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opencc-by-4.0Apr 2022View details →

maxATAC Blacklist Resources

This data upload contains the hg38 resources uses to make the maxATAC blacklist.  Files Included: ENCFF356LFX.bed: hg38 Blacklist from Anshul curation hg38_maxatac_blacklist.bed: V1 maxATAC blacklist hg38-blacklist.v2.bed: V2 blacklist from ENCODE project + <a href="https://github.com/Boyle-Lab/Blacklist/blob/master/lists/hg38-blacklist.v2.bed.gz">Boyle lab</a> hg38_gaps.bed: UCSC table browser list of annotated gaps hg38_centromeres.bed: UCSC table browser list of annotated centromeres hg38_segmental_dups_chrM.bed: UCSC table browser list of segmental duplications that are specific to chrM hg38_maxatac_blacklist_V2.bed: V2 maxATAC blacklist

opencc-zeroApr 2022View details →

Chipmunk body mass variations and life-histories in a pulsed resource ecosystem

Phenotypic plasticity is the most immediate mechanism of adaptative response to environmental change. Studying plastic changes in response to fluctuating environments provides insights into how such adjustments may impact life-history traits. Here, we used a 14-year dataset of repeated body mass measurements in male eastern chipmunks (Tamias striatus) to assess the extent of plastic changes for this trait in a resource pulse ecosystem. We first determined the magnitude of variation in body mass at the population level in response to the drastic change in food resource availability from American beech tree seeds (Fagus grandifolia). Males that emerged in the spring from winter torpor following a non-mast year had a lower body mass than males emerging after a mast year, but they tended to recover this loss by mid-June. We found significant among-individual variation in spring body mass plasticity (i.e., individual by environment interaction, I x E). We then investigated the relationships between individual spring body mass plasticity, longevity and lifetime reproductive success. Interestingly, heavier males lived longer than lighter males, but more plastic males had a lower longevity and lower lifetime reproductive success than less plastic males. The report of such plastic response in a stochastic resource system provides valuable insights into the interplay between the costs and benefits of phenotypic plasticity as an adaptation to environmental fluctuations.

opencc-zeroApr 2022View details →

Resource-dependent investment in male sexual traits in a viviparous fish

Exaggerated and conspicuous sexually selected traits are often costly to produce and maintain. Costly traits are expected to show resource-dependent expression, since limited resources prevent animals from investing maximally in multiple traits simultaneously. However, there may be critical periods during an individual's life where the expression of traits is altered if resources are limited. Moreover, costly sexual traits may arise from sexual selection acting both before (pre-copulatory) and after mating (post-copulatory). Gaining a robust understanding of resource-dependent trait expression therefore requires an approach that examines both episodes of sexual selection following resource limitation during different times in an individual's life. Yet few studies have taken such an approach. Here, we examine how resource restriction influences a set of pre- and post-copulatory traits in male pygmy halfbeaks (Dermogenys collettei), which invest in sexual ornaments and routinely engage in male-male contests and sperm competition. Critically, we examined responses in males when resources were restricted during development and after reaching sexual maturity. Both pre- and post-copulatory traits are resource-dependent in male halfbeaks. Body size, beak size, courtship behavior, and testes size were reduced by diet restriction, while, unexpectedly, the restricted-diet group had a larger area of red color on the beak and fins after diet treatment. These patterns were generally consistent when resources were restricted during development and after reaching sexual maturity. The study reinforces the role of resource acquisition in maintaining variation among sexual traits.

Data for: "Above and below ground trait coordination in tree seedlings depend on the most limiting resource: A test comparing a wet and a dry tropical forest in Mexico" by L. Sanaphre-Villanueva, F. Pineda-Garcia, W. Dattilo, L. F. Pinzon-Perez, A. Ricaño Rocha, H. Paz.

These data represent those published in “Above and below ground trait coordination in tree seedlings depend on the most limiting resource: A test comparing a wet and a dry tropical forest in Mexico” by L. Sanaphre-Villanueva, F. Pineda-Garcia, W. Dattilo, L. F. Pinzon-Perez, A. Ricaño Rocha, H. Paz. PeerJ. 2022.

A computational toolbox to investigate the metabolic potential and resource allocation in fission yeast

Computational models and figure data for the publication "A computational toolbox to investigate the metabolic potential and resource allocation in fission yeast" (preprint on <a href="https://doi.org/10.1101/2022.05.04.490403">bioRxiv</a>). Data put together by Pranas Grigaitis, p.grigaitis [at] vu.nl.   Abstract The fission yeast Schizosaccharomyces pombe is a popular eukaryal model organism for cell division and cell cycle studies. With this extensive knowledge of its cell and molecular biology, S. pombe also holds promise for use in metabolism research and industrial applications. However, unlike the baker’s yeast Saccharomyces cerevisiae, a major workhorse in these areas, cell physiology and metabolism of S. pombe remain less explored. One way to advance understanding of organism-specific metabolism is construction of computational models and their use for hypothesis testing. To this end, we leverage existing knowledge of S. cerevisiae to generate a manually-curated high-quality reconstruction of S. pombe’s metabolic network, including a proteome-constrained version of the model. Using these models, we gain insights into the energy demands for growth, as well as ribosome kinetics in S. pombe. Furthermore, we predict proteome composition and identify growth-limiting constraints that determine optimal metabolic strategies under different glucose availability regimes, and reproduce experimentally determined metabolic profiles. Notably, we find similarities in metabolic and proteome predictions of S. pombe with S. cerevisiae, which indicate that similar cellular resource constraints operate to dictate metabolic organization. With these use cases, we show, on the one hand, how these models provide an efficient means to transfer metabolic knowledge from a well-studied to a lesser-studied organism, and on the other, how they can successfully be used to explore the metabolic behaviour and the role of resource allocation in driving different strategies in fission yeast.

opencc-by-4.0Mar 2022View details →

Supporting Data for: Resource requirements for ecosystem conservation: A combined industrial and natural ecology approach to quantifying natural capital use in nature

Data used to derive allometric equations for land area use by mammals, birds, reptiles, and insects, and data for the analysis of natural resource use at the Natural Capital Laboratory site.

Data from: Building communities of teaching practice and data-driven open education resources with NEON faculty mentoring networks

With the growing availability and accessibility of big data in ecology, we face an urgent need to train the next generation of scientists in data science practices and tools. One of the biggest barriers for implementing a data-driven curriculum in undergraduate classrooms is the lack of training and support for educators to develop their own skills and time to incorporate these principles into existing courses or develop new ones. Alongside the research goals of the National Ecological Observatory Network (NEON), providing education and training are key components for building a community of scientists and users equipped to utilize large-scale ecological and environmental data. To address this need, the NEON Data Education Fellows program formed as a collaborative Faculty Mentoring Network (FMN) between scientists from NEON and university faculty interested in using NEON data and resources in their ecology classrooms. Like other FMNs, this group has two main goals: 1) to provide tools, resources, and support for faculty interested in developing data-driven curriculum, and (2) to make teaching materials that have been implemented and tested in the classroom available as open educational resources for other educators. We hosted this program using an open education and collaboration platform from the Quantitative Undergraduate Biology Education and Synthesis (QUBES) project. Here, we share lessons learned from facilitating five FMN cohorts and emphasize the successes, pitfalls, and opportunities for developing open education resources through community-driven collaborations.

Data from: Implementation of a pediatric telemedicine and medication delivery service in a resource-limited setting: A pilot study for clinical safety and feasibility

Objective: Determine the clinical safety and feasibility of implementing a telemedicine and medication delivery service (TMDS) to address gaps in nighttime healthcare access for children in low-resource settings. Results: A total of 391 cases were enrolled from September 9th, 2019 to January 19th, 2021; 89% (347) received a household visit. Most cases were triaged as mild or moderate (92%; 361). Among the severe cases, 83% (20) sought subsequent referred care. The most common complaint was a respiratory problem (63%; 246). At 10-days, 95% (329) of parents reported their child's condition as "improved" or "recovered". Ninety-nine percent (344) rated the TMDS as "good" or "great". The median phone consultation was 20 minutes, time to arrival at the household was 73 minutes and total workflow per case was 114 minutes. Conclusion: The TMDS was a feasible healthcare delivery model with high rates of improved clinical status at 10-days.

Architectural effects regulate resource allocation within the inflorescences with nonlinear blooming patterns

These data were generated to investigate the resource allocation pattern within the inflorescence of Salvia przewalskii, a perennial herb with 4-ouvle ovary flowers and flowering sequence-floral position decoupled inflorescences. Spatial and temporal resource allocations within inflorescences have been well-studied in many plants based on flowering sequence or floral position. However, there have been few attempts to investigate architectural effects and resource competition in species where the blooming pattern does not follow a linear positional pattern within the inflorescence. Moreover, most flowering plants show female-biased sex allocation in early or basal flowers, but it is unclear in species with inherent and changeless ovule production. The data demonstrated that pollen production and dry mass deceased from bottom to top flowers but didn't significantly differ following flowering sequence, resulting in male-biased sex allocation in basal flowers. The seed production, fruit set, bud developmental exhibited significant declining trends from proximal to distal positions regardless of the thinning and pollen treatments. Meanwhile, the seed production, fruit set, bud developmental success did not significant difference when thinning conducted according to flowering sequence. Thus, architectural effects plays a crucial role in resource allocation within decoupled flowering inflorescences. Moreover, the inherent floral traits, such as changeless ovule production, may modify architectural effects on sex allocation.

Behavioural and morphological traits influence sex-specific floral resource use by hummingbirds

Research on resource partitioning in plant-pollinator mutualistic systems is mainly concentrated at the levels of species and communities, whereas differences between males and females are typically ignored. Nevertheless, pollinators often show large sexual differences in behaviour and morphology, which may lead to sex-specific patterns of resource use with the potential to differentially affect plant reproduction and diversification. We investigated variation in behavioural and morphological traits between sexes of hummingbird species as potential mechanisms underlying sex-specific flower resource use in ecological communities. To do so, we compiled a dataset of plant-hummingbird interactions based on pollen loads for 31 hummingbird species from 13 localities across the Americas, complemented by data on territorial behaviour (territorial or nonterritorial) and morphological traits (bill length, bill curvature, wing length and body mass). We assessed the extent of intersexual differences in niche breadth and niche overlap in floral resource use across hummingbird species. Then, we tested whether floral niche breadth and overlap between sexes are associated with sexual dimorphism in behavioural or morphological traits of hummingbird species, while accounting for evolutionary relatedness among the species. We found striking differences in patterns of floral resource use between sex. Females had a broader floral niche breadth and were more dissimilar in the plant species visited with respect to males of the same species, resulting in a high level of resource partitioning between sexes. We found that both territoriality and morphological traits were related to sex-specific resource use by hummingbird species. Notably, niche overlap between sexes was greater for territorial than nonterritorial species, and moreover, niche overlap was negatively associated with sexual dimorphism in bill curvature across hummingbird species. These results reveal the importance of behavioural and morphological traits of hummingbird species in sex-specific resource use and that resource partitioning by sex is likely to be an important mechanism to reduce intersexual competition in hummingbirds. These findings highlight the need for better understanding the putative role of intersexual variation in shaping patterns of interactions and plant reproduction in ecological communities.

Effect of resource limitation on host post-infection survival and systemic pathogenic growth

In the experiments presented here, we explore the effect of resource limitation, in form of starvation (which leads to decrease in accessible resources and depletion of reserves) and sexual activity (which leads to reallocation of resources from somatic defence towards reproduction), on immune function of female Drosophila melanogaster flies. We infected females with five bacterial pathogens and measured their post-infection survival when subjected to either starvation or sexual activity (mating). Additionally, we measured within host pathogen levels in case of three of these pathogens. Based on previous literature, we predicted that both modes of resource limitation will increase post-infection mortality, but only sexual activity will lead to increase of pathogen load (because of compromised immune function), while starvation will either not affect or reduce pathogen loads (because of reduced availability of resources for the pathogen to proliferate within the host). Our results indicate that both starvation and sexual activity can lead to increased within-host pathogen levels, in addition to increased post-infection mortality, but in a pathogen-specific manner.

Monks relax sibling competition over parental resources in Tibetan populations

Why parents in some societies induce some of their sons to become religious celibates is an evolutionary puzzle. Some have speculated that this might be associated with brother competition for family resources. However, the behavioral ecology of monks and the possible links with competition between brothers remains unexplored. Here, we use demographic data from Amdo Tibetan agropastoralists in western China to evaluate what factors determine the probability of becoming a monk and explore the possible association between wealth and having a monk brother. We found that boys with at least one older brother are more likely to be induced by their parents to become celibate monks. Patrilocal heads of household, who inherit parental property, are more likely to be first-born sons, whereas men who marry uxorilocally, that is they move to their wife's household, are generally second or later born sons. Moreover, we find that men with at least one monk brother are wealthier than men who only have non-celibate brothers. Together, these results suggest that sending a son to the monastery is way for parents to decrease competition between brothers over family resources. Harsh and resource-limited environments, like the one we consider, can lead to the emergence of communal households, including polyandrous families, which used to be common in Tibetan areas. Directing one son to become a religious celibate offers a potentially effective solution to brother competition in our population.

Data from: Comparing the importance of farming resource endowments and agricultural livelihood diversification for agricultural sustainability from the perspective of the food–energy–water nexus

Household Survey Data for journal article 'Comparing the importance of farming resource endowments and agricultural livelihood diversification for agricultural sustainability from the perspective of the food–energy–water nexus', without protected data.

Full list of publications dealing with resources nutritional quality in ecology

Our understanding of ecosystem functioning is strongly linked to the study of predator-prey relationships and food web structures. However, trophic ecology has often focused on identifying taxonomic relationships and quantifying the biomass or energy ingested by consumers, but has often failed to integrate the importance of the nutritional quality of resources in ecological dynamics. Underlying this gap is the multi-dimensional nature of resource quality which has hampered any consensus on the definition of resource nutritional quality. In this special issue, we aimed at gathering a subset of articles exemplifying the diversity of variables by which resources quality is quantified, the diversity of research topics that can be tackled in ecology - from physiological or evolutionary aspects to ecosystem processes - and propose some perspectives on the integration of nutritional quality within broader ecological concepts. Using a semi-automated literature analysis, we map the current landscape of the "resources nutritional quality" research of the last 30 years. We depict how it has been quantified through physical, biological or chemical indicators, the use of these parameters being largely dependent on the type of ecosystem studied and on the investigated ecological process. We then position the articles published in this special issue of Oikos within this landscape, showing they cover a small but relatively well representative subset of the domains of resources quality-related issues. Articles in this special issue browse a range of individual and population-level approaches (embracing evolutionary questions) to community related questions, include methodological issues and ecosystem-wide approaches using trophic quality indicators as tracers of resources origin. Based on these studies and on the literature review, we identify a non-exhaustive list of challenges and perspectives of research that we consider of highest priority in the large topic of trophic ecology.

Energetic constraints on body-size niches in a resource-limited marine environment

Body size of life on Earth spans many orders of magnitude, and with it scales the energetic requirements of organisms. Thus, changes in environmental energy should impact community body-size distributions in predictable ways by reshaping ecological and niche dynamics. We examine how carbon, oxygen, and temperature, three energetic drivers, impact community size-based assembly in deep-sea bivalves. We demonstrate that body-size distributions are influenced by multiple energetic constraints. Relaxation in these constraints leads to an expansion of body-size niche space through the addition of novel large size classes, increasing the standard deviation and mean of the body-size distribution. With continued Anthropogenic increases in temperature and reductions in carbon availability and oxygen in most ocean basins, our results point to possible radical shifts in invertebrate body size with the potential to impact ecosystem function.

Data and code from: Mixed infection, risk projection and misdirection: Interactions among pathogens alter links between host resources and disease

A growing body of literature links resources of hosts to their risk of infectious disease. Yet most hosts encounter multiple pathogens, and projections of disease risk based on resource availability could be fundamentally wrong if they do not account for interactions among pathogens within hosts. Here, we measured infection risk of grass hosts (Avena sativa) exposed to three naturally-co-occurring viruses either singly or jointly (barley and cereal yellow dwarf viruses [B/CYDVs]: CYDV-RPV, BYDV-PAV, and BYDV-SGV) along experimental gradients of nitrogen and phosphorus supply. We asked whether disease risk (i.e., infection prevalence) differed in single versus co-inoculations, and whether these differences varied with rates and ratios of nitrogen and phosphorus supply. In single inoculations, the viruses did not respond strongly to nitrogen or phosphorus. However, in co-inoculations, we detected illustrative cases of 1) resource-dependent antagonism (RPV with increasing N; possibly due to competition), 2) resource-dependent facilitation (SGV with decreasing N:P; possibly due to immunosuppression), and 3) weak or no interactions within hosts (for PAV). Together, these within-host interactions created emergent patterns for co-inoculated hosts, with both infection prevalence and viral richness increasing with the combination of low nitrogen and high phosphorus supply. We demonstrate that knowledge of multiple pathogens is essential for predicting disease risk from host resources, and that projections of risk that fail to acknowledge resource-dependent interactions within hosts could be qualitatively wrong. Expansions of theory from community ecology theory may help anticipate such relationships linking host resources to diverse pathogen communities.

Natural selection favours drought escape and an acquisitive resource‐use strategy in semi‐arid Mediterranean shrubs

<ol> <li>Natural selection is the major force driving adaptive evolution in natural populations, varying in strength, direction, and form through space and time, especially in highly variable environments such as Mediterranean ecosystems. Although a conservative resource-use strategy has been hypothesized to be adaptive in Mediterranean taxa, patterns of selection at the intraspecific level, i.e., the suite of traits determining individual fitness, are largely unknown.</li> <li>Using a phenotypic selection experiment in natural semiarid conditions, we measured direct and indirect selection acting through two different fitness components (survival and reproduction), to assess the adaptive value of 20 ecophysiological traits on individuals of two gypsum endemic species, Centaurea hyssopifolia and Helianthemum squamatum, dwelling in environments with contrasting abiotic conditions (south- and north-facing slopes) during two climatically contrasting years (dry and mesic). This allowed quantifying the magnitude and direction of natural selection at different spatiotemporal scales.</li> <li>Our results revealed that different abiotic conditions did not alter selection patterns, being the magnitude of selection more strongly affected by temporal environmental variation. Selection through reproduction indicated consistent selection for early phenology, low water use efficiency, high specific leaf area, low leaf dry matter content, and high leaf N across slopes and years in both species. In contrast, phenotypic trait variation was not linked to survival in either species. Furthermore, while individual reproductive output was higher or similar in environments with higher abiotic stress in both species and years, survival was similar across environmental conditions, and it was neither affected by plant size nor reproductive output.</li> <li>Contrary to our expectations, natural selection via reproductive fitness consistently favoured a drought-escape, acquisitive resource-use strategy in Mediterranean semiarid plants, rather than a conservative resource-use strategy, even under conditions of higher abiotic stress (i.e., south slopes and dry year). Such acquisitive strategy could allow rapid development by maximizing resource assimilation and reproduction before the most limiting climatic conditions of mid-late summer. Our results shed light on adaptive functional strategies of Mediterranean taxa at the intraspecific level, providing insight on future responses to environmental change, and highlight remarkable differences in selection acting through different fitness components.</li> </ol>

Data from: Resource supply and organismal dominance are associated with high secondary production in temperate agricultural streams

Agricultural land use affects the environmental and biological characteristics of stream ecosystems through multiple pathways including nutrient and pesticide contamination, riparian clear-cutting, and hydromorphological degradation. These changes in the abiotic environment can have a direct effect on the productivity of macroinvertebrate communities through environmental filtering and via altered resource conditions encompassing a shift from allochthonous to autochthonous primary production and changes in elemental stoichiometry and food quality. Additionally, macroinvertebrate productivity can be affected indirectly via biological mechanisms, such as changes in species interactions, richness, competition, and predation. We studied the effects of agriculture on structural and functional descriptors of macroinvertebrate communities by assessing environmental characteristics and macroinvertebrate secondary production (MSP), biomass, and density in two forested and two agricultural streams and investigated underlying biotic mechanisms. On average, MSP was 1.6–3.6, biomass 2.8–6.2, and density 5–13 times higher in agricultural than in forested streams. This pattern was associated with higher nutrient concentrations, standing crops of riparian herbaceous vegetation, suspended particulate organic carbon, quantity and quality of epilithic biofilms, and chlorophyll-a concentrations in seston and biofilm of the agricultural streams. Species richness and evenness were significantly lower in agricultural than in forested streams. A negative relationship between MSP and species richness and evenness indicated that density compensation and trait dominance were the prevalent mechanisms facilitating higher MSP in agricultural streams. Our findings suggest that the loss of riparian canopy and excess nutrient conditions are the major environmental drivers contributing to homogenization of ecological niches and dominance of highly productive non-insect generalist species. This study highlights the importance of an ecosystem approach to understanding how complex aggregate stressors affect the regulation of consumer-resource interactions. There is an urgent need to preserve or restore natural riparian vegetation, fostering habitat and resource diversity and limiting nutrient contamination to stream ecosystems.

Latitudinal resource gradient shapes multi-variate defense strategies in a long-lived shrub

Herein lies the data and R code for the analyses for the manuscript titled, "Latitudinal resource gradient shapes multi-variate defense strategies in a long-lived shrub", published in Ecology.

Trophic structure and origin of resources of soil macrofauna in the salt marsh of the Wadden Sea: a stable isotope (15N,13C) study

Salt marshes exist along the gradient of the marine mudflat to the terrestrial dunes, with a gradient of shore height and associated plant zonation. The lower salt marsh (LSM) extends from the mean high tidal level to 35 cm above that level and is followed by the upper salt marsh (USM). Despite changes in the amount of allochthonous marine input and in abiotic conditions, little is known about changes in the trophic structure and used of basal resources by the soil macrofauna along marine – terrestrial boundaries. Natural variations in carbon stable isotope ratios (δ¹³C signatures) allow insight into basal resources of consumers such as marine algae, terrestrial C3 and C4 photosynthesising plants. Furthermore, variations in nitrogen stable isotope ratios (δ¹5N signatures) allow insight into the trophic position of consumers. We investigated spatial and temporal changes in stable isotope signatures in salt marsh soil macrofauna of the island of Spiekeroog, German Wadden Sea. The range of δ¹⁵N signatures indicated no changes in food chain length across salt marsh zones with consumers in both zones comprising primary decomposer, secondary decomposer and first order predators. However, the trophic position of individual species changed between zones, but in particular with season. Contrasting δ¹⁵N signatures, the range in δ¹³C signatures in the LSM was twice that in the USM indicating a wider range of resources consumed. Bayesian mixing models indicated predominant autochthonous resource use in both the LSM and USM, with the use of marine allochthonous resources never exceeding 29.6%. However, the models also indicate an increase in the use of marine resources in certain species in the LSM with no use in the USM. Overall, the results indicate that the resource use of salt marsh macrofauna varies more in space than in time, with the food web being generally based on autochthonous rather than allochthonous resources. However, there also is trophic plasticity in certain species across both temporal and spatial scales including variations in the use of allochthonous resources. Generally, however, marine input contributes little to the nutrition of salt marsh soil macroinvertebrates.