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.
1,073
datasets available to search
ShareScore release 0.9.0
Dataset results
1,073 results for “taxon”
Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul
Background: Tree squirrels (Sciuridae, Sciurini), in particular the highly diverse Neotropical lineages, are amongst the most rapidly diversifying branches of the mammal tree of life but also some of the least known. Negligence of this group by phylogeneticists is likely a product of the scarcity or unavailability of fresh tissue samples for DNA sequencing. Lack of comprehensive phylogenies result in highly discrepant taxonomic arrangements that are based exclusively on morphological data—impressively, these are the only classification schemes available for the group. Here we used high-throughput sequencing and an unprecedented sampling effort of museum specimens to provide the first comprehensive phylogenetic analysis of tree squirrels, with a special emphasis on Neotropical taxa. Results: We gathered mitochondrial genome data from 232 modern and historical samples, representing 40 out of the 43 currently recognized species of Sciurini. We found no correlation between specimen age and completeness of mitogenomes recovered for historical samples. Our phylogenetic analyses—performed with datasets differing on levels of missing data and taxa under distinctanalytical methods— strongly support the monophyly of Sciurini and consistently recovered 12 major clades within the tribe. We found evidence that the diversity of Neotropical tree squirrels is underestimated, with at least seven lineages that might represent taxa to be named or revalidated. Ancestral state reconstructions of number of upper premolars and number of pairs of mammae indicated that alternative conditions of both characters must have evolved multiple times along the evolutionary history of tree squirrels. Conclusions: We were able to obtain complete mitogenomes for samples as old as 120 years, reinforcing the potential of historical samples for phylogenetic and evolutionary inferences of elusive lineages of the tree of life. None of the taxonomic arrangements ever proposed for tree squirrels fully corresponded to our phylogenetic reconstruction, with only a few of the currently recognized genera recovered as monophyletic. By investigating the evolution of two morphological traits widely employed in the taxonomy of the group, we revealed that their homoplastic nature can help to explain the incongruence between phylogenetic results and classification schemes presented so far, and we recommend a substantial taxonomic overhaul.
Comparative population genetics of the federally endangered Relict Darter, and its sister taxon the Clarks Darter (Teleostei: Percidae)
<p><span>The southeastern United States harbors one of the most diverse temperate freshwater fish faunas of the world. Unfortunately, due to improper land use practices and habitat degradation, many of the species in this region are imperiled and may become extinct without appropriate conservation efforts. This study examined the population dynamics of an endangered endemic darter of southwest Kentucky, the Relict Darter (</span><span>Etheostoma chienense</span><span>) and its sister taxon, the undescribed Clarks Darter (</span><span>Etheostoma </span><span>cf. </span><span>oophylax</span><span>). Mitochondrial sequence data coupled with SNP data were used to infer population structure, gene flow, genetic variation, and effective population sizes of both species. The results from this study, based on 160 individuals from nine localities, indicate that the endangered Relict Darter possesses limited genetic variation based on mitochondrial DNA haplotypes (N=4). In addition, SNP data (6.8k markers) further indicates limited genetic structure (K=1), as well as a low effective population size (143-918), suggesting that the Relict Darter can be managed as a single, panmictic conservation unit. It is suggested that conservation efforts be taken to protect remaining habitats, augment the system with artificial spawning substrates, and, as a last resort (if needed), supplement the natural population with captive reared individuals. </span><span>Ethesotoma </span><span>cf. </span><span>oophylax </span><span>showed some genetic variation among distant sites, but more samples are needed throughout the range in order to fully understand the population dynamics of this species.</span></p>
Taxon pulse dynamics, episodic dispersal, and host colonization across Beringia drive diversification of a holarctic tapeworm assemblage
Aim: We test the predictions of the Stockholm Paradigm, a synthesis of eco-evolutionary theory explaining the nature of faunal assembly, host range and parasite diversification. Faunal diversification and assembly, manifested in patterns of host colonization, co-adaptation and parasite speciation, is predicted to emerge as a consequence of alternating episodes of ecological disruption and stability. Specifically, for a diverse cestode genus (Arostrilepis), we evaluate the number and direction of Pleistocene dispersal events across Beringia, the number and relative timing of host colonization events, and the relationship between host and parasite biogeographic histories and associations through time. Location: Beringia and adjacent temperate to arctic biomes in North America and Eurasia. Taxon: Arostrilepis (Cyclophyllidea: Hymenolepididae) and its rodent hosts. Methods: Multi-locus phylogenetic reconstruction and biogeographic ancestral range estimation. Results: Arostrilepis lineages crossed Beringia eastward into North America a minimum of four times and westward into Asia twice in association with temporally disjunct geographic expansions of three major tribes of cricetid rodents (Arvicolini, Myodini, Lemmini). Inferences of ancestral host associations support at least nine instances of host-colonization involving shifts from one rodent tribe or family to another. Several previously unrecognized lineages of Arostrilepis are revealed. Main conclusions: Consistent with expectations of the Stockholm Paradigm, episodes of intercontinental dispersal were both frequent in the history of Arostrilepis and preceded a majority of inferred host-colonization events. Events of historical geographic expansion created numerous opportunities for development of novel host-parasite associations through ecological fitting, as parasites tracked historically conserved resources available across diverse host taxa. Beringia played a major role in shaping rodent/parasite assemblages by mediating dispersal between the northern continents during glacial episodes of the Pleistocene, rather than by serving as a zone of refugial isolation.
FIGURE 3 in Apennocoris pilosulus: rediscovery of a forgotten big-eyed bug taxon from New Caledonia (Heteroptera: Lygaeoidea: Geocoridae)
FIGURE 3. Details of Apennocoris pilosulus, macropterous male: A. labial trough, B. metapleurite with structures of metathoracic scent efferent apparatus (indicated with red arrow), C. detail of thorax and abdomen in lateral view with dorsal setosity. (scale bar: 1 mm).
FIGURE 2. Apennocoris pilosulus Montandon, 1907 in Apennocoris pilosulus: rediscovery of a forgotten big-eyed bug taxon from New Caledonia (Heteroptera: Lygaeoidea: Geocoridae)
FIGURE 2. Apennocoris pilosulus Montandon, 1907, macropterous male (MNHN): A. dorsal habitus, B. lateral view (scale bar: 1 mm).
FIGURE 1. Apennocoris pilosulus Montandon, 1907 in Apennocoris pilosulus: rediscovery of a forgotten big-eyed bug taxon from New Caledonia (Heteroptera: Lygaeoidea: Geocoridae)
FIGURE 1. Apennocoris pilosulus Montandon, 1907, coleopterous female (lectotype, KNHM): A. dorsal habitus, B. lateral view, C. labels (scale bar: 1 mm).
FIGURE 4. Stylogeocoris biroi Montandon, 1913 in Apennocoris pilosulus: rediscovery of a forgotten big-eyed bug taxon from New Caledonia (Heteroptera: Lygaeoidea: Geocoridae)
FIGURE 4. Stylogeocoris biroi Montandon, 1913 (lectotype, HNHM): A. dorsal habitus, B. labels, C. Thoracic pleurites, with metathoracic scent efferent apparatus (indicated with red arrow) (scale bar: 1 mm).
Data from: Comparison of taxon-specific versus general locus sets for targeted sequence capture for plant phylogenomics
Premise of the study: Targeted sequence capture can be used to efficiently gather sequence data for large numbers of loci, such as single-copy nuclear loci. Most published studies in plants have used taxon-specific locus sets developed individually for a clade using multiple genomic and transcriptomic resources. General locus sets can also be developed from loci that have been identified as single-copy and having orthologs in large clades of plants. Methods: We identify and compare a taxon-specific locus set and three general locus sets (COSII, APVO SSC, PPR) for targeted sequence capture in Buddleja (Scrophulariaceae) and outgroups. We evaluate their performance in terms of assembly success, sequence variability, and resolution and support of inferred phylogenetic trees. Results: The taxon-specific locus set had the most target loci. Assembly success was high for all locus sets in Buddleja samples. For outgroups, general locus sets had greater assembly success. Taxon-specific and PPR loci had the highest average variability. The taxon-specific dataset produced the best supported tree, but all datasets showed improved resolution over previous non-sequence capture datasets. Discussion: General loci can be a useful source of sequence capture targets, especially if multiple genomic resources are not available for a taxon.
Data from: Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes.
Rodentia is the largest order of placental mammals, with approximately 2,050 species divided into 28 families. It is also one of the most controversial with respect to its monophyly, relationships between families, and divergence dates. Here, we have analyzed and compared the performance of three nuclear genes (von Willebrand Factor, interphotoreceptor retinoid-binding protein, and Alpha 2B adrenergic receptor) for a large taxonomic sampling, covering the whole rodent and placental diversity. The phylogenetic results significantly support rodent monophyly, the association of Rodentia with Lagomorpha (the Glires clade), and a Glires + Euarchonta (Primates, Dermoptera, and Scandentia) clade. The resolution of relationships among rodents is also greatly improved. The currently recognized families are divided here into seven well-defined clades (Anomaluromorpha, Castoridae, Ctenohystrica, Geomyoidea, Gliridae, Myodonta, and Sciuroidea) that can be grouped into three major clades: Ctenohystrica, Gliridae + Sciuroidea, and a mouse-related clade (Anomaluromorpha, Castoridae + Geomyoidea, and Myodonta). Molecular datings based on these three genes suggest that the rodent radiation took place at the transition between Paleocene and Eocene. The divergence between rodents and lagomorphs is placed just at the K-T boundary and the first splits among placentals in the Late Cretaceous. Our results thus tend to reconcile molecular and morphological-paleontological insights.
Data from: Experimental N and P additions alter stream macroinvertebrate community composition via taxon‐level responses to shifts in detrital resource stoichiometry
1. Increases in nitrogen (N) and phosphorus (P) availability are changing animal communities, partly by altering stoichiometric imbalances between consumers and their food. Testing relationships between resource stoichiometry and consumer assemblage structure requires ecosystem-level manipulations that have been lacking to date. 2. We analyzed patterns of macroinvertebrate community composition in five detritus-based headwater streams subject to experimental whole-stream N and P additions that spanned a steep gradient in dissolved N:P ratio (2:1, 8:1, 16:1, 32:1, 128:1) over two years, following a one-year pre-treatment period. 3. We predicted that shifts in leaf litter stoichiometry would drive overall patterns of community composition via greater responses of shredders to enrichment than other taxa, as shredders dominate primary consumer biomass and experience larger consumer-resource elemental imbalances than other functional groups in stream ecosystems. Specifically, we expected litter C:P to be a significant predictor of shredder biomass given the greater relative imbalances between shredder and litter C:P than C:N. Finally, we tested whether shredder responses to enrichment were related to other taxon-level traits, including body size and stoichiometry, larval lifespan and growth rate. 4. Whole-community composition shifted similarly across the five streams after enrichment, largely driven by increased shredder and predator biomass. These shifts were limited to the autumn/winter seasons and related to decreased leaf litter C:P, highlighting important links between the quality of seasonal litter subsidies and community phenology. 5. Among 10 taxa that drove structural shifts, two declined while other taxa from the same functional/taxonomic groups responded positively, suggesting that specific life-history traits may determine sensitivity to enrichment. 6. Increases in total shredder biomass, and in biomass of several common shredders, were associated with lower litter C:P. Body C:P did not predict shredder response to enrichment. However, weak negative relationships between shredder response and body size, and larval lifespan, suggest that small-bodied and short-lived taxa may be more responsive to shifting resource stoichiometry. 7. Moderate anthropogenic increases in N and P availability affect resource stoichiometry and can alter animal communities, influencing additional food-web and ecosystem properties. We provide support for ecological stoichiometry as a framework for predicting such outcomes based on changes in the elemental composition of resource pools.
Data from: Towards resolving and redefining Amphipyrinae (Lepidoptera, Noctuoidea, Noctuidae): a massively polyphyletic taxon
Amphipyrinae have long been a catchall taxon for Noctuidae, with most members lacking discernible morphological synapomorphies that would allow their assignment to one of the many readily diagnosable noctuid subfamilies. Here data from seven gene regions (>5,500 base pairs) for more than 120 noctuid genera are used to infer a phylogeny for Amphipyrinae and related subfamilies. Sequence data for 57 amphipyrine genera—most represented by the type species of the genus—are examined. Presented here are: the first large-scale molecular phylogenetic study of Amphipyrinae and largest molecular phylogeny of Noctuidae to date; several proposed nomenclatural changes for well supported results; and the identification of areas of noctuid phylogeny where greater taxon sampling and/or genomic-scale data are needed. Adult and larval morphology, along with life history traits, for taxonomic groupings most relevant to the results are discussed. Amphipyrinae are significantly redefined; many former amphipyrines, excluded as a result of these analyses, are reassigned to other noctuid subfamily-level taxa. Four genera, Chamaeclea Grote, Heminocloa Barnes & Benjamin, Hemioslaria Barnes & Benjamin, and Thurberiphaga Dyar are transferred to the tribe Chamaecleini Keegan & Wagner New Tribe in Acontiinae. Stiriina is elevated to Stiriinae Revised Status, Grotellina is elevated to Grotellinae Revised Status, and Annaphilina is elevated to Annaphilini Revised Status. Acopa Harvey is transferred to Bryophilinae, Aleptina Dyar is transferred to Condicinae, Leucocnemis Hampson and Oxycnemis gracillinea (Grote) are transferred to Oncocnemidinae, Nacopa Barnes & Benjamin is transferred to Noctuinae, and Narthecophora Smith is transferred to Stiriinae. Azenia Grote (and its subtribe Azeniina), Cropia Walker, Metaponpneumata Möschler, Sexserrata Barnes & Benjamin, and Tristyla Smith are transferred to Noctuidae incertae sedis. Hemigrotella Barnes & McDunnough (formerly in subtribe Grotellina) is retained in Amphipyrinae.
Data from: A new taxon of cistecephalid dicynodont from the upper Permian Kundaram Formation of India
A new cistecephalid dicynodont, Sauroscaptor tharavati gen. et sp. nov., is described from the upper Permian Kundaram Formation of India. This taxon is represented by specimens formerly referred to the African dicynodont genera Cistecephalus and Emydops. Sauroscaptor can be distinguished from other cistecephalids by the extremely posterior position of the pineal foramen (overhanging the edge of the occiput), bipartite nuchal crest, and relatively narrow skull roof. The recognition of Sauroscaptor as a distinct cistecephalid taxon adds to the increasing evidence for high levels of basinal endemism in this family. However, dicynodont biogeographical patterns are complex, and there is no simple relationship between inferred dispersal ability based on body size and levels of endemicity within clades.
Data from: Revision of the genus Anasibirites Mojsisovics (Ammonoidea): an iconic and cosmopolitan taxon of the late Smithian (Early Triassic) extinction
The family Prionitidae Hyatt represents a major component of ammonoid faunas during the Smithian (Early Triassic), and the genus Anasibirites Mojsisovics is the most emblematic taxon of this family. Its stratigraphical range is restricted to the beginning of the late Smithian (Wasatchites distractus Zone). The genus is also characterized by an unusual cosmopolitan distribution, thus contrasting with most earlier Smithian ammonoid distributions that were typically restricted by latitude. Because the late Smithian witnessed an extinction of the nekton (e.g. ammonoids, conodonts) whose amplitude is equal to or larger than that of the end-Permian crisis, the number of valid species that should be included in the genus Anasibirites becomes a highly relevant question when addressing this extinction at the highest possible taxonomic resolution. Based on a new extensive collection from Timor, the composition of the genus Anasibirites is herein revised with respect to its intraspecific and ontogenetic variations. Comprehensive morphological and biometric studies (c. 950 measured specimens) indicate that, of the c. 60 available species names, only two are valid, namely A. kingianus (Waagen) and A. multiformis Welter. Continuous ranges of intraspecific variation enable us to synonymize A. nevolini Zakharov, 1968 and A. angulosus (Waagen) with A. kingianus. The contribution of Anasibirites to species diversity during the late Smithian extinction is thus significantly less than previously estimated, therefore accentuating the severity of this event.
Data from: Molecular profiling of diatom assemblages in tropical lake sediments using taxon-specific PCR and Denaturing High-Performance Liquid Chromatography (PCR-DHPLC)
Here we present a protocol to genetically detect diatoms in sediments of the Kenyan tropical Lake Naivasha, based on taxon-specific PCR amplification of short fragments (approx. 100 bp) of the small subunit ribosomal (SSU) gene and subsequent separation of species-specific PCR products by PCR-based DHPLC. An evaluation of amplicons differing in primer specificity to diatoms and length of the fragments amplified demonstrated that the number of different diatom sequence types detected after cloning of the PCR products critically depended on the specificity of the primers to diatoms and the length of the amplified fragments whereby shorter fragments yielded more species of diatoms. The DHPLC was able to discriminate between very short amplicons based on the sequence difference, even if the fragments were of identical length. and if the amplicons differed only in a small number of nucleotides. Generally the method identified the dominant sequence types from mixed amplifications. A comparison with microscopic analysis of the sediment samples revealed that the sequence types identified in the molecular assessment corresponded well with the most dominant species. In summary, the PCR-based DHPLC protocol offers a fast, reliable, and cost-efficient possibility to study DNA from sediments and other environmental samples with unknown organismic content, even for very short DNA fragments.
Data from: Extensive yellow crusts below limestone overhangs: a new taxon close to a minute epiphytic lichen
A conspicuous yellow crust forming extensive covers on some dry and shaded limestone rocks in Europe is described here as Caloplaca substerilis subsp. orbicularis M. Haji Moniri, Vondrák & Malíček subsp. nov. Based on nuITS rDNA, 28S nuLSU rDNA and mtSSU rDNA sequence data, the new taxon is closely related to Caloplaca sterilis and C. ulcerosa. The three taxa form a supported clade in the subfamily Xanthorioideae (Teloschistaceae), but none of the recent genera are suitable for them. In the ITS phylogeny, the new taxon forms a monophylum nested within C. substerilis. Its extensive yellow thalli and absence of vegetative diaspores clearly distinguish it from Caloplaca substerilis (subsp. substerilis). Indeed, if it had not been for the molecular evidence, we would have described it at the rank of species. We suggest that the substrate switch and accompanying processes are responsible for the striking phenotype difference between Caloplaca substerilis subsp. substerilis and C. substerilis subsp. orbicularis.
Data from: Beyond surrogacy: A multi-taxon approach to conservation biogeography
Biogeographic analysis of species turnover (β diversity) of plants and animals among regions often yields conflicting results, with regions of high β diversity identified for some taxonomic groups but not others. Such discordance calls into question use of surrogate taxa to forge conservation plans. This discordance begs for a means of comparing multiple taxa across phyla in a manner that is cost-effective, considers limitations in computer resources in certain global regions, and is understood by policy makers and land managers. As a test case for a method taking into account these considerations, we used species lists for ten organismal groups (spanning plants, vertebrates, and invertebrates) to identify regions of high β diversity using Monmonier's algorithm, a spatially explicit technique that is readily implemented and interpreted. Data were for montane (>1000 m elevation) species across the Eastern Arc of Tanzania and Kenya and surrounding areas. Our results indicate that surrogacy does not make for the most effective expenditure of conservation efforts. We also show that to use a multi-taxon approach one need not to rely on intensive surveys of areas in order to make conservation decisions, including reserve selection. Our approach also eliminates the need for complex modeling and comparisons common to many GIS-based complementarity techniques. Additionally, a wide variety of socioeconomic, political, demographic, geological, climatological, and evolutionary factors can be incorporated into the technique to help shape conservation biogeography from a local and regional perspective. This technique can bridge the gap between conservation biogeography theory and application in tropical regions and beyond.
Data from: The indicator side of tree microhabitats: a multi-taxon approach based on bats, birds and saproxylic beetles
1. National and international forest biodiversity assessments largely rely on indirect indicators, based on elements of forest structure that are used as surrogates for species diversity. These proxies are reputedly easier and cheaper to assess than biodiversity. Tree microhabitats – tree-borne singularities such as cavities, conks of fungi or bark characteristics – have gained attention as potential forest biodiversity indicators. However, as with most biodiversity indicators, there is a lack of scientific evidence documenting their quantitative link with the biodiversity they are supposed to assess. 2. We explored the link between microhabitat indices and the richness and abundance of three taxonomic groups: bats, birds, and saproxylic beetles. Using a nation-wide multi-taxon sampling design in France, we compared 213 plots located inside and outside strict forest reserves. We hypothesized that the positive effect setting aside forest reserves has on biodiversity conservation is indirectly due to an increase in the proportion of large structural elements (e.g. living trees, standing and lying deadwood). These, in turn, are likely to favour the quantity and diversity of microhabitats. We analysed the relationship between the abundance and species richness of different groups and guilds (e.g. red-listed species, forest specialists, cavity dwellers) and microhabitat density and diversity. We then used confirmatory structural equation models to assess the direct and indirect effects of management abandonment, large structural elements and microhabitats on the biodiversity of the target species. 3. For several groups of birds and bats, the indirect effect of management abandonment and large structural elements on biodiversity was mediated by microhabitats. However, the magnitude of the link between microhabitat indices and biodiversity was moderate. In particular, saproxylic beetles' biodiversity was poorly explained by microhabitats, large structural elements or management abandonment. 4. Synthesis and applications: Tree microhabitats may serve as indicators for bats and birds, but they are not a universal biodiversity indicator. Rather, compared to large structural elements, they most likely have a complementary role to biodiversity. In terms of forest management and conservation, preserving diversity of microhabitats at the local scale benefits several groups of both bats and birds.
Data from: The arrangement of possible muscle fibres in the Ediacaran taxon Haootia quadriformis
Haootia quadriformis from Newfoundland, Canada, is one of the most unusual impressions of a soft-bodied macro-organism yet described from the late Ediacaran Period. Interpreted as a metazoan of cnidarian grade, the body impression of H. quadriformis possesses features interpreted as fibrous structures that represent possible evidence for muscular tissue. Evidence both in support of and against a relationship between H. quadriformis and the Staurozoa, one of the cnidarian groups to which Haootia was compared in Liu et al., is outlined by Miranda et al.. Our intention in our original paper was to illustrate the staurozoan body plan for comparative purposes, rather than suggest homology or direct ancestry. Nevertheless, fresh insights from workers with expertise in the biology of extant cnidarians are welcomed.
Data from: Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): testing for key innovation with incomplete taxon sampling
Replicate radiations provide powerful comparative systems to address questions about the interplay between opportunity and innovation in driving episodes of diversification and the factors limiting their subsequent progression. However, such systems have been rarely documented at intercontinental scales. Here, we evaluate the hypothesis of multiple radiations in the genus Lupinus (Leguminosae), which exhibits some of the highest known rates of net diversification in plants. Given that incomplete taxon sampling, background extinction, and lineage-specific variation in diversification rates can confound macroevolutionary inferences regarding the timing and mechanisms of cladogenesis, we used Bayesian relaxed clock phylogenetic analyses as well as MEDUSA and BiSSE birth–death likelihood models of diversification, to evaluate the evolutionary patterns of lineage accumulation in Lupinus. We identified 3 significant shifts to increased rates of net diversification (r) relative to background levels in the genus (r = 0.18–0.48 lineages/myr). The primary shift occurred approximately 4.6 Ma (r = 0.48–1.76) in the montane regions of western North America, followed by a secondary shift approximately 2.7 Ma (r = 0.89–3.33) associated with range expansion and diversification of allopatrically distributed sister clades in the Mexican highlands and Andes. We also recovered evidence for a third independent shift approximately 6.5 Ma at the base of a lower elevation eastern South American grassland and campo rupestre clade (r = 0.36–1.33). Bayesian ancestral state reconstructions and BiSSE likelihood analyses of correlated diversification indicated that increased rates of speciation are strongly associated with the derived evolution of perennial life history and invasion of montane ecosystems. Although we currently lack hard evidence for "replicate adaptive radiations" in the sense of convergent morphological and ecological trajectories among species in different clades, these results are consistent with the hypothesis that iteroparity functioned as an adaptive key innovation, providing a mechanism for range expansion and rapid divergence in upper elevation regions across much of the New World.
FIGURE 2 in Salamandridae) using molecular and morphological data. Revalidation of the taxon Pleurodeles nebulosus (Guichenot, 1850)
FIGURE 2. Schematic drawing showing all eight morphometric measurements used in the present study. SVL—snoutvent length; TL—tail length; Sp3T—right hind limb shank length; 3T—right hand third toe length; AL—length of the anterior right arm; HW—head width; IOW— interorbital width; HL—head length.
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.