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176 results for “Biological communities”
Kellogg Biological Station site, station Treatment SF, old field successional community, never tilled, study of plant species richness 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 Kellogg Biological Station (KBS) contains plant species richness measurements in numberPerMeterSquared units and were aggregated to a yearly timescale.
Estimates of surface layer net community production based on underway Lagrangian measurements of the dissolved O2/Ar ratio using Equilibrator Inlet Mass Spectrometry (EIMS), based on both steady-state and non-steady-state assumptions of the mixed-layer biological oxygen budget. Also included are estimates of the potential contribution of vertical fluxes: advection, eddy diffusion, and entrainment.
The ratio of dissolved oxygen to argon in surface seawater is frequently employed to estimate rates of net community production (NCP) in the oceanic mixed layer. The in situ O2/Ar-based method accounts for many physical factors that influence oxygen concentrations in the surface ocean, permitting isolation of the biological oxygen signal produced by the balance of photosynthesis and respiration. However, this technique traditionally relies upon several assumptions when calculating the mixed layer O2/Ar budget, most notably the absence of vertical fluxes of O2/Ar and the existence of a steady-state balance between net productivity and the air-sea gas exchange of biological oxygen. Employing a Lagrangian study design and leveraging data outputs from a regional physical oceanographic model, we conducted in situ measurements of O2/Ar in the California Current Ecosystem in spring 2016 and summer 2017 to evaluate these assumptions within a ‘worst-case’ field environment. Quantifying the magnitude of vertical fluxes and comparing NCP estimates obtained using steady-state versus non-steady-state assumptions, we find the importance of the non-steady-state term to be considerable, also observing significant potential effects from vertical flux terms, particularly advection. Additionally, we observe strong diel variability in O2/Ar and calculated NCP rates at multiple stations. Our results reemphasize the importance of accounting for vertical fluxes when interpreting O2/Ar-derived NCP data as well as the potentially large effect of non-steady-state conditions, including diel cycles in surface O2/Ar that can bias interpretation of NCP data based on local productivity and the time of day at which measurements were made.
Dataset used for the submitted manuscript "The hump-shaped effect of plant functional diversity on the biological control of a multi-species pest community"
<p>Dataset</p>
Data from: Identification of migratory bird flyways in North America using community detection on biological networks
Migratory behavior of waterfowl populations in North America has traditionally been broadly characterized by four north-south flyways, and these flyways have been central to the management of waterfowl populations for more than 80 years. However, previous flyway characterizations are not easily updated with current bird movement data and fail to provide assessments of the importance of specific geographical regions to the identification of flyways. Here, we developed a network model of migratory movement for four waterfowl species —mallard (Anas platyrhnchos), northern pintail (A. acuta), American green-winged teal (A. carolinensis), and Canada goose (Branta canadensis) — in North America using bird band and recovery data. We then identified migratory flyways using a community detection algorithm and characterize the importance of smaller geographic regions in identifying flyways using a novel metric, the consolidation factor. We identified four main flyways for mallards, northern pintails, and American green-winged teal with the flyway identification in Canada geese exhibiting higher complexity. For mallards, flyways were relatively consistent through time. However, consolidation factors revealed that for mallards and green-winged teal the presumptive Mississippi flyway was potentially a zone of high mixing between other flyways. Our results demonstrate that the network approach provides a robust method for flyway identification that is widely applicable given the relatively minimal data requirements and is easily updated with future movement data to reflect changes in flyway definitions and management goals.
Direct and indirect effects of noise pollution alter biological communities in and near noise-exposed environments
<p>Noise pollution is pervasive across every ecosystem on Earth. Although decades of research have documented a variety of negative impacts of noise to organisms, key gaps remain, such as how noise affects different taxa within a biological community and how effects of noise propagate across space. We experimentally applied traffic noise pollution to multiple roadless areas and quantified the impacts of noise on birds, grasshoppers, and odonates. We show that acoustically-oriented birds have reduced species richness and abundance and different community compositions in experimentally noise-exposed areas relative to comparable quiet locations. We also found both acoustically-oriented grasshoppers and odonates without acoustic receptors to have reduced species richness and/or abundance in relatively quiet areas that abut noise-exposed areas. These results suggest that noise pollution not only affects acoustically-oriented animals, but that noise may reverberate through biological communities through indirect effects to those with no clear links to the acoustic realm, even in adjacent quiet environments.</p>
Data from: Assemblage Accumulation Curves: A framework for resolving species accumulation in biological communities using chloroplast genome sequences
The timing and tempo of the processes involved in community assembly are of substantial concern to community ecologists and conservation managers. The fossil record is a valuable source of data for studying past changes in community composition, but it is not always detailed enough to allow the process of community assembly to be resolved at regional or site scales while tracing the trajectories of known species with associated known traits. We present a three‐step framework for studying present‐day species accumulation through time: DNA sampling from multiple individuals from multiple species within a community; estimates of coalescence times for each species using molecular dating methods; and plotting the accumulation of present‐day species through time using the inferred population ages. Our approach is illustrated using whole chloroplast genomes from plants from three rainforest communities in eastern Australia. Expected times to coalescence for multiple species in each community were inferred from pooled high‐throughput sequence libraries. Local assemblage accumulation curves for each community were constructed. We also explored the variation in assemblage accumulation curves of species with different functional traits. Models of equilibrium species richness informed our null hypothesis and largely explained the shape of the assemblage accumulation curves and indicated that the complexities of the accumulation process should be explored with additional parameters, for example allowing species classes with different extinction rates. The assemblage accumulation curves for the study sites showed evidence of recent population expansions within each of the communities. This signal of recent accumulation is consistent with the increase in suitable rainforest habitat that followed the Last Glacial Maximum. Our method of constructing assemblage accumulation curves provides a simple approach for visualizing species‐accumulation data. It can be used to test hypotheses such as the relative survival potential of species‐specific ecological attributes. Although our example used single‐nucleotide polymorphisms derived from whole‐chloroplast sequencing, this framework can be applied to mitochondrial genomes and to communities of other organisms.
FIGURE 5. Left side shows a in The amphibian community at Yanayacu Biological Station, Ecuador, with a comparison of vertical microhabitat use among Pristimantis species and the description of a new species of the Pristimantis myersi group
FIGURE 5. Left side shows a power spectrum (top), sonogram (middle), and oscillogram (bottom) of a series of advertisement calls of Pristimantis bicantus (QCAZ 18983). Right side shows a sonogram (middle) and oscillogram (bottom) of a single long call (the eighth of the 11 long calls shown on the left, marked with an asterisk). This is an example of a call series consisting of three short calls (each with two pulses) and 11 long calls (each with 17–23 more rapid pulses). The power spectrum was measured along the entire duration of the call series.
FIGURE 2 in The amphibian community at Yanayacu Biological Station, Ecuador, with a comparison of vertical microhabitat use among Pristimantis species and the description of a new species of the Pristimantis myersi group
FIGURE 2. Dorsal and ventral color variation of Pristimantis bicantus in ethanol. (A, E) QCAZ 19024 (female holotype); (B) QCAZ 16186, adult female; (C) QCAZ 18988, adult female; (D, F) QCAZ 16201, adult female.
FIGURE 1 in The amphibian community at Yanayacu Biological Station, Ecuador, with a comparison of vertical microhabitat use among Pristimantis species and the description of a new species of the Pristimantis myersi group
FIGURE 1. (A) Head, (B) hand, and (C) foot of Pristimantis bicantus, holotype, adult female, QCAZ 19024.
FIGURE 3 in The amphibian community at Yanayacu Biological Station, Ecuador, with a comparison of vertical microhabitat use among Pristimantis species and the description of a new species of the Pristimantis myersi group
FIGURE 3. Map of Ecuador showing the type locality of Pristimantis bicantus (Yanayacu Biological Station, 0°36' S, 77°53' W, 2100–2300 m).
Results of the community survey associated with manuscript "Knowledge gaps in quantifying the climate change response of biological storage of carbon in the ocean" by Henson et al.
<p><span><span>Full anonymised results of the community survey are available as part of the Supporting Information (Data Set S1)</span></span> for manuscript "Knowledge gaps in quantifying the climate change response of biological storage of carbon in the ocean" by Stephanie Henson, Chelsey A. Baker, Paul Halloran, Abigail McQuatters-Gollop, Stuart Painter, Alban Planchat, Alessandro Tagliabue</p> <p><strong> </strong></p>
Code and data sets analysed in: "Marine heatwave bleaching causes mass mortality and drives a microbial community reorganisation in an ecologically important temperate sponge" Bell et al. (2024). Global Change Biology
<p>The attached zipped folder contains in-situ, satellite, reanalysis and laboratory measurements, together with R and MATLAB scripts, to reproduce the results in Bell et al. (2024). Marine heatwave bleaching causes mass mortality and drives a microbial community reorganisation in an ecologically important temperate sponge. Global Change Biology. Each folder contains a read me file that describes the enclosed data sets and scripts.</p>
Moored ADCP Cape Canaveral from Sep 2013 to Sep 2016, part of BOEM's project "Ecological Function and Recovery of Biological Communities within Dredged Ridge-Swale Habitats in the South-Atlantic Bight"
<p>Bottom-mounted ADCP data (mooring data) for "Ecological Function and Recovery of Biological Communities within Dredged Ridge-Swale Habitats in the South-Atlantic Bight"</p> <p>All ADCP mooring deployments are detailed in the spreadsheet "Canaveral_Mooring_Deployment_details_BOEM_project" appearing with the zipped folders. These zipped folders have been separated by deployment number, as indicated by their names.The great majority of ADCP records were obtained with Teledyne instrumentation. A few records were secured with Aquadopp and AWAC (Nortek) ADPs.</p> <p>Most data have been transformed to Matlab format. Only some downward pointing ADCPs, those not in Matlab format, have been left (and uploaded) in their original format (binary from Teledyne), typically with extension '000' or '001'. These files are Gigabytes big and can be visualized with the 'WinADCP' program that can be downloaded for free from the Teledyne website.</p> <p>Missing files, still appearing in the spreadsheet, are a consequence of instrument malfunction, platform destruction, or instrument lost.</p> <p> </p>
Description and Comparison of Biological Vulnerability in Small Vulnerable Newborns Versus Healthy Community Controls in Urban Burkina Faso
ClinicalTrials.gov study NCT05730569. IPD Sharing: YES. Countries: 1. Publications: 17.
The Impact of Lifestyle Medicine on the Sense Of Coherence and Biological Age in a Community Sample
ClinicalTrials.gov study NCT06671301. IPD Sharing: NO. Countries: 1. Publications: 4.
Data from: Assemblage Accumulation Curves: A framework for resolving species accumulation in biological communities using chloroplast genome sequences
Open the record for dataset details and reuse information.
Data from: Identification of migratory bird flyways in North America using community detection on biological networks
Open the record for dataset details and reuse information.
Direct and indirect effects of noise pollution alter biological communities in and near noise-exposed environments
Open the record for dataset details and reuse information.
Figure 3 from: Souza Silva M, Iniesta LFM, Ferreira RL (2020) Invertebrates diversity in mountain Neotropical quartzite caves: which factors can influence the composition, richness, and distribution of the cave communities? Subterranean Biology 33: 23-43. https://doi.org/10.3897/subtbiol.33.46444
Figure 3 Obligate cave species found in the Ibitipoca Estadual Park, Brazil. AHypogastruridaeBBlattodeaCBrasilomma enigmatica (Prodidomidae) DProjapygidaeEEukoenenia ibitipoca (Palpigradi).
Figure 2 from: Souza Silva M, Iniesta LFM, Ferreira RL (2020) Invertebrates diversity in mountain Neotropical quartzite caves: which factors can influence the composition, richness, and distribution of the cave communities? Subterranean Biology 33: 23-43. https://doi.org/10.3897/subtbiol.33.46444
Figure 2 Higher taxa invertebrate abundance, taxonomic diversity (richness) (A) and average taxonomic distinctness (Δ+) (B) in all 20 quartzite caves placed above 1200 m high in Minas Gerais (Brazil).
ScienceDex guides
Understand access before you commit
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.