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903 results for “Domestication”
Axiom canine microarray data from Australian dingoes and domestic dogs for admixture and population structure analysis
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Ecology of domestic dogs Canis familiaris as an emerging reservoir of Guinea worm Dracunculus medinensis infection
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Cuisine in transition? Organic residue analysis of domestic containers from 9th-14th century Sicily
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Does prey scarcity increase the risk of wolf attacks on domestic dogs?
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Leaf trait covariation and controls on leaf mass per area (LMA) following cotton domestication
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Supplementary material and data from: Cranial volume and palate length of cats, Felis spp., under domestication, hybridisation and in wild populations
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The influence of domestic dogs on the spatial and temporal distribution of tayra
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Drought stress and high heat tolerance in domesticated Phaseolus beans
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Epigenetic models developed for plains zebras predict age in domestic horses and endangered equids
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Supplementary material 1 from: McPartland JM, Small E (2020) A classification of endangered high-THC cannabis (Cannabis sativa subsp. indica) domesticates and their wild relatives. PhytoKeys 144: 81-112. https://doi.org/10.3897/phytokeys.144.46700
A classification of endangered high-THC cannabis (Cannabis sativa subsp. indica) domesticates and their wild relatives
Evolutionary genomics of structural variation in Asian rice (Oryza sativa) domestication
<p>DATA from Kou et al. 2020 Evolutionary Genomics of Structural Variation in Asian Rice (<em>Oryza sativa</em>) Domestication, <em>Molecular Biology and Evolution</em>, Volume 37, Issue 12, December 2020, Pages 3507–3524, <a href="https://doi.org/10.1093/molbev/msaa185">https://doi.org/10.1093/molbev/msaa185</a> </p> <p>Gene and TE annotation of Nipponbare (<em>Oryza sativa </em>ssp.<em> japonica</em> ) genome V5.0 updated using SMRT long reads</p> <p>Raw SV calls jointly detected in Asian rice (<em>Oryza sativa</em>) and its wild progenitor (<em>O. rufipogon</em>)</p> <p> </p>
Genomic signatures of domestication in Old World camels
<p>Domestication begins with the selection of animals showing less fear of humans. In most domesticates, selection signals for tameness have been superimposed by intensive breeding for economical or other desirable traits. Old World camels, conversely, have maintained high genetic variation and lack these secondary bottlenecks associated with breed development. By re-sequencing multiple genomes from dromedaries, Bactrian camels, and their endangered wild relatives, we show that positive selection for candidate genes underlying traits collectively referred to as 'domestication syndrome' is consistent with neural crest deficiencies and altered thyroid hormone-based signaling. Comparing our results with other domestic species, we postulate that the core set of domestication genes is considerably smaller than the pan-domestication set – and overlapping genes are likely a result of chance and redundancy. These results, along with the extensive genomic resources provided, are an important contribution to understanding the evolutionary history of camels and the genomic features of their domestication.</p>
Functional genetic diversity of domestic and wild American mink (Neovison vison )
<p>The release of domestic organisms to the wild threatens biodiversity because the introduction of domestic genes through interbreeding can negatively impact wild conspecifics via outbreeding depression. In North America, farmed American mink (<i>Neovison vison</i>) frequently escape captivity, yet the impact of these events on functional genetic diversity of wild mink populations is unclear. We characterized domestic and wild mink in Ontario at 17 microsatellites located in functional genes and in a promoter region that is non-coding but thought to be associated with traits affected by domestication. We found low functional genetic diversity in both mink types, as only 4 of 17 genes were variable, and the number of alleles per locus were generally lower in captive mink than in wild mink. To determine if allele frequencies of wild populations were affected by domestic release events, we performed redundancy analysis and spatial analysis of principal components on four polymorphic loci (AR, ATN1, IGF-1, and TOB1). We found evidence to suggest domestic release events are affecting the functional genetic diversity of wild mink, as sPCA showed clear distinctions between wild individuals near mink farms and those located in areas without mink farms. This is further substantiated through RDA, where spatial location was associated with genetic variation of AR, ATN1, and IGF1.</p>
Scenario Input files for "The Domestic and International Implications of Future Climate for U.S. Agriculture in GCAM"
<p>The GCAM scenario input files needed for the experiments described in the paper "The Domestic and International Implications of Future Climate for U.S. Agriculture in GCAM".</p>
Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites
<p>STRUCTURE remains the most applied tool aimed at recovering the true, but unknown, population structure from observed microsatellite data or other genetic markers. About 30% of <span class="Program"><span>STRUCTURE</span></span>-based studies could not be reproduced (Gilbert et al., 2012). Here we use a large set of data from 2323 horses from 93 domestic breeds plus the Przewalski horse, typed at 15 microsatellite markers, to evaluate how program settings, in particular the so far insufficiently evaluated number of replicates, impact the estimation of the optimal number of population clusters <i>K</i><sub>opt</sub> that best describe the observed data. Domestic horses are suited as a test case as there is extensive knowledge of the history of many breeds, extensive phylogenetic analyses. Different methods based on different genetic assumptions and statistical procedures (<span class="Program"><span>DAPC</span></span>, <span class="Program"><span>FLOCK</span></span>, PCoA and <span class="Program"><span>STRUCTURE</span></span> with different run scenarios) all revealed the general, broad-scale relationships among the breeds that largely reflect known breed histories but diverged largely how they characterized small-scale patterns. <span class="Program"><span>STRUCTURE</span></span> failed to consistently identify <i>K</i><sub>opt</sub> using the most widespread approach, the ΔK method, despite very large numbers of MCMCs (3,000,000) and replicates (100). The interpretation of breed structure over increasing numbers of<i> K</i>, without assuming a <i>K</i><sub>opt</sub>, was consistent with known breed histories. The over-reliance on <i>K</i><sub>opt</sub> should be replaced by a qualitative description of clustering over increasing <i>K</i>, which is scientifically more honest and has the advantage of being much faster and less computer intensive as lower numbers of MCMC iterations and repetitions suffice for stable results. Very large data sets are highly challenging for cluster analyses, especially when populations with complex genetic histories are investigated.</p>
Evidence for two main domestication trajectories in Saccharomyces cerevisiae linked to distinct bread-making processes
<p>Data and code supporting the manuscript "Evidence for two main domestication trajectories in <em>Saccharomyces cerevisiae</em> linked to distinct bread-making processes" by Bigey et al. (2020)</p>
Data from: A strong east-west Mediterranean divergence supports a new phylogeographic history of the carob tree (Ceratonia siliqua, Leguminosae) and multiple domestications from native populations
Aim: Phylogeography of fruit trees is challenging due to the recurrent exchanges between domesticated and wild populations. Here we tested the eastern refugium hypothesis (ERH) for the carob tree, Ceratonia siliqua, which supports its natural and domestication origins in the Eastern Mediterranean and a feral origin in the West. Location: Mediterranean basin Taxon: Ceratonia siliqua L., Leguminosae Methods: Divergence time of the divergence between the carob tree and its sister species (C. oreothauma) was estimated based on two nuclear and one plastid sequences. Variation from four plastid regions and 17 nuclear microsatellite loci were used to decipher genetic structure in the carob tree and to test coalescent-based models by an Approximate Bayesian Computation (ABC) approach. We assessed our hypotheses by examining palaeobotanical records and hindcasting the past distribution of the carob tree at the Mid-Holocene, Last Glacial Maximum (LGM) and Last Interglacial (LIG) using species distribution modelling (SDM). Results: The split between C. oreothauma and C. siliqua was estimated at 6.4 Ma, and a first divergence within C. siliqua at 1.3 Ma. After a presence since the Oligocene, Ceratonia was found in the Western and the Eastern Mediterranean in the fossil records during the Pleistocene. Plastid and nuclear markers, characterized by low allelic richness, revealed a strong west-east genetic structuring. Approximate Bayesian computation (ABC) analyses rejected the ERH. Main conclusions: Our study supports a severe population decline during LIG. The strong west-east divergence and the occurrence of four lineages within C. siliqua provided support for a new hypothesis of multiple domestications of the carob tree from native populations throughout the Mediterranean basin.
VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species
<p>Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a "protracted period" of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available.</p>
Data from: Signatures of selection and environmental adaptation across the goat genome post-domestication
<p>Background: Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip. These animals were partitioned into groups based on geographical area, production uses, available records on solid coat color and environmental variables including the sampling geographical coordinates, to investigate the role of natural and/or artificial selection in shaping the genome of goat breeds.</p> <p>Results: Several signatures of selection on different chromosomal regions were detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk-, meat- or fiber-related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. Our results confirm previous findings in other species on adaptation to extreme environments and human purposes and provide new genes that could explain some of the differences between goat breeds according to their geographical distribution and adaptation to different environments.</p> <p>Conclusions: These analyses of signatures of selection provide a comprehensive first picture of the global domestication process and adaptation of goat breeds and highlight possible genes that may have contributed to the differentiation of this species worldwide.</p>
Data from: Distinct spread of DNA and RNA viruses among mammals amid prominent role of domestic species
<p><b>Aim:</b> Emerging infectious diseases arising from pathogen spillover from mammals to humans comprise a substantial health threat. Tracing virus origin and predicting the most likely host species for future spillover events are major objectives in One Health disciplines.</p> <p>We assessed patterns of virus sharing among a large diversity of mammals, including humans and domestic species.</p> <p><b>Location:</b> Global.</p> <p><b>Time period:</b> Current.</p> <p><b>Major taxa studied:</b> Mammals and associated viruses.</p> <p><b>Methods:</b> We used network centrality analysis and trait-based Bayesian hierarchical models to explore patterns of virus sharing among mammals. We analysed a global database that compiled the associations between 1,785 virus species and 725 mammalian host species as sourced from automatic screening of meta-data accompanying published nucleotide sequences between 1950 – 2019.</p> <p><b>Results:</b> We show that based on current evidence, domesticated mammals hold the most central positions in networks of known mammal-virus associations. Among entire host-virus networks, Carnivora and Chiroptera hold central positions for mainly sharing RNA viruses, while Ungulates hold central positions for sharing both RNA and DNA viruses with other host species. We revealed strong evidence that DNA viruses were phylogenetically more host specific than RNA viruses. RNA viruses exhibited low functional host specificity despite an overall tendency to infect phylogenetically related species, signifying high potential to shift across hosts with different ecological niches. The frequencies of sharing viruses among hosts and the proportion of zoonotic viruses in hosts were larger for RNA than DNA viruses.</p> <p><b>Main conclusions:</b> Acknowledging the role of domestic species in addition to host and virus traits in patterns of virus sharing is necessary to improve our understanding of virus spread and spillover in times of global change. Understanding multi-host virus sharing pathways adds focus to curtail disease spread.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.