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105 results for “Invertebrates collections”
Interagency Ecological Program: Drift invertebrate and ichthyoplankton catch and water quality from the Sacramento River channel, and Sacramento River floodplain and tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998-2022
Largely supported by the Interagency Ecological Program (IEP), California Department of Water Resources (DWR) has operated a fish monitoring program in the Yolo Bypass, a seasonal floodplain and tidal slough, since 1998. The objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to: 1. Collect baseline data on water quality, chlorophyll, lower trophic level biota, and fish in the Yolo Bypass to monitor spatial and temporal changes in trends and abundance. 2. Analyze and communicate Yolo Bypass data with interested parties and the scientific and management communities to address pertinent management-related questions. 3. Provide technical expertise on Yolo Bypass aquatic ecology and monitoring and sampling methods. Aquatic and terrestrial insects are an important component in the diet of juvenile and adult fishes within the San Francisco Estuary, including two important native fishes: juvenile Chinook Salmon and Sacramento Splittail. The YBFMP collects drift invertebrates year-round from two sites. Currently, samples are collected biweekly (every other week) to weekly (during floodplain inundation) using a rectangular aquatic drift net that sits at the surface of the water. Invertebrates are identified and enumerated by contractors (currently EcoAnalysts, Inc.). The goals of the monitoring program are to compare the seasonal variations in densities and species trends of aquatic and terrestrial insects/non-insects within the Sacramento River channel and the Yolo Bypass, the river’s seasonal floodplain. Drift invertebrate Key findings to date include: (1) Chinook Salmon sampled in the floodplain had diets comprised of 90% Dipterans and zooplankton, with Chironomidae being the dominant Diptera family (Sommer et al., 2001), (2) The floodplain of the Yolo Bypass contains significantly higher densities of Diptera (Diptera densities being positively associated with flow) and terrestrial invertebrates than the adjacent Sacramento River (Sommer et al. 2001b: Sommer
Interagency Ecological Program: Benthic invertebrate monitoring in the Sacramento-San Joaquin Bay-Delta, collected by the Environmental Monitoring Program, 1975-2024.
The Interagency Ecological Program’s (IEP) Environmental Monitoring Program (EMP) was initiated in compliance with the Water Right Decision D-1379 (now mandated by Water Right Decision D-1641) and has monitored benthic invertebrate macrofauna in the upper San Francisco Estuary (SFE) since 1975. The objectives of the EMP are to obtain consistent and accurate monthly data at established monitoring stations and to report this information for the purpose of management and conservation of the upper San Francisco Estuary. While the EMP also collects discrete and continuous water quality data, along with phytoplankton and zooplankton data, this dataset only includes the benthic invertebrate data collected by the EMP from 1975-2024. EMP monitors invertebrate communities in the benthos of the SFE by collecting dredge samples with a Ponar sampler. Sediment and particles smaller than 0.5mm are removed from the sample using a sieve table. The invertebrates present are preserved in formalin, identified to the lowest possible taxonomic level, and enumerated. Currently, samples are collected monthly at 10 sites across the range of salinities found in the SFE. Four replicate dredge samples are collected at each site. The frequency of sampling, number and identity of sampling sites, and number of replicate samples has changed through the 45+ years of monitoring effort, in response to changes in perceived need for data. Links to other EMP datasets can be found on the EMP website: https://emp-des.github.io/emp-reports/data-links.html, or can be found on EDI for searching for "Environmental Monitoring Program" and "San Francisco".
UC Santa Barbara Invertebrate Zoology Collection (UCSB-IZC) Data Archive and Biodiversity Dataset Graph hash://md5/10663911550bb52a0f5741993f82db9d hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c
<p>A biodiversity dataset graph: UCSB-IZC</p> <p>The intended use of this archive is to facilitate (meta-)analysis of the UC Santa Barbara Invertebrate Zoology Collection (UCSB-IZC). UCSB-IZC is a natural history collection of invertebrate zoology at Cheadle Center of Biodiversity and Ecological Restoration, University of California Santa Barbara.</p> <p>This dataset provides versioned snapshots of the UCSB-IZC network as tracked by Preston [2,3] between 2021-10-08 and 2021-11-04 using [preston track "https://api.gbif.org/v1/occurrence/search/?datasetKey=d6097f75-f99e-4c2a-b8a5-b0fc213ecbd0"].</p> <p>This archive contains 14349 images related to 32533 occurrence/specimen records. See included sample-image.jpg and their associated meta-data sample-image.json [4].</p> <p>The images were counted using:</p> <p>$ preston cat hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c\<br> | grep -o -P ".*depict"\<br> | sort\<br> | uniq\<br> | wc -l</p> <p>And the occurrences were counted using:</p> <p>$ preston cat hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c\<br> | grep -o -P "occurrence/([0-9])+"\<br> | sort\<br> | uniq\<br> | wc -l</p> <p>The archive consists of 256 individual parts (e.g., preston-00.tar.gz, preston-01.tar.gz, ...) to allow for parallel file downloads. The archive contains three types of files: index files, provenance files and data files. Only two index and provenance files are included and have been individually included in this dataset publication. Index files provide a way to links provenance files in time to establish a versioning mechanism.</p> <p>To retrieve and verify the downloaded UCSB-IZC biodiversity dataset graph, first download preston-*.tar.gz. Then, extract the archives into a "data" folder. Alternatively, you can use the Preston [2,3] command-line tool to "clone" this dataset using:</p> <p>$ java -jar preston.jar clone --remote https://archive.org/download/preston-ucsb-izc/data.zip/,https://zenodo.org/record/5557670/files,https://zenodo.org/record/5660088/files/</p> <p>After that, verify the index of the archive by reproducing the following provenance log history:</p> <p>$ java -jar preston.jar history<br> <urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36> .<br> <hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c> <http://purl.org/pav/previousVersion> <hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36> .</p> <p>To check the integrity of the extracted archive, confirm that each line produce by the command "preston verify" produces lines as shown below, with each line including "CONTENT_PRESENT_VALID_HASH". Depending on hardware capacity, this may take a while.</p> <p>$ java -jar preston.jar verify<br> hash://sha256/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c file:/home/jhpoelen/ucsb-izc/data/ce/1d/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c OK CONTENT_PRESENT_VALID_HASH 66438 hash://sha256/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c<br> hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844 file:/home/jhpoelen/ucsb-izc/data/f6/8d/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844 OK CONTENT_PRESENT_VALID_HASH 4093 hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844<br> hash://sha256/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef file:/home/jhpoelen/ucsb-izc/data/3e/70/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef OK CONTENT_PRESENT_VALID_HASH 5746 hash://sha256/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef<br> hash://sha256/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b file:/home/jhpoelen/ucsb-izc/data/99/58/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b OK CONTENT_PRESENT_VALID_HASH 6147 hash://sha256/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b</p> <p>Note that a copy of the java program "preston", preston.jar, is included in this publication. The program runs on java 8+ virtual machine using "java -jar preston.jar", or in short "preston".</p> <p>Files in this data publication:</p> <p>--- start of file descriptions ---</p> <p>-- description of archive and its contents (this file) --<br> README</p> <p>-- executable java jar containing preston [2,3] v0.3.1. --<br> preston.jar</p> <p>-- preston archive containing UCSB-IZC (meta-)data/image files, associated provenance logs and a provenance index --<br> preston-[00-ff].tar.gz</p> <p>-- individual provenance index files --<br> 2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a</p> <p>-- example image and meta-data --<br> sample-image.jpg (with hash://sha256/916ba5dc6ad37a3c16634e1a0e3d2a09969f2527bb207220e3dbdbcf4d6b810c)<br> sample-image.json (with hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844)</p> <p>--- end of file descriptions ---</p> <p><br> References</p> <p>[1] Cheadle Center for Biodiversity and Ecological Restoration (2021). University of California Santa Barbara Invertebrate Zoology Collection. Occurrence dataset https://doi.org/10.15468/w6hvhv accessed via GBIF.org on 2021-11-04 as indexed by the Global Biodiversity Informatics Facility (GBIF) with provenance hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36 hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c.<br> [2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 .<br> [3] MJ Elliott, JH Poelen, JAB Fortes (2020). Toward Reliable Biodiversity Dataset References. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2020.101132<br> [4] Cheadle Center for Biodiversity and Ecological Restoration (2021). University of California Santa Barbara Invertebrate Zoology Collection. Occurrence dataset https://doi.org/10.15468/w6hvhv accessed via GBIF.org on 2021-10-08. https://www.gbif.org/occurrence/3323647301 . hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844 hash://sha256/916ba5dc6ad37a3c16634e1a0e3d2a09969f2527bb207220e3dbdbcf4d6b810c</p>
Raw data supporting Identifying invertebrates from pitfall, flight interception traps and hand collecting
<p>Raw data supporting identifying invertebrates from pitfall, flight interception traps and hand collecting: comparing metabarcoding with traditional methods.</p> <p>Two step PCRs were performed on each sample replicate using modified primers mICOIintF and jgHCO2198 followed by the Nextera XT index kit v2 Set A (Illumina).</p> <p>The pool was loaded onto an illumina MiSeq using a MiSeq Reagent Kit v2 500 cycle kit (Illumina), with 10% Phi-X to generate 250-bp paired-end reads.</p>
Abundance of major taxonomic groups of invertebrates (arthropods and gastropods) collected with pitfall traps at four sites near Toolik Field Station Arctic LTER, Alaska in the summer of 2010.
Invertebrates (spiders, insects and slugs) were collected weekly using pitfall traps at four sites near the Arctic LTER at Toolik Field Station, Alaska. Traps were placed along transects in shrub (shrub-dominant) and open (tussock-dominant) tundra sites. Pitfall traps were placed for 48-hour intervals once per week from early June until mid-July 2010. Collected invertebrates were counted and identified to class (all invertebrates), order or family (for some of the most common families collected).
Plecoptera of the Daniel L. Gustafson Aquatic Invertebrate Collection, Montana Entomology Collection, Montana State University
<p>The adults and nymphs of Plecoptera, an order of aquatic insects commonly named stoneflies, are emulated in fly fishing patterns and the nymphs are used in water quality assessments. They are encountered in the flowing freshwaters of Montana and the state has relatively high species richness for this group. From 2018 to 2022, Montana Entomology Collection (MTEC), funded by the Council on Library and Information Resources “Hidden Collections” grant, digitized stonefly (Insecta: Plecoptera) specimens housed in its museum. This produced over 2000 records detailing sampling localities, collecting dates, number of individuals, and identifications of stoneflies collected mainly from Montana, USA. The records reveal the efforts of 40 collectors, spanning 60 years of sampling. This dataset makes information associated with 22,600 individual specimens from over 90 species stored in the MTEC available.</p>
Ephemeroptera of the Daniel L. Gustafson Aquatic Invertebrate Collection, Montana Entomology Collection, Montana State University
<p>Ephemeroptera (commonly called mayflies) is an order of insects well-recognized by fishing enthusiasts and regularly used in water quality assessments. From 2018 to 2022, Montana Entomology Collection (MTEC), funded by the Council on Library and Information Resources “Hidden Collections” grant, digitized mayfly specimens housed in its museum. Digitization of label data produced over 2900 records detailing sampling localities, collecting dates, number of individuals, and identifications of mayflies collected mainly from Montana, USA. The records reveal the efforts of 29 collectors, contributing specimens since the 1970s. The digital records make information associated with 37,000 individual specimens from approximately 100 species stored in the MTEC available.</p>
Linked collectors and determiners for: University of Puerto Rico Mayagüez Invertebrate Collection.
Natural history specimen data linked to collectors and determiners held within, "University of Puerto Rico Mayagüez Invertebrate Collection". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="http://bionomia.net/dataset/43e54c60-d6e0-41df-80a3-ca9487a3342a">https://bionomia.net/dataset/43e54c60-d6e0-41df-80a3-ca9487a3342a</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/43e54c60-d6e0-41df-80a3-ca9487a3342a">https://gbif.org/dataset/43e54c60-d6e0-41df-80a3-ca9487a3342a</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Freshwater benthic invertebrates ecological collection NTNU University Museum.
Natural history specimen data linked to collectors and determiners held within, "Freshwater benthic invertebrates ecological collection NTNU University Museum". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="http://bionomia.net/dataset/33591b80-0e31-480c-82ce-2f57211b10e6">https://bionomia.net/dataset/33591b80-0e31-480c-82ce-2f57211b10e6</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/33591b80-0e31-480c-82ce-2f57211b10e6">https://gbif.org/dataset/33591b80-0e31-480c-82ce-2f57211b10e6</a>. Formatted as a Frictionless Data package.
FIGURE 6 in Anthropologically introduced biases in natural history collections, with a case study on the invertebrate paleontology collections from the middle Cambrian Spence Shale Lagerstätte
FIGURE 6. Publications over time that refer specifically to Spence Shale specimens or use quantitative data from the Spence Shale in an analysis.
FIGURE 4 in Anthropologically introduced biases in natural history collections, with a case study on the invertebrate paleontology collections from the middle Cambrian Spence Shale Lagerstätte
FIGURE 4. Specimens in the KUMIP collections by locality, breaking down number of specimens of biomineralizing and soft-bodied taxa from each locality.
FIGURE 1 in Anthropologically introduced biases in natural history collections, with a case study on the invertebrate paleontology collections from the middle Cambrian Spence Shale Lagerstätte
FIGURE 1. Examples of anthropological actions that create bias in natural history collections and when they occur.
Linked collectors and determiners for: NEON Biorepository Invertebrate Bycatch Collection (Archive Pooling).
Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Invertebrate Bycatch Collection (Archive Pooling)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="http://bionomia.net/dataset/596bde6d-0df5-46cb-8eef-92dc3f169ceb">https://bionomia.net/dataset/596bde6d-0df5-46cb-8eef-92dc3f169ceb</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/596bde6d-0df5-46cb-8eef-92dc3f169ceb">https://gbif.org/dataset/596bde6d-0df5-46cb-8eef-92dc3f169ceb</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Field Museum of Natural History (Geology) Fossil Invertebrates Collection.
Natural history specimen data linked to collectors and determiners held within, "Field Museum of Natural History (Geology) Fossil Invertebrates Collection". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="http://bionomia.net/dataset/6595e04b-13d2-4eac-933f-73786627b5a2">https://bionomia.net/dataset/6595e04b-13d2-4eac-933f-73786627b5a2</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/6595e04b-13d2-4eac-933f-73786627b5a2">https://gbif.org/dataset/6595e04b-13d2-4eac-933f-73786627b5a2</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Royal BC Museum - Invertebrates Collection.
Natural history specimen data linked to collectors and determiners held within, "Royal BC Museum - Invertebrates Collection". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="http://bionomia.net/dataset/34fbcf59-d9bb-47e7-9672-99e13ea8c736">https://bionomia.net/dataset/34fbcf59-d9bb-47e7-9672-99e13ea8c736</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/34fbcf59-d9bb-47e7-9672-99e13ea8c736">https://gbif.org/dataset/34fbcf59-d9bb-47e7-9672-99e13ea8c736</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Evan Waite Invertebrate Collection.
Natural history specimen data linked to collectors and determiners held within, "Evan Waite Invertebrate Collection". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/8b0665a6-e35f-4d57-a493-481111d15f14">https://bionomia.net/dataset/8b0665a6-e35f-4d57-a493-481111d15f14</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/8b0665a6-e35f-4d57-a493-481111d15f14">https://gbif.org/dataset/8b0665a6-e35f-4d57-a493-481111d15f14</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: KUBI Invertebrate Zoology Collection.
Natural history specimen data linked to collectors and determiners held within, "KUBI Invertebrate Zoology Collection". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/95c6d414-f762-11e1-a439-00145eb45e9a">https://bionomia.net/dataset/95c6d414-f762-11e1-a439-00145eb45e9a</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/95c6d414-f762-11e1-a439-00145eb45e9a">https://gbif.org/dataset/95c6d414-f762-11e1-a439-00145eb45e9a</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Database of invertebrates collected in Mongolia.
Natural history specimen data linked to collectors and determiners held within, "Database of invertebrates collected in Mongolia". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/867dbe0a-f762-11e1-a439-00145eb45e9a">https://bionomia.net/dataset/867dbe0a-f762-11e1-a439-00145eb45e9a</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/867dbe0a-f762-11e1-a439-00145eb45e9a">https://gbif.org/dataset/867dbe0a-f762-11e1-a439-00145eb45e9a</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Cleveland Museum of Natural History Invertebrate Paleontology Collection.
Natural history specimen data linked to collectors and determiners held within, "Cleveland Museum of Natural History Invertebrate Paleontology Collection". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/53e9eca5-6831-4a43-a109-130feecfcd9c">https://bionomia.net/dataset/53e9eca5-6831-4a43-a109-130feecfcd9c</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/53e9eca5-6831-4a43-a109-130feecfcd9c">https://gbif.org/dataset/53e9eca5-6831-4a43-a109-130feecfcd9c</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: University of Vermont Zadock Thompson Zoological Collection-Invertebrates.
Natural history specimen data linked to collectors and determiners held within, "University of Vermont Zadock Thompson Zoological Collection-Invertebrates". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/68bcf659-9aa6-43a3-aed3-4e1140faa1b5">https://bionomia.net/dataset/68bcf659-9aa6-43a3-aed3-4e1140faa1b5</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/68bcf659-9aa6-43a3-aed3-4e1140faa1b5">https://gbif.org/dataset/68bcf659-9aa6-43a3-aed3-4e1140faa1b5</a>. Formatted as a Frictionless Data package.
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OpenNeuro
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