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Data from: Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula
Sequence data for >20 000 annotated genes from 56 accessions of Medicago truncatula were used to identify potential targets of positive selection, the determinants of evolutionary rate variation and the relative importance of positive and purifying selection in shaping nucleotide diversity. Based upon patterns of intraspecific diversity and interspecific divergence, c. 50–75% of nonsynonymous polymorphisms are subject to strong purifying selection and 1% of the sampled genes harbour a signature of positive selection. Combining polymorphism with expression data, we estimated the distribution of fitness effects and found that the proportion of deleterious mutations is significantly greater for expressed genes than for genes with undetected transcripts (nonexpressed) in a previous RNA-seq experiment and greater for broadly expressed genes than those expressed in only a single tissue. Expression level is the strongest correlate of evolutionary rates at nonsynonymous sites, and despite multiple genomic features being significantly correlated with evolutionary rates, they explain less than 20% of the variation in nonsynonymous rates (dN) and <15% of the variation in either synonymous rates (dS) or dN:dS. Among putative targets of selection were genes involved in defence against pathogens and herbivores, genes with roles in mediating the relationship with rhizobial symbionts and one-third of annotated histone-lysine methyltransferases. Adaptive evolution of the methyltransferases suggests that positive selection in gene expression may have occurred through evolution of enzymes involved in epigenetic modification.
Data from: A framework for elucidating the temperature dependence of fitness
Climate warming is predicted to cause large-scale extinctions of ectothermic species. A striking difference between tropical and temperate ectotherms is that tropical species exhibit an upper temperature limit for survival (T_max) that is closer to the temperature at which fitness is maximized (T_opt). Thus, even a small increase in environmental temperature could put tropical ectotherms at high risk of extinction, whereas temperate ectotherms have a wider temperature cushion. Although this pattern is widely observed, the mechanisms that produce it are not well-understood. We develop a mathematical framework to partition the temperature response of fitness into its components (fecundity, mortality and development) and test model predictions with data for insects. We find that fitness declines at high temperatures because the temperature responses of fecundity and mortality act in opposite ways: fecundity decreases with temperature once temperatures exceed the optimal range, whereas mortality continues to increase. The proximity of T_opt to T_max depends on how the temperature response of development mediates the interaction between fecundity and mortality. When development is highly temperature-sensitive, mortality exceeds reproduction only after fecundity has started to decline with temperature, which causes fitness to decline rapidly to zero once temperatures exceed T_opt. The model correctly predicts empirically observed fitness-temperature relationships in insects from different latitudes. It potentially explains the widely-reported phenological shifts and latitudinal differences in fitness responses.
Data from: Extra-pair paternity and the variance in male fitness in song sparrows (Melospiza melodia)
The variance in fitness across population members can influence major evolutionary processes. In socially monogamous but genetically polygynandrous species, extra-pair paternity (EPP) is widely hypothesized to increase the variance in male fitness compared to that arising given the socially monogamous mating system. This hypothesis has not been definitively tested because comprehensive data describing males' apparent (social) and realized (genetic) fitness have been lacking. We used 16 years of comprehensive social and genetic paternity data for an entire free-living song sparrow (Melospiza melodia) population to quantify and compare variances in male apparent and realized fitness, and to quantify the contribution of the variances in within-pair and extra-pair reproductive success and their covariance to the variance in realized fitness. Overall, EPP increased the variance in male fitness by only 0-27% across different fitness and variance measures. This relatively small effect reflected the presence of socially unpaired males with zero apparent and low realized fitness, small covariance between within- and extra-pair reproductive success and large variance in within-pair reproductive success that was relatively unaffected by EPP. Therefore, although EPP altered individual males' contributions to future generations, its impact on population-level parameters such as the opportunity for selection and effective population size was limited.
Data from: Population size-structure dependent fitness and ecosystem consequences in Trinidadian guppies
1. Decades of theory and recent empirical results have shown that evolutionary, population, community and ecosystem properties are the result of feedbacks between ecological and evolutionary processes. The vast majority of theory and empirical research on these eco-evolutionary feedbacks has focused on interactions among population size and mean traits of populations. 2. However, numbers and mean traits represent only a fraction of the possible feedback dimensions. Populations of many organisms consist of different size classes that differ in their impact on the environment and each other. Moreover, rarely do we know the map of ecological pathways through which changes in numbers or size structure cause evolutionary change. The goal of this study was to test the role of size structure in eco-evolutionary feedbacks of Trinidadian guppies and to begin to build an eco-evolutionary map along this unexplored dimension. 3. We used a factorial experiment in mesocosms wherein we crossed high- and low-predation guppy phenotypes with population size structure. We tested the ability of changes in size structure to generate selection on the demographic rates of guppies using an integral projection model (IPM). To understand how fitness differences among high- and low-predation phenotypes may be generated, we measured the response of the biomass of lower trophic levels and nutrient cycling to the different phenotype and size structure treatments. 4. We found a significant interaction between guppy phenotype and the size structure treatments for absolute fitness. Size structure had a very large effect on invertebrate biomass in the mesocosms, but there was little or no effect of the phenotype. The effect of size structure on algal biomass depended on guppy phenotype, with no difference in algal biomass in populations with more, smaller guppies, but a large decrease in algal biomass in mesocosms with phenotypes adapted to low-predation risk. 5. These results indicate an important role for size structure partially driving eco-evolutionary feedbacks in guppies. The changes in the ecosystem suggest that the absence of a steep decline in guppy fitness of the low-predation risk populations is likely due to higher consumption of algae when invertebrates are comparatively rare. Overall, these results demonstrate size structure as a possible dimension through which eco-evolutionary feedbacks may occur in natural populations.
Data from: Temperature-sensitive fitness cost of insecticide resistance in Chinese populations of the diamondback moth Plutella xylostella
Alleles conferring a higher adaptive value in one environment may have a detrimental impact on fitness in another environment. Alleles conferring resistance to pesticides and drugs provide textbook examples of this trade-off as, in addition to conferring resistance to these molecules, they frequently decrease fitness in pesticide/drug-free environments. We show here that resistance to chlorpyrifos, an organophosphate (OP), in Chinese populations of the diamondback moth, Plutella xylostella, is conferred by two mutations of ace1 – the gene encoding the acetylcholinesterase enzyme targeted by OPs – affecting the amino acid sequence of the corresponding protein. These mutations were always linked, consistent with the segregation of a single resistance allele, ace1R, carrying both mutations, in the populations studied. We monitored the frequency of ace1R (by genotyping more than 20 000 adults) and the level of resistance (through bioassays on more than 50 000 individuals) over several generations. We found that the ace1R resistance allele was costly in the absence of insecticide and that this cost was likely recessive. This fitness costs involved a decrease in fecundity: females from resistant strains laid 20% fewer eggs, on average, than females from susceptible strains. Finally, we found that the fitness costs associated with the ace1R allele were greater at high temperatures. At least two life history traits were involved: longevity and fecundity. The relative longevity of resistant individuals was affected only at high temperatures and the relative fecundity of resistant females – which was already affected at temperatures optimal for development – decreased further at high temperatures. The implications of these findings for resistance management are discussed.
Data from: Modeling and quantifying frequency-dependent fitness in microbial populations with cross-feeding interactions
Coexistence of two or more populations by frequency-dependent selection is common in nature, and it often arises even in well-mixed experiments with microbes. If ecology is to be incorporated into models of population genetics, then it is important to represent accurately the functional form of frequency-dependent interactions. However, measuring this functional form is problematic for traditional fitness assays, which assume a constant fitness difference between competitors over the course of an assay. Here, we present a theoretical framework for measuring the functional form of frequency-dependent fitness by accounting for changes in abundance and relative fitness during a competition assay. Using two examples of ecological coexistence that arose in a long-term evolution experiment with Escherichia coli, we illustrate accurate quantification of the functional form of frequency-dependent relative fitness. Using a Monod-type model of growth dynamics, we show that two ecotypes in a typical cross-feeding interaction—such as when one bacterial population uses a byproduct generated by another—yields relative fitness that is linear with relative frequency.
Data from: Vertically transmitted symbiont reduces host fitness along temperature gradient
Parasites with exclusive vertical transmission from host parent to offspring are an evolutionary puzzle. With parasite fitness entirely linked to host reproduction, any fitness cost for infected hosts risks their selective elimination. Environmental conditions likely influence parasite impact, and thereby the success of purely vertical transmission strategies. We tested for temperature-dependent virulence of Caedibacter taeniospiralis, a vertically transmitted bacterial symbiont of the protozoan Paramecium tetraurelia. We compared growth of infected and cured host populations at five temperatures (16-32°C). Infection reduced host density at all temperatures, with a peak at 28°C. These patterns were largely consistent across five infected Paramecium strains. Similar to Wolbachia symbionts, C. taeniospiralis may compensate fitness costs by conferring to the host a 'killer trait', targeting uninfected competitors. Considerable loss of infection at 32°C suggests that killer efficacy is not universal and that limited heat tolerance restricts the conditions for persistence of C. taeniospiralis.
Data from: Here's to the losers: evolvable residents accelerate the evolution of high fitness invaders
Recent work has shown that evolvability plays a key role in determining the long-term population dynamics of asexual clones. However, simple considerations suggest that the evolvability of a focal lineage of bacteria should also be influenced by the evolvability of its competitors. First, evolvable competitors should accelerate evolution by impeding the fixation of the focal lineage through a clonal interference–like mechanism. Second, evolvable competitors should increase the strength of selection by rapidly degrading the environment, increasing selection for adaptive mutations. Here we tested these ideas by allowing a high-fitness clone of the bacterium Pseudomonas aeruginosa to invade populations of two low-fitness resident clones that differ in their evolvability. Both competition from mutations in the resident lineage and environmental degradation lead to faster adaptation in the invader through fixing single mutations with a greater fitness advantage. The results suggest that competition from mutations in both the successful invader and the unsuccessful resident shapes the adaptive trajectory of the invader through both direct competition and indirect environmental effects. Therefore, to predict evolutionary outcomes, it will be necessary to consider the evolvability of all members of the community and the effects of adaptation on the quality of the environment. This is particularly relevant to mixed microbial communities where lineages differ in their adaptive potential, a common feature of chronic infections.
Data from: Female density-dependent chemical warfare underlies fitness effects of group sex ratio in flour beetles
In animals, skewed sex ratios can affect individual fitness either via sexual (e.g. intersexual conflict or intrasexual mate competition) or non-sexual interactions (e.g. sex-specific resource competition). Because most analyses of sex ratio focus on sexual interactions, the relative importance of sexual vs. non-sexual mechanisms remains unclear. We tested both mechanisms in the flour beetle Tribolium castaneum, where male-biased sex ratios increase female fitness relative to unbiased or female-biased groups. Although flour beetles show both sexual and non-sexual (resource) competition, we found that sexual interactions did not explain female fitness. Instead, female fecundity was dramatically reduced even after a brief exposure to flour conditioned by other females. Earlier studies suggested that secreted toxins might mediate density-dependent population growth in flour beetles. We identified ethyl- and methyl- benzoquinone (EBQ and MBQ; "quinones"), as components of adult stink glands that regulate female fecundity. In female-biased groups (i.e. at high female density), females upregulated quinones and suppressed each other's reproduction. In male-biased groups, low female density and associated low quinone levels maximized fecundity. Thus, females appear to use quinones as weapons for female-specific, density-dependent interference competition. Our results underscore the importance of non-sexual interference competition that may often underlie the fitness consequences of skewed sex ratios.
Data from: Fitness trade-offs explain low levels of persister cells in the opportunistic pathogen Pseudomonas aeruginosa
Microbial populations often contain a fraction of slow-growing persister cells that withstand antibiotics and other stress factors. Current theoretical models predict that persistence levels should reflect a stable state in which the survival advantage of persisters under adverse conditions is balanced with the direct growth cost impaired under favourable growth conditions, caused by the nonreplication of persister cells. Based on this direct growth cost alone, however, it remains challenging to explain the observed low levels of persistence (<<1%) seen in the populations of many species. Here, we present data from the opportunistic human pathogen Pseudomonas aeruginosa that can explain this discrepancy by revealing various previously unknown costs of persistence. In particular, we show that in the absence of antibiotic stress, increased persistence is traded off against a lengthened lag phase as well as a reduced survival ability during stationary phase. We argue that these pleiotropic costs contribute to the very low proportions of persister cells observed among natural P. aeruginosa isolates (3 × 10−8–3 × 10−4) and that they can explain why strains with higher proportions of persister cells lose out very quickly in competition assays under favourable growth conditions, despite a negligible difference in maximal growth rate. We discuss how incorporating these trade-offs could lead to models that can better explain the evolution of persistence in nature and facilitate the rational design of alternative therapeutic strategies for treating infectious diseases.
Data from: Impaired sperm quality, delayed mating but no costs for offspring fitness in crickets winning a fight
The outcome of male-male contest competition is known to affect male mating success and is believed to confer fitness benefits to females through preference for dominant males. However, by mating with contest winners, females can incur significant costs spanning from decreased fecundity to negative effects on offspring. Hence identifying costs and benefits of male dominance on female fitness is crucial to unravel the potential for a conflict of interests between the sexes. Here we investigated males' pre- and post-copulatory reproductive investment and its effect on female fitness after a single contest a using the field cricket Gryllus bimaculatus. We allowed males to fight, and immediately measured their mating behaviour, sperm quality, and offspring viability. We found that males experiencing a fight, independently of the outcome, delayed matings but their courtship effort was not affected. However, winners produced sperm of lower quality (viability) compared to losers and to males that did not experience fighting. Results suggest a trade-off in resource allocation between pre- and post-mating episodes of sexual selection. Despite lower ejaculate quality we found no fitness costs (fecundity and viability of offspring) for females mated to winners. Overall our findings highlight the importance of considering fighting ability when assessing male reproductive success, as winners may be impaired in their competitiveness at a post-mating level.
Data from: Selection on floral design in Polemonium brandegeei (Polemoniaceae): female and male fitness under hawkmoth pollination
Plant-pollinator interactions promote the evolution of floral traits that attract pollinators and facilitate efficient pollen transfer. The spatial separation of sex-organs, herkogamy, is believed to limit sexual interference in hermaphrodite flowers. Reverse herkogamy (stigma recessed below anthers) and long narrow corolla-tubes are expected to promote efficiency in male function under hawkmoth pollination. We tested this prediction by measuring selection in six experimental arrays of Polemonium brandegeei, a species that displays continuous variation in herkogamy, resulting in a range of recessed to exserted stigmas. Under glasshouse conditions, we measured pollen removal and deposition, and estimated selection gradients (ß) through female fitness (seeds set) and male fitness (siring success based on 6 polymorphic microsatellite loci). Siring success was higher in plants with more nectar sugar and narrow corolla-tubes. However, selection through female function for reverse herkogamy was considerably stronger than was selection through male function. Hawkmoths were initially attracted to larger flowers, but overall preferred plants with reverse herkogamy. Greater pollen deposition and seed set also occurred in reverse herkogamous plants. Thus, reverse herkogamy may be maintained by hawkmoths through female rather than male function. Further, our results suggest that pollinator attraction may play a considerable role in enhancing female function.
Data from: Primary care management of headaches and how direct-access MRI fits: a qualitative study of UK general practitioners' views
Objectives To develop a better understanding of General Practitioners' (GPs) views and experiences of the management of patients with headaches and use of direct access magnetic resonance imaging (MRI) scans, and observe outcomes of an educational session offered by a GP with a Special Interest (GPwSI) to GPs. Design A qualitative study using semi-structured interviews, analysed using thematic analysis. A GPwSI in headaches visited practices delivering a talk on headache medication, diagnosis, and management. Setting Sixteen (16) primary care family practices in South London, United Kingdom. Participants Twenty (20) General Practitioners. Results Not all GPs were aware of the availability of direct access MRI, but all acknowledged having used referral or direct-scans to manage patients' concern about their headaches. A normal scan result helped resolve uncertainty for patient and GP, and helped management towards discussion of preventative treatment. However, patients with psychological and/or severe headache symptoms could not necessarily be reassured. GPs reported difficulty interpreting radiology reports, particularly incidental abnormalities. Those who received the educational talk gained knowledge in diagnosis and medication, improving their confidence in management. Conclusions Increased access to imaging, training in headache management, addressing physical and psychological symptoms, and standardized reporting of scans, may improve GP use of direct access MRI in future.
Data from: Socially selected ornaments and fitness: signals of fighting ability in paper wasps are positively associated with survival, reproductive success, and rank
Many animals have ornaments that mediate choice and competition in social and sexual contexts. Individuals with elaborate sexual ornaments typically have higher fitness than those with less elaborate ornaments, but less is known about whether socially selected ornaments are associated with fitness. Here, we test the relationship between fitness and facial patterns that are a socially-selected signal of fighting ability in Polistes dominula wasps. We found wasps that signal higher fighting ability have larger nests, are more likely to survive harsh winters, and obtain higher dominance rank than wasps that signal lower fighting ability. In comparison, body weight was not associated with fitness. Larger wasps were dominant over smaller wasps, but showed no difference nest size or survival. Overall, the positive relationship between wasp facial patterns and fitness indicates that receivers can obtain diverse information about a signaler's phenotypic quality by paying attention to socially selected ornaments. Therefore, there are surprisingly strong parallels between the information conveyed by socially and sexually selected signals. Similar fitness relationships in social and sexually selected signals may be one reason it can be difficult to distinguish the role of social versus sexual selection in ornament evolution.
Data from: Post-copulatory opportunities for sperm competition and cryptic female choice provide no offspring fitness benefits in externally fertilizing salmon
There is increasing evidence that females can somehow improve their offspring fitness by mating with multiple males, but we understand little about the exact stage(s) at which such benefits are gained. Here, we measure whether offspring fitness is influenced by mechanisms operating solely between sperm and egg. Using externally fertilizing and polyandrous Atlantic salmon (Salmo salar), we employed split-clutch and split-ejaculate in vitro fertilization experiments to generate offspring using designs that either denied or applied opportunities for sperm competition and cryptic female choice. Following fertilizations, we measured 140 days of offspring fitness after hatch, through growth and survival in hatchery and near-natural conditions. Despite an average composite mortality of 61%, offspring fitness at every life stage was near-identical between groups fertilized under the absence versus presence of opportunities for sperm competition and cryptic female choice. Of the 21 551 and 21 771 eggs from 24 females fertilized under monandrous versus polyandrous conditions, 68% versus 67.8% survived to the 100-day juvenile stage; sub-samples showed similar hatching success (73.1% versus 74.3%), had similar survival over 40 days in near-natural streams (57.3% versus 56.2%) and grew at similar rates throughout. We therefore found no evidence that gamete-specific interactions allow offspring fitness benefits when polyandrous fertilization conditions provide opportunities for sperm competition and cryptic female choice.
Data from: Direct and indirect causal effects of heterozygosity on fitness-related traits in Alpine ibex
Heterozygosity–fitness correlations (HFCs) are a useful tool to investigate the effects of inbreeding in wild populations, but are not informative in distinguishing between direct and indirect effects of heterozygosity on fitness-related traits. We tested HFCs in male Alpine ibex (Capra ibex) in a free-ranging population (which suffered a severe bottleneck at the end of the eighteenth century) and used confirmatory path analysis to disentangle the causal relationships between heterozygosity and fitness-related traits. We tested HFCs in 149 male individuals born between 1985 and 2009. We found that standardized multi-locus heterozygosity (MLH), calculated from 37 microsatellite loci, was related to body mass and horn growth, which are known to be important fitness-related traits, and to faecal egg counts (FECs) of nematode eggs, a proxy of parasite resistance. Then, using confirmatory path analysis, we were able to show that the effect of MLH on horn growth was not direct but mediated by body mass and FEC. HFCs do not necessarily imply direct genetic effects on fitness-related traits, which instead can be mediated by other traits in complex and unexpected ways.
Data from: Reduced genetic variance among high fitness individuals: inferring stabilizing selection on male sexual displays in D. serrata
Directional selection is prevalent in nature yet phenotypes tend to remain relatively constant, suggesting a limit to trait evolution. However, the genetic basis of this limit is unresolved. Given widespread pleiotropy, opposing selection on a trait may arise from the effects of the underlying alleles on other traits under selection, generating net stabilizing selection on trait genetic variance. These pleiotropic costs of trait exaggeration may arise through any number of other traits, making them hard to detect in phenotypic analyses. Stabilizing selection can be inferred, however, if genetic variance is greater among low compared to high fitness individuals. We extend a recently suggested approach to provide a direct test of a difference in genetic variance for a suite of cuticular hydrocarbons (CHCs) in Drosophila serrata. Despite strong directional sexual selection on these traits, genetic variance differed between high and low fitness individuals and was greater among the low fitness males for seven of eight CHCs, significantly more than expected by chance. Univariate tests of a difference in genetic variance were non-significant but likely have low power. Our results suggest that further CHC exaggeration in D. serrata in response to sexual selection is limited by pleiotropic costs mediated through other traits.
Data from: Genetic diversity, virulence and fitness evolution in an obligate fungal parasite of bees
Within-host competition is predicted to drive the evolution of virulence in parasites, but the precise outcomes of such interactions are often unpredictable due to many factors including the biology of the host and the parasite, stochastic events and co-evolutionary interactions. Here, we use a serial passage experiment (SPE) with three strains of a heterothallic fungal parasite (Ascosphaera apis) of the Honey bee (Apis mellifera) to assess how evolving under increasing competitive pressure affects parasite virulence and fitness evolution. The results show an increase in virulence after successive generations of selection and consequently faster production of spores. This faster sporulation, however, did not translate into more spores being produced during this longer window of sporulation; rather, it appeared to induce a loss of fitness in terms of total spore production. There was no evidence to suggest that a greater diversity of competing strains was a driver of this increased virulence and subsequent fitness cost, but rather that strain-specific competitive interactions influenced the evolutionary outcomes of mixed infections. It is possible that the parasite may have evolved to avoid competition with multiple strains because of its heterothallic mode of reproduction, which highlights the importance of understanding parasite biology when predicting disease dynamics.
Data from: Fitness consequences of larval traits persist across the metamorphic boundary
Metamorphosis is thought to provide an adaptive decoupling between traits specialised for each life-history stage in species with complex life cycles. However, an increasing number of studies are finding that larval traits can carry-over to influence post-metamorphic performance, suggesting that these life-history stages may not be free to evolve independently of each other. We used a phenotypic selection framework to compare the relative and interactive effects of larval size, time to hatching, and time to settlement on post-metamorphic survival and growth in a marine invertebrate, Styela plicata. Time to hatching was the only larval trait found to be under directional selection, individuals that took more time to hatch into larvae survived better after metamorphosis but grew more slowly. Non-linear selection was found to act on multivariate trait combinations, once again acting in opposite directions for selection acting via survival and growth. Individuals with above average values of larval traits were the most likely to survive, but surviving individuals with intermediate larval traits grew to the largest size. These results demonstrate that larval traits can have multiple, complex fitness consequences that persist across the metamorphic boundary; and thus post-metamorphic selection pressures may constrain the evolution of larval traits.
Data from: Consistency pays: sex differences and fitness consequences of behavioural specialisation in a wide ranging seabird
Specialists and generalists often coexist within a single population, but the biological drivers of individual strategies are not fully resolved. When sexes differ in their foraging strategy, this can lead them to different environmental conditions and stability across their habitat range. As such, sexual segregation, combined with dominance, may lead to varying levels of specialization between the sexes. Here, we examine spatial and temporal niche width (intraindividual variability in aspects of foraging behaviour) of male and female black-browed albatrosses (Thalassarche melanophrys), and its consequences for fitness. We show that females, where maximum foraging range is under fluctuating selection, exhibit more variable behaviours and appear more generalist than males, who are under directional selection to forage close to the colony. However within each sex, successful birds had a much narrower niche width across most behaviours, suggesting some specialization is adaptive in both sexes. These results demonstrate that while there are sex differences in niche width, the fitness benefit of specialization in spatial distribution is strong in this wide-ranging seabird.
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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)
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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.
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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.