Selection models with monotone weight functions in meta analysis

Publication bias, the fact that studies identified for inclusion in a meta analysis do not represent all studies on the topic of interest, is commonly recognized as a threat to the validity of the results of a meta analysis. One way to explicitly model publication bias is via selection models or weighted probability distributions. We adopt the nonparametric approach initially introduced by Dear (1992) but impose that the weight function $w$ is monotonely non-increasing as a function of the $p$-value. Since in meta analysis one typically only has few studies or "observations", regularization of the estimation problem seems sensible. In addition, virtually all parametric weight functions proposed so far in the literature are in fact decreasing. We discuss how to estimate a decreasing weight function in the above model and illustrate the new methodology on two well-known examples. The new approach potentially offers more insight in the selection process than other methods and is more flexible than parametric approaches. Some basic properties of the log-likelihood function and computation of a $p$-value quantifying the evidence against the null hypothesis of a constant weight function are indicated. In addition, we provide an approximate selection bias adjusted profile likelihood confidence interval for the treatment effect. The corresponding software and the datasets used to illustrate it are provided as the R package selectMeta. This enables full reproducibility of the results in this paper.Comment: 15 pages, 2 figures. Some minor changes according to reviewer comment

A global synthesis of fire effects on pollinators

Understanding fire effects on pollinators is critical in the context of fire regime changes and the global pollination crisis. Through a systematic and quantitative review of the literature, we provide the first global assessment of pollinator responses to fire. We hypothesize that pollinators increase after fire and during the early postfire succession stages; however, high fire frequency has the opposite effect, decreasing pollinators. Location: Terrestrial ecosystems, excluding Antarctica. Time period: Data collected from 1973 to 2017. Major taxa studied: Insects (Coleoptera, Diptera, Hymenoptera and Lepidoptera) and a few bird species. Methods: We first compiled available studies across the globe that assessed fire effects on pollinator communities. Then, by means of hierarchical meta-analyses, we evaluated how different fire regime parameters (fire frequency, postfire time and fire type) and habitat characteristics affect the abundance and richness of animals that act as pollinators. We also explored to what extent the responses vary among taxa groups and life history traits of pollinators (sociality system, nest location and feeding specialization), and among biomes. The overall effect size of fire on pollinator abundance and richness across all studies was positive. Fire effect was especially clear and significant in early postfire communities, after wildfires, and for Hymenoptera. Taxonomic resolution influenced fire effects, where only studies at the species/genus and family levels showed significant effects. The main exceptions were recurrent fires that showed a negative effect, and especially wildfire effects on Lepidoptera abundance that showed a significant negative response. Main conclusions: Pollinators tend to be promoted after a wildfire event. However, short fire intervals may threat pollinators, and especially lepidopterans. Given the current fire regime changes at the global scale, it is imperative to monitor postfire pollinators across many ecosystems, as our results suggest that fire regime is critical in determining the dynamics of pollinator communities.Fil: Carbone, Lucas Manuel. Universidad Nacional de Córdoba; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Tavella, Julia Rita. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Pausas, Juli G.. Universidad de Valencia; EspañaFil: Aguilar, Ramiro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentin

Salvage logging effects on regulating ecosystem services and fuel loads

We thank several authors who generously provided data for this meta-analysis (WebPanel 2). ABL acknowledges the support of mobility grants from Universidad de Alcalá and Spanish Ministry of Education, postdoctoral fellowships from the Spanish Ministry of Economy and the Alexander von Humboldt Foundation, and Project AS2013/MAE-2719 “REMEDINAL-3” from the Government of Madrid. The data underlying this paper are available through an institutional repository (http://hdl.handle.net/10481/62260).Salvage logging, or logging after natural disturbances such as wildfires, insect outbreaks, and windstorms, is carried out to recover some of a forest’s natural and/or economic capital. However, trade-offs between management objectives and a lack of consensus on the ecological consequences of salvage logging impair science-based decision making on the management of forests after natural disturbances. We conducted a global meta-analysis of the impacts of salvage logging on regulating ecosystem services and on fuel loads, as a frequent post-disturbance objective is preventing subsequent wildfires that could be fueled by the accumulation of dead trunks and branches. Salvage logging affected ecosystem services in a moderately negative way, regardless of disturbance type and severity, time elapsed since salvage logging, intensity of salvage logging, and the group of regulating ecosystem services being considered. However, prolonging the time between natural disturbance and salvage logging mitigated negative effects on regulating ecosystem services. Salvage logging had no overall effect on surface fuels; rather, different fuel types responded differently depending on the time elapsed since salvage logging. Delaying salvage logging by ~2–4 years may reduce negative ecological impacts without affecting surface fuel loads.Project AS2013/MAE-2719 “REMEDINAL-3” from the Government of Madri

Effectiveness of agri‐environmental management on pollinators is moderated more by ecological contrast than by landscape structure or land‐use intensity

Agri-environment management (AEM) started in the 1980s in Europe to mitigate biodiversity decline, but the effectiveness of AEM has been questioned. We hypothesize that this is caused by a lack of a large enough ecological contrast between AEM and non-treated control sites. The effectiveness of AEM may be moderated by landscape structure and land-use intensity. Here, we examined the influence of local ecological contrast, landscape structure and regional land-use intensity on AEM effectiveness in a meta-analysis of 62 European pollinator studies. We found that ecological contrast was most important in determining the effectiveness of AEM, but landscape structure and regional land-use intensity played also a role. In conclusion, the most successful way to enhance AEM effectiveness for pollinators is to implement measures that result in a large ecological improvement at a local scale, which exhibit a strong contrast to conventional practices in simple landscapes of intensive land-use regions

Jumping to Conclusions About the Beads Task? A Meta-analysis of Delusional Ideation and Data-Gathering

It has been claimed that delusional and delusion-prone individuals have a tendency to gather less data before forming beliefs. Most of the evidence for this "jumping to conclusions" (JTC) bias comes from studies using the "beads task" data-gathering paradigm. However, the evidence for the JTC bias is mixed. We conducted a random-effects meta-analysis of individual participant data from 38 clinical and nonclinical samples (n = 2,237) to investigate the relationship between data gathering in the beads task (using the "draws to decision" measure) and delusional ideation (as indexed by the "Peters et al Delusions Inventory"; PDI). We found that delusional ideation is negatively associated with data gathering (r(s) = -0.10, 95% CI [-0.17, -0.03]) and that there is heterogeneity in the estimated effect sizes (Q-stat P = .03, I² = 33). Subgroup analysis revealed that the negative association is present when considering the 23 samples (n = 1,754) from the large general population subgroup alone (r(s) = -0.10, 95% CI [-0.18, -0.02]) but not when considering the 8 samples (n = 262) from the small current delusions subgroup alone (r(s) = -0.12, 95% CI [-0.31, 0.07]). These results provide some provisional support for continuum theories of psychosis and cognitive models that implicate the JTC bias in the formation and maintenance of delusions.9 page(s

Linking micro‐ and macroevolutionary perspectives to evaluate the role of Quaternary sea‐level oscillations in island diversification

With shifts in island area, isolation, and cycles of island fusion–fission, the role of Quaternary sea‐level oscillations as drivers of diversification is complex and not well understood. Here, we conduct parallel comparisons of population and species divergence between two island areas of equivalent size that have been affected differently by sea‐level oscillations, with the aim to understand the micro‐ and macroevolutionary dynamics associated with sea‐level change. Using genome‐wide datasets for a clade of seven Amphiacusta ground cricket species endemic to the Puerto Rico Bank (PRB), we found consistently deeper interspecific divergences and higher population differentiation across the unfragmented Western PRB, in comparison to the currently fragmented Eastern PRB that has experienced extreme changes in island area and connectivity during the Quaternary. We evaluate alternative hypotheses related to the microevolutionary processes (population splitting, extinction, and merging) that regulate the frequency of completed speciation across the PRB. Our results suggest that under certain combinations of archipelago characteristics and taxon traits, the repeated changes in island area and connectivity may create an opposite effect to the hypothesized “species pump” action of oscillating sea levels. Our study highlights how a microevolutionary perspective can complement current macroecological work on the Quaternary dynamics of island biodiversity.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141544/1/evo13384.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/141544/2/evo13384_am.pd

Large-scale distribution patterns of mangrove nematodes: A global meta-analysis

Mangroves harbor diverse invertebrate communities, suggesting that macroecological distribution patterns of habitat-forming foundation species drive the associated faunal distribution. Whether these are driven by mangrove biogeography is still ambiguous. For small-bodied taxa, local factors and landscape metrics might be as important as macroecology. We performed a meta-analysis to address the following questions: (1) can richness of mangrove trees explain macroecological patterns of nematode richness? and (2) do local landscape attributes have equal or higher importance than biogeography in structuring nematode richness? Mangrove areas of Caribbean-Southwest Atlantic, Western Indian, Central Indo-Pacific, and Southwest Pacific biogeographic regions. We used random-effects meta-analyses based on natural logarithm of the response ratio (lnRR) to assess the importance of macroecology (i.e., biogeographic regions, latitude, longitude), local factors (i.e., aboveground mangrove biomass and tree richness), and landscape metrics (forest area and shape) in structuring nematode richness from 34 mangroves sites around the world. Latitude, mangrove forest area, and forest shape index explained 19% of the heterogeneity across studies. Richness was higher at low latitudes, closer to the equator. At local scales, richness increased slightly with landscape complexity and decreased with forest shape index. Our results contrast with biogeographic diversity patterns of mangrove-associated taxa. Global-scale nematode diversity may have evolved independently of mangrove tree richness, and diversity of small-bodied metazoans is probably more closely driven by latitude and associated climates, rather than local, landscape, or global biogeographic patterns.Marco C. Brustolin, Ivan Nagelkerken, Gustavo Fonsec

Evolutionary expansion of the Ras switch regulatory module in eukaryotes

Ras proteins control many aspects of eukaryotic cell homeostasis by switching between active (GTP-bound) and inactive (GDP-bound) conformations, a reaction catalyzed by GTPase exchange factors (GEF) and GTPase activating proteins (GAP) regulators, respectively. Here, we show that the complexity, measured as number of genes, of the canonical Ras switch genetic system (including Ras, RasGEF, RasGAP and RapGAP families) from 24 eukaryotic organisms is correlated with their genome size and is inversely correlated to their evolutionary distances from humans. Moreover, different gene subfamilies within the Ras switch have contributed unevenly to the module’s expansion and speciation processes during eukaryote evolution. The Ras system remarkably reduced its genetic expansion after the split of the Euteleostomi clade and presently looks practically crystallized in mammals. Supporting evidence points to gene duplication as the predominant mechanism generating functional diversity in the Ras system, stressing the leading role of gene duplication in the Ras family expansion. Domain fusion and alternative splicing are significant sources of functional diversity in the GAP and GEF families but their contribution is limited in the Ras family. An evolutionary model of the Ras system expansion is proposed suggesting an inherent ‘decision making’ topology with the GEF input signal integrated by a homologous molecular mechanism and bifurcation in GAP signaling propagation

Precipitation Constrains Amphibian Chytrid Fungus Infection Rates in a Terrestrial Frog Assemblage in Jamaica, West Indies

We model Batrachochytrium dendrobatidis (Bd) infection rates in Jamaican frogs—one of the most threatened amphibian fauna in the world. The majority of species we surveyed were terrestrial direct‐developing frogs or frogs that breed in tank bromeliads, rather than those that use permanent water bodies to breed. Thus, we were able to investigate the climatic correlates of Bd infection in a frog assemblage that does not rely on permanent water bodies. We sampled frogs for Bd across all of the major habitat types on the island, used machine learning algorithms to identify climatic variables that are correlated with infection rates, and extrapolated infection rates across the island. We compared the effectiveness of the machine learning algorithms for species distribution modeling in the context of our study, and found that infection rate rose quickly with precipitation in the driest month. Infection rates also increased with mean temperature in the warmest quarter until 22 °C, and remained relatively level thereafter. Both of these results are in accordance with previous studies of the physiology of Bd . Based on our environmental results, we suggest that frogs occupying high‐precipitation habitats with cool rainy‐season temperatures, though zcurrently experiencing low frequencies of infection, may experience an increase in infection rates as global warming increases temperatures in their habitat.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106115/1/btp12093.pd