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opencc-by-4.0Aug 2022View details →

Extreme weather events threaten biodiversity and functions of river ecosystems: dataset for conducting the meta-analysis

This repository contains the code and dataset to replicate the meta-analysis conducted by Sabater et al. entitled "Extreme weather events threaten biodiversity and functions of river ecosystems: evidence from a meta-analysis" Metadata: - metaanalysis_GlobalEvidenceRivers_Rscript.R - R Script to conduct the meta-analysis - structural_resp.csv - table with data to perform the species richness, density, and biomass meta-analysis. It includes the mean, SD (or SE), and sample number of the studies included in the meta-analysis, as well as information on the paper authors, year of publication, and type of study (experimental or observational). It also includes co-variates and the author who subtracts the information from the paper. - functional_resp.csv - table with data to perform the primary productivity, respiration, and decomposition meta-analysis. It includes the mean, SD (or SE), and sample number of the studies included in the meta-analysis, as well as information on the paper authors, year of publication, and type of study (experimental or observational). It also includes co-variates and the author who subtracts the information from the paper. -refMap.csv - Geographical information of the papers included in the meta-analysis.

opencc-zeroDec 2021View details →

Pollination deficits and contributions of pollinators in apple production: a global meta-analysis

1. Apple is one of the most widely cultivated fruit crops worldwide, and apple yield benefits from pollination by insects. The global decline in wild pollinator populations raises concern about the adequacy of pollination services in apple production. 2. Here, we present a global meta-analysis of pollination in apple. We assembled from the literature a dataset comprising results of 48 studies across five continents on fruit set and seed set in apple with insect pollination, artificial pollination and pollinator exclusion, and analysed the effects of explanatory factors such as variety and continent. 3. Fruit set was on average 41% lower with open pollination than with artificial pollination, while seed set was 20% lower. These pollination deficits varied across continents and cultivars. Pollination deficits for fruit set were greatest in Asia (63%) followed by Europe (30%), whereas pollination deficits for seed set were greatest in Asia (47%) and South America (40%). Important differences in pollination deficit were also identified between cultivars but these differences were confounded with continent effects. 4. Fruit set and seed set were 71% and 62% higher, respectively, when insects had open access to flowers than when they were artificially excluded, while results varied among cultivars. 5. Synthesis and Applications. Globally, there are substantial contributions of pollinators to fruit set and seed set in apple, as well as considerable limitations in apple pollination services, particularly in Asia, Europe and South America. Several management strategies could be applied to reduce the pollination deficits in apple production: (1) conserving wild bees and enhancing their abundance and diversity, (2) using managed bees for pollination, (3) using varieties with low pollinator dependency, and/or (4) artificial pollination. These strategies should be tailored to the regional situation, considering the potential of landscapes for restoring wild pollinators, the acceptability of cultivated varieties for available pollinators, the acceptance in the market of self-compatible varieties, and the costs of management, such as artificial pollination, pollinator conservation, beekeeping and planting self-compatible varieties. Conservation of wild pollinators is preferred in regions with sufficient potential for wild pollinators as it contributes to biodiversity conservation and improves pollination in both crops and wild plants.

opencc-zeroAug 2022View details →

Data from: Worldwide impacts of landscape anthropization on mosquito abundance and diversity: a meta-analysis

In recent decades, the emergence and resurgence of vector-borne diseases have been well documented worldwide, especially in tropical regions where protection and defence tools for human populations are still very limited. In this context, the dynamics of pathogens are influenced by landscape anthropization (i.e., urbanization, deforestation, and agricultural development), and one of the mechanisms through which this occurs is a change in the abundance and/or diversity of the vectors. An increasing number of empirical studies have described heterogeneous effects of landscape anthropization on vector communities; therefore, it is difficult to have an overall picture of these effects on a global scale. Here, we performed a meta-analysis to quantify the impacts of landscape anthropization on a global scale on the presence/abundance and diversity of mosquitoes, the most important arthropods affecting human health. We obtained 338 effect sizes on 132 mosquito species, compiled from 107 studies in 52 countries that covered almost every part of the world. The results of the meta-analysis showed an overall decline of mosquito presence/abundance and diversity in response to urbanization, deforestation, and agricultural development, except for a few mosquito species that have been able to exploit landscape anthropization well. Our results highlighted that these few favoured mosquito species are those of global concern. They thus provide a better understanding of the overall effect of landscape anthropization on vector communities and, more importantly, suggest a greater risk of emergence and transmission of vector-borne diseases in human-modified landscapes.

opencc-zeroAug 2022View details →

Quantifying the ecological impacts of alien aquatic macrophytes: A global meta‐analysis of effects on fish, macroinvertebrate and macrophyte assemblages

Biological invasions constitute a pervasive and growing threat to the biodiversity and functioning of freshwater ecosystems. Macrophytes are key primary producers and ecosystem engineers in freshwaters, meaning that alien macrophyte invasions have the capacity to alter the structure and function of recipient aquatic ecosystems profoundly. Although prevailing wisdom holds that alien macrophyte invasions tend to compromise freshwater ecosystem structure and function, the ecological impacts of alien macrophyte invasion have not been quantitatively reviewed to date. Here we present a global meta-analysis of 202 cases from 53 research articles, exploring the impacts of alien macrophyte invasion on the abundance and diversity of three ubiquitous and ecologically important focal groups, which together comprise the bulk of non-microbial freshwater biodiversity: resident macrophytes, macroinvertebrates and fish. Our synthesis includes data from all continents except Antarctica and Asia, covering 25 alien macrophyte species, but reveals considerable taxonomic and geographical biases in knowledge. Meta-analysis results reveal that invasion by alien macrophytes has an overall negative impact on taxonomic diversity of the three focal groups, but no consistent effect on abundance. At a finer resolution, we detect a strong negative effect of alien macrophyte invasion on resident macrophyte abundance and diversity, and a significant but smaller positive effect of submerged alien macrophyte invasion on macroinvertebrates. Effects on fish appear inconsistent. Our findings emphasise the importance of context- and taxon-specific ecological research in informing appropriate and proportionate management of alien macrophyte invasions, since alien macrophyte impacts are not consistently negative. We also identify significant geographical and taxonomic limitations in existing studies, quantitative data being lacking for many alien taxa.

opencc-zeroOct 2022View details →

Data and code – Effects of climate on salmonid productivity: A global meta-analysis across freshwater ecosystems

Salmonids are of immense socio-economic importance in much of the world but are threatened by climate change. This has generated a substantial literature documenting effects of climate variation on salmonid productivity in freshwater ecosystems, but there has been no global quantitative synthesis across studies. We conducted a systematic review and meta-analysis to gain quantitative insight into key factors shaping the effects of climate on salmonid productivity, ultimately collecting 1,321 correlations from 156 studies, representing 23 species across 24 countries. Fisher's Z was used as the standardized effect size, and a series of weighted mixed-effects models were compared to identify covariates that best explained variation in effects. Patterns in climate effects were complex, and were driven by spatial (latitude, elevation), temporal (time-period, age-class), and biological (range, habitat type, anadromy) variation within and among study populations. These trends were often consistent with predictions based on salmonid thermal tolerances. Namely, warming and decreased precipitation tended to reduce productivity when high temperatures challenged upper thermal limits, while opposite patterns were common when cold temperatures limited productivity. Overall, variable climate impacts on salmonids suggest that future declines in some locations may be counterbalanced by gains in others. In particular, we suggest that future warming should (1) increase salmonid productivity at high latitudes and elevations (especially >60° and >1,500m), (2) reduce productivity in populations experiencing hotter and dryer growing season conditions, (3) favor non-native over native salmonids, and (4) impact lentic populations less negatively than lotic ones. These patterns should help conservation and management organizations identify populations most vulnerable to climate change, which can then be prioritized for protective measures. Our framework enables broad inferences about future productivity that can inform decision-making under climate change for salmonids and other taxa, but more widespread, standardized, and hypothesis-driven research is needed to expand current knowledge.

opencc-zeroOct 2022View details →

Elemental and biochemical nutrient limitation of zooplankton: A meta-analysis

Primary consumers in aquatic ecosystems are frequently limited by the quality of their food, often expressed as phytoplankton elemental and biochemical composition. However, effects of these food quality indicators vary across studies, and we lack an integrated understanding of how elemental (e.g., nitrogen, phosphorus) and biochemical (e.g., fatty acid, sterol) limitations interactively influence aquatic food webs. Here we present results of a meta-analysis using >100 experimental studies, confirming that limitation by N, P, fatty acids, and sterols all have significant negative effects on zooplankton performance. However, effects varied by grazer response (growth versus reproduction), specific manipulation, and across taxa. While P limitation had greater effects on zooplankton growth than fatty acids overall, P and fatty acid limitation had equal effects on reproduction. Furthermore, we show that: nutrient co-limitation in zooplankton is strong; effects of essential fatty acid limitation depend on P availability; indirect effects induced by P limitation exceed direct effects of mineral P limitation; and effects of nutrient amendments using laboratory phytoplankton isolates exceed those using natural field communities. Our meta-analysis reconciles contrasting views about the role of various food quality indicators, and their interactions, for zooplankton performance, and provides a mechanistic understanding of trophic transfer in aquatic environments.

Meta-analysis reveals challenges and gaps for genome-to-phenome research underpinning plant drought response.

Data used to identify species occurring in hyperarid environments for analyses described in "Meta-analysis reveals challenges and gaps for genome-to-phenome research underpinning plant drought response." The "PlantsLackingHumanUse_PrelimQCd_Data.csv" contains data for all plants queried, while "HyperArid_Occurrences.csv" contains the subset of data corresponding to plants occurring in hyperarid environments.

Meta-analysis of diurnal transcriptomics reveals strong patterns of concordance and discordance in mouse liver: processed data

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, 43 public mouse liver tissue timeseries totaling 805 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, while phase distributions of other periodic genes were generally less consistent. Overlap of genes identified as rhythmic across studies was generally low, with around 50% between some of the highest sample count studies. Distributions of phases of significant genes were remarkably inconsistent across studies, but genes consistently identified as rhythmic clustered near ZT0 and ZT12 in acrophase. 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. This revealed the extent of asymmetric and multimodal genes. This supplemental file provides preprocessed RNA-seq quantifications of all reviewed datasets, as well as results of multiple analyses.

opencc-zeroOct 2022View details →

Limited sex differences in plastic responses suggest evolutionary conservatism of thermal reaction norms: A meta-analysis in insects

Temperature has a profound effect on the growth and development of ectothermic animals. However, the extent to which ecologically-driven selection pressures can adjust thermal plastic responses in growth schedules is not well understood. Comparing temperature-induced plastic responses between sexes provides a promising but underexploited approach to evaluating the evolvability of thermal reaction norms: males and females share largely the same genes and immature environments but typically experience different ecological selection pressures. We proceed from the idea that substantial sex differences in plastic responses could be interpreted as resulting from sex-specific life-history optimization, whereas similarity among the sexes should rather be seen as evidence of an essential role of physiological constraints. In this study, we performed a meta-analysis of sex-specific thermal responses in insect development times, using data on 161 species with comprehensive phylogenetic and ecological coverage. As a reference for judging the magnitude of sex-specificity in thermal plasticity, we compared the magnitude of sex differences in plastic responses to temperature with those in response to diet. We show that sex-specific responses of development times to temperature variation are broadly similar. We also found no strong evidence for sex-specificity in thermal responses to depend on the magnitude or direction of sex differences in development time. Sex differences in temperature-induced plastic responses were systematically less pronounced than sex differences in responses induced by variations in larval diet. Our results point to the existence of substantial constraints on the evolvability of thermal reaction norms in insects as the most likely explanation. If confirmed, the low evolvability of thermal response is an essential aspect to consider in predicting evolutionary responses to climate warming.

opencc-by-4.0May 2024View details →

Optimized summary-statistic-based single-cell meta-analysis. Input files

This dataset contains information about the input files used in the Optimized summary-statistic-based single-cell meta-analysis research project.

opencc-by-4.0May 2024View details →

Dataset related to article: QUALITY ASSESSMENT OF THE MRI-RADIOMICS STUDIES FOR MGMT PROMOTER METHYLATION PREDICTION IN GLIOMA: A SYSTEMATIC REVIEW AND META-ANALYSIS

This table contains the raw data used to generate the heatmap illustrated in Fig 2. Each row of the table shows the distribution of the scores achieved by the studies for a domain. Colors from red to green denote progressive increase from minimum to maximum score obtainable for each domain.

opencc-by-4.0Jun 2024View details →

Data and code for "Salomon et al. 2024: Effects of dissolved organic matter on the toxicity of micro- and nanoplastic particles to Daphnia - a meta-analysis."

<div> All data and R code for Salomon S, Grubmüller E, Kropf P, Nickl E, Rühl A, Weigel S, Becker F, Antonio Vital AL, Laforsch C, Schott M, Mair MM. (2024). Effects of dissolved organic matter on the toxicity of micro- and nanoplastic particles to Daphnia - a meta-analysis. Microplastics and Nanoplastics. (<a href="https://doi.org/10.1186/s43591-024-00088-4" target="_blank" rel="noopener">https://doi.org/10.1186/s43591-024-00088-4</a>) Abstract Effects of micro- and nanoplastic particles (MNP) on organisms have been increasingly reported in recent years, with a large number of studies conducted on water fleas of the genus Daphnia. Most of the available studies used pristine particles that have not been exposed to the environment or to organic substances. In natural environments, however, organic substances like dissolved organic matter (DOM) attach to the MNP, forming an ecocorona on the particles’ surface. How the formation of an ecocorona influences MNP toxicity is still uncertain. While some studies suggest that DOM can mitigate the negative effects of MNP on organisms, other studies did not find such associations. In addition, it is unclear whether the DOM attached to the particles’ surface is attenuating the effects of MNP directly or whether co-exposure with DOM solved in the medium attenuates MNP toxicity indirectly, for instance by increasing Daphnia‘s resilience to stressors in general. To draw more solid conclusions about the direction and size of the mediating effect of DOM on MNP-associated immobilization in Daphnia spp., we synthesized evidence from the published literature and compiled 305 data points from 13 independent studies. The results of our meta-analysis show that the toxic effects of MNP are likely reduced in the presence of certain types of DOM in the exposure media. We found similar mediating effects when MNP were incubated in media containing DOM before the exposure experiments, although to a lesser extent. Future studies designed to disentangle the effects of DOM attached to the MNP from the general effects of DOM in the exposure medium will contribute to a deeper mechanistic understanding of MNP toxicity in nature and enhance the reliability of MNP risk assessment. </div>

Figure 7 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis

Figure 7. Results from the sensitivity analysis depicting variations in the overall effect size estimates (mean ± 95% confidence intervals [CIs]) of water-stress effects on (A) weed germination/emergence, (B) seedling radicle/root length, (C) plant height, and (D) leaf area when a particular study is omitted from the analysis. The vertical black solid and dashed lines represent overall effect sizes (mean ± 95% CIs) with all studies included.

Figure 3 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis

Figure 3. Overall water-stress effects on germination/emergence of grass and broadleaf weeds (top) and six weed families—Asteraceae, Fabaceae, Convolvulaceae, Amaranthaceae, Rubiaceae, and Poaceae (bottom). The vertical black dashed line represents zero effect. The black dots are overall mean effect sizes, and the black lines are 99% confidence intervals (CIs).The values in parentheses are the number of observations followed by the number of studies for each pair-wise comparison. The mean effect sizes were considered significantly different when their 99% CIs did not include zero.

Figure 4 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis

Figure 4. The log response ratio for germination and seedling radicle length of broadleaf (green dots/line) and grass (red dots/line) weed species as a function of water-stress intensity. Water stress increased as solution osmotic potential (ψsolution) decreased and vice versa.The subgroups for germination are 0 to −0.2, −0.2 to −0.4, −0.4 to −0.6, −0.6 to −0.8, −0.8 to −1.0, −1.0 to −1.4, and <−1.4 MPa, while the subgroups for radicle length are 0 to −0.2, −0.2 to −0.4, −0.4 to −0.6, −0.6 to −1.0, and <−1.0 MPa. Only ψsolution-based studies were used in this analysis. For each subgroup, the solid dots and lines represent mean effect sizes and their corresponding 99% confidence intervals (CIs).The mean effect sizes were considered significantly different when their 99% CIs did not include zero. Similarly, the water-stress effects were significantly different for each subgroup and among weed types only when their 99% CIs did not overlap with one another. The fitted lines represent a four-parameter logistic regression model, and the coefficients of the models are presented in Table 2.

Figure 1 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis

Figure 1. PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses; Page and McKenzie 2021) flow diagram highlighting the selection procedure of 86 scientific published papers included in the meta-analysis.

Figure 8 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis

Figure 8. Results from the sensitivity analysis depicting variations in the overall effect size estimates (mean ± 95% confidence intervals [CIs]) of water-stress effects on (A) branches/tillers per plant, (B) leaves per plant, (C) inflorescences per plant, (D) seeds per plant, (E) total biomass, (F) root biomass, (G) shoot biomass, and (H) root:shoot ratio, when a particular study is omitted from the analysis. The vertical black solid and dashed lines represent overall effect sizes (mean ± 95% CIs) with all studies included.

Figure 6 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis

Figure 6. Density plots depicting the distribution of the individual effect sizes for all 12 response variables considered in this meta-analysis: (A) weed seed germination/emergence; (B) radicle/root length, plant height, and leaf area; (C) branches/tillers per plant, leaves per plant, inflorescences per plant, and seeds per plant; and (D) total biomass, root biomass, shoot biomass, and root:shoot ratio.

Figure 2 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis

Figure 2. Overall water-stress effects on weed germination/emergence, growth characteristics, and seed production. The vertical black dashed line represents zero effect. The black dots are overall mean effect sizes, and the black lines are 95% confidence intervals (CIs). The values in parentheses are the number of observations followed by the number of studies for each pair-wise comparison. The mean effect sizes were considered significantly different when their 95% CIs did not include zero.

Figure 5 in Effect of water stress on weed germination, growth characteristics, and seed production: a global meta-analysis

Figure 5. The log response ratio for weed growth characteristics (plant height, leaf area, branches/tillers per plant, leaves per plant,root biomass, shoot biomass, and root:shoot ratio) and seed production (inflorescences per plant and seeds per plant) as a function of water-stress intensity. Water stress increased as soil moisture (% field capacity) decreased and vice versa. The green and red dots represent broadleaf and grass weed species, respectively. The solid black points and the lines represent mean effect sizes and their 99% confidence intervals (CIs) for low (>60%), moderate (30%–60%), and severe (<30% field capacity) water-stress subgroups. The mean effect sizes were considered significantly different when their 99% CIs did not include zero. Similarly, the water-stress effects were significantly different for each subgroup and among weed types only when their 99% CIs did not overlap with one another.