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.
54
datasets available to search
ShareScore release 0.9.0
Dataset results
54 results for “threatened habitats”
Population genomics reveals differences in genetic structure between two endemic arboreal rodent species in threatened cloud forest habitat
<p>SNPs obtained by UNEAK pipeline for <em>Habromys schmidlyi </em>and <em>Reithrodontomys microdon</em>. </p> <p>Pleae cite as: </p> <p>Colunga-Salas P., T Marines-Macías, G Hernández-Canchola, S Barbosa, C Ramírez, JB Searle, L León-Paniagua. 2022. <strong>Population genomics reveals differences in genetic structure between two endemic arboreal rodent species in threatened cloud forest habitat</strong>. Mammalian Reasearch. Doi: 10.1007/s13364-022-00667-x</p>
Habitat Protection Indexes - new monitoring measures for the conservation of threatened marine habitats - Datasets and supporting files
<p>The supporting datasets, scripts, and supplementary information for the manuscript, "Habitat Protection Indexes - new monitoring measures for the conservation of threatened marine habitats," are available within this repository.</p> <p>We conduct an analysis on the coverage of protected areas that cover six threatened marine and coastal and developed two indexes, the Local Proportion of Habitat Protected Index and the Global Proportion of Habitat Protected Index, describing the protection of these habitats locally and globally. The habitats considered are the following: cold corals, warm water corals, knolls and seamounts, mangroves, saltmarshes, and seagrasses.</p> <p>The index scores of each jurisdiction are made available for download in the dataset: <em>habitat_protection_indexes_average.csv</em></p> <p>The habitat specific index scores for each jurisdiction are made available for download in the dataset: <em>habitat_protection_indexes.csv. </em></p> <p>Column name descriptions are available in the text file: <em>Column_name_descriptions_20220301</em></p> <p>The scripts used to run the workflow to calculate the indexes, create figures, and calculate statistics for the manuscript are also included. The script <em>01_Workflow sources</em> the first 9 scripts in the <em>scripts</em> folder to calculate the indexes which relies on the functions script within the functions folder. The rest of the scripts in the folder create the figures and calculate the statistics for the manuscript.</p> <p>A readme pdf file is included here to ease with reproducing the workflow, but we strongly suggest to please visit our github (<a href="https://github.com/jkumagai96/Marine_Habitat_protection">https://github.com/jkumagai96/Marine_Habitat_protection</a>) to reproduce the entire calculation where we provide detailed information on how to run the workflow and package management.</p>
Data from: Digging deeper: habitat selection within the home ranges of a threatened marsupial
<p>While resource selection varies according to the scale and context of study, gathering data representative of multiple scales and contexts can be challenging especially when a species is small, elusive, and threatened. We explore resource selection in a small, nocturnal, threatened species—the greater bilby (<em>Macrotis lagotis</em>)—to test <strong>(a)</strong> which resources best predict bilby occupancy, and <strong>(b) </strong>whether responses are sex-specific and/or vary over time. We tracked a total of 20 bilbies and examined within home range resource selection over multiple seasons in a large (110ha) fenced sanctuary in temperate Australia. We tested a set of plausible models for bilby resource selection, showing that food biomass (terrestrial and subterranean invertebrates, and subterranean plants) and soil textures (% sand, clay and silt) best predicted bilby resource selection for all sampling periods. Selection was also sex-specific; female resource use, relative to males, was more closely linked to the location of high-quality resources (sandier soils, and terrestrial invertebrate biomass). Bilby selection for roads was independent of season but varied over time with females selecting for areas closer to roads when plants increased in density off roads. Our findings demonstrate the importance of considering resource selection over multiple contexts and highlight a method to collect such data on a difficult to study, threatened species. Collecting such data is critical to understanding the habitat required by species.</p>
When resilience is not enough: 2022 extreme marine heatwave threatens climatic refugia for a habitat-forming Mediterranean octocoral
<p>Climate change is impacting ecosystems worldwide, and the Mediterranean Sea is no exception. Extreme climatic events, such as marine heat waves (MHWs), are increasing in frequency, extent, and intensity during the last decades, which has been associated with an increase in mass mortality events for multiple species. Coralligenous assemblages, where the octocoral <em>Paramuricea clavata</em> lives, are strongly affected by MHWs. The Medes Islands Marine Reserve (NW Mediterranean) was considered a climate refugia for <em>P. clavata</em>, as their populations were showing some resilience to these changing conditions. In this study, we assessed the impacts of the MHWs that occurred between 2016 and 2022 in seven shallow populations of the octocoral <em>P. clavata</em> from a Mediterranean Marine Protected Area. The years that the mortality rates increased significantly were associated with the ones with strong MHWs, 2022 being the one with higher mortalities. In 2022, with 50 MHW days, the proportion of total affected colonies was almost 70%, with a proportion of the injured surface of almost 40%, reaching levels never attained in our study site since the monitoring was started. We also found spatial variability between the monitored populations. Whereas few of them showed low levels of mortality, others lost around 75% of their biomass. The significant impacts documented here raise concerns about the future of shallow <em>P. clavata</em> populations across the Mediterranean, suggesting that the resilience of this species may not be maintained to sustain these populations face the ongoing warming trends.</p>
Improving the application of Important Plant Areas to conserve threatened habitats: a case study of Uganda
<p><strong>This data set relates to the publication: Richards, S. L., Kalema, J., Ojelel, S., Williams, J., & Darbyshire, I. (2024). Improving the application of Important Plant Areas to conserve threatened habitats: A case study of Uganda. Conservation Science and Practice, e13246. https://doi.org/10.1111/csp2.13246<br></strong></p> <p><strong>Abstract:</strong></p> <p>Important Plant Areas (IPAs) are a successful method of identifying priority areas for plant conservation. Assessment of IPAs, however, often relies on criteria related to species, while incorporation of habitats has been less consistent. Using Uganda as a case study, we test the application of the threatened habitat criterion – criterion C. We identified nationally threatened habitats using Red List of Ecosystems criteria and assess, for the first time, how differing application of thresholds under IPA criterion C can influence IPA network outcomes. Eleven threatened habitats were identified, with declines switching from predominantly forest to savanna after the mid-20<sup>th</sup> century. Significantly, we found current IPA guidance on use of criterion C needlessly limits the number of sites that qualify as IPAs. The “five best sites” IPA threshold is reserved for countries where quantitative data is unavailable, however, the application of the relevant numerical thresholds (site contains ≥10% of national resource or site is among the best quality examples required to collectively prioritisie up to 20% of the national resource) to quantitative data largely generated fewer than five IPAs, comparably limiting conservation opportunities identified. We recommend, therefore, that the “five best” threshold is available for application on both qualitative and quantitative data. This will bolster the value of IPAs in conserving and restoring threatened and ecologically important habitats under the Kunming-Montreal Global Biodiversity Framework.</p> <p><strong>Dataset:</strong></p> <p>Within this dataset is a shapefile of the estimated extent of threatened habitats in Uganda. Each polygon represents a single "site" for each threatened habitat, with methodology for site identification given in the manuscript. Feature area and percentage national resource are given for each site, enabling users to identify those that trigger the different IPA criterion C thresholds.</p> <p><strong>In this study, we have preliminarily identified the threatened habitats and IPAs for Uganda. However, it is important to seek the expertise and views of stakeholders, consider other IPA criteria met and any complementarity between sites when identifying IPAs. In addition, ground-truthing or more localised data could validate the threat status of a vegetation type as well as identifying which sites are best to conserve these habitats. </strong></p>
Fig. 1 in Representation Of Threatened Vertebrates By A Protected Area System In Southeast Asia: The Importance Of Non-Forest Habitats
Fig. 1. Percentage of habitat use by amphibians, reptiles, birds, mammals and all taxa combined. The habitat types include Evr (evergreen forest), MD (mixed deciduous forest), Dip (dry dipterocarp forest), Mngrv (mangrove forest), Swmp (swamp forest), Bmbo (bamboo forest), Grss (grassland & shrub), Wet (wetland), SltF (salt flat), Strm (freshwater), Wtrf (waterfall), LmCv (limestone cave), and Bch (beach)
Fig. 2 in Representation Of Threatened Vertebrates By A Protected Area System In Southeast Asia: The Importance Of Non-Forest Habitats
Fig. 2. Map showing areas of underrepresented habitats in Thailand still lacking official protection. The light grey areas represent protected areas, while the black areas are underrepresented habitats outside the protected area system.
Data from: Digging deeper: habitat selection within the home ranges of a threatened marsupial
Open the record for dataset details and reuse information.
When resilience is not enough: 2022 extreme marine heatwave threatens climatic refugia for a habitat-forming Mediterranean octocoral
Open the record for dataset details and reuse information.
Science to inform policy: linking population dynamics to habitat for a threatened species in Canada
<p>Abstract</p> <p>1. Boreal forests provide numerous ecological services, including the ability to store large amounts of carbon, and are of significance to global biodiversity. Increases in industrial activities in boreal landscapes since the mid-20th century have added to concerns over biodiversity loss and climate change. Boreal forests are home to dwindling populations of boreal caribou (Rangifer tarandus caribou) in Canada, a species at risk that requires large, undisturbed landscapes for persistence. In 2012, the Canadian government defined critical habitat for boreal caribou by relating calf recruitment to disturbances. Some have questioned whether the recruitment-relationship can be extrapolated beyond the environmental conditions represented in the analysis.</p> <p>2. We examined the effects of human disturbances and fire (alone and in combination) on variation in recruitment and adult female survival using data from 58 study areas in Canada. Top models were used in aspatial scenarios of landscape change to evaluate the efficacy of the critical habitat definition in achieving the recovery objectives for boreal caribou in two contrasting landscapes: Little Smoky, dominated by high levels of human disturbances, and SK1, dominated by fire.</p> <p>3. The top recruitment model suggested the negative effect of fire was 3-4 times smaller than human disturbances. The top adult female survival model included human disturbances only. These results re-affirm that human disturbances are the primary factor contributing to boreal caribou declines.</p> <p>4. Our aspatial scenarios suggested that undisturbed habitat would have to increase to ≥68% for Little Smoky to maintain a self-sustaining population of boreal caribou with some degree of certainty. In contrast, the SK1 population was self-sustaining with 40% undisturbed habitat when fire disturbance predominates, but could become vulnerable with increases in human disturbances (8–9%). 5. Policy implications: Our results suggest that the 65% undisturbed critical habitat designation may serve as a reasonable proxy for achieving boreal caribou recovery in landscapes dominated by human disturbances. However, some populations may be less or more vulnerable, as illustrated by the SK1 scenarios. Continued population monitoring will be essential to assessing the effectiveness of land management strategies developed for boreal caribou recovery, especially with climate change.</p>
Data associated with: Climate change will likely threaten areas of suitable habitats for the most relevant medicinal plants native to the Caatinga dry forest
<p>Medicinal plants play an important role in providing ecosystem services, such as local cultural and economic value, and human well-being, especially in poor regions. The use of plants to improve living conditions and increase the chances of survival comes from the beginning of human life. Climate change has the potential to contract areas of suitable habitat for medicinal plant species across different regions. As a consequence of climate change, the possibility of treating diseases can be compromised, and even interrupted. <em>We collected data from the medicinal applications and the parts that are used of 10 species of medicinal plants native to the Caatinga dry forest [i.e., </em><em>Myracrodruon urundeuva</em><em> Allemão (Anacardiaceae), </em><em>Cereus jamacaru </em><em>DC (Cactaceae), </em><em>Neocalyptrocalyx longifolium</em><em> (Mart) Cornejo & Iltis (Caparaceae),</em><em> Maytenus rigida </em><em>Mart (Celastraceae), </em><em>Operculina hamiltonii</em><em> (G Don) DF Austin Staples, </em><em>Operculina macrocarpa</em><em> (L) Urb (Convolvulaceae), </em><em>Amburana cearensis </em><em>(Allemao) AC Sm, </em><em>Anadenantehra colubrina</em><em> (Vell) Brenan, </em><em>Bauhinia cheilantha</em><em> (Bong) Steud and </em><em>Erythrina velutina</em><em> Willd (Legimonosae). </em>In addition, we also collected precise georeferenced data (native occurrence) of these medicinal plant species, that was accessed in 1) The Global Biodiversity Information Facility platform (GBIF) is an international data network funded by governments around the world, providing open access to data on all life on Earth (https:// www.gbif.org, accessed May 2022); 2) REFLORA - Herbário Virtual, virtual herbarium network that contains information on Brazilian plants that are deposited in 63 herbaria in Brazil and 10 international herbaria (http://reflora.jbrj.gov.br/reflora/herbarioVirtual, accessed May 2022); 3) Botanical Information and Ecology Network Platform (BIEN), a global information network that helps to document patterns of plant diversity, trait records and distribution, which includes georeferenced plant observation data from herbarium records, plots, survey inventories (https://bien .nceas.ucsb.edu/bien/biendata, accessed May 2022) and 4) 95 botanical monographs and floras. We excluded all repeated and mismatch occurrence data for each species. We collected all the available points for the studied species.</p>
Data for: High focus on threatened species and habitats may undermine biodiversity conservation: evidence from the northern Baltic Sea
<p><span>Conservation policies and environmental impact assessments commonly target threatened species and habitats. Nevertheless, macroecological research provides reasons why also common species should be considered. </span><span>We investigate the consequences of focusing solely on legally protected species and habitats in a spatial conservation planning context using a comprehensive, benthic marine dataset from the northern Baltic Sea</span><span>. </span><span>Using spatial prioritization and surrogacy analysis, we </span><span>show that the common approach in conservation planning, where legally listed threatened species and habitats are the focus of conservation efforts, could lead to poor outcomes for common species (and therefore biodiversity as a whole), allowing them to decline in the future.</span> <span> </span><span>If conservation efforts were aimed solely at threatened species, common species would experience a loss of 62% coverage. In contrast, if conservation plans were based only on common species, threatened species would suffer a loss of 1%.</span><span> Threatened species are rare and their ecological niches distinct, making them poor surrogates for biodiversity. The best results are achieved by unified planning for all species and habitats. The minimal step towards acknowledging common species in conservation planning would be the inclusion of the richness of common species, complemented by information on indicator species or species of high importance for ecosystem functioning. The trade-off between planning for rare and common species should be evaluated, to minimize losses to biodiversity. </span></p>
Data for: Vegetation and soil ecology of threatened Himalayan Trillium habitats in Kashmir, Himalaya
<p>Understanding the vegetation and soil ecology of natural habitats harbouring threatened species is critical in conservation planning and restoration. The present study investigated the vegetation composition and soil physico-chemical attributes of natural habitats of <em>Trillium govanianum</em> – a threatened Himalayan endemic species. We laid 120 quadrats across eight randomly selected sites where the species was growing in the Kashmir Himalaya. We collected the soil samples from these sites and determined soil physico-chemical attributes using standard methods. Across all the sites, we found a total of 57 plant species with dominance of Rosaceae and Ranunculaceae. The IVI results revealed that <em>Fragaria nubicola</em>, <em>Corydalis diphylla</em>, <em>Galium aparine</em>, and <em>Leucanthemum vulgare</em>, were the dominant species in <em>T. govanianum</em> communities. The density, abundance and IVI of 3-leaf vegetative plants was higher than 1-leaf vegetative and 3-leaf reproductive plants across all the study sites. We found that T. govanianum alone forms 23.5 % positive, 0 negative, 76.4% random co-occurrences with other associated species in its community. Our results reveal that the variations in vegetation composition among the sites was influenced by differences in soil properties. Principal component analysis revealed that several soil parameters such as organic carbon, nitrogen, potassium, and sulphur were concentrated in five sites, namely Dara, Drung, Bangus, Gulmarg, and Doodhpathri, which also showed the highest density, frequency, and abundance of <em>T. govanianum</em>. Overall, our study contributes quantitative information on the vegetation and soil ecology of <em>T. govanianum</em>-assemblages, which in turn can help in developing conservation strategies for this threatened species, and its sustainable management and habitat restoration.</p>
Data for: Vegetation and soil ecology of threatened Himalayan Trillium habitats in Kashmir, Himalaya
Open the record for dataset details and reuse information.
Warm winters lead to early breeding, increased breeding effort, but lower reproductive success, in a threatened habitat specialist
Open the record for dataset details and reuse information.
Hibernation habitat selection by the threatened Chinese softshell turtle (Pelodiscus sinensis) in the Yellow River wetlands of Northwest China: Implications for conservation management
Open the record for dataset details and reuse information.
Data for: High focus on threatened species and habitats may undermine biodiversity conservation: evidence from the northern Baltic Sea
Open the record for dataset details and reuse information.
Data and code for: Identifying fine-scale habitat preferences of threatened butterflies using airborne laser scanning
Open the record for dataset details and reuse information.
Science to inform policy: linking population dynamics to habitat for a threatened species in Canada
Open the record for dataset details and reuse information.
Data from: Floral display and habitat fragmentation: effects on the reproductive success of the threatened mass-flowering Conospermum undulatum (Proteaceae)
1. Fragmentation of natural vegetation is currently one of the largest threats to plant populations and their interactions with pollinators. Plant reproductive susceptibility to habitat fragmentation has been investigated in many species; however, the response of wild mass-flowering species is poorly known, with research limited to mainly boreal plant species. 2. Here we studied twelve remnant populations of the threatened mass-flowering shrub Conospermum undulatum in the southwest Australian biodiversity hotspot, each presenting different population size, level of isolation, and floral display. We assessed the impact of fragmentation on: 1) fruit and seed production; and 2) seed germination. To gain a deeper understanding of factors influencing the reproductive success of C. undulatum we performed pollinator exclusion and self-pollination treatments to experimentally assess the mating system of this threatened shrub. 3. We found C. undulatum to be strictly self-incompatible and totally reliant on pollinators visiting with an outcrossed pollen load to complete the reproductive cycle. Further, we found that fruit production significantly decreased with decreasing floral display. A decrease in population size and floral display led to a decrease in seed output, while increasing isolation also led to a reduced production of seeds. Overall, seed germination was positively related to population size, and a negative relationship was found between germination and isolation. 4. Our results demonstrate the important relationship between pollinators and floral morphology in plants of southwest Australia that have coevolved with native pollinators and developed characteristic flower morphologies over long timeframes. The self-incompatible C. undulatum cannot rely on its mass-flowering trait to attract pollinators from co-flowering species, neither can it compensate for the lack of visitors by promoting geitonogamy. Consequently, fragmentation has a significant effect on the reproductive output of C. undulatum, and size, isolation, and floral display of populations should be considered when planning conservation actions for the species.
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.