Cannibalism among generalist predators has implications for the dynamics of terrestrial food webs. Spiders are common, ubiquitous arthropod generalist predators in most natural and managed ...terrestrial ecosystems. Thus, the relationship of spider cannibalism to food limitation, competition, and population regulation has direct bearing on basic ecological theory and applications such as biological control. This review first briefly treats the different types of spider cannibalism and then focuses in more depth on evidence relating cannibalism to population dynamics and food web interactions to address the following questions: Is cannibalism in spiders a foraging strategy that helps to overcome the effects of a limited supply of calories and/or nutrients? Does cannibalism in spiders reduce competition for prey? Is cannibalism a significant density-dependent factor in spider population dynamics? Does cannibalism dampen spider-initiated trophic cascades?
Abstract
Motivation
The secondary structure of RNA is of importance to its function. Over the last few years, several papers attempted to use machine learning to improve de novo RNA secondary ...structure prediction. Many of these papers report impressive results for intra-family predictions but seldom address the much more difficult (and practical) inter-family problem.
Results
We demonstrate that it is nearly trivial with convolutional neural networks to generate pseudo-free energy changes, modelled after structure mapping data that improve the accuracy of structure prediction for intra-family cases. We propose a more rigorous method for inter-family cross-validation that can be used to assess the performance of learning-based models. Using this method, we further demonstrate that intra-family performance is insufficient proof of generalization despite the widespread assumption in the literature and provide strong evidence that many existing learning-based models have not generalized inter-family.
Availability and implementation
Source code and data are available at https://github.com/marcellszi/dl-rna.
Supplementary information
Supplementary data are available at Bioinformatics online.
Although invasive plants are a major source of terrestrial ecosystem degradation worldwide, it remains unclear which trophic levels above the base of the food web are most vulnerable to plant ...invasions. We performed a meta‐analysis of 38 independent studies from 32 papers to examine how invasive plants alter major groupings of primary and secondary consumers in three globally distributed ecosystems: wetlands, woodlands and grasslands. Within each ecosystem we examined if green (grazing) food webs are more sensitive to plant invasions compared to brown (detrital) food webs. Invasive plants have strong negative effects on primary consumers (detritivores, bacterivores, fungivores, and/or herbivores) in woodlands and wetlands, which become less abundant in both green and brown food webs in woodlands and green webs in wetlands. Plant invasions increased abundances of secondary consumers (predators and/or parasitoids) only in woodland brown food webs and green webs in wetlands. Effects of invasive plants on grazing and detrital food webs clearly differed between ecosystems. Overall, invasive plants had the most pronounced effects on the trophic structure of wetlands and woodlands, but caused no detectable changes to grassland trophic structure.
Arthropods in the leaf litter layer of forest soils influence ecosystem processes such as decomposition. Climate‐change models predict both increases and decreases in average rainfall. Increased ...drought may have greater impacts on the litter arthropod community. In addition to affecting survival or behaviour of desiccation‐sensitive species, lower rainfall may indirectly lower abundances of consumers that graze drought‐stressed fungi, with repercussions for higher trophic levels.
We tested the hypothesis that trophic structure will differ between the two rainfall scenarios. In particular, we hypothesized that densities of several broadly defined trophic groupings of arthropods would be lower under reduced rainfall.
To test this hypothesis, we used sprinklers to impose two rainfall treatments during three growing seasons in roofed, fenced 14‐m2 plots and documented changes in abundance from initial, pre‐treatment densities of 39 arthropod taxa. Experimental plots were subjected to either LOW (fortnightly) or HIGH (weekly) average rainfall based upon climate models and the previous 100 years of regional weekly averages. Unroofed open plots, our reference treatment (REF), experienced higher than average rainfall during the experiment.
The two rainfall extremes produced clear negative effects of lowered rainfall on major trophic groups. Broad categories of fungivores, detritivores and predators were more abundant in HIGH than LOW plots by the final year. Springtails (Collembola), which graze fungal hyphae, were 3× more abundant in the HIGH rainfall treatment. Taxa of larger‐bodied fungivores and detritivores, spiders (Araneae), and non‐spider predators were 2× more abundant under HIGH rainfall. Densities of mites (Acari), which include fungivores, detritivores and predators, were 1.5× greater in HIGH rainfall plots. Abundances and community structure of arthropods were similar in REF and experimental plots, showing that effects of rainfall uncovered in the experiment are applicable to nature.
This pattern suggests that changes in rainfall will alter bottom‐up control processes in a critical detritus‐based food web of deciduous forests. Our results, in conjunction with other findings on the impact of desiccation on arthropods and fungal growth, suggest that drier conditions will depress densities of fungal consumers, causing declines in higher trophic levels, with possible impacts on soil processes and the larger forest food web.
This experiment revealed how rainfall extremes predicted by climate‐change models may impact bottom‐up control processes in the leaf litter food web. Comparing results with reference plots demonstrated that effects uncovered in experimental mesocosms can be extrapolated to nature, and incorporating different sites in the design uncovered spatial variation in treatment effects.
Intraguild predation (IGP)-predation between generalist predators (IGPredator and IGPrey) that potentially compete for a shared prey resource-is a common interaction module in terrestrial food webs. ...Understanding temporal variation in webs with widespread IGP is relevant to testing food web theory. We investigated temporal constancy in the structure of such a system: the spider-focused food web of the forest floor. Multiplex PCR was used to detect prey DNA in 3,300 adult spiders collected from the floor of a deciduous forest during spring, summer, and fall over four years. Because only spiders were defined as consumers, the web was tripartite, with 11 consumer nodes (spider families) and 22 resource nodes: 11 non-spider arthropod taxa (order- or family-level) and the 11 spider families. Most (99%) spider-spider predation was on spider IGPrey, and ~90% of these interactions were restricted to spider families within the same broadly defined foraging mode (cursorial or web-spinning spiders). Bootstrapped-derived confidence intervals (BCI's) for two indices of web structure, restricted connectance and interaction evenness, overlapped broadly across years and seasons. A third index, % IGPrey (% IGPrey among all prey of spiders), was similar across years (~50%) but varied seasonally, with a summer rate (65%) ~1.8x higher than spring and fall. This seasonal pattern was consistent across years. Our results suggest that extensive spider predation on spider IGPrey that exhibits consistent seasonal variation in frequency, and that occurs primarily within two broadly defined spider-spider interaction pathways, must be incorporated into models of the dynamics of forest-floor food webs.
▶ Experiment reveals complex impact of coarse woody debris (CWD) on leaf-litter spiders ▶ Removing fallen CWD affects spider community in litter adjacent to and far from CWD ▶ Spider responses to CWD ...removal cannot always be predicted by pre-treatment gradients ▶ CWD as small as Ø
=
14
cm can affect major spider genera in forest-floor leaf litter ▶ Experimental removal of CWD is needed to assess CWD thresholds for litter arthropods
Purely observational studies have documented differences in the abundance and diversity of several litter-dwelling arthropods between sites adjacent to, and far from, CWD, which suggests that reduction of fallen coarse woody debris (CWD) in temperate forests by traditional forestry practices may affect the litter arthropod community. As few field experiments have directly tested the impact of CWD on arthropods inhabiting the litter at different distances from CWD, we removed CWD from replicated open plots on the floor of a second-growth deciduous forest in order to reveal the causal connection between CWD and litter-dwelling spiders, often the most diverse and abundant predators among the litter macrofauna of temperate forests. We also documented the impact of the CWD manipulation on spider prey and several other major macroarthropod groups. Before removing CWD (∅
=
14.3
±
0.7
cm), we measured response variables as a function of distance (0.5–1.5
m) from CWD in both removal and control plots. In agreement with results of previous research that solely utilized this observational approach in temperate forests, volume and dry mass of litter, spider diversity, overall spider density, and densities of 8 of 16 major spider genera were higher adjacent to CWD before experimental manipulations. Removing CWD reduced the amount of litter and the density of spiders in litter close to where the CWD had been. Removing CWD also altered spider community structure, which had differed between litter sites adjacent to, and far from, CWD prior to the experimental removal of CWD. The patterns, though, were not completely congruent, as some of the taxa affected by the manipulation had not differed between sites prior to the removal of CWD, and vice-versa. Our findings suggest that complex interactions among structural, biotic and microclimatic factors underlie the observed responses to CWD removal by spiders and other arthropods in the litter layer. We also conclude that drawing inferences solely from observational studies is not a reliable approach for predicting the impact of changes in the amount of CWD on arthropods of forest-floor leaf litter. Further field experiments manipulating different volumes of CWD are needed in order to determine the minimum amount of CWD that should be kept on the forest floor of managed forests in order to maintain densities and diversities of major leaf-litter arthropods.
We examined the contribution of social disadvantage to the black-white disparity in preterm birth. Analyses included linked vital and hospital discharge records from 127,358 black and 615,721 white ...singleton California births from 2007-11. Odds ratios (OR) were estimated by 4 logistic regression models for 2 outcomes: early (<32 wks) and moderate (32-36 wks) spontaneous preterm birth (ePTB, mPTB), stratified by 2 race-ethnicity groups (blacks and whites). We then conducted a potential impact analysis. The OR for less than high school education (vs. college degree) was 1.8 (95% confidence interval 1.6, 2.1) for ePTB among whites but smaller for the other 3 outcome groups (ORs 1.3-1.4). For all 4 groups, higher census tract poverty was associated with increased odds (ORs 1.03-1.05 per 9% change in poverty). Associations were less noteworthy for the other variables (payer, and tract percent black and Gini index of income inequality). Setting 3 factors (education, poverty, payer) to 'favorable' values was associated with lower predicted probability of ePTB (25% lower among blacks, 31% among whites) but a 9% higher disparity, compared to probabilities based on observed values; for mPTB, respective percentages were 28% and 13% lower probability, and 17% lower disparity. Results suggest that social determinants contribute to preterm delivery and its disparities, and that future studies should focus on ePTB and more specific factors related to social circumstances.
Long-term treatment with supplemental oxygen has unknown efficacy in patients with stable chronic obstructive pulmonary disease (COPD) and resting or exercise-induced moderate desaturation.
We ...originally designed the trial to test whether long-term treatment with supplemental oxygen would result in a longer time to death than no use of supplemental oxygen among patients who had stable COPD with moderate resting desaturation (oxyhemoglobin saturation as measured by pulse oximetry Spo
, 89 to 93%). After 7 months and the randomization of 34 patients, the trial was redesigned to also include patients who had stable COPD with moderate exercise-induced desaturation (during the 6-minute walk test, Spo
≥80% for ≥5 minutes and <90% for ≥10 seconds) and to incorporate the time to the first hospitalization for any cause into the new composite primary outcome. Patients were randomly assigned, in a 1:1 ratio, to receive long-term supplemental oxygen (supplemental-oxygen group) or no long-term supplemental oxygen (no-supplemental-oxygen group). In the supplemental-oxygen group, patients with resting desaturation were prescribed 24-hour oxygen, and those with desaturation only during exercise were prescribed oxygen during exercise and sleep. The trial-group assignment was not masked.
A total of 738 patients at 42 centers were followed for 1 to 6 years. In a time-to-event analysis, we found no significant difference between the supplemental-oxygen group and the no-supplemental-oxygen group in the time to death or first hospitalization (hazard ratio, 0.94; 95% confidence interval CI, 0.79 to 1.12; P=0.52), nor in the rates of all hospitalizations (rate ratio, 1.01; 95% CI, 0.91 to 1.13), COPD exacerbations (rate ratio, 1.08; 95% CI, 0.98 to 1.19), and COPD-related hospitalizations (rate ratio, 0.99; 95% CI, 0.83 to 1.17). We found no consistent between-group differences in measures of quality of life, lung function, and the distance walked in 6 minutes.
In patients with stable COPD and resting or exercise-induced moderate desaturation, the prescription of long-term supplemental oxygen did not result in a longer time to death or first hospitalization than no long-term supplemental oxygen, nor did it provide sustained benefit with regard to any of the other measured outcomes. (Funded by the National Heart, Lung, and Blood Institute and the Centers for Medicare and Medicaid Services; LOTT ClinicalTrials.gov number, NCT00692198 .).
While aboveground impacts of invasive plants are well documented, their influence on soil food webs remains less understood. Previous research has revealed that bottom-up forces are widespread in ...soil food webs of woodlands. Thus, an invasive plant that negatively impacts the base of the food web will likely decrease primary consumers as well as their predators. We examined how a North American plant invader, garlic mustard (Alliaria petiolata), affects arthropod primary (springtails and oribatid mites) and secondary (predaceous mites) consumers of the soil food web via changes to fungal resources. We measured the abundances of plants, soil fungi, fungivores, and predators in garlic mustard-invaded and uninvaded 1-m² plots in five Midwestern USA woodlands. We then conducted a mesocosm (0.25-m² plots) experiment to tease apart the direct and indirect effects of garlic mustard by manipulating plant identity (garlic mustard vs. native plant), soil history (invaded vs. uninvaded), and fungicide application (fungicide vs. no fungicide). Our first study revealed that plots without garlic mustard had 2.8 and 1.4 × more fungi and fungivores, respectively. Predator densities did not differ. Fungal composition and structural equation modeling (SEM) revealed the garlic mustard effects on fungivores were correlated with fungal declines. The mesocosm experiment confirmed that the impacts were indirect, as fungicide plots harbored similar fungivore densities, whereas fungivore densities differed according to plant identity and soil history in the fungicide-free plots. Our results reveal that by altering soil fungal abundance, an invasive plant can indirectly affect primary consumers in soil food webs, but this indirect effect does not influence predators.
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