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1,155 results for “loci”
Genotype of expression quantitative loci (eQTL) analyses for bovine blood and liver
<p>To identify expression quantitative loci (eQTL) operating in bovine blood and liver, 238 animals were genotyped uisng Illumina BovineHD genotyping arrary. For this file minor allele is used as ref as the default in plink.</p>
Data from: Genomic landscapes of divergence among island bird populations: evidence of parallel adaptation but at different loci?
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Supplementary materials to: Nano-Strainer: a workflow for identification of single-copy nuclear loci for plant systematic studies, using target capture kits and Oxford Nanopore long reads
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A two-tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae
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Gene loci fluctuations reveal bacterial chromosome dynamical organization
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Data from: Do genetic loci that cause reproductive isolation in the lab inhibit gene flow in nature?
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Novel major loci shape habitat-associated flowering time variation in Yellowstone monkeyflowers
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Data from: A few essential genetic loci distinguish Penstemon species with flowers adapted to pollination by bees or hummingbirds
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Evolution of putative barrier loci at an intermediate stage of speciation with gene flow in campions (Silene)
Understanding the origin of new species is a central goal in evolutionary biology. Diverging lineages often evolve highly heterogeneous patterns of genetic differentiation; however, the underlying mechanisms are not well understood. We investigated evolutionary processes governing genetic differentiation between the hybridizing campions <i>Silene dioica</i> (L.) Clairv. and <i>S. latifolia</i> Poiret. Demographic modeling indicated that the two species diverged with gene flow. The best-supported scenario with heterogeneity in both migration rate and effective population size suggested that a small proportion of the loci evolved without gene flow. Differentiation (F<sub>ST</sub>) and sequence divergence (d<sub>XY</sub>) were correlated and both tended to peak in the middle of most linkage groups, consistent with reduced gene flow at highly differentiated loci. Highly differentiated loci further exhibited signatures of selection. In between-species population pairs, isolation by distance was stronger for genomic regions with low between-species differentiation than for highly differentiated regions that may contain barrier loci. Moreover, differentiation landscapes within and between species were only weakly correlated suggesting that linked selection due to shared recombination and gene density landscapes is not the dominant determinant of genetic differentiation in these lineages. Instead, our results suggest that divergent selection shaped the genomic landscape of differentiation between the two <i>Silene </i>species, consistent with predictions for speciation in the face of gene flow.
Data from: Integrative genomic analysis in African American children with asthma finds 3 novel loci associated with lung function
<p>Bronchodilator drugs are commonly prescribed for treatment and management of obstructive lung function present with diseases such as asthma. Administration of bronchodilator medication can partially or fully restore lung function as measured by pulmonary function tests. The genetics of baseline lung function measures taken prior to bronchodilator medication has been extensively studied, and the genetics of the bronchodilator response itself has received some attention. However, few studies have focused on the genetics of post-bronchodilator lung function. To address this gap, we analyzed lung function phenotypes in 1,103 subjects from the Study of African Americans, Asthma, Genes, and Environment (SAGE), a pediatric asthma case-control cohort, using an integrative genomic analysis approach that combined genotype, locus-specific genetic ancestry, and functional annotation information. We integrated genome-wide association study (GWAS) results with an admixture mapping scan of three pulmonary function tests (FEV1, FVC, and FEV1/FVC) taken before and after albuterol bronchodilator administration on the same subjects, yielding six traits. We identified 18 GWAS loci, and 5 additional loci from admixture mapping, spanning several known and novel lung function candidate genes. Most loci identified via admixture mapping exhibited wide variation in minor allele frequency across genotyped global populations. Functional fine-mapping revealed an enrichment of epigenetic annotations from peripheral blood mononuclear cells, fetal lung tissue, and lung fibroblasts. Our results point to three novel potential genetic drivers of pre- and post-bronchodilator lung function: ADAMTS1, RAD54B, and EGLN3. </p>
Genomic landscape of reproductive isolation in Lucania killifish: The role of sex loci and salinity
<p>Adaptation to different environments can directly and indirectly generate reproductive isolation between species. Bluefin killifish (<i>Lucania goodei</i>) and rainwater killifish (<i>L. parva</i>) are sister species that have diverged across a salinity gradient and are reproductively isolated by habitat, behavioral, extrinsic, and intrinsic postzygotic isolation. We asked if salinity adaptation contributes indirectly to other forms of reproductive isolation via linked selection and hypothesized that low recombination regions, such as sex chromosomes or chromosomal rearrangements, might facilitate this process. We conducted QTL mapping in backcrosses between <i>L. parva </i>and <i>L. goodei</i> to explore the genetic architecture of salinity tolerance, behavioral isolation, and intrinsic isolation. We mapped traits relative to a chromosome that has undergone a centric fusion in <i>L. parva</i> (relative to <i>L. goodei</i>). We found that the sex locus appears to be male determining (XX-XY), was located on the fused chromosome, and was implicated in intrinsic isolation. QTL associated with salinity tolerance were spread across the genome and did not overly co-localize with regions associated with behavioral or intrinsic isolation. This preliminary analysis of the genetic architecture of reproductive isolation between <i>Lucania</i> species does not support the hypothesis that divergent natural selection for salinity tolerance led to behavioral and intrinsic isolation as a byproduct. Combined with previous studies in this system, our work suggests that adaptation as a function of salinity contributes to habitat isolation and that reinforcement may have contributed to the evolution of behavioral isolation instead, possibly facilitated by linkage between behavioral isolation and intrinsic isolation loci on the fused chromosome.</p>
Genome-wide association mapping to identify genetic loci for cold tolerance and cold recovery during germination in rice
<p>To investigate the genetic architecture underlying cold tolerance during germination in rice (<i>Oryza sativa</i>), we conducted a genome-wide association study (GWAS) using a novel diversity panel of 257 rice accessions from around the world and 5,185 SNP markers from a 7K SNP marker array. Genotyping was performed using a 7K Illumina iSelect custom-designed array by following the Infinium HD Array Ultra Protocol. The 7K array, called the C7AIR, was designed by Dr. Susan McCouch's Lab at Cornell University and consists of 7,098 SNPs (Morales et al. 2020, under review). After genotyping 257 rice accessions with the 7K array (C7AIR), poor-performing SNP markers (SNPs of call rate <90%; minor allele frequency <5%; or heterozygosity >20%) were removed from the dataset. For our study, a subset of 5,185 high-quality SNP markers obtained after filtering was used to perform the genome-wide association analysis. The dataset representing the genotype data of 5,185 SNP markers by 257 rice accessions is presented here.</p>
Data from: Cryptic diversity in the Mexican highlands: thousands of UCE loci help illuminate phylogenetic relationships, species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus)
With the continued adoption of genome-scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent-based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element (UCE) data set (>3000 loci) from rattlesnakes of the Crotalus triseriatus group to delimit lineages and estimate species trees using concatenation and several coalescent-based methods. Unpartitioned and partitioned maximum-likelihood and Bayesian analysis of the concatenated matrix yield a topology identical to coalescent analysis of a subset of the data in bpp. ASTRAL analysis on a subset of the more variable loci also result in a tree consistent with concatenation and bpp, whereas the SVDquartets phylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species-tree inference using SVDquartets, warranting additional investigation on optimal data characteristics for this method. Species-delimitation analyses suggest up to 16 unique lineages may be present within the C. triseriatus group, with divergences occurring during the Neogene and Quaternary. Network analyses suggest hybridization within the group is relatively rare. Altogether, our results reaffirm the Mexican highlands as a biodiversity hotspot and suggest that coalescent-based species-tree inference on data subsets can provide a strongly supported species tree consistent with concatenation of all loci with a large amount of missing data.
Data from: Mapping reduced introgression loci to the X chromosome of the hybridizing field crickets, Gryllus firmus and G. pennsylvanicus
The genomic architecture of barriers to gene exchange during the speciation process is poorly understood. The genomic islands model suggests that loci associated with barriers to gene exchange prevent introgression of nearby genomic regions via linkage disequilibrium. But few analyses of the actual genomic location of non-introgressing loci in closely related species exist. In a previous study Maroja et al. showed that in the hybridizing field crickets, Gryllus firmus and G. pennsylvanicus, 50 non-introgressing loci are localized on two autosomal regions and the X chromosome, but they were not able to map the loci along the X chromosome because they used a male informative cross. Here, we localize the introgressing and non-introgressing loci on the X chromosome and reveal that all X-linked non-introgressing loci are restricted to a 50-cM region with 10 of these loci mapped to a single location. We discuss the implications of this finding to speciation.
Dataset for Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas, 330 markers, sequences included
<p>Dataset for Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas, 330 markers, sequences included.</p>
Treefile of a Klebsormidiophyceae phylogenomic analysis based on 845 loci
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Alignment of 845 loci for phylogenomic analysis of Klebsormidiophyceae
<p>Improved alignment with more informative loci (845)</p>
The genomes of Hercules beetles reveal putative adaptive loci and distinct demographic histories in pristine North American forests
<p><span>Beetles, despite their remarkable biodiversity and a long history of research, remain lacking in reference genomes annotated with structural variations of loci of adaptive significance. We sequenced and assembled high-quality chromosome-level genomes of four Hercules beetles which exhibit divergence in male horn size and shape, and body coloration. The four Hercules beetle genomes were assembled to 11 pseudo-chromosomes, where the three genomes assembled using Nanopore data (<em>Dynastes grantii,</em> <em>D. hyllus</em>, and <em>D. tityus</em>) were mapped to the genome assembled using PacBio + Hi-C data (<em>D. maya</em>). </span><span>We demonstrated a striking similarity in genome structure among the four species. This conservative genome structure may be attributed to our use of the <em>D. maya</em> assembly as the reference; however, it is worth noting that such a conservative genome structure is a recurring phenomenon among scarab beetles</span><span>. We further identified homologs of nine and three candidate-gene families that may be associated with the evolution of horn structure and body coloration, respectively. Structural variations in <em>Scr</em> and <em>Ebony2</em> were detected and discussed for their putative impacts on generating morphological diversity in beetles. We also reconstructed the demographic histories of the four Hercules beetles using heterozygosity information from the diploid genomes. We found that the demographic histories of the beetles closely recapitulated historical changes in suitable forest habitats driven by climate shifts. </span></p>
Pleiotropic Expression Quantitative Trait Loci Are Enriched in Enhancers and Transcription Factor Binding Sites and Impact More Genes
<p>This dataset comprises two files that accompany the article (link to be added upon publication).</p> <h2>1. gwas2eqtl_colocalization_full.tar.gz</h2> <p>This file contains the complete colocalization dataset generated using the code from the following GitHub repository: gwas2eqtl. This dataset is used as input for the pleiotropic eQTL analysis available at gwas2eqtl_pleiotropy, which produces the figures in the article.</p> <p><strong>File structure:</strong></p> <blockquote> <p>.<br>└── gwas417<br> └── coloc<br> ├── ebi-a-GCST000998<br> │ └── pval_5e-08<br> │ └── r2_0.1<br> │ └── kb_1000<br> │ └── window_1000000<br> │ ├── Alasoo_2018_ge_macrophage_IFNg+Salmonella.tsv<br> │ ├── Alasoo_2018_ge_macrophage_IFNg.tsv<br>...</p> </blockquote> <p>Each TSV file contains the following columns:</p> <blockquote> <p>chrom pos rsid ref alt eqtl_gene_id gwas_beta gwas_pval gwas_id eqtl_beta eqtl_pval eqtl_id PP.H4.abf SNP.PP.H4 nsnps PP.H3.abf PP.H2.abf PP.H1.abf PP.H0.abf coloc_variant_id coloc_region<br>1 109272258 rs4970834 C T ENSG00000168765 -0.12874.25001047052626e-09 ebi-a-GCST000998 -0.250697 0.0893351 Alasoo_2018_ge_macrophage_IFNg+Salmonella 0.108283426725895 0.0520205502224409 6 0.000552728832012655 2.09397277427793e-07 0.890881419183881 0.000282215860934432 1_109279544_G_A 1:108779544-109779543<br>1 109274968 rs12740374 G T ENSG00000168765 -0.103341 1.63998546891446e-09 ebi-a-GCST000998 -0.197397 0.172673Alasoo_2018_ge_macrophage_IFNg+Salmonella 0.108283426725895 0.0857585178966856 6 0.000552728832012655 2.09397277427793e-07 0.890881419183881 0.000282215860934432 1_109279544_G_A 1:108779544-109779543<br>1 109275216 rs660240 T C ENSG00000168765 0.1044492.78997299740827e-09 ebi-a-GCST000998 0.214165 0.139318 Alasoo_2018_ge_macrophage_IFNg+Salmonella 0.108283426725895 0.0557749486050279 6 0.000552728832012655 2.09397277427793e-07 0.890881419183881 0.000282215860934432 1_109279544_G_A 1:108779544-109779543<br>1 109275684 rs629301 G T ENSG00000168765 0.1054716.129993302249e-10 ebi-a-GCST000998 0.197397 0.172673 Alasoo_2018_ge_macrophage_IFNg+Salmonella 0.108283426725895 0.22229240584331 6 0.000552728832012655 2.09397277427793e-07 0.890881419183881 0.000282215860934432 1_109279544_G_A 1:108779544-109779543<br>1 109278889 rs602633 T G ENSG00000168765 0.1034352.15998134341707e-09 ebi-a-GCST000998 0.226329 0.102673 Alasoo_2018_ge_macrophage_IFNg+Salmonella 0.108283426725895 0.0782482718431504 6 0.000552728832012655 2.09397277427793e-07 0.890881419183881 0.000282215860934432 1_109279544_G_A 1:108779544-109779543<br>...</p> </blockquote> <p> </p> <p>The dataset provides colocalization statistics for GWAS-eQTL pairs, including posterior probabilities and variant annotations.</p> <h2>2. gwas2eqtl0.1.3.tsv.gz</h2> <p>This file is a filtered version of the colocalization dataset, refined based on cutoffs of PP.H4.abf ≥ 0.75 and SNP.PP.H4 ≥ 0. This subset is utilized in the gwas2eqtl web application for data visualization.</p> <p>Sample Columns:</p> <blockquote> <p>chrom pos19 pos38 cytoband rsid ref alt gwas_trait gwas_class gwas_beta eqtl_gene_symbol eqtl_beta eqtl_id eqtl_gene_id gwas_id gwas_pval eqtl_pval pp_h4_abf snp_pp_h4 tophits_variant_id nsnps<br>1 1163804 1228424 1p36.33 rs7515488 C T Inflammatory bowel disease Autoimmune dis. 0.0874308 ANKRD65 -0.175816 BrainSeq_ge_brain ENSG00000235098 ebi-a-GCST003043 2.85292266979231e-10 0.000841046 0.978425254116226 6.18454060493069e-12 1_1312114_T_C 3<br>1 1163804 1228424 1p36.33 rs7515488 C T Inflammatory bowel disease Autoimmune dis. 0.0874308 ANKRD65 -0.175816 BrainSeq_ge_brain ENSG00000235098 ieu-a-294 2.85292266979231e-10 0.000841046 0.974019788384412 7.52286530905187e-12 1_1312114_T_C 4<br>1 1163804 1228424 1p36.33 rs7515488 C T Inflammatory bowel disease Autoimmune dis. 0.0874308 ANKRD65 -0.293529 CommonMind_ge_DLPFC_naive ENSG00000235098 ebi-a-GCST003043 2.85292266979231e-10 2.30452e-06 0.953333690803618 6.9758581004380506e-15 1_1312114_T_C 6<br>1 1163804 1228424 1p36.33 rs7515488 C T Inflammatory bowel disease Autoimmune dis. 0.0874308 ANKRD65 -0.293529 CommonMind_ge_DLPFC_naive ENSG00000235098 ieu-a-294 2.85292266979231e-10 2.30452e-06 0.951092499048109 7.0876793540547e-15 1_1312114_T_C 7<br>1 1163804 1228424 1p36.33 rs7515488 C T Inflammatory bowel disease Autoimmune dis. 0.0874308 ANKRD65 -0.510549 FUSION_ge_adipose_naive ENSG00000235098 ebi-a-GCST003043 2.85292266979231e-10 1.2212e-06 0.974412793352836 1.70246427912903e-11 1_1312114_T_C 6</p> </blockquote> <p> </p> <p>This filtered dataset focuses on high-confidence colocalization events for functional exploration of genetic associations and regulatory mechanisms.</p>
Genotype data of 1970 Pedunculate oak trees (Quercus robur L.) in 13 European countries at 381 gene loci covering the nuclear and organelle genome
<p>The data set is the result of genetic inventory on 1970 Pedunculate oak trees from 197 locations in Europe. The samples are from the countries: Belarus, Bosnia, Bulgaria, Croatia, Finland, France, Germany, Hungary, Italy, Latvia, Poland, Russia and Ukraine. At each location ten individual trees were collected. The data set includes the location ID and geographic coordinates of each sampled tree (longitude and latitude in decimal degrees) and the genotype data. All samples were screened with a targeted sequencing approach on a set of 381 polymorphic loci (356 nuclear SNPs, 3 nuclear InDels, 17 chloroplast SNPs and five mitochondrial SNPs).</p> <p>The genotype of each individual is one row in the csv-file "genotypes". The genotypes at the nuclear markers are diploid and represented by two columns per gene marker. The genetic information at the organelle genome is haploid. For each of these gene markers one column is used. Genotypes are coded by Arabic numbers. The meaning of the numbers is explained in the table "coding genotypes" in a second csv-file.</p>
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.