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.
3,225
datasets available to search
ShareScore release 0.9.0
Dataset results
3,225 results for “Case of study”
Data from: Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: a case-study in Carex sect. Racemosae
PREMISE OF THE STUDY: Relationships among closely related and recently diverged taxa can be especially difficult to resolve. Here we use both Sanger sequencing and next-generation RADseq data sets to estimate phylogenetic relationships among species of Carex section Racemosae (Cyperaceae), a clade largely restricted to high latitudes and elevations. Interest in relationships among these taxa derives from questions about the species' biogeographic histories and possible links between diversification and Pleistocene glaciations. METHODS: A combination of approaches and molecular markers were used to estimate relationships among Carex species within sect. Racemosae and taxa from closely related sections. Nuclear and chloroplast loci generated by Sanger sequencing were analyzed with *BEAST, and SNP data from RADseq loci were analyzed as a concatenated data set using maximum likelihood and as independent loci using SVDquartets. KEY RESULTS: Sanger sequencing data sets resolved relationships among taxa at intermediate phylogenetic depths (albeit with low levels of support). Only the RADseq data resolved relationships with strong support at all phylogenetic depths. Moreover, different methods and data partitions of the RADseq data resulted in nearly identical topologies. Carex sect. Racemosae is a strongly supported clade, although a handful of species were found to group with closely related sections. Herbarium specimens up to 35 yr old successfully produced informative RADseq data. CONCLUSIONS: Despite the short read lengths of RADseq data, they nevertheless resolved relationships that Sanger sequencing data did not. Resolution of the phylogenetic relationships among recently and rapidly diversifying taxa within sect. Racemosae clades suggest a role for the Pleistocene glaciations in clade diversification.
Data from: Thelomma ocellatum, a range extension to the Yukon Territory and case study in the use of molecular data to recognize asexually reproducing crustose lichens
An unusual sterile, asexually reproducing crustose lichen was encountered during fieldwork in the Yukon Territory of Canada. Genus and family level placement of the taxon were precluded by a lack of both sexual characters and any non-sexual characters that would have suggested an unambiguous generic affiliation. Examination of mtSSU and nrITS sequence data of the taxon revealed it to be a member of the Caliciaceae, with a sister relationship to the genus Tholurna. Subsequent molecular phylogenetic analyses of mtSSU sequence data suggested conspecificity with Thelomma ocellatum, one of the few calicioid lichens that reproduce asexually via lichenized diaspores. Comparison of the material from the Yukon with reference specimens and descriptions of T. ocellatum confirmed the identification of these populations, which extend the known distribution of T. ocellatum considerably northward in North America.
Data from: Are landscape attributes a useful shortcut for classifying vegetation in the tropics? A case study of La Amistad International Park
Effective vegetation classification schemes identify the processes determining species assemblages and support the management of protected areas. They can also provide a framework for ecological research. In the tropics, elevation-based classifications dominate over alternatives such as river catchments. Given the existence of floristic data for many localities, we ask how useful floristic data are for developing classification schemes in species-rich tropical landscapes and whether floristic data provide support for classification by river catchment. We analyzed the distribution of vascular plant species within 141 plots across an elevation gradient of 130 to 3200 m asl within La Amistad National Park. We tested the hypothesis that river catchment, combined with elevation, explains much of the variation in species composition. We found that annual mean temperature, elevation, and river catchment variables best explained the variation within local species communities. However, only plots in high-elevation oak forest and Páramo were distinct from those in low- and mid-elevation zones. Beta diversity did not significantly differ in plots grouped by elevation zones, except for low-elevation forest, although it did differ between river catchments. None of the analyses identified discrete vegetation assemblages within mid-elevation (700–2600 m asl) plots. Our analysis supports the hypothesis that river catchment can be an alternative means for classifying tropical forest assemblages in conservation settings.
Data from: Continental-scale patterns of pathogen prevalence: a case study on the corncrake
Pathogen infections can represent a substantial threat to wild populations, especially those already limited in size. To determine how much variation in the pathogens observed among fragmented populations is caused by ecological factors, one needs to examine systems where host genetic diversity is consistent among the populations, thus controlling for any potentially confounding genetic effects. Here, we report geographic variation in haemosporidian infection among European populations of corncrake. This species now occurs in fragmented populations, but there is little genetic structure and equally high levels of genetic diversity among these populations. We observed a longitudinal gradient of prevalence from western to Eastern Europe negatively correlated with national agricultural yield, but positively correlated with corncrake census population sizes when only the most widespread lineage is considered. This likely reveals a possible impact of local agriculture intensity, which reduced host population densities in Western Europe and, potentially, insect vector abundance, thus reducing the transmission of pathogens. We conclude that in the corncrake system, where metapopulation dynamics resulted in variations in local census population sizes, but not in the genetic impoverishment of these populations, anthropogenic activity has led to a reduction in host populations and pathogen prevalence.
Data from: The unexpected depths of genome-skimming data: a case study examining Goodeniaceae floral symmetry genes
Premise of the study: The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae. Methods: Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their utility in mining low-copy nuclear genes involved in floral symmetry, specifically the CYCLOIDEA (CYC)-like genes. De novo assemblies were generated using multiple assemblers, and BLAST searches were performed for CYC1, CYC2, and CYC3 genes. Results: Overall Trinity, SOAPdenovo-Trans, and SOAPdenovo implementing lower k-mer values uncovered the most data, although no assembler consistently outperformed the others. Using SOAPdenovo-Trans across all 24 data sets, we recovered four CYC-like gene groups (CYC1, CYC2, CYC3A, and CYC3B) from a majority of the species. Alignments of the fragments included the entire coding sequence as well as upstream and downstream regions. Discussion: Genome-skimming data sets can provide a significant source of low-copy nuclear gene sequence data that may be used for multiple downstream applications.
Data from: Combining human acceptance and habitat suitability in a unified socio-ecological suitability model: a case study of the wolf in Switzerland
Habitat suitability models (HSMs) are commonly used in conservation practise to assess the potential of an area to be occupied and colonised. A major limitation of these models, however, is the omission of spatially explicit understanding of human acceptance towards the focal species. As wildlife is more and more subject to human-dominated landscapes, ignoring the sociological component will result in misrepresentation of the observed processes and inappropriate management. We distributed 10 000 questionnaires across Switzerland and identified key socio-demographical factors correlated with human acceptance of the wolf. We then created a spatially explicit acceptance model based on geo-referenced socio-demographical, social and geographical information. Finally, we combined our acceptance model with a HSM to obtain a unified socio-ecological suitability model, which included human and ecological components. We showed that the key factors associated with human acceptance were perception of how harmful the wolf is, interest in wolf-related issues, need for livestock protection, and fear of the wolf. Perceived harmfulness was in turn correlated with direct and indirect experience with the wolf, and level of education. Our acceptance map predicted decreasing acceptance with increasing altitude of residency and proximity to locations of confirmed wolf presence. This resulted in the overall opposition to the wolf for the Alpine region, albeit substantial regional differences. We found little spatial overlap (6% of Switzerland) between areas where the wolf was accepted and areas of suitable habitat. These areas of socio-ecological suitability were concentrated in the Jura Mountains and in the eastern and southern Alps, and were absent in the western and central Alps. Particularly in the Jura region, which is yet to be colonised, management of human acceptance will be a crucial conservation target. Synthesis and applications. We developed an integrative, socio-ecological approach that allowed us to accurately reproduce recent wolf recolonisation. We anticipate our framework to be a powerful tool to reliably evaluate overall suitable habitats and predict short to medium-term range expansion for species whose distribution is also dependent on human attitudes. Because our approach is sensitive to both the ecological and human component, it is ideally suited to identify key regions where proactive and targeted socio-ecological management plans are needed.
Data from: Shifting niches of marine predators due to human exploitation: the diet of the South American sea lion (Otaria flavescens) since the late Holocene as a case study
Stable isotope ratios of carbon and nitrogen in archaeological and modern bone samples have been used to reconstruct the dietary changes of the South American sea lion Otaria flavescens from the late Holocene to the present in the southwestern Atlantic. We sampled bones from archaeological sites in northern-central and southern Patagonia, Argentina, and bones housed in modern scientific collections. Additionally, we analyzed the stable isotope ratios in ancient and modern shells of intertidal molluscs to explore changes in the isotope baseline and allow comparison between bone samples from different periods after correction for baseline shifts. Results confirmed the trophic plasticity of the South American sea lion, demonstrated the much larger impact of modern exploitation of marine resources as compared with that of hunter-gatherers, and underscored the dissimilarity between the past and modern niches of exploited species. These conclusions are supported by the rather stable diet of South American sea lions during several millennia of aboriginal exploitation, in both northern-central and southern Patagonia, and the dramatic increase in trophic level observed during the twentieth century. The recent increase in trophic level might be related to the smaller population size resulting from modern sealing and the resulting reduced intraspecific competition. These results demonstrate how much can be learned about the ecology of modern species thanks to retrospective studies beyond the current, anthropogenically modified setting where ecosystem structure is totally different from that in the pristine environments where current species evolved.
Data from: Species discrimination of co-occurring small fossil mammals: a case study of the Cretaceous-Paleogene multituberculate genus Mesodma
The mammalian fossil record is largely composed of isolated teeth and tooth-bearing elements. In vertebrate microfossil assemblages with closely related, co-occurring species of mammals, it can be difficult to identify isolated teeth to species level because morphological differences among species may be slight and based on a single tooth position. Here we investigate the utility of the allegedly diagnostic lower fourth premolar (p4) for species-level identification in the genus Mesodma (Multituberculata, Neoplagiaulacidae). We conducted linear and geometric morphometrics on 86 p4s representing four Cretaceous-Paleogene (K-Pg) species of Mesodma that are common in deposits of the western interior of North America. Although Mesodma has been extensively discussed in the literature, these four species overlap considerably in p4 size and shape, making species-level identifications challenging. Using linear measurements, landmarks, and semilandmarks, we quantified p4 size and shape to understand morphological variation across the genus and uncover practical sources of morphological differentiation among the species represented here. Our results indicate (1) size is more important than shape for identifying p4s of Mesodma species; p4 shape varies across the genus, but cannot be used alone to identify isolated p4s to species; (2) M. garfieldensis and M. thompsoni cannot be distinguished from each other using p4 size or shape; we therefore subsume M. garfieldensis within M. thompsoni; and (3) M. formosa increased in size across the K-Pg boundary. In light of these results, we recommend that taxonomic diagnoses relying on isolated teeth incorporate quantitative analyses of morphology whenever possible to increase the accuracy of species-level identifications and paleofaunal studies that employ them.
Data from: Dealing with allometry in linear and geometric morphometrics: a taxonomic case study in the Leporinus cylindriformis group (Characiformes: Anostomidae) with description of a new species from Suriname
To achieve maximum efficacy, taxonomic studies that seek to distinguish amongst species must first account for allometric shape variation within species. Two recently developed software packages (SMATR and MorphoJ) offer regression-based allometric approaches that are notable for their statistical power and ease of use and that may prove highly useful to taxonomists working with linear or geometric morphometric data. We investigate species delimitation of the slender-bodied fishes in the Leporinus cylindriformis group using these programs and demonstrate the utility of the allometric corrections that they provide. Without allometric correction, many pairs of species are difficult to distinguish on the basis of morphometrics, but once regressions are used to account for marked allometric variation within species, most of the recognized species in this group can be readily distinguished with linear or geometric morphometrics, particularly using variation in the depth of the body. Both approaches returned congruent patterns of separation amongst putative species, but the geometric approach in MorphoJ distinguished amongst four more pairs of species than did the linear approach in SMATR and appears to provide slightly more statistical power. Based on distinctive morphometrics, meristics, and coloration, a highly elongate species of Leporinus from the Suriname, Corantijn, and Coppename rivers of Suriname is described herein as a new species, Leporinus apollo sp. nov. The unique L. cylindriformis holotype from Porto de Moz, Brazil differs in morphology, meristics, and pigmentation from specimens commonly referred to that species from the main basin of the Amazon; the latter specimens may represent an additional undescribed species. The L. cylindriformis holotype itself may represent a rare species or a specimen collected at the edge of its native range. Measurements of the holotype and paratype of Leporinus niceforoi, which were collected in the Amazonian slope of Colombia, differ substantially from similarly pigmented and putatively conspecific specimens from Amazonian portions of Ecuador and Peru. Recently collected specimens from Colombia are needed to determine whether the observed morphometric variation encompassed by the current concept of L. niceforoi indicates a morphocline within a single species, suggests the presence of multiple cryptic species, or results from shrinkage of the types. In all these cases, linear or geometric morphometric data can reliably differentiate amongst species, but only after one accounts for allometric shape variation. The new SMATR and MorphoJ software packages both offer easy and effective approaches to such allometrically informed taxonomy, and may prove useful to any systematist working on taxa that change shape as they grow.
Schizophrenia and Bartonella spp. infection: A pilot case–control study
<p>Recently, infections with emerging zoonotic bacteria of the genus Bartonella have been reported in association with a range of CNS symptoms. Currently, it remains unknown if Bartonella spp. infection is associated with symptoms of schizophrenia/schizoaffective disorder (SCZ/SAD). The objective of this study was to determine if there is an association between Bartonella species infection and SCZ/SAD. A secondary objective was to determine if SCZ/SAD symptoms were more severe among participants with documented Bartonella spp. infection. Using a case–control study design, 17 cases and 13 controls were evaluated with a series of clinical and cognitive assessments. Blood samples were collected and tested for Bartonella spp. infection using serological, microbiological, and molecular techniques. People with SCZ/SAD were more likely than healthy volunteers to have Bartonella spp. DNA in their bloodstream, with 11 of 17 cases (65%) positive by Bartonella spp. droplet digital PCR (ddPCR). In comparison, only one healthy volunteer was Bartonella spp. ddPCR positive (8%, p = 0.0024). Based on serology, Bartonella spp. exposure was common among people with SCZ/SAD (12 of 17) as well as among healthy volunteers (12 of 13), with no significant difference between the groups ( p = 0.196). Within the case group of people with SCZ/SAD, there was no significant difference in SCZ/SAD severity scores between people with and without ddPCR evidence of Bartonella spp. infection. This pilot study provides preliminary evidence in support of future investigations that should examine a potential contribution of Bartonella spp. infection to SCZ/SAD.</p>
Figure 3 in Amphibian taxonomy: early 21st century case studies
Figure 3. (a) Bar plot depicting number of new species of Amphibia described during 2015–2019 from global biodiversity hotspots. (b) Map depicting the distribution of hotspots that new amphibians were described from during 2015–2019. (c) Bar plot depicting number of new species of Amphibia described from broad geographical regions during 2015–2019. Europe and Central Asia have been combined due to geographic proximity and small sample sizes from Central Asia (N = 1).
Figure 2 in Amphibian taxonomy: early 21st century case studies
Figure 2. (a) Bar plot depicting number of new species of Amphibia described from each family across three extant orders (Anura, Caudata, and Gymnophiona) during 2015–2019. (b) Relationship between the number of new species described from each family and the overall number of species known from each family according to Frost (2020). Data have been fitted with a linear smoother using the 'lm' function from ggplot2 (Wickham 2016).
Figure 1 in Amphibian taxonomy: early 21st century case studies
Figure 1. (a) Description of new species of Amphibia from 2004 to 2019. Note that the number of species described has been similar during this timeframe and that there is no clear trend of increase or decrease. Data obtained amphibiaweb.org. (b) Types of data used to describe new species of Amphibia from 2015 to 2019. See text for definitions of data types. Proportion is out of 732 new species surveyed for our study. (c) Proportion of integrative studies (using two or more lines of evidence) to describe species of Amphibia from 2015 to 2019. Proportion is out of 732 new species surveyed for our study. Note general increase over the survey period. (d) Approximate DNA sequence alignment lengths used to describe species of Amphibia from 2015 to 2019 for mitochondrial (mtDNA) and nuclear DNA (nDNA). Alignment lengths have been Log10-transformed. Note increase in size of nDNA datasets in 2019.
Development of a versatile source apportionment analysis based on positive matrix factorization: a case study of the seasonal variation of organic aerosol sources in Estonia
<p>This work presents an advanced source apportionment approach that estimates the uncertainties of the positive matrix factorization model. The selection of the environmentally meaningful solutions is challenging in such models and a systematic approach to identify and sort the factors is important. We applied this method to a novel data set covering one yearly cycle at three sites in Estonia. The main results showed that biomass burning dominates in winter, while biogenic sources prevail in summer.</p>
Trasncripts and Survey from Case Study of Small Collaboration
<p>To identify the particularities of the small collaboration we used an exploratory case study methodology. The case study followed an embedded case study design and we collected data via semi-structured interviews and the SDR’s logs. In the study, we explored three topics: the scientific collaboration process, the collaboration’s data-sharing practices and attitudes.</p> <p>We found that, on the topic of collaboration, the collaborations suffered the common problems of geographically distributed collaborations. In terms of data- sharing practices and attitudes, we found that collaborators were solely motivated by extrinsic incentives. They showed a very restricted awareness of potential benefits, and sharing only occurred under low risk scenarios.</p> <p>We begin this section with the description of the exploratory study. We then present the results and a discussion of this exploration and propose three empirical claims.</p> <p> </p>
FIGURE 3 in Copepods associated with scleractinian corals: a worldwide checklist and a case study of their impact on the reef-building coral Pocillopora damicornis (Linnaeus, 1758) (Pocilloporidae)
FIGURE 3. Multidimensional scaling (MDS) plot of 75% similarity in species composition and abundance of symbiotic copepods amongst various sampling periods.
FIGURE 4 in Copepods associated with scleractinian corals: a worldwide checklist and a case study of their impact on the reef-building coral Pocillopora damicornis (Linnaeus, 1758) (Pocilloporidae)
FIGURE 4. Principal component analysis (PCA) of square root-transformed data from five functional categories of copepods (see text for descriptions.) defined based on behaviour (endo-/ectoparasitic or benthic) and the structure of the feeding appendages (mandibles vs. siphon) at various sampling periods. PC1 accounted for 77.2% of the variability, and PC2 accounted for 13.7%.
FIGURE 2 in Copepods associated with scleractinian corals: a worldwide checklist and a case study of their impact on the reef-building coral Pocillopora damicornis (Linnaeus, 1758) (Pocilloporidae)
FIGURE 2. Relationships between copepod infection and the amount of resources (Symbiodinium densities and surface areas) provided by host corals. A–E: Mean densities of symbiotic copepods (A: Siphonostomatoida, B: Cyclopoida, C: Harpacticoida, D: all copepods) among 480 Pocillopora damicornis colonies with varying Symbiodinium densities. E–H: Relationship between mean densities of symbiotic copepods (E: Siphonostomatoida, F: Cyclopoida, G: Harpacticoida, H: all copepods) and surface areas of host corals.
FIGURE 1 in Copepods associated with scleractinian corals: a worldwide checklist and a case study of their impact on the reef-building coral Pocillopora damicornis (Linnaeus, 1758) (Pocilloporidae)
FIGURE 1. Variation in seawater temperature and Symbiodinium density (mean ± SE) observed in Pocillopora damicornis colonies of Nanwan Bay, Southern Taiwan between July 2007 and November 2008. Lowercase and uppercase letters (a, b, c, and d) refer to the results of Tukey's post-hoc comparisons of monthly temperature and Symbiodinium density means, respectively, as a significant effect of time was detected in the overall ANOVA models (p <0.05 for both parameters).
FIGURE 2 in Phloeocharis subtilissima Mannerheim (Staphylinidae: Phloeo charinae) and Cephennium gallicum Ganglbauer (Scydmaenidae) new to North America: a case study in the introduction of exotic Coleoptera to the port of Halifax, with new records of other species
FIGURE 2: Phloeocharis subtilissima Mannerheim, Point Pleasant Park, Halifax, Nova Scotia, Canada. Living specimen in bark of red maple (Acer rubrum).
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.