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1,549 results for “invertebrate”
Supplementary data: The added value of Bayesian inference for estimating biotransformation rates of organic contaminants in aquatic invertebrates.
<p>Supporting information for the article "<strong>The added value of Bayesian inference for estimating biotransformation rates of organic contaminants in aquatic invertebrates.</strong>"</p> <p>This provides all the R script and .csv files for each dataset. </p>
Data and R Code for 'Domestication via the commensal pathway in a fish-invertebrate mutualism'
<p>This document contains all data and R code required to replicate the analyses in 'Domestication via the commensal pathway in a fish-invertebrate mechanism' as published in Nature Communications. The R Markdown provided includes descriptions of all variables and the code used for the analysis of the following eight datasets:</p> <p>1. Transects<br> 2. Census of farms<br> 3. Paired choice experiments<br> 4. Predation experiment 1<br> 5. Predation experiment 2<br> 6. Timed observations<br> 7. Farm algae composition<br> 8. Longfin damselfish body condition</p> <p>In addition, the R Markdown also includes descriptions of all variables for two additional datasets:</p> <p>9. Estimates of mysid swarm density<br> 10. Mysid waste excretion and nutrient availability</p> <p>A PDF version of the R Markdown with all output is also provided. Please see the methods section of the associated manuscript for further information on data collection and analysis procedures.</p> <p>Author contributions to data collection and analysis: RMB, JMC, ZLC, TLS & WEF collected the data; WEF, RMB, JMC, ZLC & AM implemented the analyses. </p> <p>Correspond with: rohan.m.brooker@gmail.com</p>
Summer and winter invertebrate and physicochemical data from the Coweeta Hydrologic Lab
<p>This resource contains data for aquatic invertebrates collected from leaf litterbags, which were deployed in 11 streams at the Coweeta Hydrologic Lab (Macon County, North Carolina, USA) during winter and summer months in 2017-2018. Litterbags consisted of fine-mesh bags (250µm) attached to coarse-mesh bags (5mm), each containing <em>Rhododendron maximum</em> leaf litter. The litterbags were deployed for two-month periods, which were as follows: 19 October - 11 or 18 December, 2017; 15 November - 5 January 2017-2018; 9 May - 5 July 2018; and 5 July - 31 August 2018. We collected invertebrate samples from the >1mm size fraction from 3 coarse-fine litterbag pairs incubated in each of our streams during the aforementioned 2-month periods. Invertebrates were preserved in ethanol, identified, and classified into functional feeding groups based on classifications in Merritt et al. 2019. We identified invertebrates in the "shredder" functional feeding group to genus and all other insects to family (Merritt et al. 2019). We also measured invertebrate lengths in mm and converted these lengths to masses using information from Benke 1999. This resource also contains daily temperature and discharge data, litter breakdown data from the coarse-mesh bags associated with the invertebrate data, and weekly nutrient concentration data from the streams during the study period. Discharge data was provided by the USFS Coweeta Hydrologic Lab and can also be found here: https://www.fs.usda.gov/rds/archive/catalog/RDS-2016-0025-2</p> <p>Discharge data citation:</p> <p>USFS Coweeta Hydrologic Laboratory. 2023. Daily streamflow data for gauged watersheds at Coweeta Hydrologic Laboratory, North Carolina. 2nd Edition. Fort Collins, CO: Forest Service Research Data Archive. https://doi.org/10.2737/RDS-2016-0025-2</p>
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>
Community science approach reveals temporal and eutrophication-related spatial patterns in bladderwrack-associated invertebrate fauna
<p>Data related to the "Community science approach reveals temporal and eutrophication-related spatial patterns in bladderwrack-associated invertebrate fauna" paper by Salo, Nieminen, Salovius-Laurén and Rinne published in Estuarine, Coastal and Shelf Science in 2024. <a href="https://doi.org/10.1016/j.ecss.2024.108822">https://doi.org/10.1016/j.ecss.2024.108822</a></p> <p>The data describes the community data collected with the community science method described in the paper. </p>
DATASET Invertebrate sounds from photic to mesophotic coral reefs reveal vertical stratification and diel diversity
<p>This dataset contains 17 wave folders. The original files were used for the study published by Raick et al. (2024) in Oecologia (10.1007/s00442-024-05572-5), while subsampled versions of these files were used for the studies published by Raick et al. (2023) in Coral Reefs (10.1007/s00338-022-02343-7) and Raick et al. (2023) in Scientia Marina (10.3989/scimar.05395.078).</p>
Echinoderms_Invertebrates_Interactions
<p>Data set with historical reports about parasitic and commensal invertebrates of echinoderms from American Tropical And Subtropical Atlantic. Data extracted to index papers and historical reports.</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>
A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples
<p>[This repository contains the source data for the manuscript "A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples" by deWaard et al., 2019. BioRxiv]</p>
Dataset from: Small-scale patches of detritus as habitat for invertebrates within a Zostera noltei meadow
<p>This dataset is related to "Small-scale patches of detritus as habitat for invertebrates within a <em>Zostera noltei</em> meadow" (Valentina Costa, Renato Chemello, Davide Iaciofano, Sabrina Lo Brutto, Francesca Rossi)</p>
Artificial reefs geographical location matters more than shape, age and depth for sessile invertebrate colonization in the Gulf of Lion (NorthWestern Mediterranean Sea)
<p>Artificial reefs (ARs) have been used to support fishing activities. Sessile invertebrates are essential components of trophic networks within ARs, supporting fish productivity. However, colonization by sessile invertebrates is possible only after effective larval dispersal from source populations, usually in natural habitat. While most studies focused on short term colonization by pioneer species, we propose to test the relevance of geographic location, shape, age and depth of immersion on the ARs long term colonization by species found in natural stable communities in the Gulf of Lion. We recorded the presence of five sessile invertebrates species, with contrasting life history traits and regional distribution in the natural rocky habitat, on ARs with different shapes deployed during two immersion time periods (1985 and the 2000s) and in two depth ranges (<20m and >20m). At the local level (~5kms), neither shape, depth nor immersion duration differentiated ARs assemblages. At the regional scale (>30kms), colonization patterns differed between species, resulting in diverse assemblages. This study highlights the primacy of geographical positioning over shape, immersion duration and depth in ARs colonization, suggesting it should be accounted for in maritime spatial planning.</p>
Supplementary material for "Increased sensitivity of marine invertebrates to metal toxicity in the past two decades linked to Climate Change and Ocean Acidification: revelations from a natural population of sea urchins in the Mediterranean Sea." by "Davide Sartori, Guido Scatena, Cristina Vrinceanu, Andrea Gaion".
<p>Satellite observations of environmental factors and effect concentration 50 for copper to sea urchin, from 2003 to 2022.</p>
Spineless and overlooked: DNA metabarcoding of autonomous reef monitoring structures reveals intra- and interspecific genetic diversity in Mediterranean invertebrates
<p>Sequence data and stepwise pipeline outputs associated with the article "Spineless and overlooked: DNA metabarcoding of autonomous reef monitoring structures reveals intra- and interspecific genetic diversity in Mediterranean invertebrates".</p> <p>Preprint available here: <a href="https://doi.org/10.22541/au.167085544.47638352/v1">10.22541/au.167085544.47638352/v1</a></p> <p>Sequence data is deposited in fastq-format in folders by region (Palinuro.tar.gz, Livorno.tar.gz, and Rovinj.tar.gz) and a separate folder for controls (Controls.tar.gz). Each fastq-file contains sequences for a single PCR replicate named by sample and replicate number. Sample names are described in spineless_sample_names.csv. Positive control sequences are described in SM1_positive_controls.csv. Stepwise pipeline outputs are available in the folder Pipeline_outputs_stepwise.zip</p> <p>Scripts used to generate pipeline outputs as well as other aspects of the final article are available at <a href="https://github.com/thomasdotter/spineless-haplotypes">https://github.com/thomasdotter/spineless-haplotypes</a>.</p> <p> </p>
Ecostack - Database on ESP invertebrate species
<p>This document is composed of two parts: a report and the associated Microsoft Access database with information collected for selected Ecosystem Service Provider (ESP) species.</p> <p>The objective of this database was to provide compiled, and ready to use, information on the biology and ecology of key Ecosystem Service Providers (ESP) within the studied EU agricultural landscapes to be modelled in ALMaSS (agent-based or subpopulation-based models that will run on ALMaSS landscapes and will be used to test Ecostack scenarios). This information was necessary to build the “formal model” for each species, a step of paramount important in model building.</p> <p>The DB contains information from species being currently modelled but is prepared to be updated with new information on the same or other ESP species. To better understand the DB, it is advisable to consult the associated report.</p>
Extra terrestrials: experimental drought creates niche space for rare invertebrates in terrestrialising stream channels
<p>The code and data for the paper entitled "Extra terrestrials: experimental drought creates niche space for rare invertebrates in terrestrialising stream channels" published in <em>Biology Letters</em>.</p>
Manipulating the hydroperiod affects plant and invertebrate communities in freshwater mesocosms, La Marque TX USA, 2019-2021
We used a mesocosm experiment with six flooding depths and seven drought durations, followed by seven months of recovery, to explore how freshwater wetlands typical of the Houston, Texas area would respond to different hydrological regimes that might occur if wetlands were drained in anticipation of a heavy rain that did not materialize, leading to a temporary period of little or no standing water. The experiment was conducted in 2019-2021. How quickly mesocosms dried out was a function of initial water depth, with mesocosms initially set with greater water depths (30 cm) taking on average 38 days to dry out. Individual plant species (14 were planted; 8 were common at the end of the recovery period) were affected drought length, flooding depth, or their interaction, with results varying among species. The composition of the plant community at the end of the drought period was strongly affected by drought length, and this effect persisted through seven months of recovery, with the 80- and 160-day drought treatments diverging most strongly from shorter drought treatments. Densities of mosquito larvae, snails and tadpoles were temporally variable, and affected more during the treatment period than after seven months of recovery. Our results indicate that managed wetlands in southeast Texas would be quite resilient to dry periods of up to 40 days in duration, especially if water was not completely drained at the beginning of the drought. In addition, some wetland species would persist in managed wetlands even if they experienced droughts of up to 160 days.
Decomissioned Site: Arthur Brook's (D01 ARTH) Legacy and Prototype Aquatic invertebrates (repackaging of occurrences published by the NEON Biorepository Data Portal)
This collection contains legacy and prototype NEON aquatic invertebrates from the decommissioned Arthur Brook's site in Worcester County, Massachusets. These samples and specimens were collected using NEON protocol NEON.DP1.20120 and are summarized in NEON Prototype dataset e7d152a1-1181-4c7e-ac75-ae707ffc7299. This data is available here.
Decomissioned Site: Ichawanochaway Creek (D03 ICHA) Legacy and Prototype Aquatic invertebrates (repackaging of occurrences published by the NEON Biorepository Data Portal)
This collection contains legacy and prototype NEON aquatic invertebrates from the decommissioned Ichawanochaway Creek site in Baker County, Georgia. These samples and specimens were collected using NEON protocol NEON.DP1.20120 and are summarized in NEON Prototype dataset 1599af29-fad4-4721-9b09-f8324b672d50. This data is available here.
Identified invertebrate bycatch from beetle pitfall traps at SJER and SOAP, 2017 - 2018 (repackaging of occurrences published by the NEON Biorepository Data Portal)
California permit requirements necessitated a more thorough identification of beetle pitfall samples than is typical of this protocol. These invertebrate bycatch samples therefore have occurrence associations that indicate their contents in both the NEON Biorepository and main NEON data portals. See NEON prototype dataset 9bc959c-148b-aaad-aa35-2d0805327428 available here.
Selected trait data for the most abundant phytoplankton, zooplankton, benthic invertebrates, and fishes of the Upper San Francisco Estuary
This data set includes selected trait data from published literature and online databases for the most common phytoplankton, zooplankton, benthic invertebrate, and fish taxa at long term monitoring stations in the Upper San Francisco Estuary, which includes the Sacramento-San Joaquin River Delta, Suisun Bay, and Grizzly Bay.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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