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3,121 results for “Resources”
Data from: Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of single nucleotide polymorphisms
Assessing the genetic variability of the tick Ixodes ricinus - an important vector of pathogens in Europe - is an essential step for setting-up anti-tick control methods. Here, we report the first identification of a set of SNPs isolated from the genome of I. ricinus, carried out by applying a genomic complexity reduction step, followed by pyrosequencing and the use new bioinformatics tools. Almost 1.4 million reads (average length : 528 nt) were generated with a full Roche 454 GS FLX run on two Reduced Representation Libraries of I. ricinus. 321,088 putative SNPs were isolated using the newly developed bioinformatics tool READ2SNPS, which identifies SNPs without requiring a reference genome. Stringent selection criteria were applied in a bioinformatics pipeline to select 1,768 SNPs for the development of specific primers. Among 384 randomly selected SNPs, tested by Fluidigm genotyping technology on 464 individual ticks, 368 SNPs loci (96%) exhibited the presence of the two expected alleles. Hardy-Weinberg equilibrium tests conducted on 6 natural populations of ticks showed that from 26 to 46 of the 384 loci exhibited significant heterozygote deficiencies. The generated SNP resource described here will be useful for a variety of applications such as the assessment of the genetic structure of I. ricinus populations.
Data from: Resource dispersion influences dispersal evolution of highly insulated insect communities
Communities in which species are obligately associated with a single host plant are ideal to test adaptive responses of community traits to selection since such communities are often highly insulated. Fig species provide oviposition resources to co-evolved fig-wasp communities. Dispersing fig-wasp communities move from one host plant to another for oviposition. We compared the spatial dispersion of two fig species and the dispersal capacities of their multitrophic wasp communities. Dispersal capacities were assessed by measuring vital dispersal correlates, namely tethered flight durations, somatic lipid contents and resting metabolic rates. We suggest that dispersal-trait distributions of congeneric wasp species across the communities are an adaptive response to host plant dispersion. Larger dispersal capacities of the entire multitrophic community are related to more widely dispersed resources. Our results provide evidence and a novel perspective for understanding the potential role of adaptation in whole-community dispersal-trait distributions.
Data from: Chlamydomonas genome resource for laboratory strains reveals a mosaic of sequence variation, identifies true strain histories, and enables strain-specific studies
Chlamydomonas reinhardtii is a widely used reference organism in studies of photosynthesis, cilia, and biofuels. Most research in this field uses a few dozen standard laboratory strains that are reported to share a common ancestry, but exhibit substantial phenotypic differences. In order to facilitate ongoing Chlamydomonas research and explain the phenotypic variation, we mapped the genetic diversity within these strains using whole-genome resequencing. We identified 524,640 single nucleotide variants and 4812 structural variants among 39 commonly used laboratory strains. Nearly all (98.2%) of the total observed genetic diversity was attributable to the presence of two, previously unrecognized, alternate haplotypes that are distributed in a mosaic pattern among the extant laboratory strains. We propose that these two haplotypes are the remnants of an ancestral cross between two strains with ∼2% relative divergence. These haplotype patterns create a fingerprint for each strain that facilitates the positive identification of that strain and reveals its relatedness to other strains. The presence of these alternate haplotype regions affects phenotype scoring and gene expression measurements. Here, we present a rich set of genetic differences as a community resource to allow researchers to more accurately conduct and interpret their experiments with Chlamydomonas.
Allocating resources for land protection using continuous optimization: an application to US biodiversity conservation
Spatial optimization approaches that were originally developed to help conservation organizations determine protection decisions over small spatial scales are now used to inform global or continental scale priority setting. However, the different decision contexts involved in large-scale resource allocation need to be considered. We present a continuous optimization approach in which a decision-maker allocates funding to regional offices. Local decision-makers then use these funds to implement habitat protection efforts with varying effectiveness when evaluated in terms of the funder's goals. We illustrate this continuous formulation by examining the relative priority that should be given to different counties in the coterminous United States (US) when acquiring land to establish new protected areas. If weighting all species equally, counties in the southwest US, where large areas can be bought cheaply, are priorities for protection. If focusing only on species of conservation concern, priorities shift to locations rich in such species, particularly near expanding exurban areas facing high rates of future habitat conversion (e.g., south-central Texas). Priorities for protection are sensitive to what is assumed about local ecological and decision-making processes. For example, decision-makers who doubt the efficacy of local land protection efforts should focus on a few key areas, while optimistic decision-makers should disperse funding more widely. Efforts to inform large-scale conservation priorities should reflect better the types of choice that decision-makers actually face when working over these scales. They also need to report the sensitivity of recommended priorities to what are often unstated assumptions about local processes affecting conservation outcomes.
Data from: Resource-driven changes to host population stability alter the evolution of virulence and transmission
What drives the evolution of parasite life history traits? Recent studies suggest that feedbacks between within-host and between-host processes can provide key insight into both disease dynamics and parasite evolution. Still, it remains difficult to understand how to mechanistically connect these cross-scale feedbacks, particularly under non-equilibrium conditions; many natural host populations inherently fluctuate and parasites themselves can strongly alter the stability of host populations. Here, we develop a general model framework that mechanistically links resources to parasite evolution across a gradient of stable and unstable conditions. First, we dynamically link resources and between-host (host density, stability, transmission) processes to virulence evolution. Then, we consider a 'nested' model where population-level processes (transmission and virulence) depend on resource-driven changes to individual-level (within-host) processes (energetics, immune function, parasite production). Contrary to 'non-nested' model predictions, the nested model reveals complex effects of host population dynamics on parasite evolution, including regions of evolutionary bistability, where evolution can push parasites toward strongly or weakly stabilizing strategies. This bistability results from tension between resource-driven changes to host density, host immune function, and parasite production. Together, these results highlight how cross-scale feedbacks can provide key insights into the structuring role of parasites and parasite evolution.
Data from: NEMBASE4: the nematode transcriptome resource
Nematode parasites are of major importance in human health and agriculture, and free-living species deliver essential ecosystem services. The genomics revolution has resulted in the production of many datasets of expressed sequence tags (ESTs) from a phylogenetically wide range of nematode species, but these are not easily compared. NEMBASE4 presents a single portal onto extensively functionally annotated, EST-derived transcriptomes from over sixty species of nematodes, including plant and animal parasites and free-living taxa. Using the PartiGene suite of tools, we have assembled the ESTs publicly available for each species into a high-quality set of putative transcripts. These transcripts have been translated to produce a protein sequence resource, and each annotated with functional information derived from comparison to well-studied nematode species such as Caenorhabditis elegans and also other non-nematode resources. By cross-comparing the sequences within NEMBASE4, we have also generated a protein family assignment for each translation. The data are presented in an openly-accessible, interactive database. To demonstrate the utility of NEMBASE4, we have used the database to examine the uniqueness of the transcriptomes of major clades of parasitic nematodes, identifying lineage-restricted genes that may underpin particular parasitic phenotypes, possible viral pathogens of nematodes, and nematode-unique protein families that may be developed as drug targets.
Data from: Mating affects resource selection and modulates associational effects between neighbouring resources
Associational effects occur when the attack rate on a resource depends on neighbouring resources in the environment. These effects are predicted to result from mismatches experienced by the consumer organism in resource selection along hierarchical search levels. As resource selection depends on sensory information used during search behaviour, we expected that different physiological states of an insect might modulate the outcome of associational effects due to differences in resource selection. We used Drosophila melanogaster, as a model organism for olfactory-guided behaviour in insects, to study the effects of mating induced behavioural changes on associational effects between two alternative resources. We found that mating has no effect on the ability of D. melanogaster to locate resource patches, but rather affects the perception of the resources within the patch. Consequently, we only found associational effects in the experiments with unmated females and not in the experiments with mated females. Our results suggest that the lack of associational effects for mated females resulted from changes in the use of short-range olfactory cues, leading to random selection among the resources. In conclusion, our results suggest that the physiological state of an insect modulates associational effects by affecting resource selection rates within the patch.
Data from: Transcriptome resources for the perennial sunflower Helianthus maximiliani obtained from ecologically divergent populations
Next generation sequencing (NGS) technologies provide a rapid means to generate genomic resources for species exhibiting interesting ecological and evolutionary variation but for which such resources are scant or nonexistent. In the current report, we utilize 454 pyrosequencing to obtain transcriptome information for multiple individuals and tissue types from geographically disparate and ecologically differentiated populations of the perennial sunflower species Helianthus maximiliani. A total of 850,275 raw reads were obtained averaging 355 bp in length. Reads were assembled, post processing, into 16,681 unique contigs with an N50 of 898 bp and a total length of 13.6 Mb. A majority (67%) of these contigs were annotated based on comparison to the Arabidopsis thaliana genome (TAIR10). Contigs were identified that exhibit high similarity to genes associated with natural variation in flowering time and freezing tolerance in other plant species and will facilitate future studies aimed at elucidating the molecular basis of clinal life history variation and adaptive differentiation in H. maximiliani. Large numbers of gene-associated simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) also were identified that can be deployed in mapping and population genomic analyses.
Data from: Effects of variation in resource acquisition during different stages of the life cycle on life-history traits and trade-offs in a burying beetle
Individual variation in resource acquisition should have consequences for life-history traits and trade-offs between them because such variation determines how many resources can be allocated to different life-history functions, such as growth, survival and reproduction. Since resource acquisition can vary across an individual's life cycle, the consequences for life-history traits and trade-offs may depend on when during the life cycle resources are limited. We tested for differential and/or interactive effects of variation in resource acquisition in the burying beetle Nicrophorus vespilloides. We designed an experiment in which individuals acquired high or low amounts of resources across three stages of the life cycle: larval development, prior to breeding and the onset of breeding in a fully crossed design. Resource acquisition during larval development and prior to breeding affected egg size and offspring survival, respectively. Meanwhile, resource acquisition at the onset of breeding affected size and number of both eggs and offspring. In addition, there were interactive effects between resource acquisition at different stages on egg size and offspring survival. However, only when females acquired few resources at the onset of breeding was there evidence for a trade-off between offspring size and number. Our results demonstrate that individual variation in resource acquisition during different stages of the life cycle has important consequences for life-history traits but limited effects on trade-offs. This suggests that, in species that acquire a fixed-sized resource at the onset of breeding, the size of this resource has larger effects on life-history trade-offs than resources acquired at earlier stages.
Data from: Consumer-resource interactions and the evolution of migration
Theoretical studies have demonstrated that selection will favor increased migration when fitnesses vary both temporally and spatially, but it is far from clear how pervasive those theoretical conditions are in nature. While consumer-resource interactions are omnipresent in nature and can generate spatial and temporal variation, it is unknown even in theory whether these dynamics favor the evolution of migration. We develop a mathematical model to address whether and how migration evolves when variability in fitness is determined at least in part by consumer-resource coevolutionary interactions. Our analyses show that such interactions can drive the evolution of migration in the resource, consumer, or both species and thus supplies a general explanation for the pervasiveness of migration. Over short time scales, we show the direction of change in migration rate is determined primarily by the state of local adaptation of the species involved: rates increase when a species is locally maladapted and decrease when locally adapted. Our results reveal that long-term evolutionary trends in migration rates can differ dramatically depending on the strength or weakness of interspecific interactions and suggest an explanation for the evolutionary divergence of migration rates among interacting species.
Data from: Pollen feeding, resource allocation and the evolution of chemical defense in passion vine butterflies
Evolution of pollen feeding in Heliconius has allowed exploitation of rich amino acid sources and dramatically reorganized life history traits. In Heliconius eggs are produced mainly from adult acquired resources, leaving somatic development and maintenance to larva effort. This innovation may also have spurred evolution of chemical defense via amino acid-derived cyanogenic glycosides. By contrast, non-pollen feeding heliconiines must rely almost exclusively on larval-acquired resources for both reproduction and defense. We tested whether adult amino acid intake has an immediate influence on cyanogenesis in Heliconius. Because Heliconius are more distasteful to bird predators than close relatives that do not utilize pollen we also compared cyanogenesis due to larval input across Heliconius species and non-pollen-feeding relatives. Except for one species, we found that varying the amino acid diet of an adult Heliconius has negligible effect on its cyanide concentration. Adults denied amino acids showed no decrease in cyanide and no adults showed cyanide increase when fed amino acids. Yet, pollen-feeding butterflies were capable of producing more defense than non-pollen feeding relatives and differences were detectable in freshly emerged adults, before input of adult resources. Our data points to a larger role of larval input in adult chemical defense. This, coupled with the compartmentalization of adult nutrition to reproduction and longevity suggests that one evolutionary consequence of pollen feeding, shifting the burden of reproduction to adults, is to allow the evolution of greater allocation of host plant amino acids to defensive compounds by larvae.
Data from: "You are not what you eat: massive parallel sequencing reveals that gut microbiome is not diet-related in larval Dilophus febrilis (Diptera: Bibionidae)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015
This article documents the public availability of metagenome sequence data from 454 amplicon sequencing of larval dipteran gut (Dilophus febrilis) and their potential food sources dwarf shrub litter (Vaccinium gaultheroides), grass litter (Dactylis glomerata), and cow dung (Bos primigenius taurus).
Data from: Resource heterogeneity, soil fertility, and species diversity: effects of clonal species on plant communities
Spatial heterogeneity in soil resources is widely thought to promote plant species coexistence, and this mechanism figures prominently in resource-ratio models of competition. However, most experimental studies have found that nutrient enhancements depress diversity regardless of whether nutrients are uniformly or heterogeneously applied. This mismatch between theory and empirical pattern is potentially due to an interaction between plant size and the scale of resource heterogeneity. Clonal plants that spread vegetatively via rhizomes or stolons can grow large and may integrate across resource patches, thus reducing the positive effect of small-scale resource heterogeneity on plant species richness. Many rhizomatous clonal species respond strongly to increased soil fertility, and they have been hypothesized to drive the descending arm of the hump-shaped productivity-diversity relationship in grasslands. We tested whether clonals reduce species richness in a grassland community by manipulating nutrient heterogeneity, soil fertility, and the presence of rhizomatous clonal species in a 6-year field experiment. We found strong and consistent negative effects of clonals on species richness. These effects were greatest at high fertility and when soil resources were applied at a scale at which rhizomatous clonals could integrate across resource patches. Thus, we find support for the hypothesis that plant size and resource heterogeneity interact to determine species diversity.
Data from: Logical validation and evaluation of practical feasibility for the SCRuM (School Clinical Rugby Measure) test battery developed for young adolescent rugby players in a resource-constrained environment
There is a growing impetus towards usage of test batteries in talent identification (TID) programmes in rugby. Consequently, there are many test batteries in existence profiling anthropometric, physiological characteristics and rugby-specific skills. There is no consensus in the literature on the constituent variables and corresponding tests required to inform TID programs. Following development of a new test battery called the SCRuM (School Clinical Rugby Measure), this study aimed at establishing face, logical validity and practical feasibility of included tests. The test battery, initially comprised of 23 items, had its face and logical validity evaluated by five (5) adolescent rugby coaches and 20 rugby experts, respectively. Logical validation was conducted in two questionnaire-based rounds with Content Validity Index (I-CVI) calculated for each variable. Subsequently, a cross-sectional study targeting 30 local rugby coaches was conducted to determine the perceived practical feasibility of each test item. The results showed excellent I-CVI (>0.78) for 17 variables (speed, weight, height and skin fold measures, repeated high-intensity exercise performance ability, prolonged high-intensity intermittent running ability, change of direction speed, anaerobic capacity, lower-and upper body muscular power and strength, muscular flexibility, reactive agility, passing for accuracy, tackling proficiency, and catching). However, three tests, namely, Reactive Agility, One Repetition Maximum Back Squat and One Repetition Maximum Bench Press had low test-feasibility indices (T-FI< 35) suggesting practicality concerns with implementation in the Zimbabwean context. Thus, these findings suggest the need for substitution or development of new practically feasible tests for upper-and lower body muscular strength and reactive agility.
Data from: Women are underrepresented on the editorial boards of journals in environmental biology and natural resource management
Despite women earning similar numbers of graduate degrees as men in STEM disciplines, they are underrepresented in upper level positions in both academia and industry. Editorial board memberships are an important example of such positions; membership is both a professional honor in recognition of achievement and an opportunity for professional advancement. We surveyed 10 highly regarded journals in environmental biology, natural resource management, and plant sciences to quantify the number of women on their editorial boards and in positions of editorial leadership (i.e., Associate Editors and Editors-in-Chief) from 1985 to 2013. We found that during this time period only 16% of subject editors were women, with more pronounced disparities in positions of editorial leadership. Although the trend was towards improvement over time, there was surprising variation between journals, including those with similar disciplinary foci. While demographic changes in academia may reduce these disparities over time, we argue journals should proactively strive for gender parity on their editorial boards. This will both increase the number of women afforded the opportunities and benefits that accompany board membership and increase the number of role models and potential mentors for early-career scientists and students.
Data from: Do larger individuals cope with resource fluctuations better? An artificial selection approach
Size determines the rate at which organisms acquire and use resources but it is unclear what size should be favoured under unpredictable resource regimes. Some theories claim smaller organisms can grow faster following a resource pulse, whereas others argue larger species can accumulate more resources and maintain growth for longer periods between resource pulses. Testing these theories has relied on interspecific comparisons, which tend to confound body size with other life-history traits. As a more direct approach, we used 280 generations of artificial selection to evolve a 10-fold difference in mean body size between small- and large-selected phytoplankton lineages of the green microalga Dunaliella tertiolecta, while controlling for biotic and abiotic variables. We then quantified how body size affected the ability of this species to grow at nutrient-replete conditions and following periods of nitrogen or phosphorous deprivation. Overall, smaller cells showed slower growth, lower storage capacity and poorer recovery from phosphorous depletion, as predicted by the "fasting endurance hypothesis". However, recovery from nitrogen limitation was independent of size – a finding unanticipated by current theories. Phytoplankton species are responsible for much of the global carbon fixation and projected trends of cell size decline could reduce primary productivity by lowering the ability of a cell to store resources.
Data from: Bottom-up and trait-mediated effects of resource quality on amphibian parasitism
Leaf litter subsidies are important resources for aquatic consumers like tadpoles and snails, causing bottom-up effects on wetland ecosystems. Recent studies have shown that variation in litter nutritional quality can be as important as litter quantity in driving these bottom-up effects. Resource subsidies likely also have indirect and trait-mediated effects on predation and parasitism, but these potential effects remain largely unexplored. We generated predictions for differential effects of litter nutrition and secondary polyphenolic compounds on tadpole (Lithobates sylvatica) exposure and susceptibility to Ribeiroia ondatrae, based on ecological stoichiometry and community-ecology theory. We predicted direct and indirect effects on key traits of the tadpole host (rates of growth, development and survival), the trematode parasite (production of the cercaria infective stages) and the parasite's snail intermediate host (growth and reproduction). To test these predictions, we conducted a large-scale mesocosm experiment using a natural gradient in the concentrations of nutrients (nitrogen) and toxic secondary compounds (polyphenolics) of nine leaf litter species. To differentiate between effects on exposure vs. susceptibility to infection, we included multiple infection experiments including one with constant per capita exposure. We found that increased litter nitrogen increased tadpole survival, and also increased cercaria production by the snail intermediate hosts, causing opposing effects on tadpole per capita exposure to trematode infection. Increased litter polyphenolics slowed tadpole development, leading to increased infection by increasing both their susceptibility to infection and the length of time they were exposed to parasites. Based on these results, recent shifts in forest composition towards more nitrogen-poor litter species should decrease trematode infection in tadpoles via density- and trait-mediated effects on the snail intermediate hosts. However, these shifts also involve increased abundance of litter species with high polyphenolic levels, which should increase trematode infection via trait-mediated effects on tadpoles. Future studies will be needed to determine the relative strength of these opposing effects in natural wetland communities.
Data from: Grazing and resource availability control soil nematode body size and abundance-mass relationship in semi-arid grassland
1. Body size is a central functional trait in ecological communities. Despite recognition of the importance of above-belowground interactions, effects of aboveground herbivores on size and abundance-size relationships in soil fauna are almost uncharted. Depending on climate and soil properties, herbivores may increase basal resources of soil food webs, or reduce pore space, mechanisms expected to have contrasting effects on soil animal body size. 2. We investigated how body size and shape of soil nematodes responded to mammalian grazers in three semi-arid grassland sites, along a gradient of soil texture and organic matter (OM) in a long-term herbivore removal study. We analysed nematode mass, length, diameter, body size distribution, and biomass distribution. We formulated two mechanistic hypotheses to assess whether resource availability or pore space was the dominant abiotic control and modulated the effects of grazing. 3. In ungrazed soils, average and maximum nematode size, as well as abundance and biomass of large nematodes, were greater in the high-OM than in the low-OM soil, and intermediate in the medium-OM soil. Grazing promoted larger sizes in the low-OM soil, where it had been shown to increase organic matter and microbial biomass, and led to more homogeneous average size and body size distribution across sites. The results support the hypothesis that nematode size was controlled by basal resource availability rather than by pore space. However, body shape might have been constrained by small pores in the fine-texture, high-OM soil, where nematodes were more elongated. 4. Grazing may facilitate larger sizes in soil nematode communities by boosting basal resources where these are limiting, with important implications for estimations of nematode biomass and contribution to carbon and nutrient cycling. These findings contribute to the insofar-limited mechanistic understanding of how herbivores can shape functional traits of soil fauna, and demonstrate that animals at one trophic level may control patterns in body size and abundance-size relationships in other trophic levels without a direct predator-prey or competitive linkage between them.
Data from: Prepupal building behavior in Drosophila melanogaster and its evolution under resource and time constraints
Structures built by animals are a widespread and ecologically important 'extended phenotype'. While its taxonomic diversity has been well described, factors affecting short-term evolution of building behavior within a species have received little experimental attention. Here we describe how, given the opportunity, wandering Drosophila melanogaster larvae often build long tunnels in agar substrates and embed their pupae within them. These embedded larvae are characterized by a longer egg-to-pupariation developmental time than larvae that pupate on the surface. Assuming that such building behaviors are likely to be energetically costly and/or time consuming, we hypothesized that they should evolve to be less pronounced under resource or time limitation. In accord with this prediction, larvae from populations evolved for 160 generations under a regime that combines larval malnutrition with limited developmental time dug shorter tunnels than larvae from control unselected populations. However, the proportion of larvae that embedded before pupation did not differ between the malnutrition-adapted and control populations, suggesting that tunnel length and likelihood of embedding before pupation are controlled by different genetic loci. The behaviors exhibited by wandering larvae of Drosophila melanogaster prior to pupation offer a model system to study evolution of animal building behaviors because the tunneling and embedding phenotypes are simple, facultative and highly variable.
Data from: Information use and resource competition: an integrative framework
Organisms may reduce uncertainty regarding how best to exploit their environment by collecting information about resource distribution. We develop a model to demonstrate how competition can facilitate or constrain an individual's ability to use information when acquiring resources. Since resource distribution underpins both selection on information use and the strength and nature of competition between individuals, we demonstrate interdependencies between the two that should be common in nature. Individuals in our model can search for resources either personally or by using social information. We explore selection on social information use across a comprehensive range of ecological conditions, generalising the producer-scrounger framework to a wide diversity of taxa and resources. We show that resource ecology – defined by scarcity, depletion rate, and monopolisability – determines patterns of individual differences in social information use. These differences suggest co-evolutionary processes linking dominance systems and social information use, with implications for the evolutionary demography of populations.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.