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.
601
datasets available to search
ShareScore release 0.9.0
Dataset results
601 results for “wild species”
WCSdb: A database of Wild Coffea Species.
<p>This the data table of the WCSdb: A database of Wild <em>Coffea</em> Species web site. The photo Gallery associated to this web site are available at <a href="https://dataverse.ird.fr/dataset.xhtml?persistentId=doi:10.23708/JZA8I2">https://doi.org/10.23708/JZA8I2</a> and the sequencing data at <a href="https://doi.org/10.23708/KWRIJJ%22%20%5Ct%20%22_blank">https://doi.org/10.23708/KWRIJJ</a></p> <p>Coffee is a beverage enjoyed by millions of people worldwide and an important commodity for millions of people. Beside the two cultivated species (<em>Coffea arabica</em> and <em>Coffea canephora</em>), the 139 wild coffee species belong to the <em>Coffea</em> genus are largely unknown to coffee scientists and breeders although these species may be crucial for future coffee crop development to face climate changes. Here we present the Wild Coffee Species database (WCSdb) hosted by Pl@ntNet platform (<a href="http://publish.plantnet-project.org/project/wildcofdb_en">http://publish.plantnet-project.org/project/wildcofdb_en</a>), providing information for 140 coffee species, for which 84 contain a photo gallery and 82 contain sequencing data (GBS, chloroplast or whole genome sequences). The objective of this database is to better understand and characterize the species (identification, morphology, biochemical compounds, genetic diversity, sequence data) in order to better protect and promote them. </p>
Seed mass data for crop species and wild progenitors
<p>Data supporting a comparison of seed masses in crop species and their wild progenitors.</p> <p>The data files which fed into the analysis reported in the paper are:</p> <ul> <li>Grass_crops_raw.csv</li> <li>Legume_crops_raw.csv</li> <li>Veg crops combined.csv</li> <li>Beet_seeds_dissected.csv - mass of true seeds of beet; the data in the main 'Veg crops' file are for beet seed capsules, which are easier to collect and weigh.</li> <li>Cassava_EMBRAPA_*.csv - extra seed mass data from cassava, analysed separately from the main data, and described in supplementary material 2.</li> </ul> <p>Scripts used in processing the data (*.py) and a Makefile controlling some processing steps are included.</p> <p>There is also some extra data collected on other species of vegetable crops: <em>Brassica </em>spp., Chicory & Endive (<em>Cichorium </em>spp.), Leek (<em>Allium ampeloprasum</em>), and on fibre crops: Kenaf & Roselle (<em>Hibiscus </em>spp.), Jute (<em>Corchorus olitorius</em>), Hemp (<em>Linum</em> spp.). The data available for these was not sufficient to include them in our analysis, but they are provided here anyway.</p>
Dataset: Auditory brainstem responses to varying stimulus presentation rates of 12 bat species in the wild and captivity
<p>Dataset for the Dataset Publication: Auditory brainstem responses to varying stimulus presentation rates of 12 bat species in the wild and captivity</p> <p>There are two datasets available: 1) the measured ABRs from Experiments 1 and 2 and 2) the extracted IOIs:</p> <ol> <li>ABR measurements:</li> </ol> <p>The filename of the ABR recordings from Experiment 1 include the species name, individual ID, sex, stimulus presentation rate (indicated as “modrate”) and recording day and time (yyyyddmm). Each recording file contains 256 measurements of the same stimulus and stimulus presentation rate in columns. An exemplary filename would be “Carollia_perspicillata_cp6male_modrate6_20190905T125903”, meaning that this is a recording of <em>Carollia perspicillata</em> individual cp6 of sex male, tested with a stimulus presentation rate of 6 Hz on the 09.05.2019, and the file was saved at 12:59:03 (the T between date and time stands for “Time”).</p> <p>The filename of the ABR recordings from Experiment 2 include the place of the Experiments (Bad Segeberg) and species name (<em>C. perspicillata</em>), individual ID, sex, stimulus presentation rate (indicated as “modrate”) and recording day and time (yyyymmdd; be aware, that the date format is different between Experiment 1 and 2). Each recording file contains 256 measurements of the same stimulus and stimulus presentation rate in columns. An exemplary filename would be “BadSegeberg_cper_1_male_modrate6_20200622T140952_stimulus_ST01_short ”, meaning that this is a recording of <em>Carollia perspicillata</em> individual cp6 of sex male, tested with a stimulus presentation rate of 6 Hz on the 09.05.2019, and the file was saved at 12:59:03 (the T between date and time stands for “Time”), the individual was presented with stimulus example 01 of the short stimuli.</p> <ol> <li>IOI recordings</li> </ol> <p>The recordings of Inter-Onset-Intervals are all in one single csv file and species and sequence ID is given per row, to be able to analyze the data further.</p> <p> </p>
Chromosomal-level genome assembly of the scimitar‐horned oryx: insights into diversity and demography of a species extinct in the wild
<p>Captive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation management. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes; however, the transfer of these approaches to applied conservation has been slow. The scimitar‐horned oryx (<i>Oryx dammah)</i> is a North African antelope that has been extinct in the wild since the early 1980s and is the focus of a large‐scale and long‐term reintroduction project. To enable the selection of suitable founder individuals, facilitate post‐release monitoring and improve captive breeding management, comprehensive genomic resources are required. Here, we used 10X Chromium sequencing together with Hi‐C contact mapping to develop a chromosomal‐level genome assembly for the species. The resulting assembly contained 29 chromosomes with a scaffold N50 of 100.4 Mb, and displayed strong chromosomal synteny with the cattle genome. Using resequencing data from six additional individuals, we demonstrated relatively high genetic diversity in the scimitar‐horned oryx compared to other mammals, despite it having experienced a strong founding event in captivity. Additionally, the level of diversity across populations varied according to management strategy. Finally, we uncovered a dynamic demographic history that coincided with periods of climate variation during the Pleistocene. Overall, our study provides a clear example of how genomic data can uncover valuable insights into captive populations and contributes important resources to guide future management decisions of an endangered species.</p>
Fig. 2 in On the proper type designation for Camelina microcarpa, a wild relative and possible progenitor of the crop species C. sativa (Brassicaceae)
Fig. 2. – Isotype of Camelina microcarpa Andrz. ex DC. [KW, Besser herbarium: KW001003104; © National Herbarium of Ukraine, Kiev]
Fig. 1 in On the proper type designation for Camelina microcarpa, a wild relative and possible progenitor of the crop species C. sativa (Brassicaceae)
Fig. 1. – Isotype of Camelina microcarpa Andrz. ex DC. [KW, Besser herbarium: KW001003103; © National Herbarium of Ukraine, Kiev]
Figure 3 in Wild Relatives of the Eggplant (Solanum melongena L.: Solanaceae): New Understanding of Species Names in a Complex Group
Figure 3. Fruit shape and colour variation in cultivars of the common eggplant, Solanum melongena. Photograph taken by J. Prohens. doi:10.1371/journal.pone.0057039.g003
Figure 2. A in Wild Relatives of the Eggplant (Solanum melongena L.: Solanaceae): New Understanding of Species Names in a Complex Group
Figure 2. A sample of form and leaf variation in Solanum campylacanthum A.Rich. from across its morphological and geographical range showing the cline in leaf shape from south to north. A. Habit with narrow elliptic leaves. B. Habit with small leaves, small flowers, and dense curved prickles. C. Habit with ovate leaves and no prickles. D. Habit with large prickles and multiple fruits per infructescence. E. Habit with lobed leaves. F. Habit with cordate leaves. G. Short-stalked trichome from abaxial side of leaf. (Based on: A, Mott 11B, country; B, Gilfillan 6056, country; C, Torre 7145, Mozambique; D, Stewart E33, country; E, G, Friis et al. 8107, Ethiopia; F, Friis 8505, Ethiopia) Scale bar: A–F = 4 cm; G = 0.4 mm. Drawn by Lucy T. Smith. doi:10.1371/journal.pone.0057039.g002
Figure 1 in Wild Relatives of the Eggplant (Solanum melongena L.: Solanaceae): New Understanding of Species Names in a Complex Group
Figure 1. Representative flower and fruit morphology of eggplant and its wild relatives. A. Solanum campylacanthum inflorescences (Kenya - Vorontsova et al. 157); B. Solanum incanum immature fruit (Kenya – Vorontsova et al. 203); C. Solanum insanum fruit cross-section (China – Wang et al. 2047); D. Solanum insanum inflorescence with several hermaphrodite flowers (China – Wang et al. 2039); E. Solanum linnaeanum with yellow mature and mottled green immature fruit, note highly dissected leaves (Spain - Knapp IM-10096); F. Solanum melongena flower with duplicated parts (China – Wang et al. 2042). Photographs: A, B taken M.S. Vorontsova; C, D, E, F taken by S. Knapp. doi:10.1371/journal.pone.0057039.g001
VCF files of common grassland plants from wild collected seeds of 19 common European grassland species with up to 4 consecutive generations grown in monoculture for seed production for restoration
<p>A growing number of restoration projects require large amounts of seeds. As harvesting natural populations cannot cover the demand, wild plants are often propagated in large-scale monocultures. There are concerns that this cultivation process may cause genetic drift and unintended selection, which would alter the genetic properties of the cultivated populations and reduce their genetic diversity. Such changes could reduce the pre-existing adaptation of restored populations, and limit their adaptability to environmental change.</p> <p>We used single nucleotide polymorphism (SNP) markers and a pool-sequencing approach to test for genetic differentiation and changes in gene diversity during cultivation in 19 wild grassland species, comparing the source populations and up to four consecutive cultivation generations. We then linked the magnitudes of genetic changes to the species' breeding systems and seed dormancy, to understand the roles of these traits in genetic change.</p> <p>The propagation changed the genetic composition of the cultivated generations only moderately. The genetic differentiation we observed as a consequence of cultivation was much lower than the natural genetic differentiation between different source regions. The propagated generations harbored even higher gene diversity than wild-collected seeds. Genetic change was stronger in self-compatible than in self-incompatible species, probably as a result of increased outcrossing in the monocultures.</p> <p><em>Synthesis and applications</em>: Our study indicates that large-scale seed production maintains the genetic integrity of natural populations. Increased genetic diversity may be indicative of increased adaptive potential of propagated seeds, which would make them especially suitable for ecological restoration. Yet, it remains to be tested whether these patterns observed on the level of molecular markers will be mirrored also in plant phenotypes. Further, we used seeds produced in Germany and Austria, where the seed production is regulated and certified. Whether other seed production systems perform equally well remains to be tested.</p>
Dataset for paper titled: Conceptual preferences can be transmitted via selective social information use between competing wild bird species
<p><a name="_Hlk66629591"></a><span>Concept learning is considered a high-level adaptive ability. Thus far, it has been studied in laboratory via asocial trial and error learning. Yet, social information use is common among animals but it remains unknown whether concept learning by observing others occurs. We tested whether pied flycatchers (</span><em><span>Ficedula hypoleuca</span></em><span>) form conceptual relationships from the apparent choices of nest-site characteristics (geometric symbol attached to the nest box) of great tits (</span><em><span>Parus major</span></em><span>). Each wild flycatcher female (n = 124) observed one tit pair that exhibited an apparent preference for either a large or a small symbol and was then allowed to choose between two nest boxes with a large and a small symbol, but the symbol shape was different to that on the tit nest. Older flycatcher females were more likely to copy the symbol size preference of tits than yearling flycatcher females when there was a high number of visible eggs or a few partially visible eggs in the tit nest. However, this depended on the phenotype; copying switched to rejection as a function of increasing body size. Possibly the quality of and overlap in resource use with the tits affected flycatchers' decisions. Hence, our results suggest that conceptual preferences can be horizontally transmitted across co-existing animals, which may increase the performance of individuals that utilize concept learning abilities in their decision-making.</span></p>
Can disease resistance evolve independently at different ages? Genetic variation in age-dependent resistance to disease in three wild plant species
<p>1. Juveniles are typically less resistant (more susceptible) to infectious disease than adults, and this difference in susceptibility can help fuel the spread of pathogens in age-structured populations. However evolutionary explanations for this variation in resistance across age remain to be tested.</p> <p>2. One hypothesis is that natural selection has optimized resistance to peak at ages where disease exposure is greatest. A central assumption of this hypothesis is that hosts have the capacity to evolve resistance independently at different ages. This would mean that hosts populations have a) standing genetic variation in resistance at both juvenile and adult stages, and b) that this variation is not strongly correlated between age-classes so that selection acting at one age does not produce a correlated response at the other age</p> <p>3. Here we evaluated the capacity of three wild plant species (Silene latifolia, S. vulgaris, and Dianthus pavonius) to evolve resistance to their anther-smut pathogens (Microbotryum fungi), independently at different ages. The pathogen is pollinator-transmitted, and thus exposure risk is considered to be highest at the adult flowering stage.</p> <p>4. Within each species we grew families to different ages, inoculated individuals with anther smut, and evaluated the effects of age, family and their interaction on infection.</p> <p>5. In two of the plant species, S. latifolia and D. pavonius, resistance to smut at the juvenile stage was not correlated with resistance to smut at the adult stage. In all three species, we show there are significant age*family interaction effects, indicating that age-specificity of resistance varies among the plant families.</p> <p>6. Synthesis: These results indicate that different mechanisms likely underlie resistance at juvenile and adult stages and support the hypothesis that resistance can evolve independently in response to differing selection pressures as hosts age. Taken together our results provide new insight into the structure of genetic variation in age-dependent resistance in three well-studied wild host-pathogen systems.</p>
Fig. 1. Copelatus species. A – C in A new Copelatus with small eyes from the Eastern Cape Wild Coast, South Africa (Coleoptera: Dytiscidae)
Fig. 1. Copelatus species. A – C. mkambati sp. nov. holotype male habitus; B – C. mkambati sp. nov., paratype female habitus; C – C. macellus Guignot, 1950, holotype male habitus; D – C. macellus, holotype labels. Scale bar applies to A–C. Figs C & D: © MNHN/Christophe Rivier.
Fig. 3. Copelatus species male genitalia. A – C. macellus Guignot, 1950 in A new Copelatus with small eyes from the Eastern Cape Wild Coast, South Africa (Coleoptera: Dytiscidae)
Fig. 3. Copelatus species male genitalia. A – C. macellus Guignot, 1950, median lobe; B – C. basilewskyi Bilardo & Pederzani, 1979, median lobe; C – C. mkambati sp. nov., median lobe and paramere. Scale bar in C = 0.5 mm. Note that lines on the paramere represent musculature, not surface ridges. A & B after GඎංGඇඈඍ (1961) and Bංඅൺඋൽඈ & Pൾൽൾඋඓൺඇං (1979), respectively.
Fig. 1 in Tick (Acarina: Ixodidae) species and life stages collected from Arkansas wild pigs
Fig. 1. Locations of Arkansas wild pig traps where ticks were collected Feb 2019 to Jan 2020. Collection sites are labeled by county. Two traps in Crawford County, 2 traps in Polk County, and 2 traps in Scott County were close geographically and appear as 1 location.
Fig. 1 in Trichinella species circulating in wild boar (Sus scrofa) populations in Poland
Fig. 1. Example of electrophoretic patterns obtained from multiplex PCR on Trichinella larvae collected from wild boar. Lane 1 and 8 molecular weight marker (Fermentas 100 bp DNA Ladder); lanes 2 and 4, T. spiralis; lanes 3 and 5, T. britovi; lane 6, T. spiralis and T. britovi mixed infection; lane 7, negative control.
Fig. 2 in Hemoparasites in a wild primate: Infection patterns suggest interaction of Plasmodium and Babesia in a lemur species
Fig. 2. Age-dependence of Babesia sp. infections (grey) and Plasmodium sp. infections (black). The lines represent the predicted values according to the two different GLMMs.
Fig. 1 in Hemoparasites in a wild primate: Infection patterns suggest interaction of Plasmodium and Babesia in a lemur species
Fig. 1. Maximum likelihood tree of malaria parasite cytochrome b sequences (P. = Plasmodium). The clade formed by lemur malaria parasites is blue. The two sequences detected in this study are highlighted with grey rectangles. Bootstrap values are reported above branches when>50. The scale is in substitution per site.
Fig. 6 in Molecular identification of two Eimeria species, E. uekii and E. raichoi as type B, in wild Japanese rock ptarmigans, Lagopus muta japonica
Fig. 6. Histopathologic sections of ceca which were obtained from dead chicks infected with Eimeria spp. Arrowhead indicates macrogametocytes with a prominent wall-forming body (A), and arrows indicate zygotes or early oocysts, which are surrounded by an oocyst wall (A and B). Pathological lesions could not be observed because of severe degradation after death. Scale bars indicate 20 μm.
Fig. 3 in Molecular identification of two Eimeria species, E. uekii and E. raichoi as type B, in wild Japanese rock ptarmigans, Lagopus muta japonica
Fig. 3. Phylogram of E. uekii, type B, other Eimeria spp., and related parasites (Cyclospora spp.) inferred by the neighbor-joining method using partial 18S rRNA gene sequences. Accession numbers and derived hosts are shown in parentheses. Scale bar represents substitutions per nucleotide, and bootstrap values are indicated (> 1000). Cystoisospora spp. are used as an outgroup taxon.
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.