Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
394
datasets available to search
ShareScore release 0.9.0
Dataset results
394 results for “Genomic Diversity”
Functional genomics and co-occurrence in a diverse tropical tree genus: The roles of drought and defense related genes
Open the record for dataset details and reuse information.
Data from: Conservation prioritisation of genomic diversity to inform management of a declining mammal species
Open the record for dataset details and reuse information.
Chromosomal-level genome assembly of the scimitar‐horned oryx: insights into diversity and demography of a species extinct in the wild
Open the record for dataset details and reuse information.
Data from: Island size shapes genomic diversity in a great speciator (Aves: Zosterops)
Open the record for dataset details and reuse information.
The Evolution and Genomic Basis of Beetle Diversity
<p>Datasets S1-S4. (each is contained in a separate .zip file)</p> <p><strong>Dataset S1.</strong></p> <p>Gene trees for plant cell wall degrading enzyme phylogenetic analyses in the directory ‘Pfam Candidate Genes trees and phy’</p> <p>1. Phylip formatted files for each gene used in ML analyses.</p> <p>2. ML tree files for each gene studied showing TBE bootstrap support (100 replicates) (corresponding to Figs. S15-S26).</p> <p>3. ML tree files for each gene studied showing ML bootstrap support (100 replicates) from IQtree (corresponding to Figs. S15-S26).</p> <p><strong>Dataset S2.</strong></p> <p>Directory (Blast_10best_hits_Pfam_Candidate_Genes) including: Blast results (10 best hits) for all sequences extracted from the transcriptome and genome assemblies for the plant cell wall degrading enzyme analysis in the directory ‘Pfam_Candidate_Genes_Fas’ (before filtering).</p> <p><strong>Dataset S3.</strong></p> <p>Directory (Pfam_Candidate_Genes_Fas) including: Candidate genes/transcripts encoding plant cell wall degrading enzymes extracted from the transcriptome and genome assemblies (before filtering).</p> <p><strong>Dataset S4.</strong></p> <p>Directory (Supermatrices_partitions) including:</p> <ul> <li>Supermatrix for Fig. 1 (amino acid and nucleotide level, PHYLIP formats) and Supermatrix for Fig. S10 (amino acid level, PHYLIP format).</li> <li>Partition schemes for supermatrix for Fig. 1 (Fig_1_Partition_finder_best_scheme).</li> <li>Partition schemes for supermatrix for Fig. 1 prior to Partitionfinder (AA_partitions).</li> <li>Partition schemes for supermatrix for NT prior to Partitionfinder (NT_partitions).</li> <li>Partition schemes for supermatrix for Fig. S10 (Fig_S10_Partition_finder_best_scheme)</li> </ul> <p><strong>Data Use Statement.</strong> Data on genetic material contained in this paper are published for non-commercial use only. Utilization by third parties for purposes other than non-commercial scientific research may infringe the conditions under which the genetic resources were originally accessed, and should not be undertaken without obtaining consent from the corresponding author of the paper and/or obtaining permission from the original provider of the genetic material.</p>
Data from: Miniaturization, genome size, and biological size in a diverse clade of salamanders
Genome size (C-value) can affect organismal traits across levels of biological organization, from tissue complexity to metabolism. Neotropical salamanders show wide variation in genome and body sizes, including several clades with miniature species. Because miniaturization imposes strong constraints on morphology and development, and genome size is strongly correlated with cell size, we hypothesize that body size has played an important role in the evolution of genome size in bolitoglossine salamanders. If this hypothesis is correct, then genome size and body size should be correlated in this group. Using Feulgen Image Analysis Densitometry (FIAD), we estimated genome sizes for 60 species of neotropical salamanders. We also estimated the "biological size" of species by comparing genome size and physical body sizes in a phylogenetic context. We found a significant correlation between C-value and physical body size using optimal regression with an Ornstein-Uhlenbeck model, and report the smallest salamander genome found to date. Our index of biological size showed that some salamanders with large physical body size have smaller biological body size than some miniature species, and that several clades showed patterns of increased or decreased biological size compared to their physical size. Our results suggest a causal relationship between physical body size and genome size and show the importance of considering the impact of both on the biological size of organisms. Indeed, biological size may be a more appropriate measure than physical size when considering phenotypic consequences of genome size evolution in many groups.
Data from: Population genomic diversity and structure at the discontinuous southern range of the Great Gray Owl in North America
<p>Species' distributions are often discontinuous near the edge of the range where the environment may be more variable than the core of the range. Range discontinuity can reduce or cut off gene flow to small peripheral populations and lead to genetic drift and subsequent loss of genetic diversity. The southern extent of the Great Gray Owl ( Strixnebulosa) range in North America is discontinuous, unlike their northern core range across the boreal forests. We sampled owls from five different locations on the periphery of the range across the western US (Wyoming, Idaho, California, northern Oregon, and southern Oregon) to investigate genetic population structure and genetic diversity. Using a reduced-representation genomic sequencing approach to genotype 123 individuals at 4,817 single nucleotide polymorphic loci, we identified four genetically differentiated populations: California, southern Oregon, northern Oregon, and Wyoming and Idaho grouped together as a single Rocky Mountain population. The four genetically differentiated populations of Great Gray Owls identified in this study display high differentiation and low genetic variation, which is suggestive of long-term isolation and lack of connectivity, potentially caused by range discontinuity. The populations that lack habitat connectivity to the rest of the breeding range (i.e. those in California and Oregon) had lower genetic diversity than the Rocky Mountain population that is connected to the core of the range. These factors and other risks (such as disease and human-caused mortality) heighten susceptibility of these range-edge populations to future habitat and climate changes, genetic diversity erosion, and potential extinction vortex. For these reasons, protecting and monitoring this species on the southern edge of their range is vital.</p>
High genomic diversity in the bank vole at the northern apex of a range expansion: the role of multiple colonizations and end-glacial refugia
<p>The history of repeated northern glacial cycling and southern climatic stability has long dominated explanations for how genetic diversity is distributed within temperate species in Eurasia and North America. However, growing evidence indicates the importance of cryptic refugia for northern colonization dynamics. An excellent geographic region to assess this is Fennoscandia, where recolonization at the end of the last glaciation was restricted to specific routes and temporal windows. We used genomic data to analyze genetic diversity and colonization history of the bank vole (<i>Myodes glareolus</i>) throughout Europe (> 800 samples) with Fennoscandia as the northern apex. We inferred that bank voles colonized Fennoscandia multiple times by two different routes; with three separate colonizations via a southern land-bridge route deriving from a 'Carpathian' glacial refugium and one via a north-eastern route from an 'Eastern' glacial refugium near the Ural Mts. Clustering of genome-wide SNPs revealed tremendous diversity in Fennoscandia, with eight genomic clusters: three of Carpathian origin and five Eastern. Time estimates revealed that the first of the Carpathian colonizations occurred before the Younger Dryas (YD), meaning that the first colonists survived the YD in Fennoscandia. Results also indicated that introgression between bank and northern red-backed voles (<i>Myodes rutilus</i>) took place in Fennoscandia just after end-glacial colonization. Therefore, multiple colonizations from the same and different cryptic refugia, temporal and spatial separations and interspecific introgression have shaped bank vole genetic variability in Fennoscandia. Together, these processes drive high genetic diversity at the apex of the northern expansion in this model species.</p>
Data from: Genome-wide diversity and habitat underlie fine-scale phenotypic differentiation in the rainbow darter (Etheostoma caeruleum)
<p>Adaptation to environmental change requires that populations harbor the necessary genetic variation to respond to selection. However, dispersal-limited species with fragmented populations and reduced genetic diversity may lack this variation and are at an increased risk of local extinction. In freshwater fish species, environmental change in the form of increased stream temperatures places many cold-water species at-risk. We present a study of rainbow darters (<i>Etheostoma caeruleum</i>) in which we evaluated the importance of genetic variation on adaptive potential and determined responses to extreme thermal stress. We compared fine-scale patterns of morphological and thermal tolerance differentiation across eight sites, including a unique lake habitat. We also inferred contemporary population structure using genomic data and characterized the relationship between individual genetic diversity and stress tolerance. We found site-specific variation in thermal tolerance that generally matched local conditions and morphological differences associated with lake-stream divergence. We detected patterns of population structure on a highly local spatial scale that could not be explained by isolation by distance or stream connectivity. Finally, we showed that individual thermal tolerance was positively correlated with genetic variation, suggesting that sites with increased genetic diversity may be better at tolerating novel stress. Our results highlight the importance of considering intraspecific variation in understanding population vulnerability and stress response.</p>
Data From: Evaluating the correlation between genome-wide diversity and the release of plastic phenotypic variation in experimental translocations to novel natural environments
<p>Phenotypic reaction norms are often shaped and constrained by selection and are important for allowing organisms to respond to environmental change. However, selection cannot constrain reaction norms for environmental conditions that populations have not experienced. This may allow cryptic neutral genetic variation for the reaction norm to accumulate such that a release of phenotypic variation occurs when it is exposed to novel conditions. Most genomic diversity behaves as if functionally neutral. Genome-wide diversity metrics may therefore correlate with levels of cryptic genetic variation and, as a result, could exhibit a positive relationship with a release of phenotypic variation in novel environments. To test this hypothesis, we conducted translocations of juvenile brook trout (Salvelinus fontinalis) from 12 populations to novel uninhabited ponds that represented a gradient of environmental conditions. We assessed reaction norms for morphological traits (body size and four morphometric relative warps) across pond environmental gradients and evaluated the effect of genome-wide heterozygosity on phenotypic variability. All traits displayed plastic reaction norms. Overall, we found some evidence that a release of phenotypic variation consistent with cryptic genetic variation can occur in novel environmental conditions. However, the extent to which this release was correlated with average genome-wide diversity was limited to only one of five morphological traits examined. Our results suggest that the link between genomic diversity and the accumulation of cryptic genetic variation in reaction norms may be limited. Similarly, reaction norms were constrained for many of the morphological traits examined. Past conditions may have constrained reaction norms in the putatively novel environments despite significant deviations from contemporary source population habitat. Additionally, as a generalist colonizing species brook trout may exhibit plastic phenotypes across a wide range of environmental conditions.</p>
Data from: Entangled fates of holobiont genomes during invasion: nested bacterial and host diversities in Caulerpa taxifolia
Successful prevention and mitigation of biological invasions requires retracing the initial steps of introduction, as well as understanding key elements enhancing the adaptability of invasive species. We studied the genetic diversity of the green alga Caulerpa taxifolia and its associated bacterial communities in several areas around the world. The striking congruence of α and ß diversity of the algal genome and endophytic communities reveals a tight association, supporting the holobiont concept as best describing the unit of spreading and invasion. Both genomic compartments support the hypotheses of a unique accidental introduction in the Mediterranean and of multiple invasion events in Southern Australia. In addition to helping with tracing the origin of invasion, bacterial communities exhibit metabolic functions that can potentially enhance adaptability and competitiveness of the consortium they form with their host. We thus hypothesize that low genetic diversities of both host and symbiont communities may contribute to the recent regression in the Mediterranean, in contrast with the persistence of highly diverse assemblages in southern Australia. This study supports the importance of scaling up from the host to the holobiont for a comprehensive understanding of invasions.
Data from: Genomic diversity of a nectar yeast clusters into metabolically, but not geographically, distinct lineages
Both dispersal limitation and environmental sorting can affect genetic variation in populations, but their contribution remains unclear, particularly in microbes. We sought to determine the contribution of geographic distance (as a proxy for dispersal limitation) and phenotypic traits (as a proxy for environmental sorting), including morphology, metabolic ability, and interspecific competitiveness, to the genotypic diversity in a nectar yeast species, Metschnikowia reukaufii. To measure genotypic diversity, we sequenced the genomes of 102 strains of M. reukaufii isolated from the floral nectar of hummingbird-pollinated shrub, Mimulus aurantiacus, along a 200-km coastline in California. Intraspecific genetic variation showed no detectable relationship with geographic distance, but could be grouped into three distinct lineages that correlated with metabolic ability and interspecific competitiveness. Despite ample evidence for strong competitive interactions within and among nectar yeasts, a full spectrum of the genotypic and phenotypic diversity observed across the 200-km coastline was represented even at a scale as small as 200 m. Furthermore, more competitive strains were not necessarily more abundant. These results suggest that dispersal limitation and environmental sorting might not fully explain intraspecific diversity in this microbe and highlight the need to also consider other ecological factors such as trade-offs, source-sink dynamics, and niche modification.
Ultra-deep sequencing of HIV-1 near full-length and partial proviral genomes reveals high genetic diversity among Brazilian blood donors
<p>Here, we aimed to gain a comprehensive picture of the HIV-1 diversity in the northeast and southeast part of Brazil. To this end, a high-throughput sequencing-by-synthesis protocol and instrument were used to characterize the near full length (NFLG) and partial HIV-1 proviral genome in 259 HIV-1 infected blood donors at four major blood centers in Brazil: Pro-Sangue foundation (São Paulo state (SP), n 51), Hemominas foundation (Minas Gerais state (MG), n 41), Hemope foundation (Recife state (PE), n 96) and Hemorio blood bank (Rio de Janeiro (RJ), n 70).</p>
Genome-resolved diversity and biosynthetic potential of the coral reef microbiome
<p>This repository hosts the supplementary data associated with the manuscript entitled "Genome-resolved diversity and biosynthetic potential of the coral reef microbiome".</p>
Genome Database: Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers
<p>This repository contains the dataset used in the publication "Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers," which is currently under revision. A pre-print can be found <a href="https://doi.org/10.1101/2022.12.29.522137">here</a>. The database is based on previously published work to create a genomic database of honeybee gut microbes by Kirsten Ellegaard (2021), found <a href="https://zenodo.org/records/4661061">here.</a></p><p>The zipped folder deposited here after unzipping, should contain the following files and directories:</p><ul><li>honeybee_genome.fasta : fasta file containing the host (<i>Apis mellifera</i>) genome sequence</li><li>beebiome_db : fasta file of 198 concatenated genomes with one genome per entry (multi-line fasta) where the headers represent the genome identifier</li><li>beebiome_red_db : fasta file of 39 species representative genomes with one genome per entry (multi-line fasta) where the headers represent the genome identifier to be used for the analysis of intra-specific variation</li><li>fna_files : directory containing genome sequence files and concatenated files where the concatenated files contain one fasta entry renamed to the genome identifier and all contigs concatenated into one entry</li><li>ffn_files : directory containing one file per genome listing the nucleotide sequence of all the predicted genes</li><li>faa_files : directory containing one file per genome listing the amino acid sequence of all the predicted genes</li><li>bed_files : directory containing bed files where the location of each of the predicted genes are indicated based on their position in the concatenated genome file</li><li>single_ortho : directory containing one file per phylotype listing all the single-copy orthogroups (OGs) identified by orthofinder where each line represents an OG id followed by a list of genes from each of the genomes of that phylotype that belong to that OG and the corresponding sequences of these genes can be found in the ffn file belonging to the respective genome</li><li>red_bed_files : directory containing bed files for species representative genomes that only list the positions genes that belong to the core orthogroups of their phylotype</li></ul><p>Further information about how this genome database was used to analyze strain-level diversity can be found in the publication and accompanying code repository.</p>
Monitoring genome-wide diversity over contemporary time with new indicators applied to Arctic charr populations
<p>Genetic diversity is fundamental to the adaptive potential and survival of species. Although its importance has long been recognized in science, it has a history of neglect within policy – until now. The new Global Biodiversity Framework recently adopted by the Convention on Biological Diversity, states that genetic diversity must be maintained at levels assuring adaptive potential of populations, and includes metrics for systematic monitoring of genetic diversity in so called indicators. Similarly, indicators for genetic diversity are being developed at national levels. Here, we apply new indicators for Swedish national use to one of the northernmost salmonid fishes, the Arctic charr (<em>Salvelinus alpinus</em>). We sequence whole genomes to monitor genetic diversity over four decades in three landlocked populations inhabiting protected alpine lakes in central Sweden. We find levels of genetic diversity, inbreeding and load to differ among lakes but remain stable over time. Effective population sizes are generally small (<500), suggesting a limited ability to maintain adaptive variability if genetic exchange with nearby populations became eliminated. We identify genomic regions potentially shaped by selection; SNPs exhibiting population divergence exceeding expectations under drift and a putative selective sweep acting within one lake to which the competitive brown trout was introduced during the sampling period. Identified genes appear involved in immunity and salinity tolerance. Present results suggest that genetically vulnerable populations of Arctic charr have maintained neutral and putatively adaptive genetic diversity despite small effective sizes, attesting the importance of continued protection and assurance of gene flow among populations.</p>
Data from: Genomic diversity and structure of a Neotropical microendemic fig tree
<p>Genetic diversity is a key component of evolution and unraveling factors that promote genetic differentiation in space and time is a central question in evolutionary biology. One of the most diverse and ecologically important tree genera in tropical forests worldwide is <em>Ficus (Moraceae)</em>. It has been suggested that, given the great dispersal capacity of pollinating fig wasps (Chalcidoidea; Agaonidae), the spatial genetic structure, particularly in monoecious fig species, should be weak. However, no studies have addressed the factors that determine the genetic structure of <em>Ficus</em> species in regions of high geological, geographic, and climatic complexity, such as the Mexican Transition Zone. Using nuclear single nucleotide polymorphisms (5,311 SNPs) derived from low-coverage whole genomes and 17 populations, we analyzed the population genomics of <em>Ficus</em> <em>pringlei</em> to characterize neutral and adaptive genetic variation and structure and its association with geographic barriers such as the Trans-Mexican Volcanic Belt, environmental heterogeneity, and wind connectivity. From genomic data of 71 individuals, high genetic diversity, and the identification of three genomic lineages were recorded (North, South, and Churumuco). The results suggest that genetic variation is primarily determined by climatic heterogeneity. <em>Ficus</em> <em>pringlei</em> populations from the north and south of the Trans-Mexican Volcanic Belt also exhibited minimal genetic differentiation (F<sub>ST</sub>= 0.021), indicating that this mountain range may not act as an insurmountable barrier to gene flow. Wind connectivity is also highlighted in structuring putative adaptive genetic variation, underscoring the intricate complexity of the various factors influencing genetic variation in the species. This study provides information on the possible mechanisms underlying the genetic variation of endemic species of the tropical dry forest of Western Mexico, such as <em>F</em>. <em>pringlei</em>.</p>
Data and code to reproduce analyses in Heinken et al, "A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites"
<p>This datasets archives the GitHub version found at https://github.com/ThieleLab/CodeBase to reproduce simulations for the article Heinken et al, "A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites", Cell Systems, in press.</p>
Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes
<p>Bacterial specialized metabolites are a proven source of antibiotics and cancer therapeutics, but whether we have sampled all the secondary metabolite chemical diversity of cultivated bacteria is not known. We analysed ~ 170,000 bacterial genomes and ~ 47,000 metagenome assembled genomes (MAGs) using a modified BiG-SLiCE and the new clust-o-matic algorithm. We found that only 3% of the natural products potentially encoded in bacterial genomes have been experimentally characterized. We show that the variation of secondary metabolite biosynthetic diversity drops significantly on a genus level, identifying it as an appropriate taxonomic rank for comparison. Equal comparison of genera based on Relative Evolutionary Distance revealed that <em>Streptomyces</em> bacteria encode the largest biosynthetic diversity by far, with <em>Amycolatopsis</em>, <em>Kutzneria</em> and <em>Micromonospora</em> also encoding substantial chemical diversity. Finally we find that several less-well-studied taxa such as Weeksellaceae (Bacteroidota), Myxococcaceae (Myxococcota), <em>Pleurocapsa</em> and Nostocaceae (Cyanobacteria) have potential to produce highly diverse secondary metabolites that warrant further investigation.</p>
Assessing population structure and genetic diversity in U.S. Suffolk sheep to define a framework for genomic selection
<p>Long-term sustainability of breeds depends on having sufficient genetic diversity for adaptability to change, whether driven by climatic conditions or by priorities in breeding programs. Genetic diversity in Suffolk sheep in the U.S. was evaluated in four ways: 1) using genetic relationships from pedigree data [(n=64,310 animals recorded in the U.S. National Sheep Improvement Program (NSIP)]; 2) using molecular data (n=304 Suffolk genotyped with the OvineHD BeadChip); 3) comparing Australian (n=109) and Irish (n=55) Suffolk sheep to those in the U.S. using molecular data; and 4) assessing genetic relationships (connectedness) among active Suffolk flocks (n=18) in NSIP. By characterizing genetic diversity, a goal was to define the structure of a reference population for use for genomic selection strategies in this breed. Pedigree-based mean inbreeding level for the most recent year of available data was 5.5%. Ten animals defined 22.8% of the current gene pool. The effective population size (N<sub>e</sub>) ranged from 27.5 to 244.2 based on pedigree and was 79.5 based on molecular data. Expected (H<sub>E</sub>) and observed (H<sub>O</sub>) heterozygosity were 0.317 and 0.306, respectively. Model-based population structure included 7 subpopulations. From Principal Component Analysis, countries separated into distinct populations. Within the U.S. population, flocks formed genetically disconnected clusters. A decline in genetic diversity over time was observed from both pedigree and genomic-based derived measures with evidence of population substructure as measured by F<sub>ST</sub>. Using these measures of genetic diversity, a framework for establishing a genomic reference population in U.S. Suffolk sheep engaged in NSIP was proposed.</p>
ScienceDex guides
Understand access before you commit
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.