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591 results for “phylogenomic data”
Data from: Forget-me-not phylogenomics: Improving the resolution and taxonomy of a rapid island and mountain radiation in Aotearoa New Zealand (Myosotis; Boraginaceae)
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Data from: Phylogenomics resolves key relationships in Rumex and uncovers a dynamic history of independently evolving sex chromosomes
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Data for: Phylogenomics and historical biogeography of Hydrangeeae (Hydrangeaceae) elucidate the effects of geologic and climatic dynamics on diversification
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Data from: A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses
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Data from: Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus)
<p>Gene flow between evolutionarily distinct lineages is increasingly recognized as a common occurrence. Such processes distort our ability to diagnose and delimit species, as well as confound attempts to estimate phylogenetic relationships. A conspicuous example is Dusky Salamanders (<i>Desmognathus</i>), a common model-system for ecology, evolution, and behavior. Only 22 species are described; 7 in the last 40 years. However, mitochondrial datasets indicate the presence of up to 45 "candidate species" presenting a complex history of reticulation. Some authors have even suggested that the search for species boundaries in the group may be in vain. Here, we analyze nuclear and mitochondrial data containing 161 individuals from at least 49 distinct evolutionary lineages that we treat as candidate species. Concatenated and species-tree methods fail to provide satisfactory resolution for relationships among these taxa. Comparing topologies and applying methods for estimating phylogenetic networks, we find strong support for numerous instances of hybridization throughout the history of the group. We suggest that these processes may be more common than previously thought across the phylogeography-phylogenetics continuum, and that while the search for species boundaries in <i>Desmognathus</i> may not be in vain, it will be complicated by factors such as crypsis, parallelism, and gene-flow.</p>
Data from: The origin of the legumes is a complex paleopolyploid phylogenomic tangle closely associated with the Cretaceous-Paleogene (K-Pg) mass extinction event
The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic.
Data from: Parallel evolution of bower-building behavior in two groups of bowerbirds suggested by phylogenomics
<p>The bowerbirds in New Guinea and Australia include species that build the largest and perhaps most elaborately decorated constructions outside of humans. The males use these courtship bowers, along with their displays, to attract females. In these species, the mating system is polygynous and the females alone incubate and feed the nestlings. The bowerbirds also include 10 species of the socially monogamous catbirds in which the male participates in most aspects of raising the young. How the bower-building behavior evolved has remained poorly understood, as no comprehensive phylogeny exists for the family. It has been assumed that the monogamous catbird clade is sister to all polygynous species. We here test this hypothesis using a newly developed pipeline for obtaining homologous alignments of thousands of exonic and intronic regions from genomic data to build a phylogeny. Our well-supported species tree shows that the polygynous, bower-building species are not monophyletic. The result suggests either that bower-building behavior is an ancestral condition in the family that was secondarily lost in the catbirds, or that it has arisen in parallel in two lineages of bowerbirds. We favor the latter hypothesis based on an ancestral character reconstruction showing that polygyny but not bower-building is ancestral in bowerbirds, and on the observation that <em>Scenopoeetes dentirostris</em>, the sister species to one of the bower-building clades, does not build a proper bower but constructs a court for male display. This species is also sexually monomorphic in plumage despite having a polygynous mating system. We argue that the relatively stable tropical and subtropical forest environment in combination with low predator pressure and rich food access (mostly fruit) facilitated the evolution of these unique life-history traits. </p>
Data from: Phylogenomic analysis of Wolbachia strains reveals patterns of genome evolution and recombination
<p><i>Wolbachia</i> are widespread intracellular bacteria that mediate many important biological processes in arthropod species. In this study, we identified 210 conserved single-copy genes in 33 genome-sequenced <i>Wolbachia</i> strains in the A, B, C, D, E and F supergroups. Phylogenomic analysis with these core genes indicate that all 33 <i>Wolbachia</i> strains maintain the supergroup relationship classified previously based on the multilocus sequence typing (MLST) genes. Using an interclade recombination screening method, 14 inter-supergroup recombination events were discovered in six genes (2.9%) among 210 single copy orthologs. This finding suggests a relatively low frequency of intergroup recombination. Interestingly, they have occurred not only between A and B supergroups (9 events), but also between A and E supergroups (5 events). Maintenance of such transfers suggests possible roles in <i>Wolbachia</i> infection related functions. Comparisons of strain divergence using the five genes of the MLST system show a high correlation (Pearson correlation coefficient r = 0.98) between MLST and whole genome divergences, indicating that MLST is a reliable method for identifying related strains when whole genome data are not available. The phylogenomic analysis and the identified core gene set in our study will serve as a valuable foundation for strain identification and the investigation of recombination and genome evolution in <i>Wolbachia</i>.</p>
Data from: Uneven missing data skew phylogenomic relationships within the lories and lorikeets
<p>Inlcuded is the supplementary data for Smith, B. T., Mauck, W. M., Benz, B., & Andersen, M. J. (2018). Uneven missing data skews phylogenomic relationships within the lories and lorikeets. <em>BioRxiv</em>, 398297. </p> <p>The resolution of the Tree of Life has accelerated with advances in DNA sequencing technology. To achieve dense taxon sampling, it is often necessary to obtain DNA from historical museum specimens to supplement modern genetic samples. However, DNA from historical material is generally degraded, which presents various challenges. In this study, we evaluated how the coverage at variant sites and missing data among historical and modern samples impacts phylogenomic inference. We explored these patterns in the brush-tongued parrots (lories and lorikeets) of Australasia by sampling ultraconserved elements in 105 taxa. Trees estimated with low coverage characters had several clades where relationships appeared to be influenced by whether the sample came from historical or modern specimens, which were not observed when more stringent filtering was applied. To assess if the topologies were affected by missing data, we performed an outlier analysis of sites and loci, and a data reduction approach where we excluded sites based on data completeness. Depending on the outlier test, 0.15% of total sites or 38% of loci were driving the topological differences among trees, and at these sites, historical samples had 10.9x more missing data than modern ones. In contrast, 70% data completeness was necessary to avoid spurious relationships. Predictive modeling found that outlier analysis scores were correlated with parsimony informative sites in the clades whose topologies changed the most by filtering. After accounting for biased loci and understanding the stability of relationships, we inferred a more robust phylogenetic hypothesis for lories and lorikeets.</p>
Data from: Phylogenomics, biogeography, and evolution of the blue- or white-fruited dogwoods
<p>In this study, we combined data from RAD-seq, morphology, fossils, and ecological niche to understand species relationships, biogeographic history, ecological niche and morphological evolution of the blue- or white-fruited dogwoods, the largest of the four major clades of Cornus. Our phylogenomic analyses with RAxML and MrBayes recovered a strongly supported and well-resolved phylogeny of the BW group with three intercontinental disjunct clades in east Asia/Eurasia and North America - of which two in subg. Kraniopsis are newly identified. Divergence time analyses with BEAST and treePL and DEC-based total evidence analysis resolved an ancestral range of the BW crown in eastern Asia or Eurasia in the Late Cretaceous and ancestral ranges of the three disjunct clades in Eurasia and North America during the Miocene, suggesting dispersal via the North Atlantic and Bering land bridges. Character mapping and comparison of ecological niche, morphospace, and rate of evolution shows evidence of different divergence patterns in morphology, ecological niche, and molecules of the disjunct sisters. The overall diversity bias towards EA cannot be explained by a greater net diversification rate but rather an early diversification of subg. Kraniopsis in EA. Although morphological stasis was observed in most of the characters across the disjuncts, evolutionary changes in vegetative, fruit, and habit traits may be attributed to continental differences in temperature, precipitation, and elevation. These findings in conjunction with previous studies suggest the EA-ENA disjunct floras are an assembly of lineages descended from the boreotropical or mesophytic flora through taxon-specific evolutionary pathways.</p>
Data from: Morphological characters can strongly influence early animal relationships inferred from phylogenomic data sets
<p>There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: The sister to all other Metazoa (SOM). Here we use published phylogenomic datasets (∼45,000-400,000 characters in size with ∼15-100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological datasets (∼15-275 characters). We additionally use small exemplar datasets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, i.e. likelihood models and their "equivalent" under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, i.e., that genomic-scale datasets will swamp out inferences from morphological data. Instead, weighting morphological data 2-10× in both likelihood and parsimony can in some cases "flip" which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular datasets (>200,000 characters and up to ∼100 taxa) showing node stability even with ≧100× up-weighting of morphological data. Accordingly, our analyses have three strong messages. A) The assumption that genomic data will automatically "swamp out" morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined datasets, even when outnumbered thousands of times by morphological data. Morphology therefore should not be counted out a priori. B.) We here quantify for the first time how the stability of the SOM node improves for several genomic datasets when the taxon sampling is increased. C.) The patterns of "flipping points" (i.e., the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of datasets that should be developed into a new sensitivity analysis tool.</p>
Data from: Phylogenomics reveals novel relationships among Neotropical crocodiles (Crocodylus spp.)
<p>Extant species in the order Crocodylia are remnants of an ancient lineage of large-bodied archosaur reptiles. Despite decades of systematic studies, phylogenetic relationships among members of the genus <i>Crocodylus</i> (true crocodiles) in the Neotropics are poorly understood. Here we estimated phylogenomic relationships among the four extant <i>Crocodylus </i>species in the Americas. Species-tree reconstructions using genotypic data from 17,538 SNPs collected for 33 individuals spanning six <i>Crocodylus </i>species (four ingroup and two outgroup) revealed novel relationships for all Neotropical species. For the first time, <i>C. acutus</i>, the American crocodile, was recovered as monophyletic when individuals from Antillean and continental populations were analyzed together. Our results also contradict previous inferences based on mitochondrial DNA data and a limited number of nuclear markers by robustly grouping Morelet's crocodile (<i>C. moreletii</i>) as the sister species to <i>C. acutus</i>., suggesting a novel phylogeographic hypothesis for the group. The present study punctuates the importance of using nuclear genome-wide information and representative sampling for resolving phylogenetic relationships, especially in broadly distributed species and those with complex evolutionary histories.</p>
Data from: A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans
Comprising over 15 000 living species, decapods (crabs, shrimp and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here, we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (greater than 86 000 bp) conserved across all lineages of Decapoda, more clade-specific molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, 'lobster' and 'crab' groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic–Jurassic, highlighting a cryptic Palaeozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behaviour, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.
Data from: Embracing discordance: phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a Mediterranean Campanula (Campanulaceae) clade
The Mediterranean Basin harbors a remarkable amount of biodiversity, a high proportion of which is endemic to this region. Here, we present an in-depth study of an angiosperm species complex, in which cryptic taxonomic diversity has been hypothesized. Specifically, we focus on four currently recognized species in the Roucela complex, a well-supported clade in the Campanulaceae/Campanuloideae: Campanula creutzburgii, C. drabifolia, C. erinus, and C. simulans. This study takes a phylogenomic approach, utilizing near-complete plastomes and 130 nuclear loci, to uncover cryptic diversity and test hypotheses regarding hybridization and polyploidy within this clade. Genome size estimates recovered tetraploid and octoploid lineages within the currently recognized, widespread species C. erinus, showing an east-west geographic pattern. Though genomic data clearly differentiate these two cytotypes, we failed to discern morphological differences. The formation of a cryptic octoploid lineage, distributed across the eastern Mediterranean, is hypothesized to be the result of an allopolyploid event in which one parental morphology is retained. The tetraploid C. erinus and C. creutzburgii (also a tetraploid) are implicated as parental lineages. Our results highlight the utility of target-enrichment approaches for obtaining genomic datasets for thorough assessments of species diversity and the importance of carefully considering gene-tree discordance within such datasets.
Data from: Phylogenomics reveals three sources of adaptive variation during a rapid radiation
Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a "PhyloGWAS" approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations.
Data from: A phylogenomic perspective to diversity, hybridization and evolutionary affinities in the stickleback genus Pungitius
<p>Hybridization and convergent evolution are phenomena of broad interest in evolutionary biology, but their occurrence poses challenges for reconstructing evolutionary affinities among affected taxa. Sticklebacks in the genus Pungitius are a case in point: evolutionary relationships and taxonomic validity of different species and populations in this circumpolarly distributed species complex remain contentious due to convergent evolution of traits regarded as diagnostic in their taxonomy, and possibly also due to frequent hybridization among taxa. To clarify the evolutionary relationships among different Pungitius species and populations globally, as well as to study prevalence and extent of introgression among recognized species, genomic datasets of both reference genome-anchored SNPs and de novo assembled RAD-tag loci were constructed with RAD-seq data. Both datasets yielded topologically identical and well-supported species trees. Incongruence between nuclear and mitochondrial DNA-based trees was found and suggested frequent hybridization and mitogenome capture during the evolution of Pungitius sticklebacks. Further analyses revealed evidence for frequent nuclear genetic introgression among Pungitius species, although the estimated proportions of autosomal introgression were low. Apart from providing evidence for frequent hybridization, the results challenge earlier mitochondrial and morphology-based hypotheses about the number of species and their affinities in this genus: at least seven extant species can be recognized on the basis of genetic data. The results also shed new light on the biogeographic history of the Pungitius-complex, including suggestion of several trans-Arctic invasions of Europe from the Northern Pacific. The well-resolved phylogeny should facilitate the utility of this genus as a model system for future comparative evolutionary studies.</p>
Data from: Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths
Butterflies and moths (Lepidoptera) are one of the major super-radiations of insects, comprising nearly 160,000 described extant species. As herbivores, pollinators, and prey, Lepidoptera play a fundamental role in almost every terrestrial ecosystem. Lepidoptera are also indicators of environmental change and serve as model organisms for research on mimicry and genetics. They have been central to the development of co-evolutionary hypotheses, such as butterflies with flowering plants, and moths' evolutionary arms race with echolocating bats. However, these hypotheses have not been rigorously tested because a robust lepidopteran phylogeny and timing of evolutionary novelties are lacking. To address these issues, we inferred a comprehensive phylogeny of Lepidoptera, using the largest data set assembled for the order (2,098 orthologous protein-coding genes from 186 species representing nearly all superfamilies), and dated it with carefully evaluated synapomorphy-based fossils. The oldest members of the Lepidoptera crown group appeared in the Late Carboniferous (~300 million years ago [Ma]) and fed on non-vascular land plants. Lepidoptera evolved the tube-like proboscis in the Middle Triassic and the proboscis allowed them to acquire nectar from flowering plants. This key morphological innovation, along with other traits, likely promoted the extraordinary diversification of superfamily-level lepidopteran crown groups. The ancestor of butterflies was likely nocturnal, and our results indicate that butterflies became day-flying in the Late Cretaceous. Moth hearing organs arose multiple times prior to the evolutionary arms race between moths and bats, perhaps initially detecting a wide range of sound frequencies before being co-opted to specifically detect bat sonar.
Data from: Leap-frog dispersal and mitochondrial introgression: phylogenomics and biogeography of Limnonectes fanged frogs in the Lesser Sundas Archipelago of Wallacea
Aim: The Lesser Sunda Islands are situated between the Sunda and Sahul Shelves, with a linear arrangement that has functioned as a two-way filter for taxa dispersing between the Asian and Australo-Papuan biogeographic realms. Distributional patterns of many terrestrial vertebrates suggest a stepping-stone model of island colonization. Here we investigate the timing and sequence of island colonization in Asian-origin fanged frogs from the volcanic Sunda Arc islands with the goal of testing the stepping-stone model of island colonization. Location: The Indonesian islands of Java, Lombok, Sumbawa, Flores, and Lembata. Taxon: Limnonectes dammermani and L. kadarsani (Family: Dicroglossidae) Methods: Mitochondrial DNA was sequenced from 153 frogs to identify major lineages and to select samples for an exon-capture experiment. We designed probes to capture sequence data from 974 exonic loci (1,235,981 bp) from 48 frogs including the outgroup species, L. microdiscus. The resulting data were analyzed using phylogenetic, population genetic, and biogeographical model testing methods. Results: The mtDNA phylogeny finds L. kadarsani paraphyletic with respect to L. dammermani, with a pectinate topology consistent with the stepping-stone model. Phylogenomic analyses of 974 exons recovered the two species as monophyletic sister taxa that diverged ~7.6 Ma with no detectable contemporary gene flow, suggesting introgression of the L. dammermani mitochondrion into L. kadarsani on Lombok resulting from an isolated ancient hybridization event ~4 Ma. Within L. kadarsani, the Lombok lineage diverged first while the Sumbawa and Lembata lineages are nested within a Flores assemblage composed of two parapatrically distributed lineages meeting in central Flores. Biogeographical model comparison found strict stepping-stone dispersal to be less likely than models involving leap-frog dispersal events. Main conclusions: These results suggest that the currently accepted stepping-stone model of island colonization might not best explain the current patterns of diversity in the archipelago. The high degree of genetic structure, large divergence times, and absent or low levels of migration between lineages suggests that L. kadarsani represents five distinct species.
Data from: Phylogenomic reclassification of the world's most venomous spiders (Mygalomorphae, Atracinae), with implications for venom evolution
Here we show that the most venomous spiders in the world are phylogenetically misplaced. Australian atracine spiders (family Hexathelidae), including the notorious Sydney funnel-web spider Atrax robustus, produce venom peptides that can kill people. Intriguingly, eastern Australian mouse spiders (family Actinopodidae) are also medically dangerous, possessing venom peptides strikingly similar to Atrax hexatoxins. Based on the standing morphology-based classification, mouse spiders are hypothesized distant relatives of atracines, having diverged over 200 million years ago. Using sequence-capture phylogenomics, we instead show convincingly that atracines are sister to actinopodids, and that hexathelids are non-monophyletic. Three new mygalomorph lineages are elevated to the family level, and a revised circumscription of the family Hexathelidae is presented. Re-writing this phylogenetic story has major implications for how we study venom evolution in these spiders, and potentially genuine consequences for antivenom development and bite treatment research. More generally, our research provides a textbook example of the applied importance of modern phylogenomic research.
Data from: Impacts of inference method and dataset filtering on phylogenomic resolution in a rapid radiation of ground squirrels (Xerinae: Marmotini)
Phylogenomic datasets are illuminating many areas of the Tree of Life. However, the large size of these datasets alone may be insufficient to resolve problematic nodes in the most rapid evolutionary radiations, because inferences in zones of extraordinarily low phylogenetic signal can be sensitive to the model and method of inference, as well as the information content of loci employed. We used a dataset of >3,950 ultraconserved element (UCE) loci from a classic mammalian radiation, ground-dwelling squirrels of the tribe Marmotini (Sciuridae: Xerinae), to assess sensitivity of phylogenetic estimates to varying per-locus information content across 4 different inference methods (RAxML, ASTRAL, NJst, SVDquartets). Persistent discordance was found in topology and bootstrap support between concatenation- and coalescent-based inferences; among methods within the coalescent framework; and within all methods in response to different filtering scenarios. Contrary to some recent empirical UCE-based studies, filtering by information content did not promote complete among-method concordance. Nevertheless, filtering did improve concordance relative to randomly selected locus sets, largely via improved consistency of two-step summary methods (particularly NJst) under conditions of higher average per-locus variation (and thus increasing gene tree precision). The benefits of dataset filtering are notably variable among classes of inference methods and across different evolutionary scenarios, reiterating the complexities of resolving rapid radiations, even with robust taxon and character sampling.
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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.