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.
8,819
datasets available to search
ShareScore release 0.9.0
Dataset results
8,819 results for “new data”
Data from: The early elasmobranch Phoebodus: phylogenetic relationships, ecomorphology, and a new time-scale for shark evolution
Anatomical knowledge of early chondrichthyans and estimates of their phylogeny are improving, but many taxa are still known only from microremains. The nearly cosmopolitan and regionally abundant Devonian genus Phoebodus has long been known solely from isolated teeth and fin spines. Here, we report the first skeletal remains of Phoebodus from the Famennian (Late Devonian) of the Maïder region of Morocco, revealing an anguilliform body, specialized braincase, hyoid arch, elongate jaws and rostrum, complementing its characteristic dentition and ctenacanth fin spines preceding both dorsal fins. Several of these features corroborate a likely close relationship with the Carboniferous species Thrinacodus gracia, and phylogenetic analysis places both taxa securely as members of the elasmobranch stem lineage. Identified as such, phoebodont teeth provide a plausible marker for range extension of the elasmobranchs into the Middle Devonian, thus providing a new minimum date for the origin of the chondrichthyan crown-group. Among pre-Carboniferous jawed vertebrates, the anguilliform body shape of Phoebodus is unprecedented, and its specialized anatomy is, in several respects, most easily compared with the modern frilled shark Chlamydoselachus. These results add greatly to the morphological, and by implication ecological, disparity of the earliest elasmobranchs.
Data from: Analysis of evolutionary relationships provides new clues to the origins of weedy rice
<p>Weedy rice (Oryza sativa f. spontanea) is considered to be a pest in modern rice production systems because it competes for resources, has poor yield characteristics, and subsequently has a negative effect on rice grain yield. The evolutionary relationships among weedy rice, landrace rice, improved rice cultivars, and wild rice are largely unknown. In this study, we conducted a population genetic analysis based on neutral markers and gene haplotypes in 524 rice accessions and a comparative transcriptomic analysis using 15 representative samples. The results showed that weedy rice populations have the highest level of genetic diversity (He=0.8386), and can be divided into two groups (japonica-type and indica-type). The japonica-type weedy rice accessions from HLJ, JL, LN, and NX provinces clustered with the landraces grown in these same provinces. The indica-types from JS province also clustered with the indica-type landraces from JS province. Comparative transcriptome analysis of weedy rice populations, improved rice populations. and landrace rice from HLJ, JL and LN provinces showed that the weedy rice still clustered with the landrace rice, and that the improved rice lines comprise a single population. Thirty-two differentially expressed genes were shared by the improved rice and landrace rice groups as well as between the improved rice and weedy rice groups. Using GO analysis, we identified 19 shared GO terms in the improved rice and landrace rice groups as well as between the improved rice and weedy rice groups. Our results suggest that weedy rice populations in China have diverse origins, and comparative transcriptome analysis of different types of rice from HLJ, JL, and LN suggests that improved rice populations have become a medium or end point in the evolution of weedy rice, which provides a new perspective for the study of weedy rice origins and lays a solid foundation for rice breeding.</p>
Data from: Descriptions of four new species of Minyomerus Horn, 1876 sec. Jansen & Franz, 2018 (Coleoptera: Curculionidae), with notes on their distribution and phylogeny
This contribution adopts the taxonomic concept approach, including the use of taxonomic concept labels (name sec. [according to] source) and region connection calculus-5 (RCC–5) articulations and alignments. Prior to this study, the broad-nosed weevil genus Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Curculionidae [non-focal]: Entiminae [non-focal]: Tanymecini [non-focal]) contained 17 species distributed throughout the desert and plains regions of North America. In this review of Minyomerus sec. Jansen & Franz, 2018, we describe the following four species as new to science: Minyomerus ampullaceus sec. Jansen & Franz, 2018 (henceforth: [JF2018]), new species, Minyomerus franko [JF2018], new species, Minyomerus sculptilis [JF2018], new species, and Minyomerus tylotos [JF2018], new species. The four new species are added to, and integrated with, the preceding revision, and an updated key and phylogeny of Minyomerus [JF2018] are presented. A cladistic analysis using 52 morphological characters of 26 terminal taxa (5/21 outgroup/ingroup) yielded a single most-parsimonious cladogram (Length = 99 steps, consistency index = 60, retention index = 80). The analysis reaffirms the monophyly of Minyomerus [JF2018] with eight unreversed synapomorphies. The species-group placements, possible biogeographic origins, and natural history of the new species are discussed in detail.
Data from: X-ray microtomography for ant taxonomy: an exploration and case study with two new Terataner (Hymenoptera, Formicidae, Myrmicinae) species from Madagascar
We explore the potential of x-ray micro computed tomography (μCT) for the field of ant taxonomy by using it to enhance the descriptions of two remarkable new species of the ant genus Terataner: T. balrog sp. n. and T. nymeria sp. n.. We provide an illustrated worker-based species identification key for all species found on Madagascar, as well as detailed taxonomic descriptions, which include diagnoses, discussions, measurements, natural history data, high-quality montage images and distribution maps for both new species. In addition to conventional morphological examination, we have used virtual reconstructions based on volumetric μCT scanning data for the species descriptions. We also include 3D PDFs, still images of virtual reconstructions, and 3D rotation videos for both holotype workers and one paratype queen. The complete μCT datasets have been made available online (Dryad, https://datadryad.org) and represent the first cybertypes in ants (and insects). We discuss the potential of μCT scanning and critically assess the usefulness of cybertypes for ant taxonomy.
Data from: Two new species of Parnassia (Celastraceae) from karst cave and Danxia landform in Southwest China
Two new species of Parnassia found in mountainous areas of Chongqing City, Southwest China, are described and illustrated: P. zhengyuanum M.X. Ren & J. Zhang and P. simianshanensis M.X. Ren, J. Zhang & Z.Y. Liu respectively. Parnassia zhengyuanum is found in a limestone cave near Mt. Jinfo, Nanchuan District, Chongqing City. This tiny plant has special spoon-shaped leaves and undivided staminodes with green apices. Parnassia simianshanensis was discovered in Mt. Simian, Jiangjin County, Chongqing City. This species grows along streams on red sandstones, i.e. in Danxia landform. It can be easily distinguished by its unique rhombic leaves and the five- or four-branched staminodes. The conservation status of P. zhengyuanum and P. simianshanensis are assessed respectively as 'Critically Endangered' (CR) and 'VU' (Vulnerable) according to IUCN criteria. The roles of karst and Danxia landforms in the speciation process are discussed.
Data from: Phylogenetic relationships among Old World Ruellia L.: a new classification and reinstatement of the genus Dinteracanthus Schinz
The genus Ruellia (Acanthaceae) consists of some ca. 350 species that are concentrated in tropical and subtropical regions of the world. Old World Ruellia have never been the focus of explicit phylogenetic study, yet comprise the earliest diverging lineages in the genus and contain upwards of 100 species. We sampled 52 accessions representing 29 OW species of Ruellia for phylogenetic analysis. Results yielded five clades that were strongly supported and marked by morphological synapomorphies. Analyses additionally recovered a newly recognized lineage within the tribe Ruellieae, a small radiation of plants in the deserts of Namibia and Angola, and the name Dinteracanthus is available for reinstatement. Divergence time analysis using a primary fossil calibration revealed relatively young estimates for crown ages of all five clades of OW Ruellia (2.5 Ma ‐ 630,000 ypb) as well as for Dinteracanthus (2.0 Ma). Ancestral state reconstruction of pollination systems among OW Ruellia suggest a minimum of two transitions from short-tongued insect pollination to nocturnal moth pollination, one from short-tongued insect to bird pollination, and one reversal from nocturnal moth pollination back to short-tongued insect pollination. We formally delimit the five clades of OW Ruellia as sections and present a key to aid in their identification: sect. Eusiphon, sect. Dipteracanthus, sect. Madagasikara, sect. Pseudoruellia, and sect. Discifolia. We provisionally treat 77 of 97 species of OW Ruellia among these five sections, with the remaining names considered to be unresolved.
Data from: Dietary responses of Sahul (Pleistocene Australia–New Guinea) megafauna to climate and environmental change
Throughout the late Quaternary, the Sahul (Pleistocene Australia–New Guinea) vertebrate fauna was dominated by a diversity of large mammals, birds, and reptiles, commonly referred to as megafauna. Since ca. 450–400Ka, approximately 88 species disappeared in Sahul, including kangaroos exceeding 200kg in size, wombat-like animals the size of hippopotamuses, flightless birds, and giant monitor lizards that were likely venomous. Ongoing debates over the primary cause of these extinctions have typically favored climate change or human activities. Improving our understanding of the population biology of extinct megafauna as more refined paleoenvironmental data sets become available will assist in identifying their potential vulnerabilities. Here, we apply a multiproxy approach to analyze fossil teeth from deposits dated to the middle and late Pleistocene at Cuddie Springs in southeastern Australia, assessing relative aridity via oxygen isotopes as well as vegetation and megafaunal diets using both carbon isotopes and dental microwear texture analyses. We report that the Cuddie Springs middle Pleistocene fauna was largely dominated by browsers, including consumers of C4 shrubs, but that by late Pleistocene times the C4 dietary component was markedly reduced. Our results suggest dietary restriction in more arid conditions. These dietary shifts are consistent with other independently derived isotopic data from eggshells and wombat teeth that also suggest a reduction in C4 vegetation after ~45 Ka in southeastern Australia, coincident with increasing aridification through the middle to late Pleistocene. Understanding the ecology of extinct species is important in clarifying the primary drivers of faunal extinction in Sahul. The results presented here highlight the potential impacts of aridification on marsupial megafauna. The trend to increasingly arid conditions through the middle to late Pleistocene (as identified in other paleoenvironmental records and now also observed, in part, in the Cuddie Springs sequence) may have stressed the most vulnerable animals, perhaps accelerating the decline of late Pleistocene megafauna in Australia.
Data from: A new null model approach to quantify performance and significance for ecological niche models of species distributions
Aim: Ecological niche modelling requires robust estimation of model performance and significance, but common evaluation approaches often yield biased estimates. Null models provide a solution but are rarely used in this field. We implemented an important modification to existing null-model tests, evaluating null models with the same withheld records that were used to evaluate the real model. We built and evaluated models across a range of modelling scenarios and for various performance measures using the algorithm Maxent and the monk parakeet (Myiopsitta monachus). Location: Native range in Southern America and global invasions predominantly in North/Central America and Europe Methods: We tested the ability of models built under 15 scenarios (five sets of calibration records and three settings that varied the level of model complexity) to predict spatially independent evaluation data in the invaded range (in effect, testing the models under spatial transfer). We quantified performance with measures of discriminatory ability and overfitting based on AUC and the omission error rate. We estimated null distributions of these measures and calculated effect size and significance. We determined how these estimates varied across modelling scenarios, comparing with two tests existing in the literature. Results: Performance varied starkly across modelling scenarios. As expected, the measures of overfitting agreed with each other and provided different information than that of discriminatory ability. However, high performance per se did not show strong association with high effect size and significance. Main Conclusions: Ecological niche models should be assessed with measures of effect size and significance based on appropriate null distributions, in contrast to several approaches existing in the literature. The proposed approach using independent evaluation data, implemented with our accompanying code, allows such estimates for either the same or a different region/time period, and it merits use and continued development.
Data from: Public questions spur the discovery of new bacterial species associated with lignin bioconversion of industrial waste
A citizen science project found that the greenhouse camel cricket (Diestrammena asynamora) is common in North American homes. Public response was to wonder "what good are they anyway?" and ecology and evolution guided the search for potential benefit. We predicted that camel crickets and similar household species would likely host bacteria with the ability to degrade recalcitrant carbon compounds. Lignocellulose is particularly relevant as it is difficult to degrade yet is an important feedstock for pulp and paper, chemical, and biofuel industries. We screened gut bacteria of greenhouse camel crickets and another household insect, a hide beetle (Dermestes maculatus) for the ability to grow on and degrade lignocellulose components as well as the lignocellulose-derived industrial waste product black liquor. From three greenhouse camel crickets and three hide beetles, 14 bacterial strains were identified capable of growth on lignocellulosic components, including lignin. Cedecea lapagei was selected for further study due to growth on most lignocellulose components. The C. lapagei secretome was identified using LC/MS/MS analysis. This work demonstrates a novel source of lignocellulose-degrading bacteria and introduces an effective workflow to identify bacterial enzymes for transforming industrial waste into value-added products. More generally, our research suggests the value of ecologically-guided discovery of novel organisms.
Data from: First discovery of the charophycean green alga Lychnothamnus barbatus (Charophyceae) extant in the New World
Premise of the study: Although some species of Characeae, known as stoneworts, can be found on every continent except Antarctica, many species and some genera have limited geographic distributions. The genus Lychnothamnus, represented by a single extant species L. barbatus, was known only from scattered localities in Europe and Australasia until it was recently discovered in North America. Methods: Morphological identifications were made from specimens collected in Minnesota and Wisconsin, U.S.A. DNA sequences were obtained for three plastid-encoded genes (atpB, psbC, rbcL) from seven putative Lychnothamnus samples from two states in the U.S.A. Distribution and abundance were estimated in each lake using point intercept surveys where surveyors sampled aquatic vegetation. Key results: Fourteen lakes in Wisconsin and two lakes in Minnesota, U.S.A., were found to harbor Lychnothamnus barbatus. These represent the first report of this rare charophycean extant in the New World. The North American specimens matched the morphological description for L. barbatus and were compared directly with the neotype. Phylogenetic results using three plastid-encoded genes confirmed the identification placing New World samples with those from Europe and Australasia. Our phylogenetic analyses also confirmed the sister relationship between L. barbatus and Nitellopsis obtusa. Conclusions: Because this taxon is not known for aggressive invasiveness in its native range, it may have existed in heretofore-undiscovered native populations, although the possibility that it is a recent introduction cannot be eliminated. The potential for discovery of novel lineages of green algae in even well studied regions is apparently far from exhausted.
Data from: Transcriptomic differences between day and night in Acropora millepora provide new insights into metabolite exchange and light-enhanced calcification in corals
The evolutionary success of reef-building corals is often attributed to their symbiotic relationship with photosynthetic dinoflagellates of the genus Symbiodinium, but metabolic interactions between the partners and the molecular bases of light-enhanced calcification (LEC) are not well understood. Here, the metabolic bases of the interaction between the coral Acropora millepora and its dinoflagellate symbiont were investigated by comparing gene expression levels under light and dark conditions at the whole transcriptome level. Among the 497 differentially expressed genes identified, a suite of genes involved in cholesterol transport was found to be upregulated under light conditions, confirming the significance of this compound in the coral symbiosis. Although ion transporters likely to have roles in calcification were not differentially expressed in this study, expression levels of many genes associated with skeletal organic matrix composition and organization were higher in light conditions. This implies that the rate of organic matrix synthesis is one factor limiting calcification at night. Thus, LEC during the day is likely to be a consequence of increases in both matrix synthesis and the supply of precursor molecules as a result of photosynthetic activity.
Data from: A worldwide molecular phylogeny provides new insight on cryptic diversity within the moonworts (Botrychium s. s., Ophioglossaceae)
The moonwort genus, Botrychium s. s., includes diploid and polyploid taxa that occur primarily in the northern hemisphere. Their evolutionary history, morphologically cryptic taxa and deep divergence of the family in the phylogeny of ferns has long fascinated pteridologists. Previous molecular studies did not include a complete taxonomic sampling of the taxa in the genus, nor multiple specimens from throughout the known geographical range of each taxon. Therefore, to investigate evolutionary relationships of the major clades of Botrychium s. s., we increased both taxonomic representativeness (multiple accessions per taxa), as well as phylogenetic resolution by including additional new chloroplast markers. To confirm identification and provide evidence from both maternal and paternal parentage of allopolyploids, we also included specimens that have been characterized by allozyme profiles determined by electrophoretic analysis of 20 nuclear enzyme loci for each taxon. We analyzed four chloroplast regions (matK intron, trnHGUG —psbA, andtrnLUAA —trnFGAA intergenic spacers, and rpL16 intron region) of 365 specimens fromAsia, Europe, North America, Oceania, and South America, sampling the geographical range of 34 of 35 accepted Botrychium s. s. taxa and thirteen putatively new taxa. We conducted a phylogenetic analysis of maternal lineages based on 2,385 aligned nucleotides using maximum likelihood and Bayesian inference to explore genetic diversity and phylogenetic relationships among taxa. We found strong support for themonophyly of three major clades: Lanceolatum, Lunaria, and Simplex-Campestre, and resolved 15 subclades. Our results suggest multiple origins for at least four polyploid taxa (B. boreale, B. michiganense, B. yaaxudakeit, and B. watertonense). The Simplex-Campestre clade had the largest number of species, despite having a similar total number of haplotypes as the Lunaria clade (62 and 59, respectively), which has the broadest worldwide distribution. In total, our new molecular phylogeny comprises 47 taxa, of which thirteen are discussed for possible taxonomic recognition.
Data from: Explaining global variation in the latitudinal diversity gradient: meta-analysis confirms known patterns and uncovers new ones
Aim: The pattern of increasing biological diversity from high latitudes to the equator [latitudinal diversity gradient (LDG)] has been recognized for > 200 years. Empirical studies have documented this pattern across many different organisms and locations. Our goal was to quantify the evidence for the global LDG and the associated spatial, taxonomic and environmental factors. We performed a meta-analysis on a large number of individual LDGs that have been published in the 14 years since Hillebrand's ground-breaking meta-analysis of the LDG, using meta-analysis and meta-regression approaches largely new to the fields of ecology and biogeography. Location: Global. Time period: January 2003–September 2015. Major taxa studied: Bacteria, protists, plants, fungi and animals. Methods: We synthesized the outcomes of 389 individual cases of LDGs from 199 papers published since 2003, using hierarchical mixed-effects meta-analysis and multiple meta-regression. Additionally, we re-analysed Hillebrand's original dataset using modern methods. Results: We confirmed the generality of the LDG, but found the pattern to be weaker than was found in Hillebrand's study. We identified previously unreported variation in LDG strength and slope across longitude, with evidence that the LDG is strongest in the Western Hemisphere. Locational characteristics, such as habitat and latitude range, contributed significantly to LDG strength, whereas organismal characteristics, including taxonomic group and trophic level, did not. Modern meta-analytical models that incorporate hierarchical structure led to more conservative and sometimes contrasting effect size estimates relative to Hillebrand's initial analysis, whereas meta-regression revealed underlying patterns in Hillebrand's dataset that were not apparent with a traditional analysis. Main conclusions: We present evidence of global latitudinal, longitudinal and habitat-based patterns in the LDG, which are apparent across both marine and terrestrial realms and over a broad taxonomic range of organisms, from bacteria to plants and vertebrates.
Research data supporting "Raman spectroscopy reveals new insights into the zonal organization of native and tissue-engineered articular cartilage"
<p>This file contains the raw research data supporting the publication above.</p>
Figure 15. from: New records of Ichneumonidae (Hymenoptera) for the Italian fauna - Biodiversity Data Journal 3: e5057 (19 June 2015) https://doi.org/10.3897/BDJ.3.e5057
Figure 15. - Poemeniacollaris (Haupt, 1917), female.
Figure 14. from: New records of Ichneumonidae (Hymenoptera) for the Italian fauna - Biodiversity Data Journal 3: e5057 (19 June 2015) https://doi.org/10.3897/BDJ.3.e5057
Figure 14. - Zatypotapicticollis (Thomson, 1888), female.
Figure 11. from: New records of Ichneumonidae (Hymenoptera) for the Italian fauna - Biodiversity Data Journal 3: e5057 (19 June 2015) https://doi.org/10.3897/BDJ.3.e5057
Figure 11. - Dicaelotus (Dicaelotus) morosator Aubert, 1969, male.
Figure 9. from: New records of Ichneumonidae (Hymenoptera) for the Italian fauna - Biodiversity Data Journal 3: e5057 (19 June 2015) https://doi.org/10.3897/BDJ.3.e5057
Figure 9. - Mesoleiustibiator Kasparyan, 2000, female.
Figure 13. from: New records of Ichneumonidae (Hymenoptera) for the Italian fauna - Biodiversity Data Journal 3: e5057 (19 June 2015) https://doi.org/10.3897/BDJ.3.e5057
Figure 13. - Lycorinatriangulifera Holmgren, 1859, male.
Figure 4. from: New records of Ichneumonidae (Hymenoptera) for the Italian fauna - Biodiversity Data Journal 3: e5057 (19 June 2015) https://doi.org/10.3897/BDJ.3.e5057
Figure 4. - Baranisobashibericus Heinrich, 1972, female habitus.
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.