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1,663 results for “BIAS”
Data from: Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding
Amplicon based metabarcoding promises rapid and cost-efficient analyses of species composition. However, it is disputed whether abundance estimates can be derived from metabarcoding due to taxon specific PCR amplification biases. PCR-free approaches have been suggested to mitigate this problem, but come with considerable increases in workload and cost. Here, we analyze multilocus datasets of diverse arthropod communities, to evaluate whether amplification bias can be countered by (1) targeting loci with highly degenerate primers or conserved priming sites, (2) increasing PCR template concentration, (3) reducing PCR cycle number or (4) avoiding locus specific amplification by directly sequencing genomic DNA. Amplification bias is reduced considerably by degenerate primers or targeting amplicons with conserved priming sites. Surprisingly, a reduction of PCR cycles did not have a strong effect on amplification bias. The association of taxon abundance and read count was actually less predictable with fewer cycles. Even a complete exclusion of locus specific amplification did not exclude bias. Copy number variation of the target loci may be another explanation for read abundance differences between taxa, which would affect amplicon based and PCR free methods alike. As read abundance biases are taxon specific and predictable, the application of correction factors allows abundance estimates.
Data from: A full annual perspective on sex-biased migration timing in long-distance migratory birds
In many taxa, the most common form of sex-biased migration timing is protandry – the earlier arrival of males at breeding areas. Here we test this concept across the annual cycle of long-distance migratory birds. Using more than 350 migration tracks of small-bodied trans-Saharan migrants, we quantify differences in male and female migration schedules and test for proximate determinants of sex-specific timing. In spring, males on average departed from the African non-breeding sites about 3 days earlier and reached breeding sites ca. 4 days ahead of females. In autumn, males started migration about 2 days earlier, but this difference did not carry-over to arrival at the non-breeding sites. A cross-species comparison revealed large variation in the level of protandry and protogyny across the annual cycle. While we found tight links between individual timing of departure and arrival within each migration season, only for males the timing of spring migration was linked to the timing of previous autumn migration. In conclusion, our results demonstrate that protandry is not exclusively a reproductive strategy but rather occurs year-round and the two main proximate determinants for the magnitude of sex-biased arrival times in autumn and spring are sex-specific differences in departure timing and migration duration.
Data from: Bias associated with the detectability of the coral-eating pest crown-of-thorns seastar and implications for reef management
Outbreaks of the predator crown-of-thorns seastar (COTS) Acanthaster planci cause widespread coral mortality across the Indo-Pacific. Like many marine invertebrates, COTS is a nocturnal species whose cryptic behaviour during the day can affect its detectability, particularly in structurally complex reef habitats that provide many refuges for benthic creatures. We performed extensive day and night surveys of COTS populations in coral reef habitats showing differing levels of structural complexity and COTS abundance. We tested whether estimations of COTS density varied between day and night observations, and if the differences were related to changes in COTS abundance, reef structural complexity, and the spatial scale of observation. Estimations of COTS density were on average 27% higher at night than during the day. Differences in COTS detection varied with changing seastar abundance but not reef structural complexity or scale of observation. Underestimation of COTS abundance in daytime was significant for a broad seastar density range, thus potentially affecting most outbreak events. Our study suggests that portions of COTS populations can be undetected during conventional surveys and control campaigns, which are exclusively conducted by day, and significantly affect the trajectory of coral reefs. Accounting for bias in COTS detection can strengthen coral reef management broadly.
Data from: Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome
Theoretical work suggests that sexual conflict should promote the maintenance of genetic diversity by the opposing directions of selection on males and females. If such conflict is pervasive, it could potentially lead to genomic heterogeneity in levels of genetic diversity an idea that so far has not been empirically tested on a genome-wide scale. We used large-scale population genomic and transcriptomic data from the collared flycatcher (Ficedula albicollis) to analyse how sexual conflict, for which we use sex-biased gene expression as a proxy, relates to genetic variability. Here, we demonstrate that the extent of sex-biased gene expression of both male-biased and female-biased genes is significantly correlated with levels of nucleotide diversity in gene sequences and that this correlation extends to diversity levels also in intergenic DNA and introns. We find signatures of balancing selection in sex-biased genes but also note that relaxed purifying selection could potentially explain part of the observed patterns. The finding of significant genetic differentiation between males and females for male-biased (and gonad-specific) genes indicates ongoing sexual conflict and sex-specific viability selection, potentially driven by sexual selection. Our results thus indicate that sexual antagonism could potentially be considered as one viable explanation to the long-standing question in evolutionary biology of how genomes can remain so genetically variable in face of strong natural and sexual selection.
Data from: Female-biased dispersal in a bat with a female-defence mating strategy
The ultimate causes for predominant male-biased dispersal (MBD) in mammals and female-biased dispersal (FBD) in birds are still subject to much debate. Studying exceptions to general patterns of dispersal, for example, FBD in mammals, provides a valuable opportunity to test the validity of proposed evolutionary pressures. We used long-term behavioural and genetic data on individually banded Proboscis bats (Rhynchonycteris naso) to show that this species is one of the rare mammalian exceptions with FBD. Our results suggest that all females disperse from their natal colonies prior to first reproduction and that a substantial proportion of males are philopatric and reproduce in their natal colonies, although male immigration has also been detected. The age of females at first conception falls below the tenure of males, suggesting that females disperse to avoid father–daughter inbreeding. Male philopatry in this species is intriguing because Proboscis bats do not share the usual mammalian correlates (i.e. resource-defence polygyny and/or kin cooperation) of male philopatry. They have a mating strategy based on female defence, where local mate competition between male kin is supposedly severe and should prevent the evolution of male philopatry. However, in contrast to immigrant males, philopatric males may profit from acquaintance with the natal foraging grounds and may be able to attain dominance easier and/or earlier in life. Our results on Proboscis bats lent additional support to the importance of inbreeding avoidance in shaping sex-biased dispersal patterns and suggest that resource defence by males or kin cooperation cannot fully explain the evolution of male philopatry in mammals.
Data from: Phenotype-associated inbreeding biases estimates of inbreeding depression in a wild bird population
Inbreeding depression is usually quantified by regressing individual phenotypic values on inbreeding coefficients, implicitly assuming there is no correlation between an individual's phenotype and the kinship coefficient to its mate. If such an association between parental phenotype and parental kinship exists, and if the trait of interest is heritable, estimates of inbreeding depression can be biased. Here we first derive the expected bias as a function of the covariance between mean parental breeding value and parental kinship. Subsequently, we use simulated data to confirm the existence of this bias, and show that it can be accounted for in a quantitative genetic animal model. Finally, we use long-term individual-based data for white-throated dippers (Cinclus cinclus), a bird species in which inbreeding is relatively common, to obtain empirical estimate of this bias. We show that during part of the study period, parents of inbred birds had shorter wings than those of outbred birds, and as wing length is heritable, inbred individuals were smaller, independent of any inbreeding effects. This resulted in the overestimation of inbreeding effects. Similarly, during a period when parents of inbred birds had longer wings, we found that inbreeding effects were underestimated. We discuss how such associations may have arisen in this system, and why they are likely to occur in others, too. Overall, we demonstrate how less biased estimates of inbreeding depression can be obtained within a quantitative genetic framework, and suggest that inbreeding and additive genetic effects should be accounted for simultaneously whenever possible.
Data from: Sex-biased dispersal at different geographical scales in a cooperative breeder from fragmented rainforest
Dispersal affects both social behavior and population structure and is therefore a key determinant of long-term population persistence. However, dispersal strategies and responses to spatial habitat alteration may differ between sexes. Here we analyzed spatial and temporal variation in ten polymorphic microsatellite DNA loci of male and female Cabanis's greenbuls (Phyllastrephus cabanisi), a cooperative breeder of Afrotropical rainforest, to quantify rates of gene flow and fine-grained genetic structuring within and among fragmented populations. We found genetic evidence for female-biased dispersal at small spatial scales, but not at the landscape level. Local autocorrelation analysis provided evidence of positive genetic structure within 300 m distance ranges, which is consistent with behavioral observations of short-distance natal dispersal. At a landscape scale, individual-based autocorrelation values decreased over time while levels of admixture increased, possibly indicating increased gene flow over the past decade.
Data from: Appearance of an early closure of the Isthmus of Panama is the product of biased inclusion of data in the metaanalysis
In their PNAS article "Biological evidence supports an early and complex emergence of the Isthmus of Panama," Bacon et al. (1 - http://dx.doi.org/10.1073/pnas.1423853112) use data from molecular comparisons of terrestrial and marine organisms taken from the literature to estimate dates of rate shifts in migration. One of their conclusions is that "events separating marine organisms in the Atlantic and Pacific oceans [occurred] at ca. 23 and 7 Ma" (1). The authors base this conclusion on two kinds of molecular dating: (i) 31 dates from phylogenies with evolutionary rates calibrated from fossils at one or more nodes, and (ii) 52 dates from mitochondrial divergence between sister species on either side of the Isthmus taken from the review by Lessios (2) (note: complete data are available from the Dryad Digital Repository at http://dx.doi.org/10.5061/dryad.6m653). For the latter, divergence was converted to time by assuming a mitochondrial DNA divergence rate of 2% per million years. Unfortunately, Bacon et al.'s metaanalysis of separations of marine organisms contains unexplained omissions of data and mistakes.
Data from: Ants show a leftward turning bias when exploring unknown nest sites
Behavioural lateralization in invertebrates is an important field of study because it may provide insights into the early origins of lateralization seen in a diversity of organisms. Here, we present evidence for a leftward turning bias in Temnothorax albipennis ants exploring nest cavities and in branching mazes, where the bias is initially obscured by thigmotaxis (wall-following) behaviour. Forward travel with a consistent turning bias in either direction is an effective nest exploration method, and a simple decision-making heuristic to employ when faced with multiple directional choices. Replication of the same bias at the colony level would also reduce individual predation risk through aggregation effects, and may lead to a faster attainment of a quorum threshold for nest migration. We suggest the turning bias may be the result of an evolutionary interplay between vision, exploration and migration factors, promoted by the ants' eusociality.
Data from: Genotyping-by-sequencing for estimating relatedness in non-model organisms: avoiding the trap of precise bias
There has been remarkably little attention to using the high resolution provided by genotyping-by-sequencing (i.e. RADseq and similar methods) datasets for assessing relatedness in wildlife populations. A major hurdle is the genotyping error, especially allelic dropout, often found in this type of dataset that could lead to downward-biased, yet precise, estimates of relatedness. Here we assess the applicability of genotyping-by-sequencing datasets for relatedness inferences given their relatively high genotyping error rates. Individuals of known relatedness were simulated under genotyping error, allelic dropout, and missing data scenarios based on an empirical ddRAD dataset, and their true relatedness was compared to that estimated by seven relatedness estimators. We found that an estimator chosen through such analyses can circumvent the influence of genotyping error, with the estimator of Ritland (1996) shown to be unaffected by allelic dropout and to be the most accurate when there is genotyping error. We also found that the choice of estimator should not rely solely on the strength of correlation between estimated and true relatedness as a strong correlation does not necessarily mean estimates are close to true relatedness. We also demonstrated how even a large SNP dataset with genotyping error (allelic dropout or otherwise) or missing data still performs better than a perfectly genotyped microsatellite dataset of tens of markers. The simulation-based approach used here can be easily implemented by others on their own genotyping-by-sequencing datasets to confirm the most appropriate and powerful estimator for their dataset.
Data from: Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias
Studies of insect assemblages are suited to the simultaneous DNA-based identification of multiple taxa known as metabarcoding. To obtain accurate estimates of diversity, metabarcoding markers ideally possess appropriate taxonomic coverage to avoid PCR-amplification bias, as well as sufficient sequence divergence to resolve species. We used in silico PCR to compare the taxonomic coverage and resolution of newly designed insect metabarcodes (targeting 16S) with that of existing markers (16S and COI) and then compared their efficiency in vitro. Existing metabarcoding primers amplified in silico less than 75% of insect species with complete mitochondrial genomes available, whereas new primers targeting 16S provided greater than 90% coverage. Furthermore, metabarcodes targeting COI appeared to introduce taxonomic PCR-amplification bias, typically amplifying a greater percentage of Lepidoptera and Diptera species, while failing to amplify certain orders in silico. To test whether bias predicted in silico was observed in vitro, we created an artificial DNA blend containing equal amounts of DNA from 14 species, representing 11 different insect orders and one arachnid. We PCR-amplified the blend using five primers sets, targeting either COI or 16S, with high-throughput amplicon sequencing yielding more than 6 million reads. In vitro results typically corresponded to in silico PCR predictions, with newly designed 16S primers detecting 11 insect taxa present, thus providing equivalent or better taxonomic coverage than COI metabarcodes. Our results demonstrate that in silico PCR is a useful tool for predicting taxonomic bias in mixed template PCR, and that researchers should be wary of potential bias when selecting metabarcoding markers.
Data from: Microwear-mesowear congruence and mortality bias in rhinoceros mass death assemblages
Although we do not know the cause of death of most fossils, mortality is often associated with ecological stress due to seasonality and other stochastic events (storms, volcanism) that may have caused shifts in feeding ecology preceding death. In these instances, dental microwear, which reflects feeding ecology in a narrow window of time, may provide a biased view of diet. Mesowear, another dental wear proxy based on the morphology of worn cusps, requires macroscopic amounts of dental wear and reflects diet for a longer interval and may be less prone to bias from near-death ecological stress. We compared congruence between microwear and mesowear of North American fossil rhinocerotid mass death assemblages and hunted collections of modern rhinocerotids to test the hypothesis that fossil assemblages yield more incongruous microwear and mesowear results as a result of near-death ecological disturbances. In extant rhinos, both microwear and mesowear are associated with diet and height of the feeding environment. Mesowear and microwear in the modern rhinocerotid collections are statistically correlated with strong relationships between average mesowear scores and labially distributed dental microwear. In contrast, a statistical relationship between mesowear and microwear was not observed among the fossil rhinocerotid assemblages. Mesowear suggests the fossil rhinos had low abrasion diets, suggesting they fed from clean, possibly tall vegetation. Some, but not all mass death assemblages produce microwear data with excessive scratches and/or pits compared to expectations based on mesowear results, suggesting that dental microwear was altered shortly before death in some but not all of the fossil assemblages. The dental wear proxies available to paleoecologists provide a mosaic of dietary evidence reflecting diet over long (mesowear) and more abbreviated (microwear) periods of time that, together, provide a richer understanding of feeding ecology and its relationship to environment, seasonal change, and other ecological disturbances.
Data from: How far is too close? Restricted, sex-biased dispersal in black-capped vireos
Understanding the interplay of dispersal and how it translates into gene flow is key to understanding population processes, and especially so for endangered species occupying fragmented habitats. In migratory songbirds, there is evidence that long-distance movement capabilities are not highly related to observed dispersal. Our objectives were to 1) define the fine-scale spatial genetic structure in the endangered black-capped vireos to shed light on dispersal patterns, and 2) to relate dispersal dynamics to overall population genetic structure using a simulation approach. We sampled 160 individuals over two years to describe the fine-scale genetic structuring, and used this information to model scenarios to compare with actual data on change in population structuring over a 100-year interval. We found that black-capped vireo exhibit male-philopatry, and restricted dispersal distances, relative to females. Our simulations support a sex-biased dispersal model. Additionally, we find that fragmentation related changes in rates of dispersal might be a likely cause for increasing levels of population structure over a 100-year period. We show that restricted dispersal can explain population structuring in this species, and that changes in dispersal rates due to fragmentation may be a continuing threat to genetic viability in this species.
Data from: Sex-biased avian host use by arbovirus vectors
Prevalence of arthropod-borne parasites often differs drastically between host sexes. This sex-related disparity may be related to physiological (primarily hormonal) differences that facilitate or suppress replication of the pathogen in host tissues. Alternately, differences in pathogen prevalence between host sexes may be owing to differential exposure to infected vectors. Here, we report on the use of PCR-based assays recognizing bird sex chromosomes to investigate sex-related patterns of avian host use from field-collected female mosquitoes from Florida, USA. Mosquitoes took more bloodmeals from male birds (64.0% of 308 sexed samples) than female birds (36.0%), deviating significantly from a hypothetical 1:1 sex ratio. In addition, male-biased host use was consistent across mosquito species (Culex erraticus (64.4%); Culex nigripalpus (61.0%) and Culiseta melanura (64.9%)). Our findings support the hypothesis that sex-biased exposure to vector-borne pathogens contributes to disparities in parasite/pathogen prevalence between the sexes. While few studies have yet to investigate sex-biased host use by mosquitoes, the methods used here could be applied to a variety of mosquito-borne disease systems, including those that affect health of humans, domestic animals and wildlife. Understanding the mechanisms that drive sex-based disparities in host use may lead to novel strategies for interrupting pathogen/parasite transmission.
Data from: Population structure and male-biased dispersal in the short-tail stingray Bathytoshia brevicaudata (Myliobatoidei: Dasyatidae)
Selective pressures driving dispersal in vagile species often differ between males and females, resulting in sex-biased dispersal. Male-biased dispersal is common in mammals, where there is greater reproductive investment by females, and there is emerging evidence for a similar pattern in elasmobranchs. We examine the population structure of the short-tail stingray (Bathytoshia brevicaudata), a large, viviparous coastal species common in southern hemisphere waters. Using 11 nuclear (nDNA) microsatellite markers from 202 individuals in comparison to mitochondrial (mtDNA) data reported by Le Port and Lavery (J Hered 103:174–185, 2012), we elucidate patterns of dispersal at both southern hemisphere and New Zealand scales. At a global scale, estimates of population differentiation were comparable across marker types (microsatellite FST = 0.148, p < 0.001, mtDNA ϕST = 0.67, p < 0.001). In contrast, New Zealand structure was much weaker for microsatellite markers (FST = 0.0026, p > 0.05) than for mtDNA (ϕST = 0.054, p < 0.05). Female-only data displayed a greater degree of population differentiation from both nDNA and mtDNA compared to male-only data, and population assignment tests indicated that males were significantly more likely to be immigrants to the population from which they were sampled. We estimate that within New Zealand, male-mediated gene flow is at least fivefold greater than female-mediated gene flow. This molecular evidence for sex-biased dispersal in a batoid species adds further support to male-biased dispersal as a recurrent pattern in viviparous elasmobranchs. Many elasmobranch species are vulnerable to extinction, and understanding movement patterns is crucial to management of threatened populations.
Data from: Dissociable sensitivity and bias mechanisms mediate behavioral effects of exogenous attention
Attention can be directed endogenously, based on task-relevant goals, or captured exogenously, by salient stimuli. While recent studies have shown that endogenous attention can facilitate behavior through dissociable sensitivity (sensory) and choice bias (decisional) mechanisms, it is unknown if exogenous attention also operates through dissociable sensitivity and bias mechanisms. We tested human participants on a multialternative change detection task with exogenous attention cues, which preceded or followed change events in close temporal proximity. Analyzing participants' behavior with a multidimensional signal detection model revealed clear dissociations between exogenous cueing effects on sensitivity and bias. While sensitivity was, overall, lower at the cued location compared to other locations, bias was highest at the cued location. With an appropriately designed post-cue control condition, we discovered that the attentional effect of exogenous pre-cueing was to enhance sensitivity proximal to the cue. In contrast, exogenous attention enhanced bias even for distal stimuli in the cued hemifield. Reaction time effects of exogenous cueing could be parsimoniously explained with a diffusion-decision model, in which drift rate was determined by independent contributions from sensitivity and bias at each location. The results suggest a mechanistic schema of how exogenous attention engages dissociable sensitivity and bias mechanisms to shape behavior.
Data from: Genetic diversity, population structure and sex-biased dispersal in three co-evolving species
Genetic diversity and spatial structure of populations are important for antagonistic coevolution. We investigated genetic variation and population structure of three closely related European ant species: the social parasite Harpagoxenus sublaevis and its two host species Leptothorax acervorum and Leptothorax muscorum. We sampled populations in 12 countries and analyzed eight microsatellite loci and an mtDNA sequence. We found high levels of genetic variation in all three species, only slightly less variation in the host L. muscorum. Using a newly introduced measure of differentiation (Jost's DEST), we detected strong population structuring in all species and less male-biased dispersal than previously thought. We found no phylogeographic patterns that could give information on post-glacial colonization routes - northern populations are as variable as more southern populations. We conclude that conditions for Thompson's geographic mosaic of coevolution are ideal in this system: all three species show ample genetic variation and strong population structure.
Data from: No place like home? A test of the natal habitat-biased dispersal hypothesis in Scandinavian wolves
Natal dispersal is an important mechanism for the viability of populations. The influence of local conditions or experience gained in the natal habitat could improve fitness if dispersing individuals settle in an area with similar habitat characteristics. This process, defined as "natal habitat-biased dispersal" (NHBD), has been used to explain distribution patterns in large carnivores, but actual studies evaluating it are rare. We tested whether gray wolf Canis lupus territory establishment was influenced by the habitat characteristics of the natal territory using the long-term monitoring of the Scandinavian wolf population. We paired the locations of natal and established territories, accounted for available habitats along the dispersing route, and compared their habitat characteristics for 271 wolves during 1998-2012. Wolves with the shortest dispersal distances established in natal-like habitat types more than expected by chance, whereas wolves that dispersed longer distances did not show NHBD. The pattern was consistent for male and female wolves, with females showing more NHBD than males. Chances to detect NHBD increased with the size of habitat defined as available. This highlights the importance of considering the biological characteristics of the studied species when defining habitat availability. Our methodological approach can prove useful to inform conservation and management to identify habitats to be selected by reintroduced or naturally expanding populations.
Data from: A further cost for the sicker sex? Evidence for male-biased parasite-induced vulnerability to predation
Males are typically the sicker sex. Data from multiple taxa indicate that they are more likely to be infected with parasites, and are less "tolerant," or less able to mitigate the fitness costs of a given infection, than females. One cost of infection for many animals is an increased probability of being captured by a predator. A clear, hitherto untested, prediction is therefore that this parasite-induced vulnerability to predation is more pronounced among males than females. We tested this prediction in the sexually size dimorphic guppy, Poecilia reticulata, in which females are typically larger than males. We either sham or experimentally infected guppies with Gyrodactylus turnbulli, elicited their escape response using an established protocol and measured the distance they covered during 60 ms. To discriminate between the effects of body size and those of other inherent sex differences, we size-matched fish across treatment groups. Infection with G. turnbulli reduced the distance covered during the escape response of small adults by 20.1%, whereas that of large fish was unaffected. This result implies that parasite-induced vulnerability to predation is male-biased in the wild: although there was no difference in escape response between our experimentally size-matched groups of males and females, males are significantly smaller across natural guppy populations. These results are consistent with Bateman's principle for immunity: Natural selection for larger body sizes and longevity in females seems to have resulted in the evolution of increased infection tolerance. We discuss the potential implications of sex- and size-biased parasite-induced vulnerability to predation for the evolutionary ecology of this host–parasite interaction in natural communities.
Data from: Breaking down the lithification bias: the effect of preferential sampling of larger specimens on the estimate of species richness, evenness, and average specimen size
Lithification, the transition of unconsolidated sediments to fully indurated rocks, can potentially bias estimates of species richness, evenness, and body size distribution derived from fossil assemblages. Fossil collections made from well-indurated rocks consistently exhibit lower species richness, lower evenness, and a specimen size distribution skewed towards larger specimens relative to collections made from unconsolidated sediments, even when collections are drawn from the same assemblage. This phenomenon is known as the lithification bias. While the bias itself has been demonstrated empirically, much less attention has been paid to its causes. Proposed causes include taphonomic processes (e.g., destruction of small specimens during early diagenesis) or methodological differences (e.g., sieving vs. counting specimens on outcrops, bedding surfaces, or mechanically split surfaces). Here we investigate the potential effects of preferential intersection that could also result in a methodologically related bias: the preferential sampling of larger specimens relative to smaller ones when fossils are counted on rock surfaces. We used an analog model to simulate preferential intersection (fossil collection via splitting fossiliferous rock) and compare the results to a random draw model that approximates the effects of sieving. The model was parameterized using nine different combinations of species abundance and species size distributions. The results show that, with rare exceptions, species richness is 5–23% lower, evenness 5-25% lower, and average specimen size 24–150% higher in preferential intersection than in random draw simulations. We conclude that preferential intersection can impose a significant bias independent of other mechanisms (e.g., preferential destruction of smaller specimens during diagenetic or sampling processes), that the magnitude of this bias is partially dependent on the species abundance and size distributions, and that this bias alone does not fully account for empirically observed lithification bias on species richness (i.e., other sources of bias are also at work).
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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.
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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.