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1,155 results for “loci”
Dataset for Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas with data for 330 markers
<p>Dataset for Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas with data for 330 markers. This dataset is associated with the dissertation entitled, Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas.</p>
Allele scores and frequencies of 66 microsatellite locus loci in Solenopsis invicta
<p>Allele scores and frequencies of 66 microsatellite loci in <em>Solenopsis invicta </em>samples were analyzed from 65 populations and 1,074 individuals.</p> <p>65 populations were collected from South Korea, China, Taiwan, and the United States.</p>
Locityper loci database, 1KGP genotypes and benchmarking data
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A comparative analysis of somatic mutations occurring at "common" loci and other loci with the TCGA somatic mutation dataset.
<p>A comparative analysis of somatic mutations occurring at "common" loci and other loci with the TCGA somatic mutation dataset.</p>
Concatenation files: 845 loci to study Klebsormidiophyceae
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The genome of Vitis vinifera cv. Mgaloblishvili reveals resistance and susceptibility factors to downy mildew in the Rpv29 and Rpv31 loci
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Microsatellite (13 loci) and plastid DNA haplotypes in a population of Antirrhinum charidemi
<p>Genotype matrix of 182 Antirrhinum charidemi individuals sampled in 2007-2009 in the Barranco del Dragoncillo Blanco population in Cabo de Gata, Almería, Spain. Genotypes are given for 13 microsatellite loci and also include 3 plastid DNA haplotypes. Details on loci and genotyping conditions can be found in Forrest et al. 2017, https://doi.org/10.1093/botlinnean/bow002. Each individual is geolocated. Additional information include its corolla colour, its ancestry score in four gene pools obtained in Bayesian genetic cluster analysis (STRUCTURE), and its assignment to geo-genetic subpopulations. Metadata are available in a separate tab in the submitted spreadsheet. The data are analysed in a paper expected to be published in AoB Plants in 2025, titled: "Fine-scale genetic differentiation in the bee-specialized Antirrhinum charidemi covaries more strongly with microenvironment than with corolla colour"</p>
Integrative genome-wide analyses identify novel loci associated with kidney stones and provide insights into its genetic architecture
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Neutral and adaptive loci reveal fine-scale population structure in Eleginops maclovinus from North Patagonia
<p>Patagonia is an understudied area, especially when it comes to population genomic studies with relevance to fishery management. However, the dynamic and heterogeneous landscape in this area can harbor important but cryptic genetic population structure. Once such information is revealed, it can be integrated into the management of infrequently investigated species. <i>Eleginops maclovinus</i> is a protandrous hermaphrodite species with economic importance for local communities that is currently managed as a single genetic unit. In this study, we sampled five locations distributed across a salinity cline from Northern Patagonia to investigate the genetic population structure of <i>E</i>. <i>maclovinus</i>. We use Restriction-site Associated DNA (RAD) sequencing and outlier tests to obtain 11,712 neutral, 338 adaptive loci, and 78 loci associated to environmental variables. We identified a spatial pattern of structuration with gene flow and spatial selection by environmental association. Neutral and adaptive loci showed two and three genetic groups, respectively. The effective population sizes estimated ranged from 572 to 14,454 and were influenced more by locality than salinity cline. We found loci putatively associated with salinity suggesting that salinity may act as a selective driver in <i>E</i>. <i>maclovinus</i> populations. These results suggest a complex interaction between genetic drift, geneflow, and natural selection in this area. Our findings suggest that at least two to three genetic units exist in this area, and the information should be integrated into the management of this species. We discuss the significance of these results for fishery management and suggest future directions to improve our understanding of how <i>E</i>. <i>maclovinus</i> is adapted to the dynamic waters of Northern Patagonia.</p>
Subtle limits to connectivity revealed by outlier loci within two divergent metapopulations of the deep-sea hydrothermal gastropod Ifremeria nautilei
<p class="MsoNormal"><span>Hydrothermal vents form archipelagos of ephemeral deep-sea habitats that raise interesting questions about the evolution and dynamics of the associated endemic fauna, constantly subject to extinction-recolonization processes. These metal-rich environments are coveted for the mineral resources they harbor, thus raising recent conservation concerns. The evolutionary fate and demographic resilience of hydrothermal species strongly depend on the degree of connectivity among and within their fragmented metapopulations. In the deep sea, however, assessing connectivity is difficult and usually requires indirect genetic approaches. Improved detection of fine-scale genetic connectivity is now possible based on </span><span>genome-wide </span><span>screening for</span><span> </span><span>genetic differentiation.</span></p> <p class="MsoNormal"><span>Here, we explored population connectivity in the hydrothermal vent snail <em>Ifremeria nautilei </em>across its species range encompassing five distinct back-arc basins in the Southwest Pacific. The global analysis, based on 10 570 single nucleotide polymorphism (SNP) markers derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), depicted two semi-isolated and homogeneous genetic clusters. Demo-genetic modeling suggests that these two groups began to diverge about 70 000 generations ago, but continue to exhibit weak and slightly asymmetrical gene flow. Furthermore, a careful analysis of outlier loci showed subtle limitations to connectivity between neighboring basins within both groups. This finding indicates that migration is not strong enough to totally counterbalance drift or local selection, hence questioning the potential for demographic resilience at this latter geographical scale. </span><span>These results illustrate the </span><span>potential</span><span> of large genomic datasets to understand </span><span>fine-scale</span><span> connectivity </span><span>patterns in</span><span> </span><span>hydrothermal vents and the deep sea</span><span>.</span></p>
12 nuclear microsatellite loci scores for 543 adult trees of Tilia cordata in Lithuainia
<p>Genetic signature of the natural genepool of <i>Tilia cordata</i> Mill. in Lithuania: compound evolutionary and anthropogenic effects</p> <p><i>Tilia cordata</i> Mill. is a valuable tree species enriching the ecological values of the coniferous dominated boreal forests in Europe. Following the historical decline, spreading of <i>Tilia</i> sp. is challenged by the elevated inbreeding and habitat fragmentation. We studied the geographical distribution of genetic diversity of <i>Tilia cordata</i> populations in Lithuania. We used 14 genomic microsatellite markers to genotype 543 individuals from 23 wild growing populations. We found that <i>Tilia cordata</i> retained high levels of genetic diversity (population F<sub>is</sub> = 0 to 0.15, H<sub>o </sub>= 0.53 to 0.69, H<sub>e </sub>= 0.56 to 0.75). AMOVA, Bayesian clustering and Monmonier's barrier detection indicate weak but significant differentiation among the populations (F<sub>st</sub> = 0.037***) into geographically interpretable clusters of (a) western Lithuania with high genetic heterogeneity but low genetic diversity, bottleneck effects, (b) relatively higher genetic diversity of <i>Tilia cordata</i> on rich and most soils of midland lowland, and (c) the most differentiated populations on poor soils of the coolest north-eastern highland possessing the highest rare allele frequency but elevated inbreeding and bottleneck effects. Weak genetic differentiation among the <i>Tilia cordata</i> populations in Lithuania implies common ancestry, absence of strong adaptive gradients and effective genetic exchange possible mediated via the riparian networks. A hypothesis on riparian networks as geneflow mediators in <i>Tilia cordata</i> was raised based on results of this study.</p>
Scoring of 13 microsatellite loci for Tetrastigma loheri in Cebu (Philippines) based on the fragment length size of their respective alleles
<p>Little is known about the effects of habitat fragmentation on the patterns of genetic diversity and genetic connectivity of species in the remaining tropical forests of Southeast Asia. This is particularly evident in Cebu, a Philippine island that has a long history of deforestation and has lost nearly all of its forest cover. To begin filling this gap, data from 13 microsatellite loci developed for Tetrastigma loheri (Vitaceae), a common vine species in Philippine forests, were used to study patterns of genetic diversity and genetic connectivity for the four largest of the remaining forest areas in Cebu. Evidence of relatively high levels of inbreeding was found in all four areas, despite no evidence of low genetic diversity. The four areas are genetically differentiated, suggesting low genetic connectivity. The presence of inbreeding and low genetic connectivity in a commonly encountered species such as T. loheri in Cebu suggests that the impact of habitat fragmentation is likely greater on rare plant species with more restricted distributions in Cebu. Conservation recommendations for the remaining forest areas in Cebu include the establishment of steppingstone corridors between nearby areas to improve the movement of pollinators and seed dispersers among them.</p>
Data from: Stepwise Threshold Clustering: a new method for genotyping MHC loci using next-generation sequencing technology
Genes of the vertebrate major histocompatibility complex (MHC) are of great interest to biologists because of their important role in immunity and disease, and their extremely high levels of genetic diversity. Next generation sequencing (NGS) technologies are quickly becoming the method of choice for high-throughput genotyping of multi-locus templates like MHC in non-model organisms. Previous approaches to genotyping MHC genes using NGS technologies suffer from two problems: 1) a "gray zone" where low frequency alleles and high frequency artifacts can be difficult to disentangle and 2) a similar sequence problem, where very similar alleles can be difficult to distinguish as two distinct alleles. Here were present a new method for genotyping MHC loci – Stepwise Threshold Clustering (STC) – that addresses these problems by taking full advantage of the increase in sequence data provided by NGS technologies. Unlike previous approaches for genotyping MHC with NGS data that attempt to classify individual sequences as alleles or artifacts, STC uses a quasi-Dirichlet clustering algorithm to cluster similar sequences at increasing levels of sequence similarity. By applying frequency and similarity based criteria to clusters rather than individual sequences, STC is able to successfully identify clusters of sequences that correspond to individual or similar alleles present in the genomes of individual samples. Furthermore, STC does not require duplicate runs of all samples, increasing the number of samples that can be genotyped in a given project. We show how the STC method works using a single sample library. We then apply STC to 295 threespine stickleback (Gasterosteus aculeatus) samples from four populations and show that neighboring populations differ significantly in MHC allele pools. We show that STC is a reliable, accurate, efficient, and flexible method for genotyping MHC that will be of use to biologists interested in a variety of downstream applications.
Data from: Identification of candidate loci for adaptive phenotypic plasticity in natural populations of spadefoot toads
<p>Phenotypic plasticity allows organisms to alter their phenotype in direct response to changes in the environment. Despite growing recognition of plasticity's role in ecology and evolution, few studies have probed plasticity's molecular bases—especially using natural populations. We investigated the genetic basis of phenotypic plasticity in natural populations of spadefoot toads (<i>Spea multiplicata</i>). <i>Spea</i> tadpoles normally develop into an 'omnivore' morph that is favored in long-lasting, low-density ponds. However, if tadpoles consume freshwater shrimp or other tadpoles, they can develop (via plasticity) into a 'carnivore' morph that is favored in shallow, high-density ponds. By combining natural variation in pond ecology and morph production with population genetic approaches, we identified candidate loci associated with morph (carnivores versus omnivores) and loci associated with adaptive phenotypic plasticity (adaptive versus maladaptive morph choice). Our candidate morph loci mapped to two genes, whereas our candidate plasticity loci mapped to 12 genes. In both cases, the identified genes tended to have functions related to their putative role in spadefoot tadpole biology. Our results thereby form the basis for future studies into the molecular mechanisms that mediate plasticity in spadefoots. More generally, these results illustrate how diverse loci might be deployed to mediate adaptive plasticity.</p>
FIGURE 4 in Physical mapping of 45S and 5S rDNA and telomeric repeat loci in eight diploid hyacinth cultivars
FIGURE 4. Dendrogram of eight hyacinths species using between-groups linkge At the Euclidean distance of 20, the eight were clustered into group I, II and III.
FIGURE. FISH karyotype pattern diagram of 8 diploid hyacinth cultivars a.'Gypsy Queen'; b.'Purple sensation' c.'Pink pearl' d.'Gypsy princess' e.'Blue pearl' f.'Odysseus' g.'Yellowstone' h.'Red pearl' Red point: 45S rDNA loci; Green point: 45S rDNA loci; Yellow point: ITR sites in Physical mapping of 45S and 5S rDNA and telomeric repeat loci in eight diploid hyacinth cultivars
FIGURE. FISH karyotype pattern diagram of 8 diploid hyacinth cultivars a.'Gypsy Queen'; b.'Purple sensation' c.'Pink pearl' d.'Gypsy princess' e.'Blue pearl' f.'Odysseus' g.'Yellowstone' h.'Red pearl' Red point: 45S rDNA loci; Green point: 45S rDNA loci; Yellow point: ITR sites
FIGURE. Results of FISH physical mapping on metaphase chromosomes of hyacinth 1. The distribution of 45S rDNA (red arrow) and 5S rDNA (green arrow) signals on the chromosomes; 2. The distribution of telomeric repeats signals on the chromosomes; 3. Chromosome karyotype with 45S rDNA and 5S rDNA; 4. Chromosome karyotype with telomeric repeats. A. 'Gypsy Queen' B.'Purple sensation' C.'Pink pearl' D.'Gypsy princess' E.'Blue pearl' F.'Odysseus' G.'Yellow stone' H.'Red pearl' in Physical mapping of 45S and 5S rDNA and telomeric repeat loci in eight diploid hyacinth cultivars
FIGURE. Results of FISH physical mapping on metaphase chromosomes of hyacinth 1. The distribution of 45S rDNA (red arrow) and 5S rDNA (green arrow) signals on the chromosomes; 2. The distribution of telomeric repeats signals on the chromosomes; 3. Chromosome karyotype with 45S rDNA and 5S rDNA; 4. Chromosome karyotype with telomeric repeats. A. 'Gypsy Queen' B.'Purple sensation' C.'Pink pearl' D.'Gypsy princess' E.'Blue pearl' F.'Odysseus' G.'Yellow stone' H.'Red pearl'
FIGURE. Eight diploid hyacinth cultivars a in Physical mapping of 45S and 5S rDNA and telomeric repeat loci in eight diploid hyacinth cultivars
FIGURE. Eight diploid hyacinth cultivars a.'Gypsy Queen'; b.'Purple Sensation' c.'Pink Pearl' d.'Gypsy Princess' e.'Blue Pearl' f.'Odysseus' g.'Yellow Stone' h.'Red Pearl'
FIGURE. Cladosporium benschii (VIC 44412, holotype). A–D. Colonies on A. Potato dextrose agar; B. Malt extract agar; C. Oatmeal agar; D. Synthetic nutrient-poor agar, after 14 days at 25 ºC, under near-ultraviolet light, respectively. E–J. Non-geniculate macronematous conidiophores and conidia. K. Conidiogenous cells with slightly protuberant loci. L. Micronematous conidiophores. M. Microcyclic conidiogenesis. Scale bars: E–M = 20 µM. in Six new species of Cladosporium associated with decayed leaves of native bamboo (Bambusoideae) in a fragment of Brazilian Atlantic Forest
FIGURE. Cladosporium benschii (VIC 44412, holotype). A–D. Colonies on A. Potato dextrose agar; B. Malt extract agar; C. Oatmeal agar; D. Synthetic nutrient-poor agar, after 14 days at 25 ºC, under near-ultraviolet light, respectively. E–J. Non-geniculate macronematous conidiophores and conidia. K. Conidiogenous cells with slightly protuberant loci. L. Micronematous conidiophores. M. Microcyclic conidiogenesis. Scale bars: E–M = 20 µM.
FIGURE. Cladosporium aulonemiae (VIC 44413, holotype). A–D. Colonies on A. Potato dextrose agar; B. Malt extract agar; C. Oatmeal agar; D. Synthetic nutrient-poor agar, after 14 days at 25 ºC, under near-ultraviolet light, respectively. E–G. Macronematous conidiophores and numerous conidia; H–I. Formation of loci in close succession; I. Spread polysaccharide-like material; J. Micronematous conidiophores; K. Ramoconidia and conidia; L. Microcyclic conidiogenesis; M. Stromatic hyphal aggregation. Scale bars: E–M = 20 µM. in Six new species of Cladosporium associated with decayed leaves of native bamboo (Bambusoideae) in a fragment of Brazilian Atlantic Forest
FIGURE. Cladosporium aulonemiae (VIC 44413, holotype). A–D. Colonies on A. Potato dextrose agar; B. Malt extract agar; C. Oatmeal agar; D. Synthetic nutrient-poor agar, after 14 days at 25 ºC, under near-ultraviolet light, respectively. E–G. Macronematous conidiophores and numerous conidia; H–I. Formation of loci in close succession; I. Spread polysaccharide-like material; J. Micronematous conidiophores; K. Ramoconidia and conidia; L. Microcyclic conidiogenesis; M. Stromatic hyphal aggregation. Scale bars: E–M = 20 µM.
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.