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25 results for “Crassostrea virginica”
Data from: Ocean acidification induces subtle shifts in gene expression and DNA methylation in mantle tissue of the Eastern oyster (Crassostrea virginica)
<p><b><span>Early evidence suggests that DNA methylation can mediate phenotypic responses of marine calcifying species to ocean acidification (OA). Few studies, however, have explicitly studied DNA methylation in calcifying tissues through time. Here, we examined the phenotypic and molecular responses in the extrapallial fluid and mantle (fluid and tissue at the calcification site) in adult eastern oyster (</span><span>Crassostrea virginica</span><span>) exposed to experimental OA over 80 days. Oysters were reared under three experimental </span><span>p</span><span>CO</span><span><span>2</span></span><span> treatments ('control', 580 μatm; 'moderate OA', 1000 μatm; 'high OA', 2800 μatm) and sampled at 6 time points (24 hours - 80 days). We found that high OA initially induced an increase in the pH of the extrapallial fluid (pH</span><span><span>EPF</span></span><span>) relative to the external seawater that peaked at day 9, but then diminished over time. Calcification rates were significantly lower in the high OA treatment compared to the other treatments. To explore how oysters regulate their extrapallial fluid, gene expression and DNA methylation were examined in the mantle-edge tissue of oysters from days 9 and 80 in the control and high OA treatments. Mantle tissue mounted a significant global molecular response (both in the transcriptome and methylome) to OA that shifted through time. Although we did not find individual genes that were significantly differentially expressed under OA, the pH</span><span><span>EPF</span></span><span> was significantly correlated with the eigengene expression of several co-expressed gene clusters. A small number of OA-induced differentially methylated loci were discovered, which corresponded with a weak association between OA-induced changes in genome-wide gene body DNA methylation and gene expression.</span><span> </span><span>Gene body methylation, however, was not significantly correlated with the eigengene expression of pH</span><span><span>EPF</span></span><span>-correlated gene clusters. These results suggest that OA induces a subtle response in a large number of genes in </span><span>C. virginica</span><span>, but also indicate that plasticity at the molecular level may be limited. Our study highlights the need to reassess our understanding of tissue-specific molecular responses in marine calcifiers</span><span>, </span><span>as well as the role of DNA methylation and gene expression in mediating physiological and biomineralization responses to OA. </span></b></p>
Data from: Genetic by environmental variation but no local adaptation in oysters (Crassostrea virginica)
Functional trait variation within and across populations can strongly influence population, community, and ecosystem processes, but the relative contributions of genetic vs. environmental factors to this variation are often not clear, potentially complicating conservation and restoration efforts. For example, local adaptation, a particular type of genetic by environmental (G*E) interaction in which the fitness of a population in its own habitat is greater than in other habitats, is often invoked in management practices, even in the absence of supporting evidence. Despite increasing attention to the potential for G*E interactions, few studies have tested multiple populations and environments simultaneously, limiting our understanding of the spatial consistency in patterns of adaptive genetic variation. In addition, few studies explicitly differentiate adaptation in response to predation from other biological and environmental factors. We conducted a reciprocal transplant experiment of first-generation eastern oyster (Crassostrea virginica) juveniles from six populations across three field sites spanning 1000 km in the southeastern Atlantic Bight in both the presence and absence of predation to test for G*E variation in this economically valuable and ecologically important species. We documented significant G*E variation in survival and growth, yet there was no evidence for local adaptation. Condition varied across oyster cohorts: Offspring of northern populations had better condition than offspring from the center of our region. Oyster populations in the southeastern Atlantic Bight differ in juvenile survival, growth, and condition, yet offspring from local broodstock do not have higher survival or growth than those from farther away. In the absence of population-specific performance information, oyster restoration and aquaculture may benefit from incorporating multiple populations into their practices.
Morphometrics and nutrient concentration of eastern oysters (Crassostrea virginica) sampled from Chesapeake Bay, USA
<p><span><strong>Acknowledgements</strong></span> Ward Slacum and Olivia Caretti from the Oyster Recovery Partnership for providing the support and resources to compile the initial oyster BMP dataset and maintenance. </p> <p><strong><u>Background Information</u></strong></p> <p>The Chesapeake Bay Program (CBP) approved the use of eastern oyster (<em>Crassostrea virginica</em>) aquaculture as a nitrogen and phosphorus reduction best management practice in December 2016. The CBP decision was based on the recommendations of the Oyster Best Management Practice Expert Panel. The approved BMP report, “Panel Recommendations on the Oyster BMP Nutrient and Suspended Sediment Reduction Effectiveness Determination Decision Framework and Nitrogen and Phosphorus Assimilation in Oyster Tissue Reduction Effectiveness for Oyster Aquaculture Practices” is available here: <a href="https://d18lev1ok5leia.cloudfront.net/chesapeakebay/documents/Oyster_BMP_1st_Report_Final_Approved_2016-12-19.pdf">https://d18lev1ok5leia.cloudfront.net/chesapeakebay/documents/Oyster_BMP_1st_Report_Final_Approved_2016-12-19.pdf</a></p> <p>And a summary fact sheet about the report and the panel’s findings is available here: <a href="https://oysterrecovery.org/wp-content/uploads/June_2018-FINAL-bmp-fact-sheet-1.pdf">https://oysterrecovery.org/wp-content/uploads/June_2018-FINAL-bmp-fact-sheet-1.pdf</a></p> <p>The panel’s recommendations were based on an analysis of two datasets: 1) available literature for eastern oyster tissue nitrogen and phosphorus concentrations (%) across the Northeast region of the United States, and 2) available literature for the relationship between shell height (mm) vs. tissue dry weight (g) for eastern oysters sampled within Chesapeake Bay, USA. The nitrogen and phosphorus concentration datasets were relatively small, and the data were published in the report. The dataset describing the relationship between oyster shell height vs. tissue dry weight was much larger (n = 6,816). The report contains summary statistics and visual representations of the data, but the data themselves were not publicly released.</p> <p>A second report was released by the Oyster Best Management Practice Expert Panel in 2023, with additional analysis of an expanded dataset for the relationship between oyster shell height vs. tissue dry weight (n = 10,786) and a new dataset for the relationship between oyster shell height vs. shell dry weight to support the development of an oyster restoration BMP. The second BMP report, “Nitrogen and Phosphorus Reduction Associated with Harvest of Hatchery-Produced Oysters and Reef Restoration: Assimilation and Enhanced Denitrification” is available here:</p> <p><a href="https://d18lev1ok5leia.cloudfront.net/chesapeakebay/documents/Oyster-BMP-Second-Report_Approved_with_Minutes.pdf">https://d18lev1ok5leia.cloudfront.net/chesapeakebay/documents/Oyster-BMP-Second-Report_Approved_with_Minutes.pdf</a></p> <p>The second report contains summary statistics and visual representations of the data, but the data themselves were not publicly released.</p> <p><strong><em><u>Data Description</u></em></strong></p> <p>This repository contains 77% of the data (n = 8,395) used by the Chesapeake Bay Program’s Oyster Best Management Practice Expert Panel to develop its recommendations for both the 2016 first report and the 2023 second report. Some of the data in this repository were previously published in the peer-reviewed literature as summary statistics, but the raw data were not archived. The remaining data are either not currently available or are published in the gray literature. Two datasets that were used in the Expert Panel analysis are not included in this repository, as the data are unpublished with the data owners intending to publish these data in the future.</p> <p>The repository is organized with individual oyster samples as rows and a combination of numerical and categorical information as columns. Each row/sample in the repository contains data on oyster shell height (mm) and oyster dry weight (g), data source, and sample collection location information. Location information is presented across columns with different levels of spatial resolution. This repository also contains additional information provided by scientists when available, such as nitrogen, carbon, or phosphorus concentration, details about the oyster source and growth conditions, and sampling time (e.g., season/date/year).</p>
Morphometrics and nutrient concentration of farmed eastern oysters (Crassostrea virginica) from the US Northeast Region
<p><strong><u>Acknowledgements</u></strong></p> <p>This work was supported by the NOAA Fisheries Northeast Fisheries Science Center and the NOAA Fisheries Office of Aquaculture. Thanks to Marta Gomez-Chiarri, PG Harris, Mark Luckenbach, and Christine Thompson for sharing data, although these data were not included in the final repository.</p> <p><strong><u>Background Information</u></strong></p> <p>The removal of excess nitrogen from eutrophic environments is an ecosystem service provided by shellfish aquaculture that is well described in the literature (Lindahl et al., 2005; Rose et al., 2014; Petersen et al., 2014; Clements and Comeau, 2019). Nitrogen removal associated with shellfish farms can occur via three mechanisms: the assimilation of nitrogen into tissue and shell, which is removed from the waterbody when animals are harvested; the enhancement of sediment denitrification through biodeposit production on farms; and the long-term burial of biodeposits.</p> <p>A robust calculation of the nitrogen removed at shellfish harvest has been previously published using relatively simple metrics: the nitrogen concentration of tissue/shell, the number and mean size of animals harvested, and a conversion of animal size to tissue and shell dry weight (Reichert-Nguyen et al., 2016; Clements and Comeau, 2019). The quantity of nitrogen removed at shellfish harvest has been previously predicted with high confidence, which has led to the integration of oyster and clam aquaculture into nutrient management programs at the local and estuary scale in the United States (Town of Mashpee, 2015; Reichert-Nguyen et al., 2016; Reitsma et al., 2017).</p> <p>The data in this repository were compiled with the intention of expanding the geographic scope of calculation of nitrogen removal associated with harvested eastern oysters (<em>Crassostrea virginica</em>), and to evaluate variation in this ecosystem service across common cultivation practices and ploidy. Data were obtained from sampling locations across the US from the state of North Carolina north to the state of Maine. Data are included for both diploid and triploid oysters, and for three common styles of cultivation: oysters grown on bottom without the use of aquaculture gear, oysters grown in bottom cages, and oysters grown in floating gear at the sea surface. Data curation was undertaken to obtain a dataset that most closely reflects on-farm conditions as possible. The highest priority was to find data collected from working oyster farms, and a second priority was to identify data collected by scientists who employed common cultivation practices in their research studies. In one state within the region (Rhode Island) we were unable to locate data that fit the previous description, and instead have included data from wild oysters from waterbodies that have oyster farms.</p> <p>This data set was used to support the development of the Aquaculture Nutrient Removal Calculator (ANRC,<a href="https://connect.fisheries.noaa.gov/ANRC/">https://connect.fisheries.noaa.gov/ANRC/</a>), a tool designed for use by both shellfish farmers and managers within the aquaculture permit review process. The ANRC is a publicly available, simple online tool that was developed in direct response to feedback from aquaculture resource managers. The ANRC accurately predicts harvest-based nitrogen removal from an eastern oyster farm located within the geographic range of North Carolina to Maine, USA. We have taken an adaptive management approach to tool development, basing our tool on current best available scientific information, with the intention of maintaining and updating this tool when new information and data become available in the future.</p> <p><strong><u>Data Description</u></strong></p> <p>This repository contains information on morphometrics and nitrogen concentration of tissue and shell for eastern oysters sampled within the US geographic region spanning the states of North Carolina to Maine. Some of the data in this repository (6 of 10 sources) were previously published as summary statistics in the peer-reviewed literature, but the raw data included here were not archived. Three datasets were not previously published in raw or summary form. One dataset is publicly available in a technical report.</p> <p>The repository is organized with individual oysters as rows and numerical/categorical information associated with those oyster samples as columns. Each sample in the repository contains data on oyster shell height (mm), tissue dry weight (g), data source, ploidy, cultivation practice, and location of sample collection. The repository also contains additional information provided by data sources as available, such as shell dry weight, nitrogen, carbon, sampling date, oyster stock, and other morphometric measurements.</p> <p><strong><u>References</u></strong></p> <p>Clements, J.C., Comeau, L.A., 2019. Nitrogen removal potential of shellfish aquaculture harvests in eastern Canada: A comparison of culture methods. Aquaculture Reports 13, 100183.</p> <p>Lindahl, O., Hart, R., Hernroth, B., Kollberg, S., Loo, L.-O., Olrog, L., Rehnstam-Holm, A.-S., Svensson, J., Svensson, S., Syversen, U., 2005. Improving marine water quality by mussel farming - a profitable solution for Swedish society. Ambio 34, 129-136.</p> <p>Petersen, J.K., Hasler, B., Timmermann, K., Nielsen, P., Tørring, D.B., Larsen, M.M., Holmer, M., 2014. Mussels as a tool for mitigation of nutrients in the marine environment. Marine Pollution Bulletin 82, 137-143.</p> <p>Reichert-Nguyen, J., Cornwell, J., Rose, J., Kellogg, L., Luckenbach, M., Bricker, S., Paynter, K., Moore, C., Parker, M., Sanford, L., Wolinski, B., Lacatell, A., Fegley, L., Hudson, K., French, E., Slacum, W., 2016. Panel recommendations on the oyster BMP nutrient and suspended sediment reduction effectiveness determination decision framework and nitrogen and phosphorus assimilation in oyster tissue reduction effectiveness for oyster aquaculture practices, Report to the Chesapeake Bay Program. Available online at <a href="https://www.oysterrecovery.org/wp-content/uploads/2017/01/Oyster-BMP-1st-Report_Final_Approved_2016-12-19.pdf">https://www.oysterrecovery.org/wp-content/uploads/2017/01/Oyster-BMP-1st-Report_Final_Approved_2016-12-19.pdf.</a></p> <p>Reitsma, J., Murphy, D.C., Archer, A.F., York, R.H., 2017. Nitrogen extraction potential of wild and cultured bivalves harvested from nearshore waters of Cape Cod, USA. Marine Pollution Bulletin 116, 175-181.</p> <p>Rose, J.M., Bricker, S.B., Tedesco, M.A., Wikfors, G.H., 2014. A Role for Shellfish Aquaculture in Coastal Nitrogen Management. Environmental Science & Technology 48, 2519-2525.</p> <p>Rose J.M.,, Morse, R., and Schillaci, C. 2024. Development and application of an online tool to quantify nitrogen removal associated with harvest of cultivated eastern oysters. PLoS ONE 19(9): e0310062. https://doi.org/10.1371/journal.pone.0310062</p> <p>Town of Mashpee Sewer Commission, 2015. Comprehensive watershed nitrogen management plan, Town of Mashpee, Available online at http://www.mashpeewaters.com/documents.html.</p>
Data from: Ocean acidification induces subtle shifts in gene expression and DNA methylation in mantle tissue of the Eastern oyster (Crassostrea virginica)
Open the record for dataset details and reuse information.
Data from: Genetic by environmental variation but no local adaptation in oysters (Crassostrea virginica)
Open the record for dataset details and reuse information.
Data from: Lack of genotype-by-environment interaction suggests limited potential for evolutionary changes in plasticity in the eastern oyster, Crassostrea virginica
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Georgia Coastal Ecosystems site, station Georgia Coastal Ecosystem LTER Study Site 10, Hunt Camp, Sapelo Island, GA, study of animal density of Crassostrea virginica in units of numberPerMeterSquared on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Georgia Coastal Ecosystems (GCE) contains animal density of Crassostrea virginica measurements in numberPerMeterSquared units and were aggregated to a yearly timescale.
Georgia Coastal Ecosystems site, station Georgia Coastal Ecosystem LTER Study Site 1, Eulonia, GA, study of animal density of Crassostrea virginica in units of numberPerMeterSquared on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Georgia Coastal Ecosystems (GCE) contains animal density of Crassostrea virginica measurements in numberPerMeterSquared units and were aggregated to a yearly timescale.
Georgia Coastal Ecosystems site, station Georgia Coastal Ecosystem LTER Study Site 2, Four Mile Island, GA, study of animal density of Crassostrea virginica in units of numberPerMeterSquared on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Georgia Coastal Ecosystems (GCE) contains animal density of Crassostrea virginica measurements in numberPerMeterSquared units and were aggregated to a yearly timescale.
Georgia Coastal Ecosystems site, station Georgia Coastal Ecosystem LTER Study Site 3, North Sapelo, Sapelo Island, GA, study of animal density of Crassostrea virginica in units of numberPerMeterSquared on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Georgia Coastal Ecosystems (GCE) contains animal density of Crassostrea virginica measurements in numberPerMeterSquared units and were aggregated to a yearly timescale.
Georgia Coastal Ecosystems site, station Georgia Coastal Ecosystem LTER Study Site 4, Meridian, GA, study of animal density of Crassostrea virginica in units of numberPerMeterSquared on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Georgia Coastal Ecosystems (GCE) contains animal density of Crassostrea virginica measurements in numberPerMeterSquared units and were aggregated to a yearly timescale.
Georgia Coastal Ecosystems site, station Georgia Coastal Ecosystem LTER Study Site 5, Folly River, GA, study of animal density of Crassostrea virginica in units of numberPerMeterSquared on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Georgia Coastal Ecosystems (GCE) contains animal density of Crassostrea virginica measurements in numberPerMeterSquared units and were aggregated to a yearly timescale.
Georgia Coastal Ecosystems site, station Georgia Coastal Ecosystem LTER Study Site 6, Dean Creek, Sapelo Island, GA, study of animal density of Crassostrea virginica in units of numberPerMeterSquared on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Georgia Coastal Ecosystems (GCE) contains animal density of Crassostrea virginica measurements in numberPerMeterSquared units and were aggregated to a yearly timescale.
Georgia Coastal Ecosystems site, station Georgia Coastal Ecosystem LTER Study Site 7, Carrs Island, GA, study of animal density of Crassostrea virginica in units of numberPerMeterSquared on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Georgia Coastal Ecosystems (GCE) contains animal density of Crassostrea virginica measurements in numberPerMeterSquared units and were aggregated to a yearly timescale.
Georgia Coastal Ecosystems site, station Georgia Coastal Ecosystem LTER Study Site 8, Alligator Creek, GA, study of animal density of Crassostrea virginica in units of numberPerMeterSquared on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Georgia Coastal Ecosystems (GCE) contains animal density of Crassostrea virginica measurements in numberPerMeterSquared units and were aggregated to a yearly timescale.
Georgia Coastal Ecosystems site, station Georgia Coastal Ecosystem LTER Study Site 9, Rockdedundy Island, GA, study of animal density of Crassostrea virginica in units of numberPerMeterSquared on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Georgia Coastal Ecosystems (GCE) contains animal density of Crassostrea virginica measurements in numberPerMeterSquared units and were aggregated to a yearly timescale.
Georgia Coastal Ecosystems site, station Zone 1, Creek Bank, study of animal density of Crassostrea virginica in units of numberPerMeterSquared on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Georgia Coastal Ecosystems (GCE) contains animal density of Crassostrea virginica measurements in numberPerMeterSquared units and were aggregated to a yearly timescale.
Georgia Coastal Ecosystems site, station Zone 2, Mid-marsh, study of animal density of Crassostrea virginica in units of numberPerMeterSquared on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Georgia Coastal Ecosystems (GCE) contains animal density of Crassostrea virginica measurements in numberPerMeterSquared units and were aggregated to a yearly timescale.
Data from: Reef-specific patterns of gene expression plasticity in eastern oysters (Crassostrea virginica)
Understanding the interaction between phenotypic plasticity and evolutionary processes is important for predicting a species' response to changing environment. Strong recurrent selection each generation may be an important process in highly fecund species with broad dispersal and extensive early mortality. We tested whether selection was associated with spatial divergence in gene expression plasticity for osmoregulation in the eastern oyster (Crassostrea virginica). We collected adult oysters from high and low salinity reefs within a single estuary and after 9 weeks of acclimation at 10 and 30 salinity, measured gene expression in 24 oysters using next-generation RNA sequencing technology. The oysters had significantly different expression (DE) in response to salinity treatments for 7936 (18.9%) transcripts overall, with planned contrasts showing 8× more DE in oysters from the high-salinity reef and 15× more DE between reefs when tested at 10 salinity. The reef-by-treatment interaction was also genomically pervasive (5858 DE transcripts, 13.9%). Inter-reef F ST for transcript SNPs averaged 0.0025 with the top 1% between 0.29 and 0.73. Transcripts containing "outlier" SNPs were significantly enriched for osmoregulatory genes and showed patterns of variation consistent with selection on the low-salinity reef. Both phenotypic plasticity and recurrent selection seem to be important factors determining the realized niche of oysters within estuaries.
ScienceDex guides
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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.