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opencc-zeroAug 2020View details →

Demographic analysis of invasible habitat fraction identifies context-dependent roles of resource availability and biotic resistance in determining invasion success

Theories of plant invasions predict that plant communities should be more easily invaded when resources increase and/or competition decreases. We tested this with an experimentally introduced plant population by manipulating precipitation and resident community biomass. We used a spatially-explicit demographic approach to develop a new population-level metric of invasibility that quantifies the invasible habitat fraction (IHF) across the landscape. The existing community was essentially uninvasible (median IHF ≈ 0%), but experimental manipulations greatly increased the range of outcomes, with maximum observed IHF values over 50%. However, changes in invasibility were often context-dependent, resulting in some outcomes that aligned with existing theory, and others that were not readily predicted. Moreover, variation in invasibility was often driven by specific sets of invader demographic vital rates. Removing competitors revealed the capacity for strong biotic resistance, but this interacted with precipitation such that little biotic resistance was detected under drought conditions. Adding precipitation typically had little positive effect on invasibility, and moderate drought relief led to relatively high invasibility. However, the latter was driven to a large extent by interactions with mammal herbivory that otherwise inhibited invasion in one year. Synthesis. Our findings show that interactions between abiotic and biotic factors, as well as legacy effects, can strongly mediate invasibility. This study also highlights the importance of incorporating spatial heterogeneity into population-level assessments of invasion, as initial population declines do not necessarily indicate resistance to invasion.

opencc-zeroAug 2020View details →

Data from: Resource acquisition strategies facilitate Gilbertiodendron dewevrei monodominance in African lowland forests

1. Tropical forests are hyperdiverse, yet extensive areas of monodominant forest occur in the tropics worldwide. Most long-lived and persistent monodominant tree species form ectomycorrhizal fungi symbioses, allowing them to obtain nutrients directly from soil organic matter. This might promote monodominance by reducing nutrient availability to co-occurring species, the majority of which form associations with arbuscular mycorrhizal fungi. 2. Gilbertiodendron dewevrei forest is the most widespread monodominant forest in tropical Africa. Its distribution appears determined in part by moisture availability, but its monodominance is not thought to be driven by its fungal partner or soil fertility. 3. Here we compare soil fertility of twenty G. dewevrei stands to mixed forest from three sites across an 8,400 km2 region of the Central African Republic and the Republic of Congo. In contrast to previous studies, we find monodominant G. dewevrei stands associated with infertile soils, as base cations (calcium, magnesium, total exchangeable bases) and extractable manganese are extremely low, and significantly lower in soils under G. dewevrei forest compared to mixed forest. Further, and consistent with ectomycorrhizal forests globally, soil carbon to nitrogen and carbon to phosphorus ratios are significantly higher in G. dewevrei stands than in mixed forest stands, providing evidence in support of direct acquisition of nitrogen and phosphorus from soil organic matter by ectomycorrhizal fungi. 4. Gilbertiodendron dewevrei recruits from the seedling bank, with its large seedlings surviving in high densities for over a decade. We tested whether light plasticity could facilitate monodominance by growing seedlings of G. dewevrei under controlled light conditions. We found that its seedlings grow well under a wide range of irradiance levels and conclude that this plasticity affords a competitive advantage. 5. Synthesis: We reframe the discussion of factors contributing to monodominance of G. dewevrei into one of resource acquisition and use efficiency. In particular, G. dewevrei is associated with moist and infertile soils and competes well under a variety of light conditions. Our data is consistent with a model where root associations with ectomycorrhizal fungi drive monodominance through the direct acquisition of nutrients from soil organic matter, promoting nutrient limitation of co-occurring species.

opencc-zeroSep 2020View details →

Data and code from: Vector demography, dispersal, and the spread of disease: Experimental epidemics under elevated resource supply

1. The spread of many diseases depends on the demography and dispersal of arthropod vectors. Classic epidemiological theory typically ignores vector dynamics and instead makes the simplifying assumption of frequency-dependent transmission. Yet vector ecology may be critical for understanding the spread of disease over space and time and how disease dynamics respond to environmental change. 2. Here, we ask how environmental change shapes vector demography and dispersal, and how these traits of vectors govern the spatiotemporal spread of disease. 3. We developed disease models parameterized by traits of vectors and fit them to experimental epidemics. The experiment featured a viral pathogen (CYDV-RPV) vectored by aphids (Rhopalosiphum padi) among populations of grass hosts (Avena sativa) under two rates of environmental resource supply (i.e., fertilization of the host). We compared a non-spatial model that ignores vector movement, a lagged dispersal model that emphasizes the delay between vector reproduction and dispersal, and a travelling wave model that generates waves of infections across space and time. 4. Resource supply altered both vector demography and dispersal. The lagged dispersal model fit best, indicating that vectors first reproduced and then dispersed among hosts in the experiment. Elevated resources decreased vector population growth rates, nearly doubled their carrying capacity per host, increased dispersal rates when vectors carried the virus, and homogenized disease risk across space. 5. Together, the models and experiment show how environmental eutrophication can shape spatial disease dynamics – for example, homogenizing disease risk across space – by altering the demography and behavior of vectors.

opencc-zeroSep 2020View details →

Foraging in nature: contrasting responses to resource heterogeneity at small and large spatial scales.

A key problem faced by foragers is how to forage when resources are distributed heterogeneously in space. This heterogeneity and associated trade-offs may change with spatial scale. Furthermore, foragers may also have to optimize acquiring multiple resources. Such complexity of decision-making while foraging is poorly understood. We studied the butterfly Ypthima huebneri to examine how foraging decisions of adults are influenced by spatial scale and multiple resources. We predicted that, at a small-spatial scale, the time spent foraging in a patch should be proportional to resources in the patch, but at large-spatial scales, due to limitations arising from large travel costs, this relationship should turn negative. We also predicted that both adult and larval resources should jointly affect foraging butterflies. To test these predictions, we laid eleven plots, and sub-divided them into patches. We mapped nectar and larval resources and measured butterfly behavior in these patches and plots. We found that adult foraging behavior showed contrasting relationships with adult resource density at small versus large-spatial scales. At the smaller-spatial scale, butterflies spent more time feeding in resource-rich patches, whereas at the large-scale, butterflies spent more time feeding in resource-poor plots. Furthermore, both adult and larval resources appeared to affect foraging decisions, suggesting that individuals may optimize search costs for different resources. Overall, our findings suggest that the variation in foraging behavior seen in foragers might result from animals responding to complex ecological conditions, such as, resource heterogeneity at multiple spatial scales and the challenges of tracking multiple resources.

opencc-zeroOct 2020View details →

Chromosome-level genome of the peach fruit moth Carposina sasakii (Lepidoptera: Carposinidae) provides a resource for evolutionary studies on moths

Here we provide scripts and parameters for genome assembly and annotation, as well as the manually annotated circadian genes of period (PER), timeless (TIM), Clock (CLK), cycle (CYC) and cryptochrome (CRY), five detoxification gene families of cytochrome P450 monooxygenase (P450s), glutathione S-transferase (GSTs), carboxyl/cholinesterases (CCEs), UDP-glycosyltransferases (UGTs) and ATP-binding cassette (ABC) transporters, IR, OR, OBP, GR genes from the genome of the peach fruit moth (PFM), Carposina sasakii Matsumura (Lepidoptera: Carposinidae, superfamily Copromorphoidea) and genomes of its related species.

opencc-zeroJul 2021View details →

Data from: Trait-based variation in host contribution to pathogen transmission across species and resource supplies

Two key knowledge gaps currently limit the development of more predictive and general models of pathogen transmission: (1) the physiological basis of heterogeneity in host contribution to pathogen transmission (reservoir potential) remains poorly understood, and (2) a general means of integrating the ecological dynamics of host communities has yet to emerge. If the traits responsible for differences in reservoir potential also modulate host community dynamics, these traits could be used to predict pathogen transmission as host communities change. In two greenhouse experiments, across 23 host species and two levels of resource supply, the reservoir potential of plant hosts increased significantly along the Leaf Economic Spectrum, a global axis of plant physiological trait covariation that features prominently in models of plant community ecology. This indicates that the traits of the Leaf Economic Spectrum underlie broad differences in reservoir potential across host species and resource supplies. Therefore, host traits could be used to integrate epidemiological models of pathogen transmission with ecological models of host community change.

opencc-zeroOct 2020View details →

Spatial mapping of root systems reveals diverse strategies of soil exploration and resource contest in grassland plants

1. When foraging and competing for belowground resources, plants have to coordinate the behaviour of thousands of root tips in a manner similar to that of eusocial animal colonies. While well described in animals, we know little about the spatial behaviour of plants, particularly at the level of individual roots. 2. Here, we employed statistical methods previously used to describe animal ranging behaviour to examine root system overlap and the efficiency of root positioning in eight grassland species grown in monocultures and mixtures along a gradient of neighbour densities. 3. Species varied widely in their ability to distribute roots efficiently, with the majority of species showing significant root aggregation at very fine spatial scales. Extensive root system overlap was observed in species mixtures, indicating a lack of territoriality at the level of whole root systems. However, with increasing density of competitors, several species withdrew roots from the periphery of foraging ranges and increased intraplant root aggregation in the remaining area, which may indicate consolidation of foraging areas under competitive pressure. 4. Several species exhibited responses consistent with resource contest in species mixtures where encounters with competitors' roots triggered increased root aggregation at the expense of foraging efficiency. Such responses only occurred in mixtures of species with comparable competitive abilities but were absent in asymmetric species combinations. 5. Synthesis. Combining fine-scale measurement of plant root distributions with spatial statistics yields new insights into plant behavioural strategies with significant potential to impact resource foraging efficiency and productivity.

opencc-zeroNov 2020View details →

Data from: Life-history theory provides a framework for detecting resource limitation: a test of the Nutritional Buffer Hypothesis

For ungulates and other long-lived species, life-history theory predicts that nutritional reserves are allocated to reproduction in a state-dependent manner because survival is highly conserved. Further, as per-capita food abundance and nutritional reserves decline (i.e., density-dependence intensifies), reproduction and recruitment become increasingly sensitive to weather. Thus, the degree to which weather influences vital rates should be associated with proximity to nutritional carrying capacity—a notion that we refer to as the Nutritional Buffer Hypothesis. We tested the Nutritional Buffer Hypothesis using six moose (Alces alces) populations that varied in calf recruitment (33-69 calves/ 100 cows). We predicted that populations with high calf recruitment were nutritionally buffered against the effects of unfavorable weather, and thus were below nutritional carrying capacity. We applied a suite of tools to quantify habitat and nutritional condition of each population and found that increased browse condition, forage quality, and body fat were associated with increased pregnancy and calf recruitment, thereby providing multiple lines of evidence that declines in calf recruitment were underpinned by resource limitation. From 2001 to 2015, recruitment was more sensitive to interannual variation in weather (e.g., winter severity, drought) and plant phenology (e.g., duration of spring) for populations with reduced browse condition, forage quality, and body fat, suggesting these populations lacked the nutritional reserves necessary to buffer demographic performance against the effects of unfavorable weather. Further, average within-population calf recruitment was determined by regional climatic variation, suggesting that the pattern of reduced recruitment near the southern range boundary of moose stems from an interaction between climate and resource limitation. When coupled with information on habitat, nutrition, weather, and climate, life-history theory provides a framework to estimate nutritional limitation, proximity to nutritional carrying capacity, and impacts of climate change for ungulates.

opencc-zeroNov 2019View details →

Data from: The Odonate Phenotypic Database, a new open data resource for comparative studies of an old insect order

We present The Odonate Phenotypic Database (OPD): an online data resource of dragonfly and damselfly phenotypes (Insecta: Odonata). Odonata is a relatively small insect order that currently consists of about 6400 species belonging to 32 families. The database consists of a variety of morphological, life-history and behavioral traits, and biogeographical information collected from literature sources. We see taxon-specific phenotypic databases from Odonata and other organismal groups as becoming an increasing valuable resource in comparative studies. Our database has phenotypic records for 1011 of all 6400 known odonate species. The database is accessible at <a href="http://www.odonatephenotypicdatabase.org/">http://www.odonatephenotypicdatabase.org/</a> and also uploaded as a supporting information file with this paper. Update on November 6 2020 A total of 397 new taxa have been added to the database (aside from wing pigmentation data, many taxa have information on morphology, distribution and behaviour). Updated (validated) pigmentation status for 20 taxa (for these taxa, columns concerning wing pigment have been changed compared to the original opdb‐file, while all other columns have not been changed).

COVID-CDR: An integrative resource for network-based investigation of COVID-19 combinatorial drug repositioning and mechanism of action

Repurposing of the existing medications has become the mainstream focus of anti-COVID-19 drug discovery as it offers rapid and cost-effective solutions for therapeutic development. However, a great effort is still required to enhance the efficacy of repurposing therapeutic options through combination therapy, in which promising drugs with varying mechanisms of action are administered together. Nonetheless, our ability to identify and validate effective combinations is limited due to the vast number of possible drug pairs. Yet, there is no available resource that can systematically guide to identify or choose the effective individual drugs or best possible synergistic drug combinations for the treatment of SARS-CoV-2 infection. To address this resource gap, we developed a web-based platform that displays the network-based mechanism of action of drug combinations, thus simultaneously providing a visual of the cellular interactome involved in modes of action of the chosen drugs. The platform allows the freedom to select two or more drug combinations and provides the options to investigate the network-based efficacy of drug combinations and understand the similarity score, primary indications, and pairwise synergistic scores on different cell-lines. In a nutshell, the platform (accessible via <a href="http://vafaeelab.com/COVID19_repositioning.html">http://vafaeelab.com/COVID19_repositioning.html</a>) is the first of its type, which provides a systematic approach for pre-clinical investigation of combination therapy for treating COVID-19 at the fingertips of the clinicians or researchers.

opencc-by-4.0Dec 2020View details →

Dataset for: Trust Assessment in 32 KiB of RAM: Multi-application Trust-based Task Offloading for Resource-constrained IoT Nodes

The dataset used to generate graphs for: Matthew Bradbury, Arshad Jhumka and Tim Watson. Trust Assessment in 32 KiB of RAM: Multi-application Trust-based Task Offloading for Resource-constrained IoT Nodes.  Proceedings of the Symposium on Applied Computing, ACM, 2021, 1-10. Also includes instructions for experiment setup. Scripts from https://github.com/MBradbury/iot-trust-task-alloc are required to analyse and graph these results.

opencc-by-4.0Dec 2020View details →

German-Swiss survey on the use of (digital) language resources

This survey on the use of (digital) language resources in German-speaking Switzerland complements the Europe-wide survey conducted by the European Network of e-Lexicography (ENeL) and was carried out in close cooperation with the Leibniz Institute for the German Language (IDS) in Mannheim. The aim was to obtain information on the use of language resources from the user's perspective.

Seasonal isotopic niche of a rodent: High between-individual variation but no changes in individual niche width during the rich-resource period

The dynamics of trophic niche width in animals at both population- and individual-level is potentially influenced by temporal variation of food resources, by between-individual differences in food-resource rank preferences, and also by competition. Using stable isotope of carbon and nitrogen (δ13C and δ15N) of fecal samples, we investigated the trophic niche dynamics and individual variation in food-resource use by the arboreal rat Rhipidomys macrurus, in the highly seasonal Brazilian savanna (Cerrado). We tested the hypothesis that dietary niche expansion during the rich-resource period (wet season) occurs via individual specialization and consequently lower individual niche overlap in contrast with niche retraction during the low-resource period (dry season) via increase in niche overlap and expansion of individual niches. The results indicated that R. macrurus is primarily frugivorous and presents a wider isotopic niche in the rich-resource period in comparison to the low-resource period. The increase in niche width was achieved by individual specialization (decrease in niche overlap), as expected. During the low-resource period, however, individual niche widths were not wider than during the rich-resource period. Additionally, individual body condition was lower in the wet season than in the dry season, suggesting higher competition in this period. We conclude that an increase in the population niche may involve only between-individual variation and not necessarily requiring changes in individual niche width. We propose that the combination of ecological opportunity (high resource diversity) in addition to a greater competition in the warm-wet season leads to expansion of the population trophic niche width via individual specialization.

Implementation and adherence of routine pertussis vaccination (DTP) in a low-resource urban birth cohort

Introduction: Reliable information on rates of up-to-date coverage and timely administration of routine childhood immunizations is critical for guiding public health efforts worldwide, yet prospective observation of vaccination programs within individual communities is rare. Here we provide a longitudinal analysis of the directly-observed administration of a 3-dose primary vaccination series to infants in a low-resource community in Lusaka, Zambia. Methods: Throughout 2015, we recruited a longitudinal birth cohort of mother/infant pairs (initial enrollment, 1,981 pairs; attending, 1,497 pairs) from the peri-urban informal settlement of Chawama compound, located in Lusaka, Zambia. We prospectively monitored the administration of scheduled Diphtheria-Tetanus-Pertussis (DTP) vaccinations across the first 14-18 weeks of life. We analyzed study attendance and vaccine coverage, both overall and stratified by age group. We employed Kaplan-Meier analyses to estimate delays in age-appropriate administration of vaccine doses. We also assessed schedule timing violations, including early and compressed dose administration. Results: At study completion, first dose (DTP1) rates were high (92.9% of attending), whereas third dose completion (DTP3) rates were far lower (61.9%). Missed vaccinations and study dropout both contributed to the low DTP3 completion rates. DTP1 was administered very late (at or after 10 weeks) to 61 infants (4.1%). DPT1 was administered too early to 64 infants (4.3%), and 77 (5.1%) received consecutive doses below the minimum recommended spacing of 28 days. Conclusions: We observe substantial individual variation in the timing of early childhood DTP doses, though following this birth cohort proved challenging. Our results indicate that timely administration of both DTP1 and DPT3 remains a challenge in this community. These directly-observed, individual-based results provide an important counterpoint to more course-grained, survey-based national and province estimates of up-to-date vaccine coverage. This study also highlights the challenges of vaccine hesitancy and sub-optimal utilization of (no-cost) healthcare services in a low-resource urban setting.

opencc-by-4.0Dec 2020View details →

Dataset accompanying paper submission for "Toward data-driven generation and evaluation of model structure for integrated representations of human behavior in water resources systems"

This data set accompanies code archived at DOI: <a href="https://doi.org/10.5281/zenodo.3833186">10.5281/zenodo.3833186</a>, which was used in the experiments for the paper submission "Toward data-driven generation and evaluation of model structure for integrated representations of human behavior in water resources systems"

Legacy effect of grazing intensity mediates the bottom-up controls of resource addition on soil food webs

1. Large-scale studies have demonstrated that nitrogen (N) and water (W) availability greatly affect terrestrial ecosystems worldwide, and this is especially true for the resource-poor semi-arid grasslands. Yet, experimental evidence is lacking for how N and W availability affect soil food webs across historical grazing intensity-altered environments at a local scale. 2. Here, we included N- and W-addition treatments in an 8-year grazing experiment (with four grazing intensities) to determine how the legacy effects of grazing intensity mediate the responses of key components of soil food webs (plants, microorganisms, and nematodes) to resource addition in a semi-arid grassland. 3. After 4 years of N- and W-addition treatments (with no grazing during that 4-year period), we found that a legacy of grazing, even light grazing, had significant negative effects on the components of plant community and soil food webs. Both N and W addition increased above- and below-ground plant biomass, especially under moderate and heavy grazing. N addition had negative effects on the biomass of bacteria under no grazing, while W addition increased the biomass of actinomycetes under light grazing. N addition decreased the abundance of omnivorous + carnivorous nematodes under light and heavy grazing, while W addition increased their abundance under heavy grazing. Overall, the effects of resource addition on soil food webs progressively decreased from the lowest trophic level (primary producers, i.e., plants), to intermediate tropic levels (microorganisms and root-feeding nematodes), to higher trophic levels (microbial-feeding nematodes and omnivorous + carnivorous nematodes). 4. Synthesis and applications. Our results, which are the first data concerning the effects of resource addition on key components of soil food webs across a historical grazing-induced environmental gradient, show that the strong bottom-up controls of resource addition on soil food webs are mediated by the legacy of grazing intensity. These finding should be useful for predicting the responses of grassland ecosystems to future climate change and suggest that the recovery of degraded grasslands will require more than restoration measure of resource inputs alone.

opencc-zeroJan 2021View details →

Asymmetric responses of resource use efficiency to previous-year precipitation in a semi-arid grassland

1. Intensified inter-annual fluctuations in precipitation could profoundly impact terrestrial ecosystems. However, how changes previous-year precipitation influence current ecosystem functioning (e.g., resource use efficiency) in semi-arid regions remains unclear. 2. In this study, water use efficiency (WUE) and light use efficiency (LUE) were investigated in a multi-year precipitation gradient experiment with seven treatment levels: 20%, 40% and 60% decreases and 20%, 40% and 60% increases in the amount of natural rainfall plus ambient precipitation. Plots receiving 60% less precipitation were representative of extreme dry years whereas the other treatment levels fell within the normal year-to-year range in precipitation change. Measurements made in both the post-treatment period (2013-2015) and the treatment period (2010-2012) provided an opportunity to quantify the legacy effects of precipitation on resource use efficiency (RUE). 3. Sensitivities of LUE to previous-year precipitation were not changed among treatments in 2013. However, asymmetric responses of RUEs (i.e., WUE and LUE) to previous-year precipitation were found in 2014-2015. WUE2014, WUE2015, LUE2014, and LUE2015 responded more strongly to previous normal decreased than increased precipitation. Importantly, they were more sensitive to previous extreme dry year (represented by 60% precipitation reduction) than normal wet year (represented by 60% precipitation increment). Aboveground net primary productivity (ANPP) rather than resource absorption (Ruptake) drove these asymmetric responses of RUE, and biomass of grasses further explained the asymmetric responses of ANPP. 4. This study reveals the non-linear responses of RUE to previous-year precipitation and highlighted that the legacy effects of precipitation on RUE can be ascribed to the changes in vegetation composition. Our findings can facilitate the prediction of the legacy effects of precipitation variation on grassland ecosystem functions in the future.

opencc-zeroJan 2021View details →

Relative impacts of gypsy moth outbreaks and insecticide treatments on forest resources and ecosystem: An experimental approach

Gypsy moth outbreaks cause severe defoliation in Holarctic forests, both in North America where it is invasive, and in its native range in Eurasia. Severe defoliation can hamper timber production and impact ecological communities and processes. Aerial insecticide applications are regularly performed in outbreak areas to mitigate economic losses. These operations can be financially costly and harmful to non-target species and may disrupt species interaction networks. However, replicated studies of the relative impacts of gypsy moth outbreaks and insecticide application on forest growth and animal communities are rare and have yet to be carried out in the species' indigenous range. Here, we review the pathways in which gypsy moth outbreaks and the chemical control of these outbreaks affect forest ecosystems. We then present an experimental design established in South Central Germany in early 2019, aiming to study the ecological and economic consequences of gypsy moth eruptions and insecticide application in oak forests. The study's full factorial design comprises forest stands with high and low defoliation risk, either treated with tebufenozide or left unsprayed, within 12 experimental blocks. Measurements of forest growth and structure, tree mortality, gypsy moth density, and composition of lepidopteran, bird, bat, ground beetle, and canopy arthropod communities will be conducted for several years. One-year intensive monitoring of gypsy moth populations and damage across the selected sites showed substantial differences in population density between plots with high and low defoliation risk and high efficacy of tebufenozide in suppressing gypsy moth populations in treated plots. In the first year of the experiment, gypsy moth density and defoliation in predicted outbreak plots differed strongly, confirming the importance of using many replicates and blocking to control spatial heterogeneity. The experiment will be running continuously during the coming years to produce short- and medium-term economic and ecological data to improve our understanding and management of gypsy moth outbreaks.

opencc-by-4.0Jan 2021View details →

Unexpected effects of local management and landscape composition on predatory mites and their food resources in vineyards

This research was funded by the project SECBIVIT. Dataset of the results in the Articel: Unexpected effects of local management and landscape composition on predatory mites and their food resources in vineyards. For further information also see:  <ul> <li>Sampled grape varieties: http://doi.org/10.5281/zenodo.4562219 </li> <li>https://www.secbivit.boku.ac.at/</li> </ul>