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230 results for “species presence”
Schoolyard ecology at North Temperate Lakes LTER: Dragonfly Species Presence at Stormwater Retention Ponds in July of 2014
This study aims to integrate scientific observations with community involvement, specifically with dragonfly species. The presence and absence of 17 dragonfly species was observed at Stormwater Retention ponds in the Madison area in July of 2014 and made into frequency distributions. This research will continue with community outreach in the area to further involve and educate the community on the biodiversity of their local ponds.
Presence observations for six tree species prioritized for forest landscape restoration in Ethiopia
<p><strong>Description:</strong></p><p>Geolocations of presence occurrences for a selection of six species (<i>Cordia africana</i>, <i>Croton macrostachyus</i>, <i>Eucalyptus globulus</i>, <i>Faidherbia albida</i>, <i>Grevillea robusta</i>, <i>Juniperus procera</i>) sourced from databases (GBIF, RAINBIO) and from the scientific literature.</p><p>Each record is associated with a DOI, link, or citation to the original source of the data. Observations were filtered using the R package <i>CoordinatesCleaner</i> (Zizka <i>et al</i>. 2019) with the <i>clean_coordinates </i>function to filter for errors that are common to biological collections.</p><p>The breakdown of the number of observations by species is: <i>Cordia africana</i> (84); <i>Croton macrostachyus</i> (129); <i>Eucalyptus globulus (</i>20); <i>Faidherbia albida </i>(31); <i>Grevillea robusta </i>(350); <i>Juniperus procera </i>(115).</p>
RivFISH - An European database on fish species presence across river basins
<p>The RivFISH database aggregates the available data on freshwater-dependent fish presence in Europe, validated at the river basin level and considering taxonomical synonyms for species names, thus allowing for a maximization of data usage and robustness. This database also promotes interoperability with other datasets, including the IUCN Red List of Threatened Species, FishBase and the Catchment Characterisation and Modelling (CCM2) – River and Catchment Database v2.1. It is, as far as the authors know, the most up-to-date and comprehensive database on the presence of freshwater-dependent fish species for European river basins. The structure of the database is also prepared to deal with future alterations in species taxonomy, as well as new records of species occurrence in river basins.</p>
Data for Marine Ecological Niche Models, for 2019 and across RCP 2.6, 4.5, and 8.5 scenarios in 2050 and 2100: Global-scale Environmental parameters at 0.1° and 0.5° resolutions, Presence and Absence Records of 1508 European-seas Species
<p>Data for Ecological Niche Models: Global-scale Environmental parameters at 0.1° and 0.5° resolutions, Presence and Absence Records of 1508 European-seas Species.</p>
Presence or absence of marsh plant species along transects through a nutrient enriched marsh receiving wastewater effluent and a reference (unenriched) marsh, Plum Island Ecosystems LTER.
Presence or absence of marsh plant species along transects through a nutrient enriched marsh receiving wastewater effluent and a reference (unenriched) marsh. Nutrient enrichment comes from the Ipswich Wastewater Treatment Facility on Greenwood Creek in Ipswich. The marsh around Clubhead Creek, Rowley, MA was used as a reference.
Presence-Absence Points for Tree Species Distribution Modelling for Europe
<p>The dataset is a collection of presence and absence points for forest tree species for Europe. Each unique combination of longitude, latitude and year was considered as an independent sample. Presence data was obtained from the harmonized tree species occurrence dataset by <a href="https://zenodo.org/record/5524611">Heisig and Hengl (2020)</a> and absence data from the <a href="https://ec.europa.eu/eurostat/web/lucas">LUCAS</a> (in-situ source) dataset.</p> <p>A set of <strong>50</strong> different forest tree species was selected from the harmonized tree species dataset and data lacking a temporal observation was overlaid with yearly forest masks derived from land cover maps produced by <a href="https://zenodo.org/record/4725429">Parente et al. (2021)</a>. We overlaid the points with the probability maps for the classes:</p> <ul> <li>311: Broad-leaved forest,</li> <li>312: Coniferous forest,</li> <li>313: Mixed forest,</li> <li>323: Sclerophyllous forest,</li> <li>324: Transitional woodland-shrub,</li> <li>333: Sparsely vegetated area.</li> </ul> <p>Points were included in the dataset only if the probability value extracted for at least one of the above classes was <strong>≥ 50%</strong> for all the years considered. An additional quality flag was added to distinguish points coming from this operation and the points with original year of observation coming from source datasets.</p> <p>The final dataset contains <strong>4,359,999</strong> observations for and a total of <strong>630 </strong>columns. <br> <br> The first <strong>8 </strong>columns of the dataset contain metadata information used to uniquely identify the points:</p> <ul> <li><strong>id</strong>: unique point identifier,</li> <li><strong>year</strong>: year of observation,</li> <li><strong>postprocess</strong>: quality flag to identify if the temporal reference of an observation comes from the original dataset or is the result of spatiotemporal overlay with forest masks,</li> <li><strong>Tile_ID</strong>: contains the tile id from the eu_tiling_system (30 km grid),</li> <li><strong>easting</strong>: longitude coordinates in Coordinate Reference System ETRS89 / LAEA Europe (= EPSG code 3035),</li> <li><strong>northing</strong>: latitude coordinates in Coordinate Reference System ETRS89 / LAEA Europe (= EPSG code 3035),</li> <li><strong>Atlas_class</strong>: name of the tree species according to the European Atlas of Forest Tree Species or NULL in case of absence point,</li> <li><strong>lc1</strong>: contains original LUCAS land cover class or NULL if it's a presence point.</li> </ul> <p>The remaining columns contain the extracted values of a series of predictor variables (temperature, precipitation, elevation, topographical information, spectral reflectance) useful for species distribution modeling applications. These points were used to model the potential and realized distribution of a series of <strong>16 target species </strong>for the period 2000 - 2020. The approach involved training three ML models to predict probability of presence (<em>i.e.</em> <a href="http://link.springer.com/article/10.1023/A:1010933404324">Random Forest</a>, <a href="http://dl.acm.org/doi/abs/10.1145/2939672.2939785">XGBoost</a>, <a href="https://rss.onlinelibrary.wiley.com/doi/abs/10.2307/2344614">GLM</a>), which served as input to train a linear meta-model (<em>i.e.</em> <a href="http://papers.nips.cc/paper/2014/file/ede7e2b6d13a41ddf9f4bdef84fdc737-Paper.pdf">Logistic regression classifier</a>), responsible for predicting the final probability of presence for each species.</p> <p>The <em>RDS </em>file is created from a data.table object and suitable for fast reading in the R-programming environment. The <em>CSV.GZ</em> file contains records as a table with easting and northing in Coordinate Reference System ETRS89 / LAEA Europe (= EPSG code 3035) and can be fed in a GIS after being unzipped.</p> <p>We provide <em>RDS </em>files for a 30km tile as an example containing raster stacks at 30m resolution of all the covariates included in the regression matrix. You can find the specific geographical location of the tile in Europe using the attached <em>GeoPackage </em>("eu_tiling_system_30km"): open it in QGIS and filter by "ID".</p> <p>In our approach we considered both static and dynamic covariates: dynamic covariates are calculated as averages of a 4 years time window (example: 2004 contains averages from 2002 to 2006). To get the predictions for a specific year, covariates contained in the <em>static</em> RDS file need to be bound with the respective year.</p> <p>To access our predictions (probabilities and uncertainties) produced for the target species access:</p> <ul> <li><strong>Open Data Science Europe viewer: <a href="https://maps.opendatascience.eu">https://maps.opendatascience.eu</a></strong></li> <li>Check the <strong>Related identifiers </strong>section of this repository to access each species individually</li> </ul> <p>If you instead would like to know more about the creation of this dataset and the modeling:</p> <ul> <li><strong>watch</strong> the talk at Open Data Science Workshop 2021 (<a href="https://doi.org/10.5446/55256">TIB AV-PORTAL</a>)</li> <li><strong>access </strong>the repository with our R/Python scripts and follow the instructions (<a href="https://gitlab.com/geoharmonizer_inea/spatial-layers/-/tree/master/veg_tree.species_anv.pnv.eml">GitLab</a>)</li> </ul> <p>A publication describing, in detail, all processing steps, accuracy assessment and general analysis of species distribution maps is available on <a href="https://doi.org/10.7717/peerj.13728">PeerJ</a>. To suggest any improvement/fix use <a href="https://gitlab.com/geoharmonizer_inea/spatial-layers/-/issues">https://gitlab.com/geoharmonizer_inea/spatial-layers/-/issues</a>.</p>
PIE LTER plant species presence along vegetation transects at the Argilla Rd. salt marsh restoration site (Ipswich) and Rough Meadows reference marsh (Rowley – Stackyard Road area), Massachusetts.
Plant species presence along vegetation transects at the Argilla Rd. salt marsh restoration site (Ipswich) and Rough Meadows reference marsh (Rowley – Stackyard Road area). A long term study not directly part of the PIE LTER, but a companion study related to tidal restrictions and hydrological alterations of salt marshes in the Plum Island ecosystem..
Figure 4. Bermudacaris britayevi n in On the presence of the alpheid shrimp genus Bermudacaris Anker and Iliffe, 2000 (Crustacea: Decapoda: Caridea) in the Pacific Ocean, with description of a new species from Vietnam
Figure 4. Bermudacaris britayevi n. sp., holotype (NHM 2006.1217). (a) Second pereiopod, lateral view; (b) third pereiopod, dorsal view; (c) fifth pereiopod, lateral view; (d) same, propodus and dactylus, mesial view. Scale bar: 1 mm.
Figure 3. Bermudacaris britayevi n in On the presence of the alpheid shrimp genus Bermudacaris Anker and Iliffe, 2000 (Crustacea: Decapoda: Caridea) in the Pacific Ocean, with description of a new species from Vietnam
Figure 3. Bermudacaris britayevi n. sp., holotype (NHM 2006.1217). (a) Left cheliped, dorsomesial view; (b) same, ventrolateral view; (c) same, chela and carpus, mesial view; (d) same, chela enlarged, lateral view; (e) same, ischium, merus, and carpus, mesial view; (f) same, ischium, ventral view. Scale bars: 1 mm.
Figure 2. Bermudacaris britayevi n in On the presence of the alpheid shrimp genus Bermudacaris Anker and Iliffe, 2000 (Crustacea: Decapoda: Caridea) in the Pacific Ocean, with description of a new species from Vietnam
Figure 2. Bermudacaris britayevi n. sp., holotype (NHM 2006.1217). (a) Mandible, mesial view; (b) same, incisor process; (c) maxillule, lateral view; (d) same, ventral endite, mesial view; (e) maxilla, lateral view; (f) first maxilliped, lateral view; (g) same, posteromesial view of endopod and proximal portion of exopod; (h) second maxilliped, lateral view; (i) third maxilliped, lateral view; (j) same, detail of coxa; (k) same, ultimate segment, dorsomesial view. Scale bar: 1 mm.
Figure 1. Bermudacaris britayevi n in On the presence of the alpheid shrimp genus Bermudacaris Anker and Iliffe, 2000 (Crustacea: Decapoda: Caridea) in the Pacific Ocean, with description of a new species from Vietnam
Figure 1. Bermudacaris britayevi n. sp., holotype (NHM 2006.1217). (a) General body without cephalic and thoracic appendages, lateral view; (b) frontal region, dorsal view; (c) same, lateral view; (d) epistomial sclerite near ventral base of antennule; (e) antennule, first two segments of peduncle, lateral view; (f) uropod, dorsal view; (g) telson, dorsal view. Scale bars: 1 mm.
FIG. 4 in Presence of the foraminifer Chapmanina gassinensis Silvestri, 1931, in the Eocene (Lutetian) of the Grignon "falunière" (Yvelines, Paris Basin). The genus Chapmanina, its species and world distribution
FIG. 4. — Distribution of Chapmanina gassinensis Silvestri,1931 in the Oligocene of Europe. The numbers correspond to the references indicated in the Appendix 1.
FIG. 5 in Presence of the foraminifer Chapmanina gassinensis Silvestri, 1931, in the Eocene (Lutetian) of the Grignon "falunière" (Yvelines, Paris Basin). The genus Chapmanina, its species and world distribution
FIG. 5. — Distribution of Chapmanina Silvestri, 1931 in the Eocene of Asia. The numbers correspond to the references indicated in the Appendix 1.
FIG. 3 in Presence of the foraminifer Chapmanina gassinensis Silvestri, 1931, in the Eocene (Lutetian) of the Grignon "falunière" (Yvelines, Paris Basin). The genus Chapmanina, its species and world distribution
FIG. 3. — Distribution of Chapmanina gassinensis Silvestri, 1931 in the Eocene of Europe and North Africa. The numbers correspond to the references indicated in the Appendix 1.
FIG. 2 in Presence of the foraminifer Chapmanina gassinensis Silvestri, 1931, in the Eocene (Lutetian) of the Grignon "falunière" (Yvelines, Paris Basin). The genus Chapmanina, its species and world distribution
FIG. 2. — The "Falunière" of Grignon section, after Guernet et al. (2012) for the section profile, lithologic units and sub-units and descriptions, Gély (1996) for the sequential units and Huyghe et al. (2012) for the correlation of sequential and lithologic units. Section profile modified from Sanders et al. 2015.
FIG. 1 in Presence of the foraminifer Chapmanina gassinensis Silvestri, 1931, in the Eocene (Lutetian) of the Grignon "falunière" (Yvelines, Paris Basin). The genus Chapmanina, its species and world distribution
FIG. 1. — Chapmanina gassinensis Silvestri, 1931 (Lutetian, Grignon falunière, Yvelines), in lateral (A) and apical (B) views (MNHN.F.F62410). Scale bars: 200 µm.
Presence data for vascular plant, bryophyte and lichen species in 100 vegetation plots (each 1 m2) from 32 shell-beds at Akerøya, Hvaler, SE Norway
<p><strong>We present a data set consisting of abundance data for 106 vascular plant species, 36 bryophyte species and 13 lichen species from 100 vegetation plots, each 1 m2, distributed on 32 shell-beds at Akerøya, Hvaler municipality, former Østfold (in 2022 Viken) county. The plots were analysed with respect to species composition in June 1979. These data formed the basis for the publication: Halvorsen, R. 1980. Numerical analysis and successional relationships of shell-bed vegetation at Akerøya, Hvaler, SE Norway. Norw. J. Bot. Vol. 27 pp. 71-95. Oslo. ISSN 0300-1156.</strong></p>
APPENDIX 3 in Molecular data reveal the presence of three Plocamium Lamouroux species with complex patterns of distribution in Southern Chile
APPENDIX 3. — Automatic Barcode Gap Discovery (ABGD) results and distribution of pairwise distances for the marker 5P-COI. A, ABGD results showing the number of groups (primary partitions) obtained for a range of prior maximum divergence of intraspecific diversity; B, bar chart showing the proportion of pairwise comparisons of 5P-COI gene at each range of sequence divergence (K2P distance). Intraspecific divergences are represented in grey bars and divergences belonging to different species are represented in yellow bars.
APPENDIX 4. — Ultrametric Bayesian tree reconstructed with the 5P in Molecular data reveal the presence of three Plocamium Lamouroux species with complex patterns of distribution in Southern Chile
APPENDIX 4. — Ultrametric Bayesian tree reconstructed with the 5P-COI marker. The dotted vertical red line indicates the maximum likelihood transition point of the switch in branching rates, as estimated by a General Mixed Yule-Coalescent (GMYC) model. The GMYC analysis was performed using a single threshold. Haplotype code as in Appendix 5.
APPENDIX 1 in Molecular data reveal the presence of three Plocamium Lamouroux species with complex patterns of distribution in Southern Chile
APPENDIX 1. — Maximum likelihood (ML) phylogram of the genus Plocamium Lamouroux based on rbcL sequences. ML bootstrap (BS)/Bayesian posterior probability (PP) values are shown above or close to each branch and only values superior to 75 and 0.75, respectively, are given. Colors correspond to oceans where individuals sequenced where sampled. Outgroup corresponds to Sarcodia ciliata Zanardini (GenBank accession: KM360040).
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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)
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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.