Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
174
datasets available to search
ShareScore release 0.9.0
Dataset results
174 results for “Biodiversity assessment”
Codes and data for the article: Biodiversity on the Line: Life Cycle Impact Assessment of Power Lines on Birds and Mammals in Norway
<p>This repository contains all input data required to run the habitat conversion, collision, and electrocution LCIA models and reproduce the results, as well as all output data generated in various formats. The models are described in the paper "Biodiversity on the Line: Life Cycle Impact Assessment of Power Lines on Birds and Mammals in Norway" (https://doi.org/10.1088/2634-4505/ad5bfd).</p> <p>"The files "01_Get_GBIF_points.R, "02_SDMs_maxent.R" describe how to create the species distribution maps.</p> <p>"03_Data_preparation.R", "04_Pylon_cleaning.py" are to prepare and modify the raw data for the analysis. The raw data are not provided, yet links to the sources are provided either in the R codes or the paper.</p> <p>To run the models, run the "05_SHR_modelling.R" and "06_Collision_electrocution_models.R" files.</p> <p>To calculate characterization factors, run the "07_Characterisation_factors.R" file.</p> <p>To export the tables in the Supporting Information 1, run the file "08_Supporting_Information.R".</p> <p>Finally, the file "09_Sensitivity_analysis.R" performs the sensitivity analyses.</p>
Phylogenomic assessment of biodiversity using a reference-based taxonomy: An example with Horned Lizards (Phrynosoma)
<p><span><span><span><span><span><span><span><span><span><span><span>Phylogenomic investigations of biodiversity facilitate the detection of fine-scale population genetic structure and the demographic histories of species and populations. However, determining whether or not the genetic divergence measured among populations reflects species-level differentiation remains a central challenge in species delimitation. One potential solution is to compare genetic divergence between putative new species with other closely related species, sometimes referred to as a reference-based taxonomy. To be described as a new species, a population should be at least as divergent as other species. Here, we develop a reference-based taxonomy for Horned Lizards (<i>Phrynosoma</i>; 17 species) using phylogenomic data (ddRADseq data) to provide a framework for delimiting species in the Greater Short-horned Lizard species complex (<i>P. hernandesi</i>). Previous species delimitation studies of this species complex have produced conflicting results, with morphological data suggesting that <i>P. hernandesi </i>consists of five species, whereas mitochondrial DNA support anywhere from 1 to 10+ species. To help address this conflict, we first estimated a time-calibrated species tree for <i>P. hernandesi </i>and close relatives using SNP data. These results support the paraphyly of <i>P. hernandesi;</i> we recommend the recognition of two species to promote a taxonomy that is consistent with species monophyly. There is strong evidence for three populations within <i>P. hernandesi</i>, and demographic modeling and admixture analyses suggest that these populations are not reproductively isolated, which is consistent with previous morphological analyses that suggest hybridization could be common. Finally, we characterize the population-species boundary by quantifying levels of genetic divergence for all 18 <i>Phrynosoma </i>species. Genetic divergence measures for western and southern populations of <i>P. hernandesi </i>failed to exceed those of other <i>Phrynosoma </i>species<i>,</i> but<i> </i>the relatively small population size estimated for the northern population causes it to appear as a relatively divergent species. These comparisons underscore the difficulties associated with putting a reference-based approach to species delimitation into practice. Nevertheless, the reference-based approach offers a promising framework for the consistent assessment of biodiversity within clades of organisms with similar life histories and ecological traits.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Fine-tuning biodiversity assessments: A framework to pair eDNA metabarcoding and morphological approaches
<p><span>Accurate quantification of biodiversity can be demanding and expensive. Although environmental DNA (eDNA) metabarcoding can facilitate biodiversity assessments through non-invasive, cost-efficient, and rapid surveys, the approach struggles to outperform traditional morphological approaches in providing reliable quantitative estimates for surveyed species (e.g., abundance and biomass).</span></p> <p><span>We present an integrated methodology for improving biodiversity surveys that pairs eDNA metabarcoding with morphological data, following a series of taxonomic and geographic filters. We demonstrate its power by applying it to a new spatiotemporal dataset generated on an Iberian-wide distributed aquatic mesocosm infrastructure that spans a wide biogeographic gradient.</span></p> <p><span>By building upon the strengths that these two approaches offer, our framework improved taxonomic resolution for 30% of the taxa and enabled species' traits (e.g., body-size) and abundance to be assigned to 85% of the taxa in hybrid datasets.</span></p> <p><span>These results indicate that eDNA-based assessments can complement, but not always replace, conventional approaches. Integrating conventional and modern eDNA metabarcoding approaches, already available in the ecologist's toolbox, will greatly enhance biodiversity assessments.</span></p>
Data for 'Assessing the value of biodiversity-specific footprinting metrics linked to South American soy trade'
<p>Underlying data for publication 'Assessing the value of biodiversity-specific footprinting metrics linked to South American soy trade'. </p>
A predictive approach to assess urban biodiversity and plan for future development scenarios
Open the record for dataset details and reuse information.
Data from: Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean
Open the record for dataset details and reuse information.
Assessing the effects of artificial light at night on biodiversity across latitude – Current knowledge gaps
Open the record for dataset details and reuse information.
Data and R code for: An experimental approach to assessing the impact of ecosystem engineers on biodiversity and ecosystem functions
Open the record for dataset details and reuse information.
Data from: Applying eDNA Metabarcoding to assess invertebrate biodiversity of Eelgrass (Zostera marina) meadows across Nova Scotia
Open the record for dataset details and reuse information.
Phylogenomic assessment of biodiversity using a reference-based taxonomy: An example with Horned Lizards (Phrynosoma)
Open the record for dataset details and reuse information.
Data from: Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding
Open the record for dataset details and reuse information.
Data from: Fine-tuning biodiversity assessments: A framework to pair eDNA metabarcoding and morphological approaches
Open the record for dataset details and reuse information.
Data from: Comparison of rapid biodiversity assessment of meiobenthos using MALDI-TOF MS and metabarcoding
Open the record for dataset details and reuse information.
Comparing eDNA and transect methods for aquatic biodiversity assessment in lakes and ponds
Open the record for dataset details and reuse information.
Assessing biodiversity of arbuscular mycorrhizal fungi: sample sites
The dataset represents data collected from a subset of the 200-point survey sites created for the Mycorrhiza study project. The project involves examination of soil samples for species richness, abundance, and composition of arbuscular mycorrhizal fungi. Comparisons between arbuscular mycorrhizal fungal community in the Phoenix metropolitan area and the surrounding desert are also being made.
Data from: A multi-taxa assessment of the effectiveness of agri-environmental schemes for biodiversity management
<p>Agri-environmental schemes (AES) aim to restore biodiversity and biodiversity-mediated ecosystem services in landscapes impoverished by modern agriculture. However, a systematic, empirical evaluation of different AES types across multiple taxa and functional groups is missing. Within one orthogonal design, we studied sown flowering AES types with different temporal continuity, size, and landscape context and used calcareous grasslands as semi-natural reference habitat. We measured species richness of twelve taxonomic groups (vascular plants, cicadas, orthopterans, bees, butterflies, moths, hoverflies, flower visiting beetles, parasitoid wasps, carabid beetles, staphylinid beetles and birds) representing five trophic levels. A total of 54,955 specimens were identified using traditional taxonomic methods and bulk arthropod samples were identified through DNA metabarcoding, resulting in a total of 1077 and 2110 taxa, respectively. Species richness of most taxonomic groups as well as multidiversity and richness of pollinators increased with temporal continuity of AES types. Some groups responded to size and landscape context but multidiversity and richness of pollinators and natural enemies were not affected. AES flowering fields supported different species assemblages than calcareous grasslands, but assemblages became more similar to those in semi-natural grasslands with increasing temporal continuity. Our results indicate that AES flowering fields and semi-natural grasslands function synergistically. Flowering fields support biodiversity even when they are relatively small and in landscapes with few remaining semi-natural habitats. We, therefore, recommend a network of smaller, temporally continuous AES flowering fields of different ages combined with permanent semi-natural grasslands to maximize benefits for biodiversity conservation and ecosystem service delivery in agricultural landscapes.</p>
Data from: Carrion fly-derived DNA as a tool for comprehensive and cost-effective assessment of mammalian biodiversity
Large-scale monitoring schemes are essential in assessing global mammalian biodiversity, and in this framework leeches have recently been promoted as an indirect source of DNA from terrestrial mammal species. Carrion feeding flies are ubiquitous and can be expected to feed on many vertebrate carcasses. Hence, we tested whether fly-derived DNA analysis may also serve as a novel tool for mammalian diversity surveys. We screened DNA extracted from 201 carrion flies collected in tropical habitats of Côte d'Ivoire and Madagascar for mammal DNA using multiple PCR systems and retrieved DNA sequences from a diverse set of species (22 in Côte d'Ivoire, 4 in Madagascar) exploiting distinct forest strata and displaying a broad range of body sizes. Deep-sequencing of amplicons generated from pools of flies performed equally well as individual sequencing approaches. We conclude that the analysis of fly-derived DNA can be implemented in a very rapid and cost-effective manner and will give a relatively unbiased picture of local mammal diversity. Carrion flies therefore represent an extraordinary and thus far unexploited resource of mammal DNA, which will likely prove useful for future inventories of wild mammal communities.
Data from: Spatial representativeness of environmental DNA metabarcoding signal for fish biodiversity assessment in a natural freshwater system
In the last few years, the study of environmental DNA (eDNA) has drawn attention for many reasons, including its advantages for monitoring and conservation purposes. So far, in aquatic environments, most of eDNA research has focused on the detection of single species using species-specific markers. Recently, species inventories based on the analysis of a single generalist marker targeting a larger taxonomic group (eDNA metabarcoding) have proven useful for bony fish and amphibian biodiversity surveys. This approach involves in situ filtering of large volumes of water followed by amplification and sequencing of a short discriminative fragment from the 12S rDNA mitochondrial gene. In this study, we went one step further by investigating the spatial representativeness (i.e. ecological reliability and signal variability in space) of eDNA metabarcoding for large-scale fish biodiversity assessment in a freshwater system including lentic and lotic environments. We tested the ability of this approach to characterize large-scale organization of fish communities along a longitudinal gradient, from a lake to the outflowing river. First, our results confirm that eDNA metabarcoding is more efficient than a single traditional sampling campaign to detect species presence, especially in rivers. Second, the species list obtained using this approach is comparable to the one obtained when cumulating all traditional sampling sessions since 1995 and 1988 for the lake and the river, respectively. In conclusion, eDNA metabarcoding gives a faithful description of local fish biodiversity in the study system, more specifically within a range of a few kilometers along the river in our study conditions, i.e. longer than a traditional fish sampling site.
Data from: Biodiversity assessment using next-generation sequencing: comparison of phylogenetic and functional diversity between Nebraska grasslands
Global biodiversity is declining rapidly as a consequence of anthropogenic changes to the environment. Traditional diversity indices such as species richness have been used to assess biodiversity, but recent arguments call for a more comprehensive assessment that includes both phylogenetic and functional diversity (PD and FD, respectively). Many PD metrics have been developed, but few empirical studies have compared metrics across sites with the goal of understanding their application to characterizing biodiversity. In this study, 17 PD metrics, four traditional diversity indices, and one measure of FD were calculated and compared between two Nebraska grasslands. PD metrics were calculated from robust phylogenies estimated from next-generation sequencing data of 45 species. Traditional indices were calculated using species abundance data, and FD was quantified by measuring the phylogenetic signal, K, of specific leaf area (SLA). Results showed that PD metrics and traditional indices were not always correlated, and various PD metrics characterized biodiversity differently. In addition, phylogenies estimated from >80 genes were more robust than single- or dual-gene phylogenies resulting in more reliable PD metrics. K of SLA indicated random trait assembly in all sites. Results suggested that metrics that identify phylogenetic structure and relatedness can provide information to conservation planners about the ability of a community to persist in an unpredictable future. A combination of these results with those of future investigations applying PD and FD metrics to varying communities will support concrete recommendations to conservation planners about how to incorporate these metrics into the selection of priority regions.
Data from: A new integrative framework for large-scale assessments of biodiversity and community dynamics, using littoral gastropods and crabs of British Columbia, Canada
Improving our understanding of species responses to environmental changes is an important contribution ecologists can make to facilitate effective management decisions. Novel synthetic approaches to assessing biodiversity and ecosystem integrity are needed, ideally including all species living in a community and the dynamics defining their ecological relationships. Here we present and apply an integrative approach that links high-throughput, multi-character taxonomy with community ecology. The overall purpose is to enable the coupling of biodiversity assessments with investigations into the nature of ecological interactions in a community-level data set. We collected 1,195 gastropods and crabs in British Columbia. First, the General mixed Yule-coalescent (GMYC) and the Poisson Tree Processes (PTP) methods for proposing primary species-hypotheses based on cox1 sequences were evaluated against an integrative taxonomic framework. We then used data on the geographic distribution of delineated species to test species co-occurrence patterns for non-randomness using community-wide and pairwise approaches. Results showed that PTP generally outperformed GMYC and thus constitutes a more effective option for producing species-hypotheses in community-level datasets. Non-random species co-occurrence patterns indicative of ecological relationships or habitat preferences were observed for grazer gastropods, whereas assemblages of opportunistic omnivorous gastropods and crabs appeared influenced by random processes. Species-pair associations were consistent with current ecological knowledge, thus suggesting that applying community assembly within a large taxonomical framework constitutes a valuable tool for assessing ecological interactions. Combining phylogenetic, morphological and co-occurrence data enabled an integrated view of communities, providing both a conceptual and pragmatic framework for biodiversity assessments and investigations into community dynamics.
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.