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76 results for “Linked selection”
The Missing Link Between Black Holes in High-Mass X-ray Binaries and Gravitational-Wave Sources: Observational Selection Effects
<p>Data tables containing the calculated binary parameters used to acquire all results in <a href="https://arxiv.org/abs/2210.01825v1">arXiv:2210.01825v1</a>. The file "xrb_params_illustris_z0.05_sample.csv" contains data for the z<0.05 sampled population and the file xrb_params_illustris_z20_sample.csv contains data for the z<20 sampled population.</p>
Linked collectors and determiners for: Flora of Sumatra: Vascular plant collection of selected families deposited at Herbarium of Andalas University (ANDA).
Natural history specimen data linked to collectors and determiners held within, "Flora of Sumatra: Vascular plant collection of selected families deposited at Herbarium of Andalas University (ANDA)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/3e0987c4-375f-4d68-b2ac-5e4e3a6d3d6d">https://bionomia.net/dataset/3e0987c4-375f-4d68-b2ac-5e4e3a6d3d6d</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/3e0987c4-375f-4d68-b2ac-5e4e3a6d3d6d">https://gbif.org/dataset/3e0987c4-375f-4d68-b2ac-5e4e3a6d3d6d</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Vascular plants of the Amur River Basin, Russia: specimen based occurrence dataset of 100 selected species.
Natural history specimen data linked to collectors and determiners held within, "Vascular plants of the Amur River Basin, Russia: specimen based occurrence dataset of 100 selected species". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/0c7bd9e3-ded7-4de4-99ec-d5145361ff48">https://bionomia.net/dataset/0c7bd9e3-ded7-4de4-99ec-d5145361ff48</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/0c7bd9e3-ded7-4de4-99ec-d5145361ff48">https://gbif.org/dataset/0c7bd9e3-ded7-4de4-99ec-d5145361ff48</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Occurrence of Heilipus squamosus from selected collections in the United States.
Natural history specimen data linked to collectors and determiners held within, "Occurrence of Heilipus squamosus from selected collections in the United States". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/17909377-6d89-41b5-bf65-807665c68a3b">https://bionomia.net/dataset/17909377-6d89-41b5-bf65-807665c68a3b</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/17909377-6d89-41b5-bf65-807665c68a3b">https://gbif.org/dataset/17909377-6d89-41b5-bf65-807665c68a3b</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Select Specimens from the Hanover High School Insect Collection.
Natural history specimen data linked to collectors and determiners held within, "Select Specimens from the Hanover High School Insect Collection". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/8e8472a9-d604-4c97-9f2f-4aee2076a140">https://bionomia.net/dataset/8e8472a9-d604-4c97-9f2f-4aee2076a140</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/8e8472a9-d604-4c97-9f2f-4aee2076a140">https://gbif.org/dataset/8e8472a9-d604-4c97-9f2f-4aee2076a140</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Plant species occurrences recorded from selected sites in the lower Tana River Basin, Kenya.
Natural history specimen data linked to collectors and determiners held within, "Plant species occurrences recorded from selected sites in the lower Tana River Basin, Kenya". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/cbc3c3cb-4351-42cd-8209-70c3f12f4dad">https://bionomia.net/dataset/cbc3c3cb-4351-42cd-8209-70c3f12f4dad</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/cbc3c3cb-4351-42cd-8209-70c3f12f4dad">https://gbif.org/dataset/cbc3c3cb-4351-42cd-8209-70c3f12f4dad</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Select Insect Specimens from Malaise Traps in Orleans County, Vermont, USA.
Natural history specimen data linked to collectors and determiners held within, "Select Insect Specimens from Malaise Traps in Orleans County, Vermont, USA". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/30968d94-12c8-48d6-9cc7-1a407f4c5e1b">https://bionomia.net/dataset/30968d94-12c8-48d6-9cc7-1a407f4c5e1b</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/30968d94-12c8-48d6-9cc7-1a407f4c5e1b">https://gbif.org/dataset/30968d94-12c8-48d6-9cc7-1a407f4c5e1b</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Plant species occurrences recorded from selected sites in the mid Tana River Basin, Kenya.
Natural history specimen data linked to collectors and determiners held within, "Plant species occurrences recorded from selected sites in the mid Tana River Basin, Kenya". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/88e15b3d-e8fa-4527-b164-83078901de99">https://bionomia.net/dataset/88e15b3d-e8fa-4527-b164-83078901de99</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/88e15b3d-e8fa-4527-b164-83078901de99">https://gbif.org/dataset/88e15b3d-e8fa-4527-b164-83078901de99</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Bitunicate ascomycetes (Dothideomycetes and Chaetothyriomycetidae) on bark and wood of selected hosts in Norway.
Natural history specimen data linked to collectors and determiners held within, "Bitunicate ascomycetes (Dothideomycetes and Chaetothyriomycetidae) on bark and wood of selected hosts in Norway". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/ca0d8107-a2bd-47a1-91a1-250179b534ec">https://bionomia.net/dataset/ca0d8107-a2bd-47a1-91a1-250179b534ec</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/ca0d8107-a2bd-47a1-91a1-250179b534ec">https://gbif.org/dataset/ca0d8107-a2bd-47a1-91a1-250179b534ec</a>. Formatted as a Frictionless Data package.
Data from: Seasonal brain regeneration and chromosome instability are linked to selection on DNA repair in Sorex araneus
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Data from: Evidence for a selective link between cooperation and individual recognition
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Data from: Linking divergence in phenotypic selection on floral traits to divergence in local pollinator assemblages in a pollination-generalized plant
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Semantic links between selected CSV datasets harvested by the European Data Portal and the DBpedia knowledge graph
<p>These dataset contains the results of the interlinking process between selected csv datasets harvested by the European DAta Portal and the DBpedia knowledge graph. </p> <p>We aim at answering the following questions:<br> What are the more popular column types? This will provide hindsight about what the datasets hold and how they can be joined. It will also provide hindsight on what specific linking schemes could be applied in future elements.<br> What datasets have columns of the same type? This will suggest datasets that may be similar or related.<br> What entities appear in most datasets (co-referent entities)? This will suggest entities for which more data is published.<br> What datasets share a particular entity? This will suggest datasets that may be joined, or are related through that particular entity</p> <p>Results are provided as augmented tables, that contain the columns of the original csv, plus a metadata file in JSON-LD format. The metadata files can be loaded in an RDF-store and queried.</p> <p>Refer to the accompanying report of activities for more details on the methodolog and how to query the dataset.</p> <p><br> </p>
Data from: Divergent and linked selection shape patterns of genomic differentiation between European and North American Atlantic salmon (Salmo salar)
<p>As populations diverge many processes can shape genomic patterns of differentiation. Regions of high differentiation can arise due to divergent selection acting on selected loci, genetic hitchhiking of nearby loci, or through repeated selection against deleterious alleles (linked background selection); this divergence may then be further elevated in regions of reduced recombination. Atlantic salmon (Salmo salar) from Europe and North America diverged >600,000 years ago and despite some evidence of secondary contact, the majority of genetic data indicate substantial divergence between lineages. This deep divergence with potential gene flow provides an opportunity to investigate the role of different mechanisms that shape the genomic landscape during early speciation. Here, using 184,295 SNPs and 80 populations, we investigate the genomic landscape of differentiation across the Atlantic Ocean with a focus on highly differentiated regions and processes shaping them. We found evidence of high (mean FST=0.26) and heterogeneous genomic differentiation between continents. Genomic regions associated with high trans-Atlantic differentiation ranged in size from single loci (SNPs) within important genes to large regions (1-3Mbp) on four chromosomes (Ssa06, Ssa13, Ssa16, and Ssa19). These regions showed signatures consistent with selection, including high linkage disequilibrium despite no local reduction in recombination. Genes and functional enrichment of processes associated with differentiated regions may highlight continental differences in ocean navigation and parasite resistance. Our results provide insight into potential mechanisms underlying differences between continents, and evidence of near fixed and potentially adaptive trans-Atlantic differences concurrent with a background of high genome-wide differentiation supports subspecies designation in Atlantic salmon.</p>
A Functional Response in Resource Selection Links Multi-Scale Responses of a Large Carnivore to Human Mortality Risk
<p>This repository contains code and data to reproduce results from the manuscript 'A Functional Response in Resource Selection Links Multi-Scale Responses of a Large Carnivore to Human Mortality Risk'. </p>
Following Darwin's footsteps: Evaluating the impact of an activity designed for elementary school students to link historically important evolution key concepts on their understanding of natural selection
<p>While several researchers have suggested that evolution should be explored from the initial years of schooling, little information is available on effective resources to enhance elementary school students' level of understanding of evolution by natural selection (LUENS). For the present study, we designed, implemented and evaluated an educational activity planned for fourth graders to explore concepts and conceptual fields that were historically important for the discovery of natural selection. Observation field notes and students' productions were used to analyse how the students explored the proposed activity. Additionally, an evaluation framework consisting of a test, the evaluation criteria and the scoring process was applied in two fourth-grade classes to estimate elementary school students' LUENS before and after engaging in the activity. Our results suggest that our activity allowed students to effectively link all of the key concepts in the classroom and produced a significant increase in their LUENS. These results indicate that our activity had a positive impact on students' understanding of natural selection. They also reveal that additional activities and minor fine-tuning of the present activity are required to further support students' learning about the concept of differential reproduction. We also observed a low level of teleological predictions for both pre- and post-tests. --</p>
Linked selection, differential introgression and recombination rate variation promote heterogeneous divergence in a pair of yellow croakers
<p><span>Understanding the mechanisms underlying heterogeneous genomic divergence is of particular interest in evolutionary biology. Highly differentiated genomic regions, known as genomic islands, often evolve between diverging lineages. These genomic islands may be related to selection promoting adaptation or reproductive isolation. Based on whole genome assembly and genome-wide RAD sequencing in a pair of yellow croakers (genus: <em>Larimichthys</em>), we investigated the evolutionary processes shaping genomic landscapes of divergence. Demographic modelling indicated that the two species diverged following a secondary contact scenario, where differential introgression and linked selection were suggested to be involved in heterogeneous genomic divergence. We identified reduced recombination rate in genomic islands and a relatively good conservation of both genetic diversity and recombination landscapes between species, which highlight the roles of linked selection and recombination rate variation in promoting heterogeneous divergence in the common ancestral lineage of the two species. In addition, we found a positive correlation between differentiation (F<sub>ST</sub>) and absolute sequence divergence (<em>D</em><sub>xy</sub>), and elevated </span><span><span><em>D</em><sub>xy</sub></span> in genomic islands, which were different from the patterns under linked selection. Restricted gene flow in highly differentiated regions has likely remodeled the landscape of heterogeneous genomic divergence. Moreover, genomic islands showed little evidence of overlapping within and between species, implying that high gene flow and divergent selection when colonizing new habitats have reshaped the patterns of intraspecific divergence. This study highlights that highly differentiated genomic regions can also be from linked selection and variation of recombination rate, and thus are not necessarily related to speciation islands or local adaptation. </span></p>
Demography and linked selection interact to shape the genomic landscape of codistributed woodpeckers during the Ice Age
<p><span>The influence of genetic drift on population dynamics during Pleistocene glacial cycles is well understood, but the role of selection in shaping patterns of genomic variation during these events is less explored. We used resequenced whole genomes to</span><span> i</span><span>nvestigate </span><span>how demography and natural selection interact to generate the genomic landscapes of Downy and Hairy Woodpeckers, species co-distributed in previously glaciated North America. First, we explored the spatial and temporal patterns of genomic diversity produced by neutral evolution. Next, we tested (1) whether levels of nucleotide diversity along the genome are correlated with intrinsic genomic properties, such as recombination rate and gene density, and (2) whether different demographic trajectories impacted the efficacy of selection. Our results revealed cycles of bottleneck and expansion and genetic structure associated with glacial refugia. Nucleotide diversity varied widely along the genome, but this variation was highly correlated between the species, suggesting the presence of conserved genomic features. In both taxa, nucleotide diversity was positively correlated with recombination rate and negatively correlated with gene density, suggesting that linked selection played a role in reducing diversity. Despite strong fluctuations in effective population size, the maintenance of relatively large populations during glaciations may have facilitated selection. Under these conditions, we found evidence that the individual demographic trajectory of populations modulated linked selection, with purifying selection being more efficient in removing deleterious alleles in large populations. These results highlight that while genome-wide variation reflects the expected signature of demographic change during climatic perturbations, the interaction of multiple processes produces a predictable and highly heterogeneous genomic landscape.</span></p>
Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin
<p>The Papain-like protease (PLpro) is a domain of a multi-functional, non-structural protein 3 of coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin and protective ISG15, composed of two ubiquitin-like (UBL) domains. Across coronaviruses, PLpro showed divergent selectivity for recognition and cleavage of posttranslational conjugates despite sequence conservation. We show that SARS-CoV-2 PLpro binds human ISG15 and K48-linked di-ubiquitin (K48-Ub<sub>2</sub>) with nanomolar affinity and detect alternate weaker-binding modes. Crystal structures of untethered PLpro complexes with ISG15 and K48-Ub<sub>2</sub> combined with solution NMR and cross-linking mass spectrometry revealed how the two domains of ISG15 or K48-Ub<sub>2</sub> are differently utilized in interactions with PLpro. Analysis of protein interface energetics predicted differential binding stabilities of the two UBL/Ub domains that were validated experimentally. We emphasize how substrate recognition can be tuned to cleave specifically ISG15 or K48-Ub<sub>2</sub> modifications while retaining capacity to cleave mono-Ub conjugates. These results highlight alternative druggable surfaces that would inhibit PLpro function.</p>
Male and female adult zebra finch (Taeniopygia guttata) gonad RNAseq associated with: Relaxed purifying selection maintains a sex-linked supergene polymorphism in zebra finches
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