Find research datasets worth reusing

opencc-by-4.0Apr 2024View details →

Data for "Willingness of rural and urban citizens to undertake pollinator conservation actions across three contrasting European countries"

Data for: "Willingness of rural and urban citizens to undertake pollinator conservation actions across three contrasting European countries" by Costanza Geppert, Cristiano Franceschinis, Thijs P.M. Fijen, David Kleijn, Jeroen Scheper, Ingolf Steffan-Dewenter, Mara Thiene, Lorenzo Marini (2024) People and Nature. This dataset was obtained by administering an online questionnaire in Germany, Italy, and the Netherlands.

opencc-by-4.0Apr 2024View details →

A Conserved Inhibitory Interdomain Interaction Regulates DNA-binding Activities of Hybrid Two-component Systems in Bacteroides

The study reveals a highly conserved inhibitory mechanism to regulate the activities of hybrid two-component systems (HTCSs) in Bacteroides. HTCSs comprise a major class of transcription regulators of polysaccharide utilization genes in Bacteroides. A conserved sequence motif has been discovered to correlate with the interdomain arrangement of HTCS domains. Presence or absence of this motif is likely predictive of the regulatory mechanism evolved for utilization of different glycans.   This dataset includes sequence analyses and structure predictions of HTCSs. List of files: ·        AlphaFold-HTCS-RR.zip                             AlphaFold results of all HTCS-RR fragments in B. theta ·        AlphaFold-HTCS-cyto-dimer.zip                AlphaFold results of all HTCS-cyto dimers in B. theta ·        HTCSbacteroides-MAFFT-fasta                  Sequence alignment of 6908 HTCSs from Bacteroides ·        HMM-AllHTCS.hmm                                  HMM of HTCSs generated from the MAFFT alignment ·        HMM-DBD-PF12833                                 HMM of HTH18 (Pfam: PF12833) from Interpro ·        HMM-REC-PF00072                                  HMM of REC (Pfam: PF00072) from Interpro ·        B_theta_RR_fasta                                       Sequence alignment of 32 HTCS-RRs in B. theta ·        B_theta_RR-tree                                         A neighbor-joining phylogenetic tree of 32 HTCS-RRs in B. theta

opencc-by-4.0Dec 2023View details →

Final products from "3D MODELING AS A CONSERVATION TOOL TO CHARACTERIZE ENDANGERED SEASONALLY FLOODED ECOSYSTEMS IN THE VOLTA GRANDE DO XINGU, AMAZON FOREST, PARÁ, BRAZIL"

In these .zip folders, you will find the products generated from flight missions carried out between November 7th to 14th, 2021, in the Volta Grande do Xingu, Pará, Brazil.  These results are presented as an integral part of the article titled '3D MODELING AS A CONSERVATION TOOL TO CHARACTERIZE ENDANGERED SEASONALLY FLOODED ECOSYSTEMS IN THE VOLTA GRANDE DO XINGU, AMAZON FOREST, PARÁ, BRAZIL' published on the doctoral thesis "Characterization and monitoring of the flooding dynamics and seasonally flooded environments of the Volta Grande do Xingu through remote sensing", available at <a href="https://doi.org/10.11606/T.106.2023.tde-02022024-211517">https://doi.org/10.11606/T.106.2023.tde-02022024-211517</a>. To understand the data processing methodology that led to these results, please refer to the thesis. Each folder represents a flight mission. They are named by date and flight number (DD_MM_YYYY_FLIGHT#). Within each folder, there are six files resulting from the processed flights: The georeferenced orthophoto and Digital Surface Model, which are raster files (.TIFs), the dense point cloud (.las), and the files composing the 3D Model generated by Agisoft Metashape (extensions .OBJ, .MTL, and .JPEG). The .OBJ file is the primary file for visualizing the model, including the three-dimensional mesh formed by the points of the point cloud and containing geometry, texture, and color information.  The .MTL file contains the material description associated with the OBJ file and includes information about the visual properties of the model, such as texture, reflections, and materials.  The .JPEG files are the texture images used on the Digital Surface Model to generate the 3D model. This information provides the model with its realistic properties. The .OBJ, .MTL and .JPEG files need to be together in the same folder for a complete 3D Model visualization (i.e., shape, color, and texture). When using this data, please cite Affonso, A. A. (2023). Caracterização e monitoramento da dinâmica de alagamento e dos ambientes sazonalmente alagáveis da Volta Grande do Xingu através de sensoriamento remoto. Tese de Doutorado, Instituto de Energia e Ambiente, Universidade de São Paulo, São Paulo. doi:10.11606/T.106.2023.tde-02022024-211517. Recuperado em 2024-04-14, de www.teses.usp.br

opencc-by-4.0Nov 2024View details →

Cetaceans sighting positions from 2009 to 2021 (animal conservation)

Sighting position of the Striped dolphin (Stenella coeruleoalba), Common bottlenose dolphin (Tursiops truncatus) and Fin whale (Balaenoptera physalus) in the 2009 - 2021 period collected buy aerial line transect distance sampling. These data coupled with other from public database are linked with the Copernicus in order to fit ensemble SDMs 16 and predict their current and future potential distribution at the Mediterranean subregional scale.

opencc-by-4.0Nov 2024View details →

BeEST single pixel data for conservative wavepacket analysis

One day of data from a single STJ pixel from the BeEST experiment.  The data file is the calibaration laser and EC signal energy spectra.  The code file produces limits on uncertainty of the energy measurement and corresponding limits on decay product wavepackets.

opencc-by-4.0Nov 2024View details →

Classification and structural analysis of value chain contracts for biodiversity conservation in the European Union

The data provided by this dataset are the raw data published in the paper "Classification and structural analysis of value chain contracts for biodiversity conservation in the European Union" (<a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.sftr.2024.100372" target="_blank" rel="noopener">https://doi.org/10.1016/j.sftr.2024.100372</a>).

opencc-by-nc-4.0Apr 2024View details →

Data from: Deciduous forests hold conservation value for birds within South Andaman Island, India

We assessed the importance of deciduous and evergreen habitats for forest birds (including several endemic and threatened species) within South Andaman Island, India. To this end, we compared the composition and diversity (taxonomic, functional and phylogenetic) of forest birds across the two habitat types, and evaluted species-specific responses to habitat variables within the island. The dataset collected and R codes used in this study are published here. Bird species traits were sourced from Tobias et al. (2022) and Wilman et al. (2014). Phylogenetic trees were sourced from <a href="https://birdtree.org/">birdtree.org</a> (Jetz et al. 2012). Taxonomic Coverage: Birds, 54 species Geographic Coverage: South Andaman Island, Andaman and Nicobar Islands, India Temporal Coverage: March-May 2022 and December 2022-April 2023   Brief summary of field methods:  We conducted line-transect surveys for forest birds across evergreen and deciduous forests in South Andaman Island, India.  Twenty-seven transects were sampled either in the morning (between 0515 – 0930 hrs) or in the afternoon (between 1515 – 1730 hrs) from March-May 2022 and December 2022-April 2023. For every bird detected, we noted species identity, group size (if visible), time of detection, and whether the bird(s) was seen or heard. Detections of flying birds and nocturnal species (owls and nightjars) were excluded. For each transect, we measured -  a. tree density and basal area (using the point-centered quarter method, or PCQ);  b. canopy cover, proportion of deciduous trees, and presence of cane, bamboo runners and clumps of standing bamboo (averaged across PCQ points); c. number of large trees and cut logs (counted within a 20m-wide belt along each transect); and  d. distance from nearest settlement/village (using Google Earth Pro). The dataset published here contains eight data files and two R code files, along with a ReadMe.txt file that explains each of these files.   Funding: Science and Engineering Research Board (Govt. of India) - SRG/2021/001523 The Rufford Foundation The Rauf Ali Fellowship Arvind Datar Rohini Nilekani Philanthropies   References: Jetz, W., G. H. Thomas, J. B. Joy, K. Hartmann, and A. O. Mooers. 2012. The global diversity of birds in space and time. Nature 491:444–448. Tobias, J. A., C. Sheard, A. L. Pigot, A. J. M. Devenish, J. Yang, et al. 2022. AVONET: morphological, ecological and geographical data for all birds. Ecology Letters 25:581–597. Wilman, H., J. Belmaker, J. Simpson, C. de la Rosa, M. M. Rivadeneira, and W. Jetz. 2014. EltonTraits 1.0: Species-level foraging attributes of the world’s birds and mammals. Ecology 95:2027–2027.

opencc-zeroNov 2021View details →

Trust in researchers and researchers' statements in large carnivore conservation

Human-wildlife interactions occur when humans and wildlife overlap in the same landscapes. Due to the growing human population, the number of interactions will continue to increase, and in some cases, develop further into social conflicts. Conflicts may occur between people disagreeing about wildlife conservation or arguing over which wildlife management measures should be taken. Social conflicts between humans are based on different attitudes, values and land-use aspirations. The success of solving these social conflicts strongly depends on building trust between the public, stakeholders, authorities, and researchers, as trust is fundamental to all communication and dialogue. Here we have examined how trust in large carnivore research differs within a geographically stratified sample of the Norwegian population. The comprehensive survey, including 2110 respondents, allows us to explore how people perceive factual statements about large carnivores depending on the source of these statements. Specifically, the respondents were given multiple statements and asked to judge them in terms of meaning and authenticity depending on whether the statements were made by a politician, the Norwegian farmers' association, the Norwegian Fish and Game association or a large carnivore researcher. Based on the variations in perceptions, we inferred that trust in large carnivore researchers and their research results varied with people's attitudes, values and direct experience of large carnivores. In general, respondents perceived 60% of the statements to be genuine when given no information of who had made them. Although this increased to 75 % when informed that the statements were made by a large carnivore researcher, there was still a 25 % probability that the statement was perceived as manipulative or political. Age, environmental values, and negative experiences of carnivores increased the probability of perceiving research statements as manipulative or political. People living in areas with high proportions of hunters showed particularly polarized views, either more strongly perceiving the statements as political, or in contrast as research. This study provides a novel perspective in understanding the role trust plays in social conflicts related to human-wildlife interactions.

opencc-by-4.0Nov 2021View details →

The soil surface food web in conservation agriculture as the foundation for conservation biocontrol

Data on Collembola (per 5 cm diameter sample), spiders (per 0.25 m2), carabid beetles (per 0.25 m2), aphids (per straw), and simulated max density of aphids from conservation agriculture fields (CA) and conventionally tilled fields (CT).

opencc-zeroNov 2021View details →

Data from: Sequential use of niche and occupancy models identifies conservation and research priority areas for two data-poor endemic birds from the Colombian Andes

The lack of high-quality information on data-poor species can hinder efforts to inform conservation actions via spatial distribution modeling. This is particularly true for tropical birds of conservation concern, for which ecological studies and assessments of their conservation status have received limited funding. Here we use a cost- and time-efficient protocol for assessing the distribution of range-restricted taxa and to identify priority areas for their conservation based on a sequential application of Environmental Niche Models (ENMs) and Occupancy-Detection Models. This approach first uses available geographical information and niche-theory to prioritize potential study sites, which can later be surveyed to obtain high-quality presence-absence data to accurately model distributional ranges with limited resources. We apply this protocol to identify priority areas for two Neotropical birds of conservation concern endemic to the Colombian Andes: Yellow-headed Brush-finch (Atlapetes flaviceps) and Tolima Dove (Leptotila conoveri). We first fitted ENMs using spatially-filtered datasets containing all available records up to 2018. We then conducted field surveys across climatically suitable areas identified for both species, carrying out a total of 1750 counts to generate input data for the occupancy models. Overall, our results suggested more extended and more continuous distribution ranges for both species than previously reported, but also identified population strongholds that are not currently represented within the national protected areas system. Both species occupied a narrow elevational belt (~1300–2600) of the Central Andes of Colombia primarily on the slopes of the Magdalena River valley, with isolated populations in the Western and Eastern Andes; these areas have undergone some of the most marked landscape transformations in Colombia. This straightforward protocol maximizes available information and minimizes costs, while allowing for estimation of occurrence probabilities for range-restricted, data-poor taxa.

opencc-by-4.0Dec 2015View details →

Fig. 5 in The vascular plant diversity of Burkina Faso (West Africa) - a quantitative analysis and implications for conservation

Fig. 5. – Species richness in Burkina Faso on a province level.

opencc-by-4.0Dec 2015View details →

Fig. 2 in The vascular plant diversity of Burkina Faso (West Africa) - a quantitative analysis and implications for conservation

Fig. 2. – The twelve most species-rich plant families in Burkina Faso.

opencc-by-4.0Dec 2015View details →

Fig. 4 in The vascular plant diversity of Burkina Faso (West Africa) - a quantitative analysis and implications for conservation

Fig. 4. – Proportion of life forms in the different phytogeographic zones of Burkina Faso.

opencc-by-4.0Jun 2012View details →

Fig. 16 in Taxonomic Review Of Euphydryas Maturna (Linnaeus, 1758) (Lepidoptera, Nymphalidae) With Description Of A New Subspecies From Dobrogea (Romania) And Notes On Conservation Biology

Fig. 16. Distribution of Euphydryas maturna in Eurasia and in SE Europe

opencc-zeroDec 2021View details →

Integrating dynamic processes into waterfowl conservation prioritization tools

Aim: Traditional approaches for including species' distributions in conservation planning have presented them as long-term averages of variation. Like these approaches, the main waterfowl conservation targeting tool in the United States Prairie Pothole Region (US PPR) is based primarily on long-term averaged distributions of breeding pairs. While this tool has supported valuable conservation, it does not explicitly consider spatiotemporal changes in spring wetland availability and does not assess wetland availability during the brood rearing period. We sought to develop a modeling approach and targeting tool that incorporated these types of dynamics for breeding waterfowl pairs and broods. This goal also presented an opportunity for us to compare predictions from a traditional targeting tool based on long-term averages to predictions from spatiotemporal models. Such a comparison facilitated tests of the underlying assumption that this traditional targeting tool could provide an effective surrogate measure for conservation objectives such as brood abundance and climate refugia. Location: US PPR Methods: We developed spatiotemporal models of waterfowl pair and brood abundance within the PPR of the US. We compared the distributions predicted by these models and assessed similarity with the averaged pair data that is used to develop the current waterfowl targeting tool. Results: Results demonstrated low similarity and correlation between the averaged pair data and spatiotemporal brood and pair models. The spatiotemporal pair model distributions served as better surrogates for brood abundance than the averaged pair data. Main conclusions: Our study underscored the contributions that the current targeting tool has made to waterfowl conservation but also suggested that conservation plans in the region would benefit from the consideration of inter- and intra-annual dynamics. We suggested that using only the averaged pair data and derived products might result in the omission of 46-98% of important pair and brood habitat, respectively, from conservation plans.

opencc-zeroDec 2021View details →

Data from: Establishing community-wide DNA barcode references for conserving mangrove forests in China

Background: Mangrove ecosystems have been the focus of global attention for their crucial role in sheltering coastal communities and retarding global climate change by sequestering 'blue carbon'. China is relatively rich in mangrove diversity, with one-third of the ca. 70 true mangrove species and a number of mangrove associate species occurring naturally along the country's coasts. Mangrove ecosystems, however, are widely threatened by intensifying human disturbances and rising sea levels. The urgent need to protect mangrove ecosystems could be assisted by using barcoding technology, which provides rapid species identification. Results: To investigate this potential, 898 plant specimens were collected from 33 of the major mangrove sites in China. Based on the morphologic diagnosis, the specimens were assigned to 72 species, including all 28 true mangrove species and all 12 mangrove associate species recorded in China. Three chloroplast DNA markers rbcL, trnH-psbA, matK, and one nuclear marker ITS2 were chosen to investigate the utility of using barcoding to identify these species. According to the criteria of barcoding gaps in genetic distance, sequence similarity and phylogenetic monophyly, we propose that a single marker, ITS2, is sufficient to barcode the species of mangroves and their associates in China. Furthermore, rbcL or trnH-psbA can also be used to gather supplement confirming data. In using these barcodes, we revealed a very low level of genetic variation among geographic locations in the mangrove species, which is an alert to their vulnerability to climate and anthropogenic disturbances. Conclusion: We suggest to use ITS2 to barcode mangrove species and terrestrial coastal plants in South China. The DNA barcode sequences we obtained would be valuable in monitoring biodiversity and the restoration of ecosystems, which are essential for mangrove conservation.

Can at-risk species serve as effective conservation surrogates? Case study in northeastern US shrublands

Targeted, single-species management and ecosystem-based management are generally considered disparate conservation approaches. In imperiled ecosystems, these approaches may be complementary, when habitat management for targeted at-risk species provides broad ecosystem benefits through an umbrella or surrogate species effect. In the northeastern United States, extensive management has been ongoing since 2011 to restore declining habitat for an at-risk shrubland habitat specialist, the New England cottontail (Sylvilagus transitionalis), with the goal that other shrubland-obligate wildlife will also benefit; yet the efficacy of these efforts has not been evaluated. In this study, we assessed whether habitat management targeting New England cottontail provides conservation benefits for shrubland-obligate birds. Specifically, we (1) identified shrubland-obligate birds that are indicative of the microhabitat conditions and habitat types suitable for New England cottontails, and (2) determined microhabitat and patch-level influences on shrubland bird occupancy at sites occupied by or managed for New England cottontail. Through avian point count surveys and indicator species analyses, we identified 12 shrubland-obligate bird species on patches occupied by New England cottontail and in microhabitat conditions suitable for New England cottontail. Occupancy models for five shrubland bird species further identified species-specific habitat associations. Generalized linear models showed that shrubland bird species richness was positively associated with herbaceous vegetation and low shrubs, indicating that shrublands managed for the purpose of cottontail colonization can also benefit a suite of shrubland birds before the habitat is dense enough to provide cover for cottontails. Our findings show that managing habitat for New England cottontail on a variety of site types can maintain a range of microhabitat conditions to support a high diversity of shrubland-obligate birds. These findings provide evidence for broad ecosystem benefits of managing for New England cottontail and exemplify the value of at-risk habitat specialists as conservation surrogates in imperiled ecosystems.

Ignorance is not bliss: Evolutionary naïveté in an endangered desert fish and implications for conservation

Predator naiveté has been invoked to explain the impacts of non-native predators on isolated populations that evolved with limited predation. Such impacts have been repeatedly observed for the endangered Pahrump poolfish, Empetrichthys latos, a desert fish species that evolved in isolation since the end of the Pleistocene. We tested Pahrump poolfish anti-predator responses to conspecific chemical alarm cues released from damaged epidermal tissue in terms of fish activity and water column position. Pahrump poolfish behavioural responses to conspecific alarm cues did not differ from responses to a dechlorinated tap water control. As a positive control, the well-studied fathead minnow, Pimephales promelas, showed significant alarm cue responses in terms of reduced activity and lowered water column position. The density of epidermal club cells, the presumptive source of alarm cues, was significantly lower in Pahrump poolfish relative to fathead minnows. Therefore, anti-predator competence mediated by conspecific alarm cues does not seem to be a component of the ecology of Pahrump poolfish. These findings provide a proximate mechanism for the vulnerability of Pahrump poolfish to non-native predators, with implications for conservation and management of insular species.

Data from: Predicting habitat suitability and connectivity for management and conservation of urban wildlife: A real-time web application for grassland water voles

<ol> <li>Natural habitats in urban areas provide benefits for both humans and biodiversity. However, to achieve biodiversity gains we require new techniques to determine habitat suitability and ecological connectivity that will inform urban planning and development.</li> <li>Using an example of an urban population of water voles (Arvicola amphibius) we developed a habitat suitability model and a resistance-surface-based model of landscape connectivity to identify potential connectivity between areas of suitable habitat. We then updated the environmental variables according to new urban development plans and used our models to generate spatially explicit predictions of both habitat suitability and connectivity.</li> <li>To make models accessible to urban and conservation planners we developed an interactive mapping tool that provided users with a graphical user interface (GUI) to inform conservation planning for this species.</li> <li>The model found that habitat suitability for water voles was related to distance from key environmental variables, such as built-up areas and urban green spaces, while the connectivity model identified important corridors connecting areas of potential distribution for this species.</li> <li>Future development plans altered the potential spatial distribution of the water vole population, reducing the extent of suitable habitat in some core areas. The interactive mapping tool made available suitable habitat and connectivity maps for conservation managers to assess new planning applications and for the development of a conservation action plan for water voles.</li> <li>Synthesis and applications: We believe this approach provides a framework for future development of nature conservation tools that can be used by planners to inform ecological decision making, increase biodiversity and reduce human-wildlife conflict in urban environments.</li> </ol>

In-situ feeding as a new management tool to conserve orphaned Eurasian lynx (Lynx lynx)

High human-caused mortality due to wildlife-vehicle-collisions and illegal killing leads to frequent cases of orphaned Eurasian lynx juveniles. Under natural conditions, this would result in starvation of the young. To avoid this, wildlife managers conventionally rear animals in captivity and release them later. However, this measure is an undesirable outcome for species conservation, managers and animals alike. Increased awareness of Eurasian lynx orphaned by human-caused mortality means managers must often intervene in endangered populations. In this study we report for the first time a successful case of in-situ feeding designed to avoid captivity of two orphaned Eurasian lynx. We exposed 13 roe deer and 7 red deer carcasses in the field to successfully support two orphans to the age of independence and confirm dispersal from the natal range. We present this management approach as a feasible and complimentary tool that can be considered in small or isolated large carnivore populations where every individual counts towards population viability.