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903
datasets available to search
ShareScore release 0.9.0
Dataset results
903 results for “Domestication”
A Single Cell Transcriptome Atlas of The Domestic Pig
GEO Series GSE193975. Sus scrofa domesticus. 45 samples. Type: Expression profiling by high throughput sequencing.
Domestication causes large-scale effects on gene expression in rainbow trout: Analysis of the liver transcriptome
GEO Series GSE16897. Osmerus mordax; Coregonus clupeaformis; Oncorhynchus tshawytscha; Oncorhynchus mykiss; Salmo salar. 14 samples. Type: Expression profiling by array.
A single-cell analysis of nasal epithelial cells development in domestic pig
GEO Series GSE274334. Sus scrofa. 2 samples. Type: Expression profiling by high throughput sequencing.
Teosinte Pollen Drive guides maize domestication and evolution by RNA interference [dna_single_pollen]
GEO Series GSE234920. Zea mays subsp. mays x Zea mays subsp. mexicana. 377 samples. Type: Other.
Evolutionary and functional genomics of DNA methylation in maize domestication and improvement
GEO Series GSE145586. Zea mays. 74 samples. Type: Other; Methylation profiling by high throughput sequencing.
MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication
GEO Series GSE254496. Zea mays subsp. parviglumis; Zea mays. 226 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Replication package for ``Trade and Domestic Production Networks"
<p>This package contains the code and public access data used to produce the figures and tables in Dhyne, Kikkawa, Mogstad, and Tintelnot (forthcoming), Trade and Domestic Production Networks, Review of Economic Studies. </p>
Data from: DNA metabarcoding reveals diet overlap between the endangered Walia ibex and domestic goats - implications for conservation
Human population expansion and associated degradation of the habitat of many wildlife species cause loss of biodiversity and species extinctions. The small Simen Mountains National Park in Ethiopia is one of the last strongholds for the preservation of a number of afro-alpine mammals, plants and birds, and it is home to the rare endemic Walia ibex, Capra walie. The narrow distribution range of this species as well as potential competition for resources with livestock, especially with domestic goat, Capra hircus, may compromise its future survival. Based on a curated afro-alpine taxonomic reference library constructed for plant taxon identification, we investigated the diet of the Walia ibex and addressed the dietary overlap with domestic goat using DNA metabarcoding of faecal samples. Faeces of both species were collected from different localities in the National Park. We show that both species are browsers, with forbs, shrubs and trees comprising the largest proportion of their diet, supplemented by grasses. There was a considerable overlap in dietary preferences. Several of the preferred diet items of the Walia ibex (Alchemilla sp., Hypericum revolutum, Erica arborea and Rumex sp.) were also among the most preferred diet items of the domestic goat. These results indicate that there is potential for competition between the two species, especially during the dry season, when resources are limited. Our findings, in combination with the expected increase in domestic herbivores, suggest that management plans should consider the potential threat posed by domestic goats to ensure future survival of the endangered Walia ibex.
Data from: Mixed-ancestry and admixture in Kaua'i's feral chickens: invasion of domestic genes into ancient Red Junglefowl reservoirs?
A major goal of invasion genetics is to determine how establishment histories shape non-native organisms' genotypes and phenotypes. While domesticated species commonly escape cultivation to invade feral habitats, few studies have examined how this process shapes feral gene pools and traits. We collected genomic and phenotypic data from feral chickens (Gallus gallus) on the Hawaiian island of Kauai to (i) ascertain their origins and (ii) measure standing variation in feral genomes, morphology and behaviour. Mitochondrial phylogenies (D-loop & whole Mt genome) revealed two divergent clades within our samples. The rare clade also contains sequences from Red Junglefowl (the domestic chicken's progenitor) and ancient DNA sequences from Kauai that predate European contact. This lineage appears to have been dispersed into the east Pacific by ancient Polynesian colonists. The more prevalent MtDNA clade occurs worldwide and includes domesticated breeds developed recently in Europe that are farmed within Hawaii. We hypothesize this lineage originates from recently feralized livestock and found supporting evidence for increased G. gallus density on Kauai within the last few decades. SNPs obtained from whole-genome sequencing were consistent with historic admixture between Kauai's divergent (G. gallus) lineages. Additionally, analyses of plumage, skin colour and vocalizations revealed that Kauai birds' behaviours and morphologies overlap with those of domestic chickens and Red Junglefowl, suggesting hybrid origins. Together, our data support the hypotheses that (i) Kauai's feral G. gallus descend from recent invasion(s) of domestic chickens into an ancient Red Junglefowl reservoir and (ii) feral chickens exhibit greater phenotypic diversity than candidate source populations. These findings complicate management objectives for Pacific feral chickens, while highlighting the potential of this and other feral systems for evolutionary studies of invasions.
Data from: Mitochondrial genomes of domestic animals need scrutiny
More than 1000 complete or near-complete mitochondrial DNA (mtDNA) sequences have been deposited in GenBank for eight common domestic animals (cattle, dog, goat, horse, pig, sheep, yak and chicken) and their close wild ancestors or relatives, as well. Nevertheless, few efforts have been performed to evaluate the sequence data quality. Herein, we conducted a phylogenetic survey of these complete or near-complete mtDNA sequences based on mtDNA haplogroup trees for the eight animals. We show that errors due to artificial recombination, surplus of mutations, and phantom mutations, do exist in 14.5% (194/1342) of mtDNA sequences and all of them should be treated with wide caution. We propose some caveats for future mtDNA studies of domestic animals.
Data from: The evolutionary road from wild moth to domestic silkworm
The Silk Road, which derives its name from the trade of silk produced by the domestic silkworm Bombyx mori, was an important episode in the development and interaction of human civilizations. However, the detailed history behind silkworm domestication remains ambiguous, and little is known about the underlying genetics with respect to important aspects of its domestication. Here, we reconstruct the domestication processes and identify selective sweeps by sequencing 137 representative silkworm strains. The results present an evolutionary scenario in which silkworms may have been initially domesticated in China as trimoulting lines, then subjected to independent spreads along the Silk Road that gave rise to the development of most local strains, and further improved for modern silk production in Japan and China, having descended from diverse ancestral sources. We find that genes with key roles in nitrogen and amino acid metabolism may have contributed to the promotion of silk production, and that circadian-related genes are generally selected for their adaptation. We additionally identify associations between several candidate genes and important breeding traits, thereby advancing the applicable value of our resources.
Structure and scaling of the middle ear in domestic dog breeds
<p>This data-set of 8-bit JPEG files represents CT scans of the ear regions of 17 dog breeds, plus a mongrel and a wolf. Each folder includes a CT parameter settings text file (.xtekct) which contains the voxel size.</p> <p>17 of the 19 JPEG stacks were based on scans of prepared skull specimens from the Veterinary Anatomy Museum and Anatomic Pathology Laboratory at the Queen’s Veterinary School Hospital, University of Cambridge. The mongrel was a preserved teaching specimen, while the Chihuahua was a euthanized animal donated to the Queen's Veterinary School, University of Cambridge, for the purposes of teaching and research.</p> <p>These CT scans were made by Matthew J. Mason as part of a project entitled "Structure and scaling of the middle ear in domestic dog breeds". An original journal article based on reconstructions made from the scan data has been published in Journal of Anatomy (volume 245, issue 2, 2024), co-authored by Matthew J. Mason and Madaleine A. Lewis. The article may be found here: <a href="https://doi.org/10.1111/joa.14049">https://doi.org/10.1111/joa.14049</a>.</p>
Data from: Extensive hybridization following a large escape of domesticated Atlantic salmon in the Northwest Atlantic
[No abstract entered]
From wild to cultivated varieties: The genetic variation and genomic domestication of Medicago polymorpha in China
<p><i>Medicago polymorpha</i> is a successful invasive plant and widespread around the world with its ability to adapt to the novel environment conditions quickly. However, the evolutionary dynamics after invasion still largely unclear so far. In this study, we performed a specific-length amplified fragments sequencing (SLAF-seq) of ten representative <i>Medicago polymorpha</i> accessions enrolled from different regions in China to infer the population structure and nucleotide diversity. As a result, total 52,237 high-quality cross-species SNPs were identified. Population structure analysis based on these SNPs suggested entire <i>Medicago polymorpha</i> accessions could be divided into three groups, that is consistent with wild, intermediate, and cultivated. Moreover, a low level of gene flow occurred between cultivated and wild subgroups, and the wild subgroup had a higher allelic variation than the cultivated subgroup, which indicated that a genetic bottleneck may occurred during <i>Medicago polymorpha</i> domestication. The genotypic structure is no significant correlation with the geographic parameters (longitude and latitude) by Mantel test, suggested a rapid evolution to adapt to different environments. Additionally, selective sweep analyses found some improvement-selective genes. Gene function analysis revealed that they were primary involved in endonuclease activity and RNA-DNA hybrid ribonuclease activity biological processes, which are correlated with plant evolution. Therefore, we speculated these genes identified from selective sweep regions may have contributed to <i>Medicago polymorpha</i> domestication from wild to cultivated. Taken together, our results suggest that <i>Medicago polymorpha</i> has rapidly evolved across the invaded range. This will help us better understand the domestication history and intraspecific relationship of <i>Medicago polymorpha</i>, and provide basic information for breeding research in the future.</p>
Data from: Survival and phenology of ducklings of Mallard, Domestic Duck and Gadwall in The Netherlands
<p>Previous analysis of demographic parameters of the Mallard (<em>Anas platyrhynchos</em>) population hinted at low duckling survival driving the decline, but no empirical data on duckling survival in the Netherlands were available. To address this knowledge gap, we initiated a citizen science project in 2016 to collect basic information about Mallard breeding biology and duckling survival. In the slipstream of this project, we also collected data for Domestic Duck (<em>A. platyrhynchos forma domestica</em>) and Gadwall (<em>Mareca strepera</em>) for comparison. </p> <p>Here we archive the research data underlying the analyses and graphs of the this publication in Limosa (2024, 97:49-61): "Survival and phenology of dablings of Mallard <em>Anas platyrhynchos</em>, Domestic Duck <em>A. platyrhynchos forma domestica</em> and Gadwall <em>Mareca strepera</em> in The Netherlands" (Dutch title: "Overleving en fenologie van kuikens van Wilde Eend, Soepeend en Krakeend in Nederland") by Erik Kleyheeg, Loes van den Bremer, Chris van Turnhout, Ties Maris, Eelke Jongejans & Niek van Rabenswaaij.</p> <p> </p> <p>The data file <strong><span>“waarnemingen 2016-2020 Limosa.csv”</span></strong><span> contains the following variables:</span></p> <p><span>year: Year of the study (2016 up to 2020)</span></p> <p><span>date: Date of observation</span></p> <p><span>time: Time of observation</span></p> <p><span>ID: Identifier of observation</span></p> <p><span>ID_family: Identifier of mallard family/brood (useful in case of successive observations)</span></p> <p><span>species: Species (dom = domestic duck/feral mallard, gad = gadwall, mal = mallard)</span></p> <p><span>N_chicks: Reported number of chicks</span></p> <p><span>age: Estimated age in weeks (1 = 0 to 1 week old, etc.)</span></p> <p><span>age_days: Estimated age in days</span></p> <p><span>observer: Anonymized observer</span></p> <p><span>remark: Remark</span></p> <p><span>latitude: Latitude of observation</span></p> <p><span>longitude: Longitude of observation</span></p> <p><span>surface: Whether ducklings were on land or water</span></p> <p><span>shore: Type of shoreline nearest to ducklings (emb = timbering/revetment, nhv = high vegetation, nlv = low </span><span>vegetation, nno = no vegetation, oth = other)</span></p> <p><span>water: Water quality (cle = clear, tur = turbid, wee = covered with duckweed, oth = other) </span></p> <p><span>N_deaths: Number of ducklings observed perishing during the observation</span></p> <p><span>cause_deaths: Observed cause of death (agg = aggression, bre = grey heron, bui = buzzard, hon = dog, kat = cat, nijl = Egyptian goose, pre = predator unknown, sno = pike, zkr = carrion crown, zon = mammal unknown, oth = other)</span></p> <p><span>breadfeeding: Whether or not ducks are fed with bread regularly at the site of the observation</span></p>
Investigating Economic Growth Catalysts: An Empirical Analysis of Determinants of Domestic Private Investment in Ethiopia
<p>This is the original data that supports the findings of the research entitled "<strong>Investigating Economic Growth Catalysts: An Empirical Analysis of Determinants of Domestic Private Investment in Ethiopia"</strong></p>
Reducing HIV & Domestic Violence Risk in Women Offenders
ClinicalTrials.gov study NCT00289939. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Effects of a Legal Support Program on Women Experiencing Domestic Violence
ClinicalTrials.gov study NCT04107025. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Clinical Controlled Study on the Efficacy of Denosumab in Treating Osteoporosis in the Domestic Population and Its Impact on Sarcopenia-related Outcomes
ClinicalTrials.gov study NCT06154707. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Randomized Clinical Study of a Mind-Body Approach to Domestic Violence Offender Treatment
ClinicalTrials.gov study NCT00983593. IPD Sharing: Not stated. Countries: 1. Publications: 0.
ScienceDex guides
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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.