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518 results for “useful plants”
Within and cross species predictions of plant specialized metabolism genes using transfer learning
<p>Datasets for <em>Within and cross species predictions of plant specialized metabolism genes using transfer learning.</em> </p> <ol> <li>Dataset 1: All gene features used in the full feature machine learning models including expression, co-expression, evolutionary, duplication, and protein domain features.</li> <li>Dataset 2: All gene features used in shared feature machine learning models including expression, evolutionary, duplication, and protein domain features.</li> <li>Table S1: All gene annotations from TomatoCyc or manual annotation.</li> <li>Table S2: All model scores.</li> <li>Table S3: All gene scores and predictions from each model.</li> <li>Table S4: Feature importance for 5 models.</li> <li>Table S5: Statistical analysis between classes for binary and continuous feature data.</li> <li>Table S6: RNAseq datasets used in analysis.</li> </ol>
High water use in desert plants exposed to extreme heat
<p>Many plant water use models predict leaves maximize carbon assimilation while minimizing water loss via transpiration. Alternate scenarios may occur at high temperature, including heat avoidance, where leaves increase water loss to evaporatively cool regardless of carbon uptake; or heat failure, where leaves non-adaptively lose water also regardless of carbon uptake. We hypothesized that these alternative scenarios are common in species exposed to hot environments, with heat avoidance more common in species with high construction-cost leaves. Diurnal measurements of leaf gas exchange and temperature for 11 Sonoran Desert species revealed 37% of these species increased transpiration in the absence of increased carbon uptake. High leaf mass per area partially predicted this behavior (<i>r</i><sup>2</sup>=0.39). These data are consistent with heat avoidance and heat failure, but failure is less likely given the ecological dominance of the focal species. These behaviors are not yet captured in any extant plant water use model.</p> <p> </p>
African sunbirds predominantly pollinate plants useful to humans
<p>Birds provide multiple ecological services that benefit humans including pollination. In Africa, sunbirds are the <span>domi- </span>nant vertebrate pollinator. Here we present a species-level assessment for African sunbirds of the number and relative frequency of their food plants that have useful properties to humans. <span>We </span>conducted this analysis by compiling and integrating known sunbird food plants with useful tropical plant and tropical cultivated plant databases. Across Africa, 68% of the 329 genera and 44% of the 468 species of sunbirds' known food plants are used by humans for medicine, food, building materials, or other uses. <span>Yet </span>most genera and species of useful plants are visited by a small number of sunbird species. The median number of sunbird species that visit a useful genus and species of plant is two and one, re- spectively. Of the 409 genera and 308 species of useful plants that are sunbird pollinated across one or more of the <span>six </span>predominant habitats for sunbirds, 67% of genera and 71% of species are pollinated by sunbird species that are forest or woodland dependent. Additionally, 58% of all genera and 83% of all species of useful plants pollinated by sunbirds are non-cultivated. In Africa, non-cultivated sunbird-pollinated useful plants are almost entirely collected, used, and traded locally rather than regionally or internationally. Our results indicate that African sunbirds provide important ecological services as pollinators that benefit humans, and these services are provided largely at a local scale. Given the decline of invertebrate and vertebrate pollinators both globally and in Africa, sunbirds are important to the long-term conservation of many useful plants in Africa and hence human well-being.</p>
Data from: Species-specific variation in germination rates contributes to spatial coexistence more than adult plant water use in four closely-related annual flowering plants
1. Spatial partitioning is a classic hypothesis to explain plant species coexistence, but evidence linking local environmental variation to spatial sorting, demography, and species' traits is sparse. If co-occurring species' performance is optimized differently along environmental gradients because of trait variation, then spatial variation might facilitate coexistence. 2. We used a system of four naturally co-occurring species of Clarkia (Onagraceae) to ask if distribution patchiness corresponds to variation in two environmental variables that contribute to hydrological variation. We then reciprocally sowed Clarkia into each patch type and measured demographic rates in the absence of congeneric competition. Species sorted in patches along one or both gradients, and in three of the four species, germination rate in the "home" patch was higher than all other patches. 3. Spatially variable germination resulted in the same three species exhibiting the highest population growth rates in their home patches. 4. Species' trait values related to plant water use, as well as indicators of water stress in home patches, differed among species and corresponded to home patch attributes. However, post-germination survival did not vary among species or between patch types, and fecundity did not vary spatially. 5. Synthesis Our research demonstrates the likelihood that within-community spatial heterogeneity affects plant species coexistence, and presents novel evidence that differential performance in space is explained by what happens in the germination stage. Despite the seemingly obvious link between adult plant water-use and variation in the environment, our results distinguish the germination stage as important for spatially variable population performance.
Data from: Inferring phylogeny and introgression using RADseq data: an example from flowering plants (Pedicularis: Orobanchaceae)
Phylogenetic relationships among recently diverged species are often difficult to resolve due to insufficient phylogenetic signal in available markers and/or conflict among gene trees. Here we explore the use of reduced-representation genome sequencing, specifically in the form of restriction-site associated DNA (RAD), for phylogenetic inference and the detection of ancestral hybridization in non-model organisms. As a case study, we investigate Pedicularis section Cyathophora, a systematically recalcitrant clade of flowering plants in the broomrape family (Orobanchaceae). Two methods of phylogenetic inference, maximum likelihood and Bayesian concordance, were applied to data sets that included as many as 40,000 RAD loci. Both methods yielded similar topologies that included two major clades: a "rex-thamnophila" clade, composed of two species and several subspecies with relatively low floral diversity, and geographically widespread distributions at lower elevations, and a "superba" clade, composed of three species characterized by relatively high floral diversity and isolated geographic distributions at higher elevations. Levels of molecular divergence between subspecies in the rex-thamnophila clade are similar to those between species in the superba clade. Using Patterson's D-statistic test, including a novel extension of the method that enables finer-grained resolution of introgression among multiple candidate taxa by removing the effect of their shared ancestry, we detect significant introgression among nearly all taxa in the rex-thamnophila clade, but not between clades or among taxa within the superba clade. These results suggest an important role for geographic isolation in the emergence of species barriers, by facilitating local adaptation and differentiation in the absence of homogenizing gene flow.
Data from: Plant water use affects competition for nitrogen: why drought favors invasive species in California
Classic resource competition theory typically treats resource supply rates as independent; however, nutrient supplies can be affected by plants indirectly, with important consequences for model predictions. We demonstrate this general phenomenon by using a model in which competition for nitrogen is mediated by soil moisture, with competitive outcomes including coexistence and multiple stable states as well as competitive exclusion. In the model, soil moisture regulates nitrogen availability through soil moisture dependence of microbial processes, leaching, and plant uptake. By affecting water availability, plants also indirectly affect nitrogen availability and may therefore alter the competitive outcome. Exotic annual species from the Mediterranean have displaced much of the native perennial grasses in California. Nitrogen and water have been shown to be potentially limiting in this system. We parameterize the model for a Californian grassland and show that soil moisture–mediated competition for nitrogen can explain the annual species' dominance in drier areas, with coexistence expected in wetter regions. These results are concordant with larger biogeographic patterns of grassland invasion in the Pacific states of the United States, in which annual grasses have invaded most of the hot, dry grasslands in California but perennial grasses dominate the moister prairies of northern California, Oregon, and Washington.
Dataset for paper "Interpreting the shifts in forest structure, plant community composition, diversity, and functional identity by using remote sensing-derived wildfire severity"
<p>Interpreting the shifts in forest structure, plant community composition, diversity, and functional identity by using remote sensing-derived wildfire severity . New collected data</p>
Data and R code used in Alonso-Crespo et al (2024) Exploring priority and year effects on plant diversity, productivity and vertical root distribution: first insights from a grassland field experiment
<p>This release contains the raw data, R code, and RootPainter model supporting the results described in Alonso-Crespo et al (2024) Exploring priority and year effects on plant diversity, productivity and vertical root distribution: first insights from a grassland field experiment.</p>
Expression analysis of targeted genes Sgt1 (A) and Hsp90 (B) in tomato plants subjected to virus-induced gene silencing using Tobacco rattle virus (TRV) vector.
<p><strong>Figure S1</strong>. Expression analysis of targeted genes Sgt1 (A) and Hsp90 (B) in tomato plants subjected to virus-induced gene silencing using Tobacco rattle virus (TRV) vector. (A) Relative expression levels of Sgt1 analyzed by Reverse Transcription-quantitative Polymerase Chain Reaction (RT-qPCR) in tomato plants infected with TRV vector alone (TRV2), TRV carrying Sgt1 silencing constructs (TRV-Sgt1), and mock-inoculated (Mock). Transcript levels were normalized using tomato genes encoding elongation factor 1-α and SAND as internal references, with Mock as the calibrator. (B) Relative expression levels of Hsp90 analyzed by RT-qPCR in tomato plants infected with TRV2, TRV-Hsp90, and Mock. Gene expression levels were normalized using the same reference genes as in (A). (C) Quantification of the relative accumulation of TRV RNA in plants infected with TRV2 and in silenced plants (TRV-Sgt1 and TRV-Hsp90). The expression levels were normalized using tomato genes for elongation factor 1-α and SAND, with TRV2 as the calibrator. All samples were collected at 19 dpi to anticipate the observed decline. Error bars represent standard errors of five biological replicates, and an asterisk indicates a significant difference, as determined by one-way ANOVA with P < 0.05</p>
The global distribution of plants used by humans datasets: list of utilised species, occurrence data and model outputs at 10 arc-minutes spatial resolution
<p>Datasets and model outputs used to map the global distribution of utilised plants by humans. The folder is composed of two subfolders <em>raw_data</em> and <em>processed_data</em> containing respectively the list of utilised plant species modelled -<em>utilised_plants_species_list.csv</em>-, and their occurrence data -<em>occurrence_data.zip-</em> and predicted distribution -<em>species_proba_per_cell.rds-.</em></p> <p> </p> <ul> <li>The file <em>utilised_plants_species_list.csv</em> in the <em>raw_data</em> folder contains a<strong> </strong>list of 35687 plant species (and hybrids) used by humans and 10 plant use categories with the following 14 fields:</li> </ul> <p><strong>plant_ID:<em> </em></strong>plant identifier number ranging from between 1-35687</p> <p><strong>binomial_acc_name:</strong> binomial accepted name of the plant species</p> <p><strong>author_acc_name</strong>: name of the author(s)</p> <p><strong>is_hybrid:</strong> logical TRUE or FALSE indicating whether the species is an hybrid or not.</p> <p><strong>AnimalFood:</strong> forage and fodder for vertebrate animals only.</p> <p><strong>EnvironmentalUses:</strong> examples include intercrops and nurse crops, ornamentals, barrier hedges, shade plants, windbreaks, soil improvers, plants for revegetation and erosion control, wastewater purifiers, indicators of the presence of metals, pollution, or underground water.</p> <p><strong>Fuels:</strong> charcoal, petroleum substitutes, fuel alcohols, etc. Given the importance of energy plants for people, those were distinguished from Materials.</p> <p><strong>GeneSources:</strong> wild relatives of major crops which may possess traits associated with biotic or abiotic resistance and may be valuable for breeding programs.</p> <p><strong>HumanFood:</strong> food for humans only, including beverages and food additives.</p> <p><strong>InvertebrateFood:</strong> plants consumed by invertebrates used by humans, such as bees, silkworms, lac insects and edible grubs.</p> <p><strong>Materials:</strong> woods, fibers, cork, cane, tannins, latex, resins, gums, waxes, oils, lipids, etc. and their derived products.</p> <p><strong>Medicines:</strong> both human and veterinary.</p> <p><strong>Poisons:</strong> plants which are poisonous to both vertebrates and invertebrates, both accidentally and intentionally, e.g., for hunting and fishing, molluscicides, herbicides, insecticides.</p> <p><strong>SocialsUses:</strong> plants used for social purposes, which cannot be defined as food or medicine, for instance, masticatories, smoking materials, narcotics, hallucinogens and psychoactive drugs, and plants with ritual or religious significance.</p> <p><strong>Totals:</strong> total number of uses recorded for a species</p> <p> </p> <ul> <li>The zipfile <em>occurrence_data.zip</em> in the <em>processed_data</em> folder contains 35687 Comma Separated Values (CSV) files, one for each species, containing curated geographic occurrence records used to build species distribution models with the following 14 fields:</li> </ul> <p><strong>Species:</strong> the binomial accepted name of the species</p> <p><strong>Fullname:</strong> same as species</p> <p><strong>decimalLongitude:</strong> the geographic longitude of the occurrence records of the species in decimal degrees</p> <p><strong>decimalLatitude:</strong> the geographic latitude of the occurrence records of the species in decimal degrees</p> <p><strong>countryCode:</strong> a three-letter standard abbreviation for the country of the occurrence locality</p> <p><strong>coordinateUncertaintyinMeters</strong>: indicator for the accuracy of the coordinate location, described as the radius of a circle around the stated point location</p> <p><strong>year:</strong> year of the observation of the occurrence record of the species</p> <p><strong>individualCount:</strong> the number of individuals present at the time of the observation</p> <p><strong>gbifID:</strong> unique identifier number for the occurrence from the original database</p> <p><strong>basisOfRecords:</strong> the type of the individual record, e.g. observation, physical specimen, fossil, living ex-situ, culture collection specimen</p> <p><strong>institutionCode</strong>: the name of the institution or organization listed as the data publisher on GBIF</p> <p><strong>establishmentMeans:</strong> statement about whether an organism has been introduced to a given place and time through the direct or indirect activity of modern humans</p> <p><strong>is_cultivated_observation:</strong> whether or not an organism is cultivated</p> <p><strong>sourceID:</strong> name of the source database</p> <p> </p> <ul> <li>The file <em>species_proba_per_cell.rds</em> in the <em>processed_data</em> folder is<em> a R Data Serialization </em>(RDS) file containing a data.table object with the following 3 fields:</li> </ul> <p><strong>plant_ID:</strong><em> </em>plant identifier number ranging from between 1-35687</p> <p><strong>proba:</strong> species occurrence probability</p> <p><strong>cell:</strong><em> </em>raster grid cell number between 1-2251762</p> <p>This object can be used in combination with a raster layer to reconstruct the modelled distribution of each species or retrieve species richness and endemism.</p>
Data from: Land-use intensity and relatedness to native plants promote exotic plant invasion in a tropical biodiversity hotspot
<p>Exotic plant invasions threaten biodiversity and are costly to farmers. Land use is a major pathway promoting the spread of exotic plant species; however, little is known about the processes underlying the success of exotic plants in tropical agricultural landscapes. Focussing on the heterogeneous smallholder landscapes of north-eastern Madagascar, we studied exotic plants of understorey communities across a land-use intensity gradient from unburned lands (old-growth forests, forest fragments, and forest-derived vanilla agroforests) to burned ones (fallow-derived vanilla agroforests, woody fallows, and herbaceous fallows). </p> <p>We quantified the absolute species richness, abundance, and cover of exotic plants across land-use types and their proportional contribution to community richness, abundance, and cover as indicators of exotic plant invasion. We tested for the effects of land-use parameters, namely land-use history, canopy closure, and landscape-level forest cover, on exotic plants. Additionally, we tested whether the phylogenetic relatedness between exotic and native species in the same plot affected invasion success, testing Darwin's naturalization and pre-adaptation hypotheses. </p> <p>All indicators of exotic plant invasion were lowest in old-growth forests and forest fragments and highest in fallow-derived vanilla agroforests, woody fallows, and herbaceous fallows. Absolute and proportional exotic richness was negatively affected by canopy closure, and landscapes with high forest cover had lower proportions of exotic plant richness. High phylogenetic relatedness between exotics and natives was associated with lower proportional richness but higher proportions of exotics in abundance and cover. However, individual exotic species showed contrasting responses to land-use parameters and relatedness to natives.</p> <p>Synthesis and applications: Our results indicate that maintaining unburned lands, land-use types with dense canopies, and landscapes with high forest cover prevents the spread of exotic plants within agricultural landscapes of north-eastern Madagascar. Supporting Darwin's pre-adaptation hypothesis, exotic plants phylogenetically closely related to native plants are more likely to become successful invaders in terms of abundance and cover. Nevertheless, individual species show different responses to land-use changes and phylogenetic relatedness. Therefore, land-use decisions and management choices can be tailored to limit the spread of exotic species and to preserve native plants in this global biodiversity hotspot.</p>
Data on soil variables (with plot IDs) and grassland species traits used for the analysis of grassland vegetation data by Pillar, V.D. (2024) Trait divergence in plant community assembly is generated by environmental factor interactions. Journal of Vegetation Science, 35, e13259. Available from: https://doi.org/10.1111/jvs.13259
<p>File <a href="../api/records/10983049/draft/files/Plot_IDs_990ua.txt/content" target="_blank" rel="noopener noreferrer">Plot_IDs_990ua.txt</a> contains the IDs of the 1-m2 plots used for the analysis of grassland vegetation data by Pillar, V.D. (2024) Trait divergence in plant community assembly is generated by environmental factor interactions. The plot data are stored in the sPlot database (PPBio South Brazilian Grassland Database).</p> <p>File <a href="../api/records/10983049/draft/files/E_990ua_21SoilVar.txt/content" target="_blank" rel="noopener noreferrer">E_990ua_21SoilVar.txt</a> contains data on soil variables evaluated in the 250 m transects, but here expanded to the 990 1-m2 plots (each transect was sampled using 10 1-m2 pots).</p> <p>File <a href="../api/records/10983049/draft/files/B_769spp_4t.txt/content" target="_blank" rel="noopener noreferrer">B_769spp_4t.txt</a> is the species trait database collected in the framework of several research projects in the Quantitative Ecology Lab (EcoQua) and Grassland Vegetation Studies Lab (LevCamp) of Universidade Federal do Rio Grande do Sul (UFRGS). Data gaps were filled by compiled from the TRY database and data imputation.</p> <p> </p> <p> </p>
Figure 6 in Colotis lais (Butler, 1876) and Colotis euippe omphale (Godart, [1819]) use Cadaba aphylla (Thunb.) Wild LC as a host-plant at Tswalu Kalahari, Northern Cape Province, South Africa)
Figure 6 – Location of Tswalu Kalahari in southern Africa.
Mesolithic Plant Processing Unveiled: Multiscale Use-Wear Analysis of the Ground Stone Tools from Vlasac (Serbia)
<p>This repository contains the raw data and code to reproduce the analyses presented in the paper "Mesolithic Plant Processing Unveiled: Multiscale Use-Wear Analysis of the Ground Stone Tools from Vlasac (Serbia)" by Zupancich et al.</p> <p>The repositiory includes:</p> <ul> <li>CSV files containing the raw data of:</li> <li>3D surface measurement of experimental and archaeological ground stone tools</li> <li>Use wear spatial distribution</li> <li>Ground stone tools techno-morphological data</li> <li>HTML files of the code utilised to perform the analyses</li> </ul>
Measuring plant biomass remotely using drones in arid landscapes
<p>Measurement of variation in plant biomass is essential for answering many ecological and evolutionary questions. Quantitative estimates require plant destruction for laboratory analyses, while field studies use allometric approaches based on simple measurement of plant dimensions. We estimated the biomass of individual shrub-sized plants, using a low cost Unmanned Aerial System (drone), enabling rapid data collection and non-destructive sampling. We compared volume measurement (a surrogate for biomass) and sampling time, from the simple dimension measurements and drone, to accurate laboratory-derived biomass weights. We focused on three Australian plant species which are ecologically important to their floodplain and terrestrial ecosystems: porcupine grass <em>Triodia scariosa, </em>Queensland bluebush<em> Chenopodium auricomum</em> and lignum <em>Duma florulenta</em>.</p> <p>Estimated volume from the drone was more accurate than simple dimension measurements for porcupine grass and Queensland bluebush, compared to estimates from laboratory analyses but, not for lignum. The latter had a sparse canopy, with thin branches, few vestigial leaves and a similar colour to the ground. Data collection and analysis consistently required more time for the drone method than the simple dimension measurements, but this would improve with automation. </p>
Data: Detecting preservation and reintroduction sites for endangered plant species using a two-step modelling and field approach
<p><span>To withstand the surge of species loss worldwide, (re)introduction of endangered plant species has become an increasingly common technique in conservation biology. Successful (re)introduction plans, however, require identifying sites that provide the optimal ecological conditions for the target species to thrive. In this study, we propose a two-step approach to identify appropriate (re)introduction sites. The first step involves modelling the niche and distribution of the species with bioclimatic and topographical predictors, both at continental and at national scales. The second step consists of refining these bioclimatic predictions by analysing stationary ecological parameters, such as soil conditions, and relating them to population-level fitness values. We demonstrate this methodology using Swiss populations of the lady's slipper orchid (<em>Cypripedium calceolus</em> L., Orchidaceae), for which conservation plans have existed for years but have generally been unfruitful. Our workflow identified sites for future (re)introductions based on the species requirements for mid-to-sunny light conditions and specific soil physico-chemical properties, such as basic to neutral pH and low soil organic matter content. Our findings show that by combining wide-scale bioclimatic modelling with fine scale field measurements it is possible to carefully identify the ecological requirements of a target species for successful (re)introductions.</span></p>
High resolution ancient sedimentary DNA shows that alpine plant diversity is associated with human land use and climate change
<p>The European Alps are highly rich in species, but their future may be threatened by ongoing changes in human land use and climate. Here, we reconstructed vegetation, temperature, human impact and livestock over the past ~12,000 years from Lake Sulsseewli, based on sedimentary ancient plant and mammal DNA, pollen, spores, chironomids, and microcharcoal. We assembled a highly-complete local DNA reference library (PhyloAlps, 3,923 plant taxa), and used this to obtain an exceptionally rich <em>sed</em>aDNA record of 366 plant taxa. Vegetation mainly responded to climate during the early Holocene, while human activity had an additional influence on vegetation from 6 ka onwards. Land-use shifted from episodic grazing during the Neolithic and Bronze Age to agropastoralism in the Middle Ages. Associated human deforestation allowed the coexistence of plant species typically found at different elevational belts, leading to levels of plant richness that characterise the current high diversity of this region. Our findings indicate a positive association between low-intensity agropastoral activities and precipitation with the maintenance of the unique subalpine and alpine plant diversity of the European Alps.</p>
Species occurrence locations and environmental parameters used for predicting the potential planting regions of Pterocarpus santalinus
<p>This study explores the habitat distribution of <em>Pterocarpus santalinus</em>, a valuable rosewood species, across China, focusing on its response to current and future climate changes. Utilizing the MaxEnt model, we assess its suitable habitat under present conditions and future climate scenarios (SSPs126, SSPs245, and SSPs585). Our findings reveal that the current suitable habitat, spanning approximately 409,600 km², is primarily located in the central and southern parts of Guangdong, Guangxi, Fujian, Yunnan, as well as in the Hainan provinces, along with the coastal regions of Taiwan, and the Sichuan-Chongqing border. The habitat's distribution is significantly influenced by climatic factors such as temperature seasonality (bio4), mean temperature of the wettest quarter (bio8), annual mean temperature (bio1), and annual precipitation (bio12), while terrain and soil factors play a lesser role. Under future climate scenarios, the suitable habitat for <em>P. santalinus</em> is projected to expand, with a northeastward shift in its distribution center. This research not only sheds light on the geoecological characteristics and geographical distribution of <em>P. santalinus</em> in China but also offers a scientific basis for planning its cultivation areas and enhancing cultivation efficiency under changing climate conditions.</p>
StArt Protocol for systematic review: Use of CRISPR technology in gene editing for tolerance to biotic factors in plants: A systematic review.
<p>StArt Protocol for systematic review: Use of CRISPR technology in gene editing for tolerance to biotic factors in plants: A systematic review.</p>
Data from: Trends in plant cover derived from vegetation-plot data using ordinal zero-augmented beta regression
<p><strong>Questions.</strong> Plant cover values in vegetation-plot data are bounded between 0 and 1, and cover is typically recorded in discrete classes with non-equal intervals. Consequently, cover data are skewed and heteroskedastic, which hampers the application of conventional regression methods. Recently developed ordinal beta regression models consider these statistical difficulties. Our primary question is if we can detect species trends in vegetation-plot time series data with this modelling approach. A second question is whether trends in cover have additional value compared to trends in occurrence, which are easier to assess for practitioners.</p> <p><strong>Location</strong>. The Netherlands, Western Europe.</p> <p><strong>Methods. </strong>We used vegetation-plot data collected from 10.000 fixed plots which were surveyed once every four years during 1999-2022. We used the ordinal zero-augmented beta regression (OZAB) model, a hierarchical model consisting of a logistic regression for presence and an ordinal beta regression for cover. We adapted the OZAB model for longitudinal data and produced estimates of cover and occurrence for each four-year period. Thereafter we assessed trends in cover and in occurrence across all periods.</p> <p><strong>Results.</strong> We found evidence of a trend in cover in 318 out of the 721 species (44%) with sufficient data. Most species showed similar directional trends in occurrence and percent cover. No trend in occurrence was detected for 64 species that had evidence of a trend in cover. Declining species had stronger relative changes in cover than in occurrence.</p> <p><strong>Conclusions. </strong>Our model enables researchers to detect trends in cover using longitudinal vegetation-plot data. Cover trends often corroborated trends in occurrence, but we also regularly found trends in cover even in the absence of evidence for trends in occurrence. Our approach thus contributes to a more complete picture of (changes in) vegetation composition based on large monitoring datasets.</p>
ScienceDex guides
Understand access before you commit
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.