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4,034 results for “Species associations”
Langenheim Plant Species Data (1953) and Associated Resurvey Datasets (2014), Gunnison Basin, Colorado, USA
Quantitative plant abundance data were collected from the same 121 sites at two time periods separated by 65 years (1948-1952 and 2012-2014) in the Colorado Rocky Mountains to examine changes in plant community composition. The sites range in elevation from 2600m to 4100m. Approximately 30 sites were sampled from each of four habitat types: sagebrush (2528-3119m, n=27 sites), spruce-fir forest understory (3001-3520m, n=31 sites) , upland herb = montane meadow (3124-3850m, n=30 sites), and alpine (3549-4013m, n=33 sites). The earlier data set was collected by Jean H. Langenheim (1953, 1962) and consisted of counts of species occurrences along approximately 100m paced transects, noting species touching her boot tip every pace (n=100 sampled points per site). The later data set was collected by Stephanie D. Zorio (2015, 2016) consisting of counts of species occurrences every 1m along 300m transects (n=300 sampled points per site). The sites resurveyed by Zorio (2015, Zorio et al. 2016) were placed as close as possible to the original sites based on the written descriptions of Langenheim, but are only approximate. The GPS coordinates given for the resurveyed sites are the centerpoint of 2 perpendicular 150m transects, one across the slope and the other perpendicular to the slope. GPS coordinates for alpine sites along narrow ridges are the start and end points of three 100m transects along the ridge. Georeferenced localities and environmental site data are presented in Table 2: Lang Zorio Env Site Data. Langenheim’s original data were extracted from tables in her thesis (Langenheim 1953). These data omitted species that occurred in fewer than 14% of sites of a given habitat type (constancy). Species that occurred at very low frequencies (<1% per site) were only denoted as an x in the tables. Zorio converted these to frequencies of 0.5 for quantitative comparative purposes. This data set contains 157 species from 27 families across all sites and habitats. Species in seve
Nekton species counts and density from flume net collections along Rowley River tidal creeks associated with long term fertilization experiments, Rowley, MA.
The flume nets were deployed with the purpose of capturing salt marsh nekton. Nekton species were identified to the lowest taxonomic level using species keys. The TIDE project aims to simulate eutrophication on a large scale by the addition of NO3- aiming to reach 70μM concentrations from May to September every year during the growing season. This fertilization of the marsh has been going on at Sweeney Creek since the 2004 growing season through 2016 and at Clubhead Creek in 2005 and from 2009 till 2016. Years 2017-2020 are enrichment recovery years.
Marsh plant species shoot height, weight and diameters for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA.
Marsh plant species shoot height, weight and diameters for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA. The TIDE project aims to simulate eutrophication on a large scale by the addition of NO3- aiming to reach 70μM concentrations from May to September every year during the growing season. This fertilization of the marsh has been going on at Sweeney Creek since the 2004 growing season through 2012 and at Clubhead Creek in 2005 and from 2009 till 2019.
Invert species counts and density along transects on the high marsh along Rowley River tidal creeks associated with long term fertilization experiments, Rowley, MA.
At PIE, mummichog (Fundulus heteroclitus) use the spring-cycle high tides to access the flooded high marsh platform and consume invertebrate prey. Invertebrate surveys were conducted before and after spring tides that flooded the high marsh area to determine the effect of mummichog predation that occurs on the high marsh during the flood events and to assess the impact of low marsh geomorphology on top-down control by mummichog. These data were included in part of the study "Cross-habitat access modifies the ‘trophic relay’ in New England saltmarsh ecosystems” (Lesser et al. 2021) as well as a part of a NEU Three Seas Master's thesis.
Coat protein (CP) and trimmed replication-associated protein (Rep) amino acid alignments, phylogenetic analyses, and associated metadata for ICTV-approved begomovirus RefSeq species exemplars
<p>DATA RETRIEVAL</p> <p>Annotated begomovirus coding sequences corresponding to each begomovirus species exemplar with a RefSeq accession number listed in the ICTV Virus Metadata Resource (VMR #18, 2021-10-19, <a href="https://ictv.global/vmr">https://ictv.global/vmr</a>) were downloaded from GenBank in protein FASTA file format. CP and Rep amino acid sequences were extracted and split into separate data sets for analysis. We confirmed the identity of misannotated ORF products by performing a BLAST search. For exemplar sequences missing ORF annotations (listed in metadata spreadsheet), ORFfinder (<a href="https://www.ncbi.nlm.nih.gov/orffinder/">https://www.ncbi.nlm.nih.gov/orffinder/</a>) was used to identify CP and Rep ORFs that were subsequently translated and added to each corresponding data set after BLAST confirmation.</p> <p>ALIGNMENTS</p> <p>Multiple sequence alignments were constructed using the MUSCLE method (Edgar, 2004) as implemented in MEGA 11 (Tamura et al., 2021) and manually corrected using AliView v1.26<strong> </strong>(Larsson, 2014). After an initial alignment inspection, exemplars with either severely truncated (i.e., length < 50% of the average length of the protein) or very divergent (i.e., causing us to doubt protein homology) CP or Rep sequences were excluded from the data set. Due to the difficulties in aligning the Rep sequences at the N- and C- terminal ends, the Rep alignment was trimmed to eliminate all residues prior to the iteron related domain (i.e., the known Rep functional region closest to the Rep start (Arguello-Astorga & Ruiz-Medrano, 2001)) in the N-terminus and after a conserved geminivirus motif found near the C-terminus, which corresponds to where other circular, Rep-encoding single-stranded DNA viruses possess an arginine finger motif (Kazlauskas et al., 2019; Krupovic et al., 2020). In total, our CP and Rep data sets contained amino acid sequences from 432 begomovirus species exemplars that met our inclusion criteria.</p> <p>PHYLOGENETIC ANALYSIS</p> <p>Maximum likelihood (ML) trees were inferred with IQ-Tree v2.0.7 (Minh et al., 2020) using the best fitting substitution model identified by the built-in ModelFinder feature (Kalyaanamoorthy et al., 2017). Tree inference was performed with 3000 ultrafast bootstrap (UFBoot) replicates, a perturbation strength of 0.2 and a stopping rule requiring an iteration interval of 500 iterations between unsuccessful improvements to the local optimum. The -bnni flag was enabled to reduce the risk of overestimating branch supports with UFBoot due to severe model violations. The provided phylogenies in NEXUS format are midpoint-rooted and branches are colored based on traditional begomovirus geographic groupings: exemplars sampled in the Americas in orange and exemplars sampled in the 'Africa, Asia, Europe and Oceania' (AAEO) region in blue. </p> <p>METADATA</p> <p>Metadata associated with each ICTV-approved species exemplar (n=445) – including country of isolation, geographic designation (i.e., AAEO/Americas), genome segmentation (i.e., monopartite/bipartite), presence/absence of V2/AV2 gene and length of genome/DNA-A segments – are included. Exemplars not incorporated into the other analyses are highlighted in red on the spreadsheet.</p> <p> </p>
MCR LTER: Coral Reef: Community Dynamics: Abundance and Species Richness of Fishes Associated with the Coral Porites rus 2000 thru 2011
These data describe the species richness and abundance as part of MCR LTER's reef fish monitoring program to track long-term patterns in species abundance and diversity. This study began in 2000 in the lagoons off of the north shore of the island of Moorea, French Polynesia and the dataset is updated annually. The abundance and life history stage (adults, juveniles or recruits) of all taxa of fishes associated with selected colonies (5-16 colonies per site) of the mound forming coral Porites rus are recorded at seven reef sites located along the north shore of Moorea. These sites are characterized by differences in water depth, distance to the fore reef and the number and types of neighboring corals. Counts are performed by a pair of divers using SCUBA and include semi-cryptic species. The collection of these data was suspended following the last survey conducted in July 2011 due to the extremely low abundance of live P. rus at these locations.
Marsh plant species percent cover for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA.
Marsh plant species percent cover for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA. The TIDE project aims to simulate eutrophication on a large scale by the addition of NO3- aiming to reach 70µM concentrations from May to September every year during the growing season. This fertilization of the marsh has been going on at Sweeney Creek since the 2004 growing season through 2011 and at Clubhead Creek in 2005 and from 2009 till 2011.
Marsh plant species C:H:N data for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA.
Marsh plant species C:H:N data for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA. The TIDE project aims to simulate eutrophication on a large scale by the addition of NO3- aiming to reach 70µM concentrations from May to September every year during the growing season. This fertilization of the marsh has been going on at Sweeney Creek since the 2004 growing season through 2011 and at Clubhead Creek in 2005 and from 2009 till 2011.
Marsh plant species frequency of occurrence along marsh transects for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA.
Marsh plant species frequency of occurrence along marsh transects for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA. The TIDE project aims to simulate eutrophication on a large scale by the addition of NO3- aiming to reach 70µM concentrations from May to September every year during the growing season. This fertilization of the marsh has been going on at Sweeney Creek since the 2004 growing season through 2011 and at Clubhead Creek in 2005 and from 2009 till 2011.
Marsh plant species stem counts for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA.
Marsh plant species stem counts for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA. The TIDE project aims to simulate eutrophication on a large scale by the addition of NO3- aiming to reach 70µM concentrations from May to September every year during the growing season. This fertilization of the marsh has been going on at Sweeney Creek since the 2004 growing season through 2012 and at Clubhead Creek in 2005 and from 2009 till 2012. The reference creeks, West and Nelson, have been sampled in pair with the nutrient enriched creeks.
Fig. 7 in Coordinated hunting behaviors of mixed-species groups of piscivores and associated species at Isla del Coco National Park (Eastern Tropical Pacific)
Fig. 7. Cluster analysis of species co-occurrences in groups based on the Ward linkage method and Pearson distance. Abbreviations for each species are defined in Tab. 1. Note two dominant clusters (cluster 1 at left and cluster 2 at right). An asterisk below species codes indicate membership in top 10 species based on mixed-species links.
Fig. 5 in Coordinated hunting behaviors of mixed-species groups of piscivores and associated species at Isla del Coco National Park (Eastern Tropical Pacific)
Fig. 5. Network visualization of the web of associations between species (33 species with 288 pair-wise links). The size of each species node is weighted relative to the frequency of each species in any group (abbreviations for each species are defined in Tab. 1). The lines between species nodes are weighted by the relative frequency of associations between each species pair.
Fig. 3 in Coordinated hunting behaviors of mixed-species groups of piscivores and associated species at Isla del Coco National Park (Eastern Tropical Pacific)
Fig. 3. Examples of mixed-species hunting groups observed to ca. 35 m depth. (A) Caranx melampygus, Dermatolepis dermatolepis and Bodianus diplotenia at a crevice. Note D. dermatolepis and B. diplotaenia are able to maneuver deep into the crevice while C. melampygus follow from above and search for escaping prey. (B) Group composed of C. melampygus, Trianodon obesus, Cephalopholis panamensis and unidentified muraenid eel (hidden within crevices) hunt for prey within crevices amongst coral and coral rubble along reef edge. (C) Lutjanus argentiventris, D. dermatolepis, C. melampygus and B. diplotaenia hunt for prey as group traverses low relief volcanic pavement along a pinnacle. (D) Group composed of D. dermatolepis, C. melampygus and Aulostomus chinensis. Note position of A. chinensis in lead over C. melampygus. (E) C. melampygus follows above a muraenid eel hunting within narrow crevices. (F) As in previous image, D. dermatolepis follows above muraenid eel hunting within narrow crevice. (G) C. melampygus follow B. diplotaenia hunting over sand and volcanic rubble habitat. (H) B. diplotaenia and A. chinensis hunt in tandem along edge of pinnacle.
Figures 9-14 in A new species of Clinodiplosis Kieffer (Diptera, Cecidomyiidae) associated with Cecropia sp. (Urticaceae) in Brazil
Figures 9-14. Clinodiplosiscecropiae Proença & Maia. (9) female abdomen, segments 6-8 (lateral view); (10) ovipositor (lateral view); (11) pupal exuviae: cephalic region and prothoracic spiracle (frontal view); (12) pupal exuviae: abdominal segment V (dorsal view); (13-14) sexual dimorphism on pupal exuviae: (13) male's pupal exuvia: terminal segment; (14) female'spupalexuvia: terminal segment.
GenBank accession numbers of the four marker genes and associated voucher specimens/tissues that were used in this study. For more details see Guo et al. (2014). Sequences of species in bold are unpublished and were provided by P. Guo as personal communication in Rediscovery of Andrea's keelback, Hebius andreae (Ziegler & Le, 2006): First country record for Laos and phylogenetic placement
GenBank accession numbers of the four marker genes and associated voucher specimens/tissues that were used in this study. For more details see Guo et al. (2014). Sequences of species in bold are unpublished and were provided by P. Guo as personal communication
Figures 1–5. Chileporter huemeri n. gen. and n in New genus and species of Yponomeutidae (Lepidoptera: Yponomeutoidea) associated with Maytenus boaria Molina (Celastraceae) from Chile, with descriptions of immature stages and natural history observations
Figures 1–5. Chileporter huemeri n. gen. and n. sp., adult. 1) Wings, dorsal view. 2) Head, side view. 3) Wing veins. Scale bar: 1 mm (1, 2, 3). 4). Sternum 2. Scale bar: 0.5 mm. 5). Tergum spiny setae. Scale bar: 0.25 mm.
Figures 12–20. Chileporter huemeri n. gen. and n in New genus and species of Yponomeutidae (Lepidoptera: Yponomeutoidea) associated with Maytenus boaria Molina (Celastraceae) from Chile, with descriptions of immature stages and natural history observations
Figures 12–20. Chileporter huemeri n. gen. and n. sp. 12–15. Adult female. Scale bar: 0.25 mm. 12) Female genitalia. 13) Ductus bursae. 14) Corpus bursae. 15) Signum. 16) Larva, dorsal view. Scale bar: 1.0 mm. 17–20. Larval structures. Scale bar: 0.20 mm. 17) Mandible. 18) Crochets. 19) Microprocesses on integument. 20) Antennae.
Fig. 1 in A new species of the genus Liljeborgia Spence Bate, 1862 (Crustacea: Amphipoda: Liljeborgiidae) associated with the burrows of the spoon worm Urechis unicinctus in the Sea of Japan
Fig. 1. Habitus of live female specimen of Liljeborgia associata sp. nov. from Vostok Bay of the Sea of Japan with geographical indication of the collection sites in the Peter the Great Bay and Posjeta Bay of the Sea of Japan.
Fig. 4 in A new species of the genus Liljeborgia Spence Bate, 1862 (Crustacea: Amphipoda: Liljeborgiidae) associated with the burrows of the spoon worm Urechis unicinctus in the Sea of Japan
Fig. 4. Liljeborgia associata sp. nov., female (LEMMI) from Vostok Bay of the Sea of Japan. a. Pereopod 3. b. Pereopod 4. c. Pereopod 5. d. Distal segments of P5. e. Pereopod 6. f. Distal segments of P6. g. Pereopod 7.
Fig. 3 in A new species of the genus Liljeborgia Spence Bate, 1862 (Crustacea: Amphipoda: Liljeborgiidae) associated with the burrows of the spoon worm Urechis unicinctus in the Sea of Japan
Fig. 3. Liljeborgia associata sp. nov., female (LEMMI) from Vostok Bay of the Sea of Japan. a. Gnathopod 1. b. Chela of Gn1. c. Gnathopod 2. d. Chela of Gn2.
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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.