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3,121 results for “Resources”
Data from: Combined effects of natural enemies and competition for resources on a forest defoliator: a theoretical and empirical analysis
Explanations for the dynamics of insect outbreaks often focus on natural enemies, on the grounds that parasitoid and pathogen attack rates are high during outbreaks. While natural enemy models can successfully reproduce outbreak cycles, experiments have repeatedly demonstrated the importance of resource quality and abundance. Experiments, however, are rarely invoked in modeling studies. Here we combine mechanistic models, observational data, and field experiments to quantify the roles of parasitoid attacks and resource competition on the jack pine budworm, Choristoneura pinus. By fitting models to a combination of observational and experimental data, we show that parasitoid attacks are the main source of larval budworm mortality at low and intermediate budworm densities, but that resource competition is the main source of mortality at high densities. Our results further show that the effects of resource competition become more severe with increasing host tree age, and that the effects of parasitoids are moderated by strong competition between parasitoids for hosts. Allowing for these effects in a model of insect outbreaks leads to realistic outbreak cycles, while a host-parasitoid model without resource competition produces an unrealistic stable equilibrium. The effects of resource competition are modulated by tree age, which in turn depends on fire regimes. Our model therefore suggests that increases in fire frequency due to climate change may interact in complex ways with budworm outbreaks. Our work shows that resource competition can be as important as natural enemies in modulating insect outbreaks, while demonstrating the usefulness of high-performance computing in experimental field ecology.
Data from: Molecular diet analysis finds an insectivorous desert bat community dominated by resource sharing despite diverse echolocation and foraging strategies
Interspecific differences in traits can alter the relative niche use of species within the same environment. Bats provide an excellent model to study niche use because they have a wide variety of behavioural, acoustic and morphological traits that may lead to multi-species, functional groups. Predatory bats have been classified by their foraging location (edge, clutter, open space), ability to aerial hawk and/or substrate glean prey and echolocation call design and flexibility, all of which may dictate their diet. For example, high frequency, broadband calls do not travel far but offer high object resolution while high intensity, low frequency calls travel further but provide lower resolution. Because these behaviours can be flexible four behavioural categories have been proposed: (1) gleaning, (2) behaviourally flexible (gleaning and hawking), (3) clutter tolerant hawking, and (4) open space hawking. Recent studies of diet in bats use molecular tools to identify prey but mainly focus on one or two species in isolation and few studies provide evidence for substantial differences in prey use despite the many behavioural, acoustic and morphological differences. Here we analyse the diet of 17 sympatric species in the Chihuahuan desert and test the hypothesis that peak echolocation frequency and behavioural categories are linked to differences in diet. We find no significant correlation between dietary richness and echolocation frequency (though it spanned close to 100kHz across species). However, our data suggest that behaviourally flexible bats that use gleaning and aerial hawking have the broadest diets and are the most differentiated from clutter-tolerant aerial hawking species.
Data from: "De novo assembled transcriptome of organs involved in reproduction in an endangered endemic Iberian cyprinid fish (Squalius pyrenaicus)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015
Sex determination systems are diverse, especially among fish, and include genetic and/or environmental components. Unexpectedly for such a basic aspect of development, sex determination systems change rapidly during evolution and gonadal fate is not ultimate, being actively maintained lifelong. Here, sequences of expressed genes involved in maintenance of gonad identity and reproduction processes were obtained through transcriptome assembly of the brain-gonadal axis tissues of a freshwater fish inhabiting highly variable environments, the gonochoristic Iberian fish Squalius pyrenaicus. Through Illumina total RNA-sequencing, male and female transcriptomes of brain and gonad tissues were assembled with Trans-ABySS software and merged to produce a more comprehensive S. pyrenaicus transcriptome. Coding sequences (CDS) predicted by TransDecoder were annotated using blastx. By means of read mapping against the reference transcriptome and CDS datasets, using Bowtie2, the accuracy of read mapping was assessed. This first endemic Iberian cyprinid transcriptome of organs involved in reproduction processes may serve as a valuable genomic resource for studying sexual mechanisms and other aspects of evolution, such as speciation and responses to environmental changes, and may be a useful tool for conservation studies since S. pyrenaicus is an endangered species.
Data from: Land use alters trophic redundancy and resource flow through stream food webs
1. The changes to physical and chemical ecosystem characteristics as a response to pervasive and intensifying land use have the potential to alter the consumer-resource interactions and to rewire the flow of energy through entire food webs. 2. We investigated these structural and functional properties of food webs in stream ecosystems distributed across woodland, agricultural and urban areas in the Zagreb region of Croatia. We compared resource availability and consumer diet composition using stable isotope mixing models and tested how the isotopic variance of basal resources, primary consumers, macroinvertebrate predators, and other food-web characteristics change with different land use types. 3. Combination of increased loading and altered composition of nutrients, lower water discharge and higher light availability at urban sites likely promoted the contribution of aquatic macrophytes to diets of primary consumers. Macroinvertebrate predators shifted their diet, relying more on active filterers at urban sites relative to woodland and agricultural sites. Urban food webs also had lower trophic redundancy (i.e. fewer species at each trophic level) and a more homogenised energy flow from lower to higher trophic levels. There was no effect of land use on isotopic variation of basal resources, primary consumers or macroinvertebrate predators, but all these trophic groups at urban and agricultural sites were 15N-enriched relative to their counterparts in woodland stream food webs. 4. The physical and chemical ecosystem characteristics associated with intensive land use altered the resource availability, trophic redundancy and the flow of energy to other trophic levels, with potentially negative consequences for community dynamics and ecosystem functioning. These empirical findings indicate that reducing nutrient pollution, agricultural runoffs and maintaining riparian vegetation can mitigate the impacts of land use on structure and function of stream ecosystems.
Data from: Extreme behavioural shifts by baboons exploiting risky, resource-rich, human-modified environments
A range of species exploit anthropogenic food resources in behaviour known as 'raiding'. Such behavioural flexibility is considered a central component of a species' ability to cope with human-induced environmental changes. Here, we study the behavioural processes by which raiding male chacma baboons (Papio ursinus) exploit the opportunities and mitigate the risks presented by raiding in the suburbs of Cape Town, South Africa. Ecological sampling and interviews conducted with 'rangers' (employed to manage the baboons' space use) revealed that baboons are at risk of being herded out of urban spaces that contain high-energy anthropogenic food sources. Baboon-attached motion/GPS tracking collars showed that raiding male baboons spent almost all of their time at the urban edge, engaging in short, high-activity forays into the urban space. Moreover, activity levels were increased where the likelihood of deterrence by rangers was greater. Overall, these raiding baboons display a time-activity balance that is drastically altered in comparison to individuals living in more remote regions. We suggest our methods can be used to obtain precise estimates of management impact for this and other species in conflict with people.
Data from: Teasing apart plant community responses to N enrichment: the roles of resource limitation, competition and soil microbes
Although ecologists have documented the effects of nitrogen enrichment on productivity, diversity and species composition, we know little about the relative importance of the mechanisms driving these effects. We propose that distinct aspects of environmental change associated with N enrichment (resource limitation, asymmetric competition, and interactions with soil microbes) drive different aspects of plant response. We test this in greenhouse mesocosms, experimentally manipulating each factor across three ecosystems: tallgrass prairie, alpine tundra and desert grassland. We found that resource limitation controlled productivity responses to N enrichment in all systems. Asymmetric competition was responsible for diversity declines in two systems. Plant community composition was impacted by both asymmetric competition and altered soil microbes, with some contributions from resource limitation. Results suggest there may be generality in the mechanisms of plant community change with N enrichment. Understanding these links can help us better predict N response across a wide range of ecosystems.
Data from: Interacting effects of predation risk and resource level on escape speed of amphibian larvae along a latitudinal gradient
Fast-growing genotypes living in time-constrained environments are often more prone to predation, suggesting that growth-predation risk trade-offs are important factors maintaining variation in growth along climatic gradients. However, the mechanisms underlying how fast growth increases predation-mediated mortality are not well understood. Here, we investigated if slow-growing, low-latitude individuals have faster escape swimming speed than fast-growing high-latitude individuals using common frog (Rana temporaria) tadpoles from eight populations collected along a 1500 km latitudinal gradient. We measured escape speed in terms of burst and endurance speeds in tadpoles raised in the laboratory at two food levels and in the presence and absence of a predator (Aeshna dragonfly larvae). We did not find any latitudinal trend in escape speed performance. In low food treatments, burst speed was higher in tadpoles reared with predators but did not differ between high food treatments. Endurance speed, on the contrary, was lower in high-food tadpoles reared with predators, and did not differ between treatments at low food levels. Tadpoles reared with predators showed inducible morphology (increased relative body size and tail depth), which had positive effects on speed endurance at low but not at high food levels. Burst speed was positively affected by tail length and tail muscle size in the absence of predators. Our results suggest that escape speed does not trade off with fast growth along the latitudinal gradient in R. temporaria tadpoles. Instead, escape speed is a plastic trait and strongly influenced by the interaction between resource level and predation risk.
Data from: Signatures of selection for bonamiosis resistance in European flat oyster (Ostrea edulis): new genomic tools for breeding programs and management of natural resources
The European flat oyster (Ostrea edulis) is a highly appreciated mollusk with an important aquaculture production throughout the 20th century, in addition to playing an important role on coastal ecosystems. Overexploitation of natural beds, habitat degradation, introduction of non-native species and epidemic outbreaks have severely affected this important resource, particularly, the protozoan parasite Bonamia ostreae, which is the main concern affecting its production and conservation. In order to identify genomic regions and markers potentially associated with bonamiosis resistance, six oyster beds distributed throughout the European Atlantic coast were sampled. Three of them have been exposed to this parasite since the early 1980's and showed some degree of innate resistance (long-term affected group, LTA), while the other three were free of B. ostreae at least until sampling date (naïve group, NV). A total of 14,065 SNPs were analyzed, including 37 markers from candidate genes and 14,028 from a medium density SNP array. Gene diversity was similar between LTA and NV groups suggesting no genetic erosion due to long term exposure to the parasite, and three population clusters were detected using the whole dataset. Tests for divergent selection between NV and LTA groups detected the presence of a very consistent set of 22 markers, located within a putative single genomic region, which suggests the presence of a major quantitative trait locus associated with B. ostreae resistance. Moreover, 324 outlier loci associated with factors other than bonamiosis were identified allowing fully discrimination of all the oyster beds. A practical tool which included the 84 highest discriminative markers for tracing O. edulis populations was developed and tested with empirical data. Results reported herein could assist the production of stocks with improved resistance to bonamiosis, and facilitate the management of oyster beds for recovery production and ecosystem services provided by this species.
The spatial analysis of biological interactions: morphological variation responding to the co-occurrence of competitors and resources
By sharing geographic space, species are forced to interact with one another and the contribution of this process to evolutionary and ecological patterns of individual species is not fully understood. At the same time, species turnover makes that species composition varies from one area to another, so the analysis of biological interaction cannot be uncoupled from the spatial context. This is particularly important for clades that show high degree of specialization such as hummingbirds, where any variation in biotic pressures might lead to changes in morphology. Here, we describe the influence of biological interactions on the morphology of Hylocharis leucotis by simultaneously considering potential competition and diet resources. We characterized the extent of local potential competition and local available floral resources by correlating two measurements of hummingbird diversity, floral resources and the size of morphological space of H. leucotis along its geographic distribution. We found that H. leucotis shows an important morphological variability across its range and two groups can be recognized. Surprisingly, morphological variation is not always linked to local hummingbird richness or the phylogenetic similarity of. Only in the southern part of its distribution, H. leucotis is morphologically more variable in those communities where it coexist with closely related hummingbird species. We also found that morphological variation in H. leucotis is independent from the availability of floral resources. Our results suggest that abiotic factors might be responsible for morphological differences across populations in Hylocharis leucotis being biological interactions of minor importance.
Data from: The dynamics of recovery and growth: how defoliation affects stored resources
Growth rate varies widely among species and the trade-off between growth rate and storage or maintenance traits is a principal axis of variation between species. Many plant species have substantial root stores, but very little is known about how growth rate modifies responses of these stores to defoliation and other stresses. Species with different growth rates are predicted to respond in distinct ways, because of variation in the pre-defoliation allocation to storage. Here, we quantified the dynamics of stored carbohydrates in seven species with varying growth rate, following defoliation in a pot experiment. For faster growing species, there was significant reduction in carbohydrate concentration following defoliation, followed by relatively fast recovery, whereas for slower growing species, carbohydrate concentration levels remained relatively invariant across treatments. Results for total carbohydrates mirrored those for concentration, but were not as significant. Our findings were consistent with the idea that faster growing species respond more rapidly than slower growers to defoliation, through changes in carbohydrate pool concentrations. Growth rate as an indicator of life-history and ecological strategy may therefore be key to understanding post-defoliation recovery and storage strategies.
Data from: Development of a genomic resource and quantitative trait loci mapping of male calling traits in the lesser wax moth, Achroia grisella
In the study of sexual selection among insects, the Lesser Waxmoth, Achroia grisella (Lepidoptera: Pyralidae), has been one of the more intensively studied species over the past 20 years. Studies have focused on how the male calling song functions in pair formation and on the quantitative genetics of male song characters and female preference for the song. Recent QTL studies have attempted to elucidate the genetic architecture of male song and female preference traits using AFLP markers. We continued these QTL studies using SNP markers derived from an EST library that allowed us to measure both DNA sequence variation and map loci with respect to the lepidopteran genome. We report that the level of sequence variation within A. grisella is typical among other Lepidoptera that have been examined, and that comparison with the Bombyx mori genome shows that macrosynteny is conserved. Our QTL map shows that a QTL for a male song trait, pulse-pair rate, is situated on the Z chromosome, a prediction for sexually selected traits in Lepidoptera. Our findings will be useful for future studies of genetic architecture of this model species and may help identify the genetics associated with the evolution of its novel acoustic communication.
Data from: Interaction networks of macrofungi and mycophagous beetles reflect diurnal variation and the size and spatial arrangement of resources
Ecological networks are useful for characterizing interspecific associations and predicting the resilience of ecological communities. We evaluated how such networks vary with the size, spatial distribution, and timing of availability of resources, with a focus on beetle-macrofungal associations. We used 2 y of field experiments to construct ecological networks based on manipulated sporocarp baits (resources; Pleurotus ostreatus) and natural communities of beetles (consumers) in a temperate forest. Centrality and interaction strength increased with resource size, but were associated weakly with resource density and isolation, and not at all with position within patches. Whole-network connectance was greater in mornings (when beetle richness and abundance were high) than evenings. Interannual differences in networks were consistent with differences in beetle communities between years. The capacity of networks to vary temporally, spatially, and as a function of resource traits is examined in light of understanding beetle-macrofungal associations, which are important components of fungal ecology.
Data from: Time-integrated habitat availability is a resource attribute that informs patterns of use in intertidal areas
In dynamic environments, resource availability may change by several orders of magnitude, over hours to months, but the duration of resource availability is not often included as a characteristic attribute of resources even though temporal resource dynamics might limit patterns of use. In our study of wading birds foraging in intertidal areas, tides cause large changes in the areal extent of shallow-water foraging habitat (i.e., the resource), but tides also constrain the duration of availability, which is often overlooked. We hypothesized that temporal constraints on habitat availability from tides would be reflected in patterns of habitat use by foraging birds. We estimated the time-integrated habitat availability and compared it to traditional habitat attributes (seagrass cover, substrate type, instantaneous water depth, and proximity to mangrove islands or deep water) that have strong evidential support for influencing patterns of use. To evaluate our hypotheses, we quantified habitat attributes at intertidal areas in the Florida Keys, U.S.A, where wading birds were observed foraging (Little Blue Heron, Egretta caerulea: N=183; Great White Heron, Ardea herodias occidentalis: N=162). We tested for non-random use by sampling habitat attributes at two spatial scales around the observed feeding locations and we analyzed the data using a conditional logistic regression model. There was no evidence that seagrass cover or substrate explained patterns of use. The proximity of foraging locations relative to mangroves and to deep water were important at both spatial scales but had lower effect sizes (odds-ratios) than time-integrated habitat availability and water depth, and the latter may only serve as a physical constraint on access. We found support that time-integrated habitat availability was a distinct resource attribute, had the greatest effect size (4-8-fold change in relative probability of use), and best explained patterns of habitat use at the largest spatial scale. In studies of resource use where changes in resource availability are non-linear or when strong constraints on access are imposed by behavior, incorporating time-integrated estimates of resource availability into analyses can improve insights into spatiotemporal patterns of resource use.
Data from: Rehabilitating the cyanobacteria – niche partitioning, resource use efficiency, and phytoplankton community structure during diazotrophic cyanobacterial blooms
1. Blooms of nitrogen-fixing cyanobacteria are recurrent phenomena in marine and freshwater habitats, and their supplying role in aquatic biogeochemical cycles is generally considered vital. The objective of this study is to analyze if an increasing proportion of nitrogen-fixing cyanobacteria affects (i) the composition of the non-diazotrophic component of ambient phytoplankton communities, and (ii) resource use efficiency (RUE; ratio of chl a to total nutrients) – an important ecosystem function. We hypothesize that diazotrophs increase community P use, and decrease N use efficiencies, as new N is brought into the system, relaxing N, and concomitantly aggravating P limitation. We test this by analyzing an extensive dataset from the Baltic Sea (> 3700 quantitative phytoplankton samples), known to harbor conspicuous and recurrent blooms of Nodularia spumigena and Aphanizomenon sp. 2. System-level phosphorus use efficiency (RUEP) was positively related with high proportion of diazotrophic cyanobacteria, suggesting aggravation of phosphorus limitation. However, concomitant decrease of nitrogen use efficiency (RUEN) was not observed. Nodularia spumigena, a dominant diazotroph and a notorious toxin producer, had a significantly stronger relationship with RUEP, compared to the competing non-toxic Aphanizomenon sp., confirming niche differentiation in P acquisition strategies between the major bloom-forming cyanobacterial species in the Baltic Sea. Nodularia occurrences were associated with stronger temperature stratification in more offshore environments, indicating higher reliance on in situ P regeneration. 3. By using constrained and unconstrained ordination, permutational multivariate analysis of variance, and local similarity analysis, we show that diazotrophic cyanobacteria explained no more than a few percent of the ambient phytoplankton community variation. The analyses furthermore yielded rather evenly distributed negative and positive effects on individual co-occurring phytoplankton taxa, with no obvious phylogenetic or functional trait-based patterns. 4. Synthesis. Our study reveals that despite the widely acknowledged noxious impacts of cyanobacterial blooms, the overall effect on phytoplankton community structure is minor. There are no predominantly positive or negative associations with ambient phytoplankton species. Species-specific niche differences in cyanobacterial resource acquisition affect important ecosystem functions, like biomass production per unit limiting resource.
Data from: Spatial overlap in a solitary carnivore: support for the land-tenure, kinship, or resource dispersion hypotheses?
1. There are several alternative hypotheses about the effects of territoriality, kinship, and prey availability on individual carnivore distributions within populations. The first is the land-tenure hypothesis, which predicts that carnivores regulate their density through territoriality and temporal avoidance. The second is the kinship hypothesis, which predicts related individuals will be clumped within populations, and the third is the resource dispersion hypothesis, which suggests that resource richness may explain variable sociality, spatial overlap, or temporary aggregations of conspecifics. 2. Research on the socio-spatial organization of animals is essential in understanding territoriality, intra- and inter-specific competition, and contact rates that influence diverse ecology, including disease transmission between conspecifics and courtship behaviors. 3. We explored these hypotheses with data collected on a solitary carnivore, the cougar (Puma concolor), from 2005 to 2012 in the Southern Yellowstone Ecosystem, Wyoming, USA. We employed 27 annual home ranges for 13 cougars to test whether home range overlap was better explained by land-tenure, kinship, resource dispersion, or some combination of the three. 4. We found support for both the land-tenure and resource dispersion hypotheses, but not for kinship. Cougar sex was the primary driver explaining variation in home range overlap. Males overlapped significantly with females, whereas the remaining dyads (F-F, M-M) overlapped significantly less. In support for the resource dispersion hypothesis, hunting opportunity (the probability of a cougar killing prey in a given location) was often higher in overlapping than in non-overlapping portions of cougar home ranges. In particular, winter hunt opportunity rather than summer hunt opportunity was higher in overlapping portions of female-female and male-female home ranges. 5. Our results may indicate that solitary carnivores are more tolerant of sharing key resources with unrelated conspecifics than previously believed, or at least during periods of high resource availability. Further, our results suggest that the resource dispersion hypothesis, which is typically applied to social species, is applicable in describing the spatial organization of solitary carnivores.
Data from: "Complete mitochondrial and partial nuclear genomes for the jack species Caranx ignobilis (Forsskål, 1775) and C. melampygus (Cuvier, 1833) (Perciformes:Carangidae) from the High Hawaiian Islands" in Genomic Resources Notes accepted 1 October 2013 – 30 November 2013
Complete mitochondrial and partial nuclear genomes for the jack species Caranx ignobilis (Forsskål, 1775) and C. melampygus (Cuvier, 1833) (Perciformes:Carangidae) from the High Hawaiian Islands are presented along with annotation and characterization of intragenomic single nucleotide polymorphism (SNPs) and indel variation.
Data from: A Mesoamerican origin of cherimoya (Annona cherimola Mill.). Implications for the conservation of plant genetic resources
Knowledge on the structure and distribution of genetic diversity is a key aspect in order to plan and execute an efficient conservation and utilization of the genetic resources of any crop as well as for determining historical demographic inferences. In this work, a large data set of 1765 accessions of cherimoya (Annona cherimola Mill, Annonaceae), an underutilized fruit tree crop native to the neotropics and used as a food source by pre-Columbian cultures, was collected from 6 different countries across the American continent and amplified with 9 highly informative microsatellite markers. The structure analyses, fine representation of the genetic diversity and an ABC approach suggest a Mesoamerican origin of the crop, contrary to previous reports, with clear implications for the dispersion of plant germplasm between Central and South America in pre-Columbian times. These results together with the potential distribution of the species in a climatic change context using two different climate models provide new insights for the history and conservation of extant genetic resources of cherimoya that can be applied to other currently underutilized woody perennial crops.
Data from: Resource allocation trade-offs and the loss of chemical defences during apple domestication
Background and Aims: Most crops have been dramatically altered from their wild ancestors with the primary goal of increasing harvestable yield. A long-held hypothesis is that increased allocation to yield has reduced plant investment in defence and resulted in crops that are highly susceptible to pests. However, clear demonstrations of these trade-offs have been elusive due to the many selective pressures that occur concurrently during crop domestication. Methods: To provide a robust test of whether increased allocation to yield can alter plant investment in defence, this study examined fruit chemical defence traits and herbivore resistance across 52 wild and 56 domesticated genotypes of apples that vary >26-fold in fruit size. Ninety-six phenolic metabolites were quantified in apple skin, pulp and seeds, and resistance to the codling moth was assessed with a series of bioassays. Key Results: The results show that wild apples have higher total phenolic concentrations and a higher diversity of metabolites than domesticated apples in skin, pulp and seeds. A negative phenotypic relationship between fruit size and phenolics indicates that this pattern is driven in part by allocation-based trade-offs between yield and defence. There were no clear differences in codling moth performance between wild and domesticated apples and no overall effects of total phenolic concentration on codling moth performance, but the results did show that codling moth resistance was increased in apples with higher phenolic diversity. The concentrations of a few individual compounds (primarily flavan-3-ols) also correlated with increased resistance, primarily driven by a reduction in pupal mass of female moths. Conclusions: The negative phenotypic relationship between fruit size and phenolic content, observed across a large number of wild and domesticated genotypes, supports the hypothesis of yield–defence trade-offs in crops. However, the limited effects of phenolics on codling moth highlight the complexity of consequences that domestication has for plant–herbivore interactions. Continued studies of crop domestication can further our understanding of the multiple trade-offs involved in plant defence, while simultaneously leading to novel discoveries that can improve the sustainability of crop production.
Data from: A curated and standardized adverse drug event resource to accelerate drug safety research
Identification of adverse drug reactions (ADRs) during the post-marketing phase is one of the most important goals of drug safety surveillance. Spontaneous reporting systems (SRS) data, which are the mainstay of traditional drug safety surveillance, are used for hypothesis generation and to validate the newer approaches. The publicly available US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) data requires substantial curation before they can be used appropriately, and applying different strategies for data cleaning and normalization can have material impact on analysis results. We provide a curated and standardized version of FAERS removing duplicate case records, applying standardized vocabularies with drug names mapped to RxNorm concepts and outcomes mapped to SNOMED-CT concepts, and pre-computed summary statistics about drug-outcome relationships for general consumption. This publicly available resource, along with the source code, will accelerate drug safety research by reducing the amount of time spent performing data management on the source FAERS reports, improving the quality of the underlying data, and enabling standardized analyses using common vocabularies.
Data from: Comparative transcriptome resources of two Dysosma species (Berberidaceae) and molecular evolution of the CYP719A gene in Podophylloideae
Dysosma species (Berberidaceae, Podophylloideae) are of great medicinal pharmacogenetic importance and used as model systems to study the drivers and mechanisms of species diversification of temperate plants in East Asia. Recently, we have sequenced the transcriptome of the low-elevation D. versipellis. In this study, we sequenced the transcriptome of the high-elevation D. aurantiocaulis and used comparative genomic approaches to investigate the transcriptome evolution of the two species. We retrieved 53 929 unigenes from D. aurantiocaulis by de novo transcriptome assemblies using the Illumina HiSeq 2000 platform. Comparing the transcriptomes of both species, we identified 4593 orthologs. Estimation of Ka/Ks ratios for 3126 orthologs revealed that none had a Ka/Ks significantly greater than 1, whereas 1273 (Ka/Ks < 0.5, P < 0.05) were inferred to be under purifying selection. A total of 51 primer pairs were successfully designed from 461 EST-SSRs contained in 4593 orthologs. Marker validation assay revealed that 26 (51%) and 41 (80.4%) produced clear fragments with the expected sizes in all Podophylloideae species. Specifically, 19 different sequences of CYP719A were identified from PCR-amplified genomic DNA of all 12 species of Podophylloideae using primers designed from the assembled transcripts. The data further indicated that CYP719A was likely subject to strong selective constraints maintaining only one copy per genome. In Dysosma, there was relaxed purifying selection or more positive selection for high-elevation species. Overall, this study has generated a wealth of molecular resources potentially useful for pharmacogenetic and evolutionary studies in Dysosma and allied taxa.
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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.