPs. However, the diversity of experimental designs in these studies makes conclusions about the general impact of NMPs on Daphnia challenging. To approach this, we systematically reviewed the literature on NMP effects on Daphnia and summarized the diversity of test organisms, experimental conditions, NMP properties and measured endpoints to identify gaps in our knowledge of NMP effects on Daphnia. We use a meta-analysis on mortality and immobilization rates extracted from the compiled literature to illustrate how NMP properties, study parameters and the biology of Daphnia can impact outcomes in toxicity bioassays. In addition, we investigate the extent to which the available data can be used to predict the toxicity of untested NMPs based on the extracted parameters. Based on our results, we argue that focusing on a more diverse set of NMP properties combined with a more detailed characterization of the particles in future studies will help to fill current research gaps, improve predictive models and allow the identification of NMP properties linked to toxicity.

opencc-zeroMay 2023View details →

The effects of urbanisation on pollinators and pollination: A meta-analysis

Urbanisation is increasing worldwide, with major impacts on biodiversity, species interactions and ecosystem functioning. Pollination is an ecosystem function vital for terrestrial ecosystems and food security; however, the processes underlying the patterns of pollinator diversity and the ecosystem services they provide in cities have seldom been quantified. Here, we perform a comprehensive meta-analysis of 133 studies examining urbanisation effects on pollinator diversity and pollination. Our results confirm the widespread negative impacts of urbanisation on pollinator richness and abundance, with Lepidoptera being the most affected group. Furthermore, pollinator responses were found to be trait-specific, with below-ground nesting and solitary Hymenoptera and spring flyers more severely affected by urbanisation. Meanwhile, cities promote non-native pollinators, which may exacerbate conservation risks to native species. Surprisingly, despite the negative effects of urbanisation on pollinator diversity, pollination service measured as seed set is enhanced in non-tropical cities likely due to abundant generalists and managed pollinators therein. We emphasize that the richness of local flowering plants could mitigate the negative impacts of urbanisation on pollinator diversity. Overall, the results demonstrate the varying magnitudes of multiple moderators on urban pollinators and pollination service provision and could help guide conservation actions for biodiversity and ecosystem function for a sustainable future.

opencc-zeroJun 2023View details →

Dryland soil restoration meta-analysis data

This dataset was used to conduct a meta-analysis on soil restoration in global drylands. It includes data collected from published literature on experiments of soil-based restoration in dryland environments. Predictor variables included in this dataset are site aridity and percent soil sand, type of restoration treatment used, whether seeding or revegetating was done, and time since restoration. Response variables include the effect of soil restoration on aggregate stability, bulk density, volumetric water content, soil organic carbon, soil nitrogen, mycorrhizal colonization, and basal respiration. The calculated effect size on each of these variables is represented as the log response ratio.

opencc-zeroJun 2023View details →

Data for: Meta analysis reveals impacts of disturbance on reptile and amphibian body condition

Ecosystem disturbance is increasing in extent, severity, and frequency across the globe. To date, research has largely focused on the impacts of disturbance on animal population size, extinction risk, and species richness. However, individual responses, such as changes in body condition, can act as more sensitive metrics and may provide early warning signs of reduced fitness and population declines. We conducted the first global systematic review and meta-analysis investigating the impacts of ecosystem disturbance on reptile and amphibian body condition. We collated 384 effect sizes representing 137 species from 133 studies. We tested how disturbance type, species traits, biome, and taxon moderate the impacts of disturbance on body condition. We found an overall negative effect of disturbance on herpetofauna body condition (Hedges' g = -0.37, 95%CI: -0.57, -0.18). Disturbance type was an influential predictor of body condition response and all disturbance types had a negative mean effect. Drought, invasive species, and agriculture had the largest effects. The impact of disturbance varied in strength and direction across biomes, with the largest negative effects found within Mediterranean and temperate biomes. In contrast, taxon, body size, habitat specialisation, and conservation status were not influential predictors of disturbance effects. Our findings reveal the widespread effects of disturbance on herpetofauna body condition and highlight the potential role of individual-level response metrics in enhancing wildlife monitoring. The use of individual response metrics alongside population and community metrics would deepen our understanding of disturbance impacts by revealing both early impacts and chronic effects within affected populations. This could enable early and more informed conservation management.

opencc-by-4.0Jul 2023View details →

Data and R code for: "Global meta-analysis shows reduced quality of food crops under inadequate animal pollination"

R code, data, and metadata for the study "Global meta-analysis shows reduced quality of food crops under inadequate animal pollination"

Towards a mechanistic understanding of variation in aquatic food chain length revealed by meta-analysis

Ecologists have long sought to understand the forces determining food chain lengths (FCLs). Multiple hypotheses have proposed a diverse array of potential environmental determinants of FCL, typically including ecosystem size, resource productivity, and disturbance. Yet, many empirical studies have found that FCL responses to these environmental variables can be positive as well as negative. To explain such mixed responses, we develop a simple yet comprehensive, site-occupancy dynamic framework for complex food webs by integrating multiple environmental drivers. With the competition-colonization tradeoff among basal species, our model shows that increasing ecosystem size results in a monotonic increase in FCL as a whole, while FCL displays a non-linear, oscillatory response to resource productivity or disturbance in benign environments. These predictions are generally supported by our meta-analysis of an empirical dataset compiled from diverse aquatic ecosystems. Therefore, this unifying framework offers a novel mechanistic explanation for observed variation in FCLs driven by multiple environmental factors.

Flower strip effectiveness for pollinating insects in agricultural landscapes depends on established contrast in habitat quality: A meta-analysis

Flower strips have become a prevalent measure in agricultural landscapes to counteract biodiversity loss and especially promote pollinators. Although their benefits for pollinating insects have been frequently evaluated and reported, generalized conclusions about optimal settings for effective flower strips are still difficult. From the perspective of pollinators, flower strips vary distinctly in habitat quality, and the same applies for the control sites selected for scientific studies. In this study, we used a meta-analytic approach based on a systematic review of recent studies (2009-2020) to analyze the relationship between flower strip effectiveness for pollinators and the contrast in habitat quality between flower strips and control sites. We extracted 350 data entries from 29 out of 172 studies based on available data for richness or abundance of the pollinator taxa groups Apiformes, Lepidoptera and Syrphidae as response variables, for both flower strips and control treatments. All flower strips and control treatments were assigned a habitat quality score including information on spatial dimension, floral resources and management. Moreover, we included information on landscape complexity as measured by percent cover of semi-natural habitats in the studied landscape. In general, our results of meta-analytical models showed an increasing effect size of flower strips on pollinators for higher contrasts in habitat quality between flower strips and control treatments. This relationship was consistent across pollinator taxa and different levels of landscape complexity. Altogether, in terms of pollinator habitat quality, high-quality flower strips were more attractive than low-quality flower strips, and the reported effectiveness of flower strips decreased from low-quality to high-quality control treatments. We recommend that results of future studies evaluating flower strips for pollinators are always linked with the contrast in habitat quality between selected flower strips and control treatments.

Data for: Developmental plasticity in anurans: meta-analysis reveals effects of larval environments on size at metamorphosis and timing of metamorphosis

Many anuran amphibians (frogs and toads) rely on aquatic habitats during their larval stage. The quality of this environment can significantly impact the overall lifetime fitness and dynamics of the population. Over 450 studies have been published on the impact of the environment on anuran developmental plasticity, yet we lack a synthesis of these effects across different environments. We conducted a meta-analysis and used a comparative approach to understand whether developmental plasticity in response to different larval environments produces predictable changes in metamorphic phenotypes. We analyzed data from 124 studies spanning 80 anuran species and six larval environments and showed that interspecific variation in mass at metamorphosis and the duration of the larval period is partly explained by the type of environment experienced during the larval period. Phylogenetic relationships among species were not associated with variation in mass at metamorphosis plasticity or duration of the larval period plasticity. Larval environments tended to reduce mass at metamorphosis relative to control conditions, with the degree of change depending on the identity and severity of environmental change. Higher temperatures and lower water levels shortened the duration of the larval period, whereas less food and higher densities increased the duration of the larval period. Our results provide a foundation for future studies on developmental plasticity, especially in response to global changes. This study provides motivation for additional work that links developmental plasticity with fitness consequences within and across life stages, as well as how the outcomes described here are altered in compounding environments.

Geographical trends of soil-associated biodiversity changes due to tree plantations in South America: biome and climate constraints revealed through meta-analysis

Aim Evaluate the interaction between climate and biome structure when explaining changes in species richness of soil-associated communities due to tree plantations developed in different biomes. Compare the response of plants, soil invertebrates, and soil microorganisms, and test whether they should be considered sensitive-coupled biotas. Location Continental South America. Time period 1996–2023 Major taxa studied Plants, soil invertebrates and soil microorganisms Methods Through a meta-analysis, the change in species richness (i.e., response ratio) associated with tree plantations was evaluated in 127 points of study across South America, considering soil-associated communities of plants, invertebrates and microorganisms. The influence of biome structure (open vs. closed habitats) on the response ratio and its interaction with the actual evapotranspiration (AET) and temperature seasonality was evaluated. Differentiated responses of different taxa were tested by comparing models with and without an interaction term referring to the taxon studied. The regional agricultural cover and plantation age were considered as anthropogenic variables. Results Models containing the AET were better at explaining the trend of change in species richness than those with temperature seasonality. The response to the change in species richness was oppositely related to the AET in open and closed biomes. Plants presented a higher loss in species richness than soil invertebrates and microorganisms. The three taxa were positively associated with AET, while seasonality was not relevant in any case. Both anthropogenic variables significantly lessened the change in species richness in all models. Main conclusions The structural contrast between the anthropogenic habitat and the biome where it is developed is a key factor influencing the response of soil-associated communities to tree plantations. Nevertheless, its influence must be assessed together with climatic and anthropogenic variables given that their interaction can explain different geographical trends in the change in species richness across regions.

opencc-by-4.0Aug 2023View details →

Plant invasion and fertilizer addition alter soil biota and their functions: A global meta-analysis

Datasets used for meta-analysis on plant invasion and fertilizer addition effects on soil biota and their functions.

opencc-zeroAug 2023View details →

Differences in pathogen resistance between diploid and polyploid plants: a systematic review and meta-analysis

Polyploidy, the state of having more than two full sets of chromosomes, has been hypothesized to provide several evolutionary advantages to flowering plants, including increased ability to resist pathogens and parasites. However, studies comparing pathogen resistance in conspecific and congeneric diploids and polyploids have produced mixed results. While the supposed relationship between polyploidy and pathogen resistance has been commented on in several narrative reviews, it has never been subjected to a systematic meta-analysis. We examined the effect of polyploidy on pathogen resistance by synthesizing 214 effect sizes from 128 studies. We find that, overall, there is no consistent effect of polyploidy on pathogen resistance. Subgroup analyses suggest that polyploids perform significantly better than diploids only in resisting hemibiotrophic pathogens, and autopolyploids tend show greater resistance than allopolyploids. This is surprising given the fact that polyploids possess extra allele copies of R-gene alleles that provide resistance to biotrophic pathogens, and this pattern may indicate that signaling cascades needed to elicit hypersensitive responses are disrupted by polyploidy. Disruption is supported by the observation that, across all pathogens, autopolyploids show significantly greater resistance compared to diploids, whereas allopolyploids do not. This is corroborated by the observation that synthetic autopolyploids perform significantly better than their allopolyploid and established counterparts. Regarding pathogen type, diploids show greater resistance than polyploids to pathogens that are fungi or nematodes. Analyses of publication bias indicate little to no bias, and analyses of heterogeneity indicate that phylogeny explains almost none of the observed heterogeneity. These results underscore the importance of not only systematic review but also the strong degree to which the effects of polyploidy depend on ecological context.

opencc-zeroAug 2023View details →

A meta-analysis investigating the effects of energy infrastructure proximity on grouse demography and space use

The increased global demand for energy will require additional tools to help guide policy and management actions to conserve wildlife. Grouse (Tetraoninae) are adversely affected by infrastructure associated with energy development, but the magnitude of effects are difficult to quantify in a singular management prescription. Advancement in monitoring and analysis techniques have allowed researchers to evaluate complex questions surrounding the effects of infrastructure on grouse populations, rapidly increasing our knowledge. To better inform management decisions, especially with the emergence of renewable energy, a quantitative synthesis of previous research evaluating the effects of infrastructure on grouse populations is needed. We reviewed studies evaluating the effect of energy infrastructure on grouse, with the main objective to determine the magnitude of effect on grouse lek attendance, resource selection, and survival to help inform future conservation actions. We modeled slope coefficients for distance to energy infrastructure, standardized by scale, on various behaviors to determine overall effect sizes in a meta-analysis. We used 93 study-result combinations from 21 studies that directly evaluated resource selection, survival, or lek attendance relative to energy infrastructure. Trends in overall effect sizes suggest an adverse effect of distance to energy infrastructure on grouse behavior; however, the combination of non-significant pooled regression slopes and high among-study heterogeneity suggest the effect of distance to energy infrastructure is context dependent. While distance to infrastructure is a common metric used in many grouse management plans, our results suggest distance to infrastructure may not be a reliable predictor of grouse behavior and the effect is context dependent making management prescriptions based solely on distance to infrastructure in a one size fits all approach difficult. Our analysis points to numerous aspects that scientists can improve upon by evaluating density in conjunction with distance to energy infrastructure as well as reporting the necessary statistics for future meta-analyses.

opencc-by-4.0Sep 2023View details →

The effect of microplastics on Daphnia fitness – systematic review and meta-analysis.

Systematic review on studies on micro/nanoplastic effect on Daphnia published up to 27 April 2022, including a meta-analysis on the effect of micro/nanoplastics on Daphnia reproduction.

opencc-by-4.0Aug 2023View details →

The Prognostic Value of COX-2 in Predicting Metastasis of Patients with Colorectal Cancer: A systematic review and meta analysis.

The Prognostic Value of COX-2 in Predicting Metastasis of Patients with Colorectal Cancer: A systematic review and meta analysis.