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25 results for “Genomic Data Commons data”
Data from: The genome of a globally invasive passerine, the common myna, Acridotheres tristis
<p>In an era of global climate change, biodiversity conservation is receiving increased attention. Conservation efforts are greatly aided by genetic tools and approaches, which seek to understand patterns of genetic diversity and how they impact species health and their ability to persist under future climate regimes. Invasive species offer vital model systems in which to investigate questions regarding adaptive potential, with a particular focus on how changes in genetic diversity and effective population size interact with novel selection regimes. The common myna (<em>Acridotheres tristis</em>) is a globally invasive passerine and is an excellent model species for research both into the persistence of low-diversity populations and the mechanisms of biological invasion. To underpin research on the invasion genetics of this species, we present the genome assembly of the common myna. We describe the genomic landscape of this species, including genome wide allelic diversity, methylation, repeats, and recombination rate, as well as an examination of gene family evolution. Finally, we use demographic analysis to identify that some native regions underwent a dramatic population increase between the two most recent periods of glaciation, and reveal artefactual impacts of genetic bottlenecks on demographic analysis.</p>
Historical NCI Genomic Data Commons data (09-14-2017)
<p>Historical NCI Genomic Data Commons data (v09-14-2017). Clinical ('phenotype') and gene expression (HTSeq FPKM-UQ).</p> <p> </p> <p><strong><a href="https://xenabrowser.net/datapages/?dataset=TCGA-COAD/Xena_Matrices/TCGA-COAD.GDC_phenotype.tsv&host=https://gdc.xenahubs.net">TCGA-COAD.GDC_phenotype.tsv</a></strong></p> <blockquote> <p>dataset: phenotype - Phenotype</p> <p>cohort<a href="https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Colon%20Cancer%20(COAD)">GDC TCGA Colon Cancer (COAD)</a><br> dataset IDTCGA-COAD/Xena_Matrices/TCGA-COAD.GDC_phenotype.tsv<br> download<a href="https://gdc.xenahubs.net/download/TCGA-COAD/Xena_Matrices/TCGA-COAD.GDC_phenotype.tsv.gz">https://gdc.xenahubs.net/download/TCGA-COAD/Xena_Matrices/TCGA-COAD.GDC_phenotype.tsv.gz</a>; <a href="https://gdc.xenahubs.net/download/TCGA-COAD/Xena_Matrices/TCGA-COAD.GDC_phenotype.tsv.json">Full metadata</a><br> samples570<br> version11-27-2017<br> hubhttps://gdc.xenahubs.net<br> type of dataphenotype<br> authorGenomic Data Commons<br> raw data<a href="https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-90">https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-90</a><br> raw data<a href="https://api.gdc.cancer.gov/data/">https://api.gdc.cancer.gov/data/</a><br> input data formatROWs (samples) x COLUMNs (identifiers) (i.e. clinicalMatrix)<br> 570 samples X 151 identifiers<a href="https://xenabrowser.net/datapages/?host=https%3A%2F%2Fgdc.xenahubs.net&dataset=TCGA-COAD%2FXena_Matrices%2FTCGA-COAD.GDC_phenotype.tsv&allIdentifiers=true">All Identifiers</a><a href="https://xenabrowser.net/datapages/?host=https%3A%2F%2Fgdc.xenahubs.net&dataset=TCGA-COAD%2FXena_Matrices%2FTCGA-COAD.GDC_phenotype.tsv&allSamples=true">All Samples</a></p> </blockquote> <p> </p> <p><strong><a href="https://xenabrowser.net/datapages/?dataset=TCGA-COAD%2FXena_Matrices%2FTCGA-COAD.htseq_fpkm-uq.tsv&host=https%3A%2F%2Fgdc.xenahubs.net">TCGA-COAD.htseq_fpkm-uq.tsv</a></strong></p> <blockquote> <p>dataset: gene expression RNAseq - HTSeq - FPKM-UQ</p> <p>cohort<a href="https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Colon%20Cancer%20(COAD)">GDC TCGA Colon Cancer (COAD)</a><br> dataset IDTCGA-COAD/Xena_Matrices/TCGA-COAD.htseq_fpkm-uq.tsv<br> download<a href="https://gdc.xenahubs.net/download/TCGA-COAD/Xena_Matrices/TCGA-COAD.htseq_fpkm-uq.tsv.gz">https://gdc.xenahubs.net/download/TCGA-COAD/Xena_Matrices/TCGA-COAD.htseq_fpkm-uq.tsv.gz</a>; <a href="https://gdc.xenahubs.net/download/TCGA-COAD/Xena_Matrices/TCGA-COAD.htseq_fpkm-uq.tsv.json">Full metadata</a><br> samples512<br> version09-14-2017<br> hubhttps://gdc.xenahubs.net<br> type of datagene expression RNAseq<br> unitlog2(fpkm-uq+1)<br> platformIllumina<br> ID/Gene Mapping<a href="https://gdc.xenahubs.net/download/probeMaps/gencode.v22.annotation.gene.probeMap.gz">https://gdc.xenahubs.net/download/probeMaps/gencode.v22.annotation.gene.probeMap.gz</a>; <a href="https://gdc.xenahubs.net/download/probeMaps/gencode.v22.annotation.gene.probeMap.json">Full metadata</a><br> authorGenomic Data Commons<br> raw data<a href="https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-80">https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/#data-release-80</a><br> raw data<a href="https://api.gdc.cancer.gov/data/">https://api.gdc.cancer.gov/data/</a><br> wranglingData from the same sample but from different vials/portions/analytes/aliquotes is averaged; data from different samples is combined into genomicMatrix; all data is then log2(x+1) transformed.<br> input data formatROWs (identifiers) x COLUMNs (samples) (i.e. genomicMatrix)<br> 60,484 identifiers X 512 samples</p> </blockquote>
Genomic data and common garden experiments reveal climate-driven selection on ecophysiological traits in two Mediterranean oaks
<p>This release includes the different genomic datasets used in the article entitled "<em>Genomic data and common garden experiments reveal climate-driven selection on ecophysiological traits in two Mediterranean oaks</em> " by Ramírez-Valiente et al.,</p> <p>File description:</p> <p><strong>Samples.xlsx</strong>: Description of individual and population codes used in the different analyses and genomic datasets.</p> <p><strong>Quercus_faginea_p12r05m05minMAF001_all_loci.str</strong>: Input file used to perform genetic clustering analyses (STRUCTURE and DAPC) for <em>Quercus faginea</em> including all loci.</p> <p><strong>Quercus_faginea_p12r05m05minMAF001_neutral_loci.str</strong>: Input file used to perform genetic clustering analyses (STRUCTURE and DAPC) for <em>Quercus faginea</em> excluding outlier loci (i.e., putatively under selection) identified by either BAYESCAN or using the FDIST method in ARLEQUIN.</p> <p><strong>Quercus_lusitanica_p7r05m05minMAF001_all_loci.str</strong>: Input file used to perform genetic clustering analyses (STRUCTURE and DAPC) for <em>Quercus lusitanica </em>including all loci.</p> <p><strong>Quercus_ lusitanica_p7r05m05minMAF001_neutral_loci.str</strong>: Input file used to perform genetic clustering analyses (STRUCTURE and DAPC) for <em>Quercus lusitanica </em>excluding outlier loci (i.e., putatively under selection) identified by either BAYESCAN or using the FDIST method in ARLEQUIN.</p> <p><strong>Quercus_faginea_p12r05m05minMAF001_BAYESCAN.txt</strong>: Input file used to perform BAYESCAN analyses for <em>Quercus faginea</em>.</p> <p><strong>Quercus_lusitanica_p7r05m05minMAF001_BAYESCAN.txt</strong>: Input file used to perform BAYESCAN analyses for <em>Quercus lusitanica</em>.</p> <p><strong>Quercus_faginea_p12r05m05minMAF001_ARLEQUIN.arp</strong>: Input file used to perform ARLEQUIN analyses for <em>Quercus faginea</em>.</p> <p><strong>Quercus_lusitanica_p7r05m05minMAF001_ARLEQUIN.arp</strong>: Input file used to perform ARLEQUIN analyses for <em>Quercus lusitanica</em>.</p> <p><strong>Quercus_faginea_p12r05m05minMAF001_all_loci.vcf</strong>: Variant call format (VCF) file for <em>Quercus faginea</em> including all loci.</p> <p><strong>Quercus_faginea_p12r05m05minMAF001_neutral_loci.vcf</strong>: Variant call format (VCF) file for <em>Quercus faginea</em> excluding outlier loci (i.e., putatively under selection) identified by either BAYESCAN or using the FDIST method in ARLEQUIN.</p> <p><strong>Quercus_lusitanica_p7r05m05minMAF001_all_loci.vcf</strong>: Variant call format (VCF) file for <em>Quercus lusitanica </em>including all loci.</p> <p><strong>Quercus_ lusitanica_p7r05m05minMAF001_neutral_loci.vcf</strong>: Variant call format (VCF) file for <em>Quercus lusitanica </em>excluding outlier loci (i.e., putatively under selection) identified by either BAYESCAN or using the FDIST method in ARLEQUIN.</p> <p><strong>Quercus_faginea_Greenhouse_DRIFTSEL.txt</strong>: Input file used to run DRIFTSEL and evaluate selection on the different studied traits for <em>Quercus faginea </em>under common garden greenhouse experiments.</p> <p><strong>Quercus_faginea_Outdoor_DRIFTSEL.txt</strong>: Input file used to run DRIFTSEL and evaluate selection on the different studied traits for <em>Quercus faginea</em> under common garden outdoor experiments.</p> <p><strong>Quercus_lusitanica_Greenhouse_DRIFTSEL.txt</strong>: Input file used to run DRIFTSEL and evaluate selection on the different studied traits for <em>Quercus lusitanica </em>under common garden greenhouse experiments.</p>
Data from: The genome of a globally invasive passerine, the common myna, Acridotheres tristis
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Data from: Landscape genomics and a common garden trial reveal adaptive differentiation to temperature across Europe in the tree species Alnus glutinosa
The adaptive potential of tree species to cope with climate change has important ecological and economic implications. Many temperate tree species experience a wide range of environmental conditions, suggesting high adaptability to new environmental conditions. We investigated adaptation to regional climate in the drought-sensitive tree species Alnus glutinosa (Black alder), using a complementary approach that integrates genomic, phenotypic and landscape data. A total of 24 European populations were studied in a common garden and through landscape genomic approaches. Genotyping-By-Sequencing was used to identify SNPs across the genome, resulting in 1990 SNPs. Although a relatively low percentage of putative adaptive SNPs was detected (2.86% outlier SNPs), we observed clear associations among outlier allele frequencies, temperature, and plant traits. In line with the typical drought avoiding nature of A. glutinosa, leaf size varied according to a temperature gradient and significant associations with multiple outlier loci were observed, corroborating the ecological relevance of the observed outlier SNPs. Moreover, the lack of isolation-by-distance, the very low genetic differentiation among populations and the high intra-population genetic variation all support the notion that high gene exchange combined with strong environmental selection promotes adaptation to environmental cues.
Data from: Genotyping by sequencing and genome–environment associations in wild common bean predict widespread divergent adaptation to drought
Drought will reduce global crop production by >10% in 2050 substantially worsening global malnutrition. Breeding for resistance to drought will require accessing crop genetic diversity found in the wild accessions from the driest high stress ecosystems. Genome–environment associations in crop wild relatives reveal natural adaptation, and therefore can be used to identify adaptive variation. We explored this approach in the food crop Phaseolus vulgaris L., characterizing 86 geo-referenced wild accessions using Genotyping by Sequencing (GBS) to discover single-nucleotide-polymorphisms (SNPs). The wild beans represented Mesoamerica, Guatemala, Colombia, Ecuador/Northern Peru and Andean groupings. We found high polymorphism with a total of 22,845 SNPs across the 86 accessions loci that confirmed genetic relationships for the groups. As a second objective, we quantified allelic associations with a bioclimatic-based drought index using 10 different statistical models that accounted for population structure. Based on the optimum model, 115 SNPs in 90 regions, widespread in all 11 common bean chromosomes, were associated with the bioclimatic-based drought index. A gene coding for an Ankyrin repeat-containing protein and a phototropic-responsive NPH3 gene were identified as potential candidates. Genomic windows of 1Mb containing associated SNPs had more positive Tajima's D scores than windows without associated markers. This indicates that adaptation to drought, as estimated by bioclimatic variables, has been under natural divergent selection, suggesting that drought tolerance may be favorable under dry conditions but harmful in humid conditions. Our work exemplifies that genomic signatures of adaptation are useful for germplasm characterization, potentially enhancing future marker-assisted selection and crop improvement.
Population genomic consequences of life history and mating system adaptation to a geothermal soil mosaic in yellow monkeyflowers (common garden phenotype data)
<p>Local selection can promote phenotypic divergence despite gene flow across habitat mosaics, but adaptation itself may generate substantial barriers to genetic exchange. In plants, life-history, phenology, and mating system divergence have been proposed to promote genetic differentiation in sympatry. In this study, we investigate phenotypic and genetic variation in <em>Mimulus guttatus</em> (yellow monkeyflowers) across a geothermal soil mosaic in Yellowstone National Park (YNP). Plants from thermal annual and nonthermal perennial habitats were heritably differentiated for life history and mating system traits, consistent with local adaptation to the ephemeral thermal-soil growing season. However, genome-wide genetic variation primarily clustered plants by geographic region, with little variation sorting by habitat. The one exception was an extreme thermal population also isolated by a 200m geographical gap of no intermediate habitat. Individual inbreeding coefficients (F<sub>IS</sub>) were higher (and predicted by trait variation) in annual plants and annual pairs showed greater isolation by distance at local (<1km) scales. Finally, YNP adaptation does not re-use a widespread inversion that underlies <em>M. guttatus</em> life-history ecotypes range-wide, suggesting a novel genetic mechanism. Overall, this work suggests that life history and mating system adaptation strong enough to shape individual mating patterns does not necessarily generate incipient speciation without geographical barriers.</p>
Data for isolation-by-environment and its consequences for range shifts with global change: Landscape genomics of the invasive common tansy
<p>Invasive species are a growing global economic and ecological problem. However, it is not well understood how environmental factors mediate invasive range expansion. In this study, we investigated the recent and rapid range expansion of common tansy across environmental gradients in Minnesota, U.S.A. We densely sampled individuals across the expanding range and performed reduced representation sequencing to generate a dataset of 3071 polymorphic loci for 176 individuals. The dataset includes additional samples from the native range in Finland that were not used in the downstream analysis but are contributed for completeness. The dataset includes the genotype calls for all individuals sampled and sequenced. The genotype file was generated by stacks2.59 running the denovo pipeline and then using the populations function where we kept loci that were in 70% of populations and had a minor allele frequency of at least 1%. We used non-spatial and spatially-explicit analyses to determine the relative influences of geographic distance and environmental variation on patterns of genomic variation. We found no evidence for isolation-by-distance (IBD) but strong evidence for isolation-by-environment (IBE), indicating that environmental factors may have modulated patterns of range expansion.</p>
Data from: Demographic histories shape population genomics of the common coral grouper (Plectropomus leopardus)
<p>Many coral reef fishes display remarkable genetic and phenotypic variation across their geographic ranges. Understanding how historical and contemporary processes have shaped these patterns remains a focal question in evolutionary biology since they reveal how diversity is generated and how it may respond to future environmental change. Here we compare the population genomics and demographic histories of a commercially and ecologically important coral reef fish, the common coral grouper (<em>Plectropomus</em> <em>leopardus</em> [Lacépède 1802]), across two adjoining regions (the Great Barrier Reef; GBR, and the Coral Sea, Australia) spanning approximately 14 degrees of latitude and 9 degrees of longitude. We analysed 4,548 single nucleotide polymorphism (SNP) markers across 11 sites and show that genetic connectivity between regions is low, despite their relative proximity (~ 100 km) and an absence of any obvious geographic barrier. Inferred demographic histories using 10,479 markers suggest that the Coral Sea population was founded by a small number of GBR individuals and that divergence occurred ~ 190 kya under a model of isolation with asymmetric migration. We detected population expansions in both regions, but estimates of contemporary effective population sizes were approximately 50 % smaller in Coral Sea sites, which also had lower genetic diversity. Our results suggest that <em>P. leopardus</em> in the Coral Sea have experienced a long period of isolation that precedes the recent glacial period (~ 10–120 kya) and may be vulnerable to localised disturbances due to their relative reliance on local larval replenishment. While it is difficult to determine the underlying events that led to the divergence of Coral Sea and GBR lineages, we show that even geographically proximate populations of a widely dispersed coral reef fish can have vastly different evolutionary histories.</p>
Population genomic consequences of life history and mating system adaptation to a geothermal soil mosaic in yellow monkeyflowers (common garden phenotype data)
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Data for isolation-by-environment and its consequences for range shifts with global change: Landscape genomics of the invasive common tansy
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Data from: Genotyping by sequencing and genome–environment associations in wild common bean predict widespread divergent adaptation to drought
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Data from: Demographic histories shape population genomics of the common coral grouper (Plectropomus leopardus)
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Data from: Landscape genomics and a common garden trial reveal adaptive differentiation to temperature across Europe in the tree species Alnus glutinosa
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Data from: Phenotypic, ecological and genomic variation in common bully (Gobiomorphus cotidianus) populations along depth gradients in New Zealand's Southern Great Lakes
<p>Depth gradients in lakes are often key drivers of population divergence and speciation in fishes. New Zealand has many deep lakes but no known profundal specialist fishes or cases of intralacustrine speciation. We sampled a native benthic fish, the common bully, from 5–90 m depth in four South Island lakes, to test for morphological, ecological, or genetic differentiation associated with depth. Deeper fish consistently had narrower bodies, while other morphological traits showed variable relationships with depth. Carbon and nitrogen stable isotope values of fish increased with depth, largely tracking isotopic trends with depth of benthic invertebrate prey. Genotyping-by-sequencing showed some genome-wide differentiation between two of the lakes, but no evidence for within-lake genetic structuring along depth gradients. These results indicate that individual bullies associate with shallower or deeper habitats within their lifetimes, but we found no evidence of progress toward genetic divergence within lakes. The apparent lack of intralacustrine genetic divergence in New Zealand's fishes may be explained by a combination of environmental factors and constraints intrinsic to its marine-derived freshwater fish fauna.</p>
Data from: Differences in the regulation of growth and biomineralization genes revealed through long-term common garden acclimation and experimental genomics in the purple sea urchin
Across heterogeneous landscapes, populations may have adaptive differences in gene regulation that adjust their physiologies to match local environments. Such differences could have origins in acclimation or in genetically fixed variation between habitats. Here we use common garden experiments to evaluate differences in gene expression between populations of the purple sea urchin, Strongylocentrotus purpuratus, spanning 1700 km and average temperature differences of 5 °C to 8 °C. Across expression profiles from 18,883 genes after three years of common conditions, we find highly correlated expression patterns (Pearson's r = 0.992) among most genes. However, sixty-six genes were differentially expressed, including many ribosomal protein and biomineralization genes, all of which had higher expression in urchins originally from the southern population. Gene function analyses revealed slight but pervasive expression differences in genes related to ribosomal function, metabolism, transport, "bone" development, and response to stimuli. In accord with gene expression patterns, a post-hoc spine re-growth experiment revealed that urchins of southern origin re-grew spines at a faster rate than northern urchins. These results suggest that there may be genetically controlled, potentially adaptive differences in gene regulation across habitats and that gene expression differences may be under strong enough selection to overcome high dispersal-mediated gene flow in this marine species.
Data from: Genome-wide investigation of adaptation to harmful algal blooms in common bottlenose dolphins (Tursiops truncatus)
Harmful algal blooms (HABs), which can be lethal in marine species and cause illness in humans, are increasing worldwide. In the Gulf of Mexico, HABs of Karenia brevis produce neurotoxic brevetoxins that cause large-scale marine mortality events. The long history of such blooms, combined with the potentially severe effects of exposure, may have produced a strong selective pressure for evolved resistance. Advances in next-generation sequencing, in particular genotyping-by-sequencing, greatly enable the genomic study of such adaptation in natural populations. We used restriction site-associated DNA (RAD) sequencing to investigate brevetoxicosis resistance in common bottlenose dolphins (Tursiops truncatus). To improve our understanding of the epidemiology and aetiology of brevetoxicosis and the potential for evolved resistance in an upper trophic level predator, we sequenced pools of genomic DNA from dolphins sampled from both coastal and estuarine populations in Florida and during multiple HAB-associated mortality events. We sequenced 129 594 RAD loci and analysed 7431 single nucleotide polymorphisms (SNPs). The allele frequencies of many of these polymorphic loci differed significantly between live and dead dolphins. Some loci associated with survival showed patterns suggesting a common genetic-based mechanism of resistance to brevetoxins in bottlenose dolphins along the Gulf coast of Florida, but others suggested regionally specific mechanisms of resistance or reflected differences among HABs. We identified candidate genes that may be the evolutionary target for brevetoxin resistance by searching the dolphin genome for genes adjacent to survival-associated SNPs.
Data from: Phenotypic, ecological and genomic variation in common bully (Gobiomorphus cotidianus) populations along depth gradients in New Zealand's Southern Great Lakes
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Data from: Developing genomic resources for the common bottlenose dolphin (Tursiops truncatus): isolation and characterisation of 153 single nucleotide polymorphisms and 53 genotyping assays
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Data from: Differences in the regulation of growth and biomineralization genes revealed through long-term common garden acclimation and experimental genomics in the purple sea urchin
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.