Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
808
datasets available to search
ShareScore release 0.9.0
Dataset results
808 results for “dogs”
Data from: Catch the wave: prairie dogs assess neighbours' awareness using contagious displays
The jump–yip display of black-tailed prairie dogs (Cynomys ludovicianus) is contagious, spreading through a prairie dog town as 'the wave' through a stadium. Because contagious communication in primates serves to assess conspecific social awareness, we investigated whether instigators of jump–yip bouts adjusted their behaviour relative to the response of conspecifics recruited to display bouts. Increased responsiveness of neighbouring town members resulted in bout initiators devoting a significantly greater proportion of time to active foraging. Contagious jump–yips thus function to assess neighbours' alertness, soliciting social information to assess effective conspecific group size in real time and reveal active probing of conspecific awareness consistent with theory of mind in these group-living rodents.
Data from: Evaluating the performance of selection scans to detect selective sweeps in domestic dogs
Selective breeding of dogs has resulted in repeated artificial selection on breed-specific morphological phenotypes. A number of quantitative trait loci associated with these phenotypes have been identified in genetic mapping studies. We analyzed the population genomic signatures observed around the causal mutations for 12 of these loci in 25 dog breeds, for which we genotyped 25 individuals in each breed. By measuring the population frequencies of the causal mutations in each breed, we identified those breeds in which specific mutations most likely experienced positive selection. These instances were then used as positive controls for assessing the performance of popular statistics to detect selection from population genomic data. We found that artificial selection during dog domestication has left characteristic signatures in the haplotype and nucleotide polymorphism patterns around selected loci that can be detected in the genotype data from a single population sample. However, the sensitivity and accuracy at which such signatures were detected varied widely between loci, the particular statistic used, and the choice of analysis parameters. We observed examples of both hard and soft selective sweeps and detected strong selective events that removed genetic diversity almost entirely over regions >10 Mbp. Our study demonstrates the power and limitations of selection scans in populations with high levels of linkage disequilibrium due to severe founder effects and recent population bottlenecks.
Data from: Denning habits of free-ranging dogs reveal preference for human proximity
Dens are crucial in the early development of many mammals, making den site selection an important component of parental care in such species. Resource availability and shelter from predators primarily govern den selection. Species inhabiting human-dominated landscapes typically den away from human disturbance, often shifting dens to avoid humans during the early life of their young. Domesticated dogs have evolved in human proximity over centuries, being bred and reared in human homes for generations. While pets rely on their owners for shelter and care, free-ranging dogs roam uncared, and typically whelp in dens. We conducted a study on 148 free-ranging dog dens in India to understand their denning habits. Distance from resources influenced den choice, but anthropogenic disturbance did not. Dens were found in areas of high human activity, and begging from humans was preferred over scavenging. A study on 15 pregnant females revealed that females actively searched for denning sites, rejecting several intermediate ones before selecting the final den. We propose that the obvious preference of dogs for denning close to humans is a behavioural adaptation that helps them to survive in the urban landscape, in spite of the high human induced mortality during the early life of pups.
Data from: True colors: commercially-acquired morphological genotypes reveal hidden allele variation among dog breeds, informing both trait ancestry and breed potential
<p>Direct-to-consumer canine genetic testing is becoming increasingly popular among dog owners. The data collected therein provides intriguing insight into the current status of morphological variation present within purebred populations. Mars WISDOM PANEL<sup>TM</sup> data from 11,790 anonymized dogs, representing 212 breeds and 4 wild canine species, were evaluated at genes associated with 7 coat color traits and 5 physical characteristics. Frequencies for all tested alleles at these 12 genes were determined by breed and by phylogenetic grouping. A sub-set of the data, consisting of 30 breeds, was divided into separate same-breed populations based on country of collection, body size, coat variation, or lineages selected for working or conformation traits. Significantly different (p ≤ 0.00167) allele frequencies were observed between populations for at least one of the tested genes in 26 of the 30 breeds. Next, standard breed descriptions from major American and international registries were used to determine colors and tail lengths (e.g. genetic bobtail) accepted within each breed. Alleles capable of producing traits incongruous with breed descriptions were observed in 143 breeds, such that random mating within breeds has probabilities of between 4.9e<sup>-7</sup> and 0.25 of creating undesirable phenotypes. Finally, the presence of rare alleles within breeds, such as those for the recessive black coloration and natural bobtail, was combined with previously published identity-by-decent haplotype sharing levels to propose pathways by which the alleles may have spread throughout dog breeds. Taken together, this work demonstrates that: 1) the occurrence of low frequency alleles within breeds can reveal the influence of regional or functional selection practices; 2) it is possible to trace the mode by which characteristics have spread across breeds during historical breed formation; and 3) the necessity of addressing conflicting ideals in breed descriptions relative to actual genetic potential is crucial.</p>
Data from: Diet adaptation in dog reflects spread of prehistoric agriculture
Adaptations allowing dogs to thrive on a diet rich in starch, including a significant AMY2B copy number gain, constituted a crucial step in the evolution of the dog from the wolf. It is however not clear if this change was associated with the initial domestication or represents a secondary shift related to the subsequent development of agriculture. Previous efforts to study this process were based on geographically limited data sets and low-resolution methods and it is therefore not known to what extent the diet adaptations are universal among dogs and whether there are regional differences associated with alternative human subsistence strategies. Here we use droplet PCR to investigate worldwide AMY2B copy number diversity among indigenous as well as breed dogs and wolves to elucidate how a change in dog diet was associated with the domestication process and subsequent shifts in human subsistence. We find that AMY2B copy numbers are bimodally distributed with high copy numbers (median 2nAMY2B=11) in a majority of dogs but no, or few, duplications (median 2nAMY2B=3) in a small group of dogs originating mostly in Australia and the arctic. We show that this patterns correlates geographically to the spread of prehistoric agriculture and conclude that the diet change may not have been associated with initial domestication but rather the subsequent development and spread of agriculture to most, but not all regions of the globe.
Data from: A genome-wide association study identifies a region strongly associated with symmetrical onychomadesis on chromosome 12 in dogs
Symmetrical onychomadesis causes periodic loss of claws in otherwise healthy dogs. Genome-wide association analysis in 225 Gordon Setters identified a single region associated with symmetrical onychomadesis on chromosome 12 (spanning about 3.3 mb). A meta-analysis including also English Setters indicated that this genomic region predisposes for symmetrical onychomadesis in English Setters as well. The associated region spans most of the major histocompatibility complex and nearly 1 Mb downstream. Like many other autoimmune diseases, associations of symmetrical onychomadesis with DLA class II alleles have been reported. In this study, no associated markers were revealed within any of the DLA-DRB1, -DQA1 or -DQB1 genes, and the odds for symmetrical onychomadesis in the Gordon Setters were much higher, carrying significant single nucleotide polymorphisms compared to the odds of any of the recorded DLA-DRB1/DQA1/DQB1 haplotypes. We noticed that some of the associated DLA haplotypes were different between the English Setters and the Gordon Setters. Interestingly, associated SNP chip markers showed a more consistent pattern of allelic variants related to cases or controls regardless of breed. In conclusion, the associated genetic markers identified in this study hold the potential to aid in selection of breeding animals to reduce the frequency of symmetrical onychomadesis in the dog.
Data from: Den site selection, pack composition, and reproductive success in endangered African wild dogs
Habitat quality is often assumed to be directly related to increased consumer density, but such assumptions cannot be made without supporting demographic data that indicate improved fitness. Habitat selection might be especially important for denning species, where vulnerable offspring are confined to a single location for extended periods, but the effect of den choice on the reproductive success of denning species is poorly understood. By combining airborne high-resolution Light Detection and Ranging (LiDAR) measurements with data on pack composition, we investigated den site selection by endangered African wild dogs in Hluhluwe-iMfolozi Park, South Africa, examining whether habitat selection based on ecological factors resulted in increased litter sizes and thus reproductive success compared with social factors known to be important. Although there was selection for den sites in areas of increased terrain ruggedness and vegetation density, only vegetation density was associated with larger litter sizes and translated into increased reproductive success. Moreover, pack size was only influential when a minimum vegetation density around den sites was achieved, indicating that although social variables have a powerful effect on reproductive success, they are mediated by ecological factors defining habitat quality. Our results demonstrate the importance of distinguishing between density- and fitness-based indicators of habitat quality, and how this can affect management actions, particularly for endangered species conservation.
Data from: Untargeted metabolomic profiling of urine from healthy dogs and dogs with chronic hepatic disease
Chronic hepatic disease can present a diagnostic challenge with different etiologies being associated with similar clinical and laboratory findings. The histopathological assessment of a liver biopsy specimen is usually required in order to make a definitive diagnosis and the availability of non-invasive prognostic biomarkers is limited. The emerging science of metabolomics is used to detect changes in endogenous low molecular weight metabolites in biological samples and offers the possibility of identifying noninvasive markers of disease. The objective of this study was to investigate differences in the urine metabolome between healthy dogs, dogs with chronic hepatitis, dogs with hepatocellular carcinoma, and dogs with a congenital portosystemic shunt. Stored urine samples from 10 healthy dogs, 10 dogs with chronic hepatitis, 6 dogs with hepatocellular carcinoma, and 5 dogs with a congenital portosystemic shunt were analyzed. The urine metabolome was analyzed by gas chromatography – quadrupole time of flight mass spectrometry and 220 known metabolites were identified. Principal component analysis and heat dendrogram plots of the metabolomics data showed clustering between groups. Random forest analysis showed differences in the abundance of various metabolites including putrescine, gluconic acid, sorbitol, and valine. Based on univariate statistics, 37 metabolites were significantly different between groups. In, conclusion, the urine metabolome varies between healthy dogs, dogs with chronic hepatitis, dogs with hepatocellular carcinoma, and dogs with a congenital portosystemic shunt. Further targeted assessment of these metabolites is needed to assess their diagnostic utility.
The Jennings Dogs
 [HR Object](https://skfb.ly/OrYs) (693k tris) displayed in the [British Museum online collection](http://bit.ly/1sqKDUa).  Remeshing with Instant Meshes and Decimate planar (-> 3.1k tris), texturing by mixing PBR textures. Baking done entirely in blender for the PBR maps. The mesh resolution is a bit low on this model, but the result still looks fine in my opinion for tests :)  Source: Objaverse 1.0 / Sketchfab
A catalog of genes, genomes and species of the dog (Canis lupus familiaris) intestinal microbiota
<p></p><h1>Data sources</h1><br>This dataset was constructed using metagenomic sequencing data from the bioproject PRJEB20308 from Coelho et al. 2018 (129 samples)<br><h1>Metagenomic assembly</h1><br>First, sequencing adapters removal and read trimming was performed with fastp. Reads mapped on the host genome (ROS_Cfam_1.0 GCF_014441545.1) with bowtie2 were removed with samtools. Finally, Metagenomic assembly was performed with metaSPAdes. Contigs of less than 1500 bp were removed.<br><h1>MAGs recovery</h1><br>MAGs were generated with COMEBin (multi-coverage mode) and MAGs quality was assessed with CheckM2. MAGs with completeness < 70% or contamination > 5% or N50 < 5Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%).<br><h1>Non-redundant gene catalog</h1><br>Genes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.<br><h1>MSPs recovery</h1><br>Reads were aligned against the non-redundant gene catalog with the Meteor software suite to produce a raw gene abundance table (1,0M genes quantified in 129 samples). Then, co-abundant genes were binned in 234 Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer.<br><h1>MAGs and MSPs taxonomic annotation</h1><br>Dereplicated MAGs were annotated with GTDB-Tk based on GTDB r220. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs.<br><h1>Construction of the phylogenetic tree</h1><br>39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).<h1>Mapping rate distribution across public cohorts</h1>We generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJEB20308 (cohort used in catalogue assembly) and PRNJNA714112 (independent cohort not used in assembly).<p></p>
Canine 230K Consortium chip data originated from the drug detection dogs
<p>Drug detection dogs play integral roles in society. However, the interplay between their behaviors and genetic characteristics underlying their performance remains uninvestigated. Herein, more than 120,000 genetic variants were evaluated in 326 German Shepherd or Labrador Retriever dogs to profile the genetic traits associated with various behavioral traits related to the successful training of drug detection dogs.</p>
The Dog with Three Names
This marble Molossian Hound is a Roman copy of the Hellenistic Greek original. #jenningsdog #duncombedog #dogofalcibiades The sculpture [2001,1010.1](https://www.britishmuseum.org/research/collection_online/collection_object_details.aspx?objectId=467443&partId=1)) can be found in Gallery 22 at the British Museum. 3D model photographed and processed by students as part of the [3D Training Session](http://jwexlerbm.github.io/festivalofarchaeology/), Festival of Archaeology organised by the [Council for British Archaeology](http://new.archaeologyuk.org/). Source: Objaverse 1.0 / Sketchfab
Dog Effigy Tetrapodal Pot (2535p16)
**Dog effigy tetrapodal pot** Location: Panama. Period: Chiriqui culture, period unknown. Material: ceramic. Dimensions: length, 17.8 cm; width, 12.3 cm; height, 12.0 cm. Notes: Catalog no. 2535p16, North Carolina Archaeological Collection, Research Laboratories of Archaeology, University of North Carolina at Chapel Hill. Model by Abigail Gancz. Source: Objaverse 1.0 / Sketchfab
dogs_vs_cats_subset_kaggle
<p>This is a subset of the well known image classification dataset for cats and dogs made by kaggle.</p> <p>https://www.microsoft.com/en-us/download/details.aspx?id=54765</p> <p>This dataset contains 1000 training images (500 cats & 500 dogs), 200 validation images (100 cats/100 dogs) and 100 unlabelled test images.</p> <p>There are other similar dataset already on zenodo like this https://zenodo.org/doi/10.5281/zenodo.5226944, but that dataset is not balanced even though it claims to be.</p> <p> </p> <p> </p>
Metagenome-assembled genomes generated from dog dental plaque microbiome
<p>Metagenome-assembled genomes generated from dog dental plaque microbiome from the study "Newly identified species from the dog dental plaque microbiome highlight little overlap with humans"</p>
Distribution. Sub-Saharan Africa; virtually eradicated from W Africa, and greatly reduced in C and NE Africa. The largest populations exist in Botswana, Tanzania, and Zimbabwe, which account for approximately half of the estimated number of African Wild Dogs remaining in the wild. Other populations occur in Central African Republic, Ethiopia, Kenya, Mozambique, Namibia, South Africa, Sudan, and Zambia. Potential small populations (less than 100 individuals) may exist in Cameroon, Chad, Senegal, and Somalia. in Canidae
Distribution. Sub-Saharan Africa; virtually eradicated from W Africa, and greatly reduced in C and NE Africa. The largest populations exist in Botswana, Tanzania, and Zimbabwe, which account for approximately half of the estimated number of African Wild Dogs remaining in the wild. Other populations occur in Central African Republic, Ethiopia, Kenya, Mozambique, Namibia, South Africa, Sudan, and Zambia. Potential small populations (less than 100 individuals) may exist in Cameroon, Chad, Senegal, and Somalia.
Determining the efficacy of camera traps, live capture traps, and detection dogs for locating cryptic small mammal species
<p>Metal box (e.g., Elliott, Sherman) traps and remote cameras are two of the most commonly employed methods presently used to survey terrestrial mammals. However, their relative efficacy at accurately detecting cryptic small mammals has not been adequately assessed. The present study therefore compared the effectiveness of metal box (Elliott) traps and vertically oriented, close range, white flash camera traps in detecting small mammals occurring in the Scenic Rim of eastern Australia. We also conducted a preliminary survey to determine effectiveness of a conservation detection dog (CDD) for identifying presence of a threatened carnivorous marsupial, <i>Antechinus arktos,</i> in present-day and historical locations, using camera traps to corroborate detections. 200 Elliott traps and 20 white flash camera traps were set for four deployments per method, across a site where the target small mammals, including <i>A. arktos</i>, are known to occur. Camera traps produced higher detection probabilities than Elliott traps for all four species. Thus, vertically mounted white flash cameras were preferable for detecting the presence of cryptic small mammals in our survey. The CDD, which had been trained to detect <i>A. arktos</i> scat, indicated in total 31 times when deployed in the field survey area, with subsequent camera trap deployments specifically corroborating <i>A. arktos</i> presence at 100% (3) indication locations. Importantly, the dog indicated twice within Border Ranges National Park, where historical (1980s-1990s) specimen-based records indicate the species was present, but extensive Elliott and camera trapping over the last 5-10 years have resulted in zero <i>A. arktos</i> captures. Camera traps subsequently corroborated <i>A. arktos</i> presence at these sites. This demonstrates that detection dogs can be a highly effective means of locating threatened, cryptic species, especially when traditional methods are unable to detect low-density mammal populations.</p>
African wild dog access to kills
<p>Patterns of food sharing in collectively hunting species are likely to influence social dynamics and evolution. Despite this, little is known about competition within social groups at carcasses and other food sources, making the social drivers and implications of food sharing difficult to assess. We quantified carcass access and feeding behavior in free-ranging African wild dogs, <i>Lycaon pictus</i>, at natural kill sites, confirming and quantifying previous descriptions of a youngest-feed-first system. Using data on feeding duration and latency to feed, we confirm that the position in the feeding queue (PFQ) runs from youngest to oldest, except the dominant pair, which generally feed after the pups. We found some evidence that older subdominants were more likely to participate in kills, perhaps because they may only gain access to carcasses at the most profitable early stages of consumption if they make the kill themselves. These dogs were no more likely to initiate hunts or sustain probable hunting-related injuries than were younger dogs with better access. We suggest that allowing younger animals uncontested access to food they have not caught themselves may be an extension of helping behaviour prioritizing those least able to catch food themselves, and that this system may provide anti-kleptoparasitism benefits. Our results contribute to the discussion on the functions and importance of food sharing more broadly.</p>
High pitch sounds small for domestic dogs dataset
<p>Humans possess intuitive associations linking certain non-redundant features of stimuli – e.g., high-pitched sounds with small object-size (or similarly, <i>low</i>-pitched sounds with <i>large</i> object-size). This phenomenon, known as crossmodal correspondence, has been identified in humans across multiple different senses. There is some evidence that non-human animals also form crossmodal correspondences, but the known examples are mostly limited to the associations between the pitch of vocalisations and the size of callers. To investigate whether domestic dogs, like humans, show abstract pitch-size association, we first trained dogs to approach and touch an object after hearing a sound emanating from it. Subsequently, we repeated the task but presented dogs with <i>two</i> objects differing in size, only one of which was playing a sound. The sound was either high- or low-pitched, thereby creating trials that were either congruent (high-pitch from small object; low-pitch from large objects) or incongruent (the reverse). We found that dogs reacted faster on congruent versus incongruent trials. Moreover, their accuracy was at chance on incongruent trials, but significantly above chance for congruent trials. Our results suggest that non-human animals show abstract pitch-sound correspondences, indicating these correspondences may not be uniquely human but rather a sensory processing feature shared by other species.</p>
Fig. 1 in Blautia argi sp. nov., a new anaerobic bacterium isolated from dog faeces
Fig. 1. Phylogenetic consensus tree based on 16S rRNA gene sequences, reconstructed with the neighbour-joining (NJ), maximumparsimony (MP) and maximum-likelihood (ML) algorithms, indicating the taxonomic positions of isolates and close relatives. Bootstrap values (>70 %, NJ/MP/ML) calculated for 1000 subsets are shown at branch nodes. Atopobium minutum served as an outgroup. Bar, 0.02 subsitutions per nucleotide position.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.