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866 results for “closely related species”
Response of distribution patterns of two closely related species in Taxus genus to climate change since last inter-glacial
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Data from: Hybridization has localized effect on genetic variation in closely related pine species
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Data from: A multi-dimensional selective landscape drives adaptive divergence between and within closely related Phlox species
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Comparative studies on genetic differentiation between two closely related species of <em>Drosophila,</em> <em>D. bipectinata</em> and <em>D. malerkotliana</em>
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Data from: Individual asymmetric competition responses across multidimensional niches may enable coexistence of closely related species
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Data from: Why does the complexity of functionally equivalent signals vary across closely related species?
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Data for: Host shift promotes divergent evolution between closely related holoparasitic species
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Molecular phenotyping uncovers differences in basic housekeeping functions among closely related species of hares (Lepus spp., Lagomorpha: Leporidae)
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Data from: Evidence for non-allopatric speciation among closely related sympatric Heliotropium species in the Atacama Desert
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Closely related tree species support distinct communities of seed-associated fungi in a lowland tropical forest
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Inbreeding depression contributes to the maintenance of habitat segregation between closely related monkeyflower species
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Evolutionary targets of gene expression divergence in a complex of closely related pine species
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Bioinformatic pipeline: Vast differences in strain-level diversity in the gut microbiota of two closely related honey bee species
<p>This data-set contains the full bioinformatic pipeline used to analyze metagenomic samples in the study "Vast differences in strain-level diversity in the gut microbiota of two closely related honey bee species" (Ellegaard et al. 2020, Current Biology). </p> <p>New metagenomic samples were generated for the study, for which the raw data is available on the NCBI Sequence Read Achive, under accession: PRJNA59809.</p> <p>The data of this submission consist of 9 tar-balls, as further described here below. Download and unpack to view the contents (tar -zxvf filename.tar.gz). For each tarball, all directories contain README.txt files, describing the contents of the directory. Due to size constraints, some intermediate files have been omitted, and some workflows are demonstrated for a subset of the data. However, the full analysis can be reproduced from the raw data, using the provided scripts.</p> <p>All scripts are included within the directories where they were applied. Perl-scripts contain documentation, which can be viewed by typing: "perl script_name.pl -h". For R scripts, the usage is indicated as a comment in the top lines of each script. Note that many of the scripts require specific input-files to be present in the run-directory. Their usage is demonstrated within the workflow directories in bash-scripts (*.sh). Commands used for generating plots and some statistics are given within workflow directories in text-files "R.commands" when applicable.</p> <p>Aside from custom code, the pipeline also utilizes various open-source Software packages, which are detailed in the file "software_dependencies.txt". Note, while many of the scripts will run fast on any computer, some steps of the pipeline are computationally demanding, and will require significant computing time, as well as storage space. When scripts are known to be time-consuming, this is indicated in the script help message.</p> <p>Description of tarballs.</p> <p>raw_data_processing.tar.gz: Describes the quality-control and trimming of raw data, and includes info on the sequencing run.</p> <p>databases.tar.gz: Contains all databases used for analysis, in addition to relevant meta-data.</p> <p>mapping_stats.tar.gz: Contains a file with the number of reads mapped to the honey bee gut microbiota database and the host genomes, for each sample. Bash-scripts are provided, detailing how the mapping was done and quantified.</p> <p>orthologs_phylogenies.tar.gz: Contains the pipeline for inferring orthologous gene-families and core genome phylogenies, as well as scripts for filtering of single-copy core gene families.</p> <p>assemblies.tar.gz: Contains the final de novo metagenome assembly files (contig fasta-files), gener<br> ated for both complete and rarefied read subsets. Bash-scripts detailing the assembly commands are also provided.</p> <p>SDP_validation.tar.gz: Contains the pipeline for metagenomic validation of candidate SDPs. Final output-files, containing the percentage identity of recruited metagenomic ORFs to database core genes, are provided for each candidate SDP. Additionally, a small example dataset is provided, where the intermediate result-files can be viewed.</p> <p>community_profiling.tar.gz: Contains the pipeline for community profiling, i.e. the quantification of individual community members (SDPs) across samples. Final output files are provided, including mapped read coverage on core gene families and corresponding plots. A small bam-file (containing data from a single subset sample), is also provided, in order to demonstrate the pipeline, together with all scripts used.</p> <p>snv_profiling.tar.gz: Contains the pipeline used for SNV profiling, including filtering and analysis. Final filtered vcf-files are provided for each SDP. Analytical output files are also provided, including data on shared SNV fractions, distance matrices, and cumulative curves.</p> <p>metagenomic_ORF_analyses.tar.gz: Contains the pipeline for analysis of metagenomic ORFs. This includes prediction of ORFs, clustering, annotation and functional characterization. ORF sequences, annotation files, and cluster-files are provided.</p>
FIGURE 4 in A new species closely related to Acartia sinjiensis (Copepoda: Calanoida), from river estuaries of northern Luzon, the Philippines
FIGURE 4. Maximum likelihood (ML) phylogenetic trees based on COI gene of Acartia cagayanensis sp. nov. from the Cagayan (CP) and Pata (PP) Rivers in the Philippines, A. sinjiensis from the Ayaragi River (AJ) in the mainland and the Yamakuni River (YJ) in Kyushu Island, Japan, and A. tsuensis (outgroup). ML bootstrap probabilities and Bayesian posterior probabilities for bipartitions with over 65% and 0.95 support, respectively, are shown. DDBJ/EMBL/GenBank accession nos. are provided in parentheses.
FIGURE 2 in A new species closely related to Acartia sinjiensis (Copepoda: Calanoida), from river estuaries of northern Luzon, the Philippines
FIGURE 2. Acartia cagayanensis sp. nov. female (A–G, I, holotype; H, paratype from the Cagayan River). A, left maxillule; B, left maxilla; C, right maxilliped; D–H, legs 1–5, posterior; I, right leg 5, right lateral.
FIGURE 2 in A new species of the porcelain crab genus Petrolisthes from the Pacific coast of Panama, with taxonomic notes on closely related species (Decapoda: Anomura Porcellanidae)
FIGURE 2. Petrolisthes lazarus sp. nov., female holotype from Isla Saboga, Las Perlas Islands, Panama (MZUSP 33807): (A) dorsal view; (B) ventral view; (C) anterior (frontal) view. Photographs by A. Anker.
FIGURE 1 in A new species of the porcelain crab genus Petrolisthes from the Pacific coast of Panama, with taxonomic notes on closely related species (Decapoda: Anomura Porcellanidae)
FIGURE 1. Petrolisthes lazarus sp. nov., female holotype from Isla Saboga, Las Perlas Islands, Panama (MZUSP 33807): (A) carapace, dorsal view; (B) fronto-orbital region of carapace, anterior view; (C) carapace, lateral view of branchiostegite; (D) right antennule, ventral view; (E) right antenna, dorsal view (flagellum omitted); (F) left Mxp 3, ventral (exterior) view (flagellum of exopod omitted); (G) left P1, dorsal view; (H) right P1, dorsal view; (I) right P2, lateral view; (J) telson, external view; (K) thoracic sternum, ventral view. Setae omitted for clarity. Scale bars: 1 mm.
FIGURE 7 in A new species of the porcelain crab genus Petrolisthes from the Pacific coast of Panama, with taxonomic notes on closely related species (Decapoda: Anomura Porcellanidae)
FIGURE 7. Mixed sand-rock intertidal at La Cruz de Huanacaxtle, Nayarit, Pacific coast of Mexico, collection locality of Petrolisthes crenulatus (Lockington, 1878): (A) general ocean view; (B) detail of rocks and sand; (C) one of the collected porcelain crabs in situ, exposed after flipping a large rock. Photographs by L.D. Santana-Moreno.
FIGURE 5. Petrolisthes crenulatus Lockington, 1878 in A new species of the porcelain crab genus Petrolisthes from the Pacific coast of Panama, with taxonomic notes on closely related species (Decapoda: Anomura Porcellanidae)
FIGURE 5. Petrolisthes crenulatus Lockington, 1878, male from La Cruz de Huanacaxtle, Nayarit, Mexico (CNCR 35708): (A) dorsal view; (B) ventral view; (C) anterior (frontal) view. Photographs by L.D. Santana-Moreno.
FIGURE 4 in A new species of the porcelain crab genus Petrolisthes from the Pacific coast of Panama, with taxonomic notes on closely related species (Decapoda: Anomura Porcellanidae)
FIGURE 4. Extensive rocky intertidal at Río Mar, Pacific coast of Panama, collection locality of paratype of Petrolisthes lazarus sp. nov.: (A) beach view, showing coastal development; (B) ocean view. Photographs by I.N. Marin.
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.