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22,445 results for “diversity”
Long-term mid-marsh grasshopper abundance and species diversity at eight GCE-LTER sampling sites
Grasshopper abundance and species diversity were investigated at eight sampling sites within the Georgia Coastal Ecosystems (GCE) LTER study area during July or August from 2000 to 2023. Visual surveys were conducted along 8-10 2m by 10m transects randomly allocated within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. These surveys were conducted as part of the GCE invertebrate monitoring program, and are performed annually to assess long-term changes in relative species abundances across the GCE study area.
USFWS Red Bluff Diversion Dam Rotary Screw Trap Juvenile Fish Monitoring Database
The United States Fish and Wildlife Service (USFWS) has conducted direct monitoring of juvenile Chinook Salmon Oncorhynchus tshawytscha passage at the Red Bluff Diversion Dam (RBDD), river kilometer (RKM) 391 on the Sacramento River, in Northern California since 1994 (Johnson and Martin 1997). Martin et al. (2001) developed quantitative methodologies for indexing juvenile Chinook passage using rotary-screw traps (RST) to assess the impacts of the United States Bureau of Reclamation’s (USBR) RBDD Research Pumping Plant. Absolute abundance (passage and production) estimates were needed to determine the level of impact from the entrainment of salmonids and other fish community populations through RBDD’s experimental ‘fish friendly’ Archimedes and internal helical pumps (Borthwick and Corwin 2001). The original project objectives were met by 2000 and funding of the project was discontinued. From 2001 to 2008, funding was secured through a CALFED Bay-Delta Program grant for annual monitoring operations to determine the effects of restoration activities in the upper Sacramento River aimed primarily at winter Chinook Salmon*. The USBR, the primary proponent of the Central Valley Project (CVP), has funded this project since 2010 due to regulatory requirements contained within the National Marine Fisheries Service’s (NMFS) Biological Opinion for the Long-term Operations of the CVP and State Water Project (NMFS 2009 and 2019). The project began sampling in 1994 with (4) 2.4-m diameter RST’s which sampled through March of 2020. From March 25, 2020 through June 25, 2020, in order to protect employee health and safety during the Coronavirus global pandemic (COVID-19), sampling ceased. Just prior to resuming sampling operations in July of 2020, (4) 1.5-m diameter and one 2.4-m diameter RSTs were re-installed across the transect at the RBDD site. This new five-trap configuration provides a solution to sampling a location that has become shallower since the RBDD gates were permanen
Species diversity and plant dominance influence grassland stability in response to extreme climatic events and anthropogenic drivers across three LTER sites: Cedar Creek, Konza Prairie, and Kellogg Biological Station, 1982-2023.
The data in this package is associated with the analysis for a manuscript titled "Multiple community properties drive ecosystem resistance and resilience to extreme climate events across mesic grasslands". The files include compiled data on plant biomass production, species abundance, experimental treatments, extreme climate event values, and calculated diversity and stability measures from grassland plots in experiments at CDR, KBS, and KNZ LTER sites.
CVPIA Predation Contact Point Study - 2021: Impacts of Water Diversions in the Sacramento – San Joaquin Delta
The Central Valley Project Improvement Act (CVPIA) has led to the implementation of a Decision Support Model (DSM) to assist in the prioritization of CVPIA restoration actions. The fall-run Chinook salmon (Oncorhynchus tshawytscha) DSM depends on a coarse-resolution salmon life-cycle model to predict the population benefits of different restoration actions and scenarios. One critical element of the life-cycle model is how to incorporate predation mortality during the juvenile rearing and outmigration portion of the salmon life-cycle in the Sacramento-San Joaquin Delta (the Delta). Of particular importance to potential restoration activities, is the predation mortality that occurs in proximity to, and as a result of contact points between predator and prey fishes. Water diversions that support agricultural and municipal use result in fish mortality through entrainment and impingement. Additionally, this infrastructure may attract both predators and prey fishes, thereby increasing predation rates and prey mortality near these anthropogenic contact points. Throughout the spring of 2021, we used ARIS (adaptive resolution imaging sonar; Sound Metrics) sonars to compare piscivore abundance at 30 small water diversions in the north Delta to adjacent shorelines. We used predation event recorders (PERs) to assess the predation risk of juvenile salmonids with linear distance (m) from diversions and other predation drivers in the north Delta. Finally, we used a boat electrofishing survey to determine the piscivore community structure and compare spatial trends in black bass (Micropterus spp.) CPUE and relative abundance throughout these waterways. Piscivore abundance was greater near small water diversions than at adjacent shorelines and the predation risk of juvenile salmonids increased with proximity to diversions. Additionally, predation risk increased with increasing piscivore abundance and decreasing water depth. The north Delta predator community was dominated by black b
Point-count bird censusing: long-term monitoring of bird abundance and diversity in central Arizona-Phoenix, ongoing since 2000
### project overview Over the past half-century, the greater Phoenix metropolitan area (GPMA) has been one of the fastest growing regions in the US, experiencing rapid urban expansion in addition to urban intensification. This backdrop provides an ideal setting to monitor biodiversity changes in response to urbanization, and the CAP LTER has been using a standardized point-count protocol to monitor the bird community in the GPMA and surrounding Sonoran desert region since 2000. The bird survey locations in this CAP LTER core monitoring program include six general site groupings: 1. ESCA. Forty bird survey locations were selected from a subset of the CAP LTER's Ecological Survey of Central Arizona (ESCA; formerly named Survey200) long-term monitoring sites. ESCA sites were located using a tessellation-stratified dual-density sampling design, and, as such, span a diversity of habitats including urban, suburban, rural, commercial areas, parks, agricultural fields, and native Sonoran desert. Earlier versions of this data package included data from the ESCA project that was intended to complement the bird data. However, while positioned in close proximity, the bird survey locations do not necessarily overlap with the 30m x 30m plot that constitutes an ESCA sampling location, and leveraging data from these two monitoring programs should be addressed carefully. ESCA data have corresponding survey location names, and those data are available through the CAP LTER and LTER network data portals. At the conclusion of the 2016 spring survey, fifteen of the ESCA-correlated sites were discontinued as the core monitoring program refocused its efforts on desert parks and PASS neighborhoods. Among the deleted locations were all agricultural and commercial sites, as well as sites where access had become restrictive. 2. North Desert Village (NDV). Additional bird survey locations were positioned in treatment areas of the North Desert Village (NDV). This was a site of intense study on t
Fall 2022 grasshopper monitoring -- mid-marsh grasshopper abundance and species diversity at eight GCE LTER sampling sites
Grasshopper abundance and species diversity were investigated at eight sampling sites within the Georgia Coastal Ecosystems (GCE) LTER study area in July 2022. Visual surveys were conducted along 8 2m by 10m transects randomly allocated within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. This survey was conducted as part of the GCE invertebrate monitoring program, and will be performed annually to assess long-term changes in relative species abundances across the GCE study area.
Fall 2023 grasshopper monitoring -- mid-marsh grasshopper abundance and species diversity at eight GCE LTER sampling sites
Grasshopper abundance and species diversity were investigated at eight sampling sites within the Georgia Coastal Ecosystems (GCE) LTER study area in August 2023. Visual surveys were conducted along 8 2m by 10m transects randomly allocated within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. This survey was conducted as part of the GCE invertebrate monitoring program, and will be performed annually to assess long-term changes in relative species abundances across the GCE study area.
Fall 2024 grasshopper monitoring -- mid-marsh grasshopper abundance and species diversity at eight GCE LTER sampling sites
Grasshopper abundance and species diversity were investigated at eight sites within the Georgia Coastal Ecosystems (GCE) LTER study area in August 2024. Visual surveys were conducted along eight 2m by 10m transects randomly located within the mid-marsh zone at each site. All grasshoppers observed within each transect were counted and identified to species, if possible. This survey is conducted annually to assess spatial patterns of grasshopper abundance and long-term changes in relative species abundances across the GCE study area. In 2024, only 3 sites were sampled due to time and weather constraints.
Ant Diversity and Vegetation Composition in Hemlock Removal Experiment at Harvard Forest 2006
Ants comprise a considerable amount of animal biomass in terrestrial ecosystems and play major roles in ecological processes ranging from seed dispersal to soil turnover. Invasion by the hemlock woolly adelgid will transform late-successional hemlock forests into earlier successional mixed hardwood-white pine forests or red-maple wetlands. Understanding how ant assemblages vary in different habitat types allows for predictions of how hemlock decline could alter the composition of ant assemblages, with implications for a wide range of ecosystem processes. An ongoing study at the Simes Tract of Harvard Forest is documenting the effects of invasion and land-use history on ant biodiversity. Surveys from 2003 to 2005 focused on ant structure in hemlock and hardwood microhabitats in the Harvard Forest Hemlock Removal Experiment, in which hemlock forest response to deforestation by the hemlock woolly adelgid (Adelges tsugae) and to selective logging is being examined (Ellison et al. 2005). In the summer of 2006, we surveyed a greater range of microhabitat types with two objectives. First, to collect rare or elusive species in hemlock and hardwood stands that may have gone uncollected in previous years. Second, to sample forest communities not included in previous years - white pine, swamp, and rocky slope - for ant species unique to these microhabitats. We found fourteen newly documented species of ants in the Simes Tract - nine of which were in an open, swamp. Aphaenogaster rudis and Camponotus pennsylvanicus were the only ant species found in all microhabitat types. In a canonical correspondence analysis, A. rudis and C. pennsylvanicus were associated most strongly with hemlock stands and low species richness of understory plants.
Fungal Diversity in Sarracenia Purpurea Pitchers at Harvard Forest 2009-2010
The carnivorous pitcher plant Sarracenia purpurea is widely distributed in the United States and Canada, and is host to a variety of symbiotic organisms, including symbiotic fungi. Culturing of S. purpurea pitcher contents in its native range uncovers diverse single-celled (yeast) communities; these yeast communities are dominated by the ascomycete yeast Candida pseudoglaebosa. We set out to understand how fungal diversity in S. purpurea pitchers changes over space and time, and how C. pseudoglaebosa might influence this diversity. In the summer of 2009, we assayed S. purpurea pitcher water fungal succession in Tom Swamp in Harvard Forest. We sequenced fungal DNA barcodes from 43 pitchers at different times throughout the growing season, and found that C. pseudoglaebosa has a strong impact on fungal diversity. It generally appears in pitchers early in succession, and once it arrives, it often becomes dominant quickly and decreases community evenness. We also identified two other culturable yeasts, Rhodotorula babjevae and Moesziomyces aphidis, which are common but not dominant in pitchers. In laboratory experiments, C. pseudoglaebosa outcompetes these two yeasts, but only if it is inoculated in large numbers, suggesting that C. pseudoglaebosa’s dominance is a consequence of early arrival during pitcher succession. The following summer (2010), we collected water from pitchers at five distant sites in the United States and Canada, and assayed fungal community diversity and C. pseudoglaebosa genetic diversity. We sampled pitcher plants from Tom Swamp in Harvard Forest, plus four other sites in British Columbia, Newfoundland, Georgia, and Florida (Floridian plants were Sarracenia rosea, a close relative of S. purpurea). Fungal communities tended to be structured geographically, with close communities resembling each other more than distant communities. In contrast, C. pseudoglaebosa exhibited three populations: one well-mixed population including isolates from Harvard F
Dataset on tree diversity metrics and aboveground carbon storage in Southeastern U.S. oak-pine forests, 2009–2019
This dataset contains measurements of tree structural and taxonomic diversity, stand attributes, and aboveground carbon storage from mixed oak-pine forests in Florida, Georgia, and Alabama, located in the southeastern United States. Data were collected from 946 mixed oak-pine, and 7224 longleaf-slash pine and oak-pine Forest Inventory and Analysis (FIA) plots respectively spanning the years 2009 to 2019. Variables include aboveground carbon, aboveground biomass, tree density, basal area, stand age, and diversity metrics such as Shannon indices for tree species and diameter-based structural classes. Functional diversity metrics—including functional dominance and functional divergence—are also included. These data were used to support a published study examining the interactive effects of diversity metrics on carbon storage using structural equation modeling. The geographic coverage represents humid subtropical forest regions of the southeastern U.S.
Point-count bird censusing: long-term monitoring of bird abundance and diversity along the Salt River in the greater Phoenix metropolitan area, ongoing since 2013 (Reformatted to the ecocomDP Design Pattern)
This data package is formatted as an ecocomDP (Ecological Community Data Pattern). For more information on ecocomDP see https://github.com/EDIorg/ecocomDP. This Level 1 data package was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-cap/641/6. The abstract below was extracted from the Level 0 data package and is included for context:
Point-count bird censusing: long-term monitoring of bird abundance and diversity along the Salt River in the greater Phoenix metropolitan area, ongoing since 2013 (Reformatted to a Darwin Core Archive)
This data package is formatted as a Darwin Core Archive (DwC-A, event core). For more information on Darwin Core see https://www.tdwg.org/standards/dwc/. This Level 2 data package was derived from the Level 1 data package found here: https://pasta.lternet.edu/package/metadata/eml/edi/252/3, which was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-cap/641/6. The abstract below was extracted from the Level 0 data package and is included for context:
Forest structural diversity at NEON sites in the continuous USA that experienced recent moderate disturbance
Disturbances can change the structural diversity of forests through time, which can be measured from three-dimensional data provided by LiDAR. Discrete-return LiDAR was used to measure a suite of 19 structural diversity metrics that describe the height, cover and openness, vegetation density, and internal and external heterogeneity of forest vegetation at NEON base plots. Discrete-return LiDAR point clouds from the NEON Aerial Observation Platform (DP1.30003.001) were downloaded September of 2020 and used to estimate the metrics within 40 x 40 m base plots. Metrics were estimated from base plots at 15 NEON forested sites from provisional LiDAR data available from 2014 to 2020. The workflow that produced the data was developed in the program R.
Gender and ethnic diversity of members of US university natural resource program external advisory board members, 2017-2022
This dataset contains deidentified demographics information for the members of external advisory boards that serve university natural resource programs. Data collected in 2017 and 2022 represents a sample of land-grant, National Association of University Forestry Program-affiliated, TIMES-ranked universities and colleges. Each row represents a member of an advisory board. Data collection was completed in two years: 2017 and 2022. Data was collected from department webpages and lists of advisory board members provided by department personnel. As needed, information was augmented through internet searches for public LinkedIn pages, organizational pages, local news stories, etc. Data include a unique respondent ID, a code for the university they are from, their employer affiliation (e.g., NGO, federal government, NR business, etc.) and their gender and ethnicity measured as binary variables.
Ant Functional Diversity in Temperate Zone Forests: A Comparison with Neotropical Ants 2010
Predicted impacts of climatic change on ant functional diversity and distributions in eastern North American forests Aims--Climatic change is expected to rearrange species assemblages and ultimately affect organism-mediated ecosystem processes. We focus on identifying patterns and relationships between common ant species (representing 99% of total ant records) richness and functional diversity; modelling how these patterns may change at local and regional scales in future climatic conditions; and interpreting how these changes might influence ant-mediated ecosystem processes. Location--Forested ecosystems of eastern North America. Methods--We used a previously published dataset to evaluate functional diversity at 67 sites in the eastern U.S. and quantified 14 taxonomic, morphometric and natural history traits for 70 common ant species in the region. We used functional diversity metrics, functional groups and species distribution modelling methods to address our aims. We used stacked species distribution models and stacked functional group models to predict species assemblages and functional richness at the 67 sites and at a regional scale for current and future climatic conditions. Results--Species richness and functional diversity are positively correlated throughout the region. Under future climate scenarios, species richness and functional group richness were predicted to decrease in southern ecoregions and increase in northern ecoregions. This may be due to increased thermal stress for species in the southern extent of their ranges and increased habitat suitability in the northern ecoregions. Decomposers, arthropod community regulators and seed dispersers are forecast to be the most threatened ant functional groups. Main Conclusions--Climate change will likely lead to major changes in ant species richness and functional group richness in the forests of the north-eastern United States, and this may substantially alter ant-mediated ecosystem processes and services
Supplementary Material to article "Molecular Diversity of Mycobacterium avium subsp. paratuberculosis in Four Dairy Goat Herds from Thuringia (Germany)"
<p>These data (supplementary material) belong to the publication "Molecular Diversity of <i>Mycobacterium avium</i> subsp. <i>paratuberculosis</i> in Four Dairy Goat Herds from Thuringia (Germany)". The study determined the diversity of <i>Mycobacterium avium</i> subsp. <i>paratuberculosis</i> (MAP) isolated from four goat herds affected by paratuberculosis in Thuringia (Germany), as well as the detailed distribution of MAP genotypes among the animals and their environment in one herd (herd 1). A combination of three methods was used to genotype isolates from fecal samples of infected goats, from various intestinal and other tissues of clinically affected goats, and from environmental samples. The six MAP-C genotypes identified could be assigned to five different phylogenetic subgroups. The results suggest individual infection strains within each herd. In herd 1, one predominant strain was found, and two strains occurred sporadically. The identified genotypes were not goat specific.</p>
Pawpaws prevent predictability: A locally-dominant tree alters understory beta-diversity and community assembly
<p>Data used in "Pawpaws Prevent Predictability: A locally-dominant tree alters understory beta-diversity and community assembly" (Wassel and Myers) accepted for publication in Ecosphere.<br><br><strong>Metadata for Zenodo.pdf </strong>contains more information on the following data files including descriptions of the columns. </p> <p>The file <strong>understory_abundance_data2021.csv</strong> contains all species abundances in 1x1m plots. This data was used for analyses in publication. Each row is a plot, each column is a speceis or plot descriptor, values for columns 5 and higher are species abundances. Data was collected July-August 2021 by Anna Wassel in Missouri, USA. </p> <p>The file <strong>understory_species_list2021.csv </strong>contains a list of the species codes used in the first file with their scientific names and their status as herbs or woody. This was used to filter out herbaceous species from the data set for herbaceous-only analyses. </p> <p> </p>
NMR screen reveals the diverse structural landscape of a G- quadruplex library
<p>This is the NMR dataset for the manuscript '<span>NMR screen reveals the diverse structural landscape of a G-</span><br><span>quadruplex library</span>'</p> <p>Abstract</p> <p><span>G-quadruplexes are noncanonical nucleic acid structures</span><br><span>formed by stacked guanosine tetrads. Despite their functional and</span><br><span>structural diversity, a single consensus model is typically used to</span><br><span>describe</span><span> </span><span>sequences</span><span> </span><span>with</span><span> </span><span>the</span><span> </span><span>potential</span><span> </span><span>to</span><span> </span><span>form</span><span> </span><span>G-quadruplex</span><br><span>structures. We are interested in developing more specific sequence</span><br><span>models</span><span> </span><span>for</span><span> </span><span>G-quadruplexes.</span><span> </span><span>In</span><span> </span><span>previous</span><span> </span><span>work,</span><span> </span><span>we</span><span> </span><span>functionally</span><br><span>characterized each sequence in a 496-member library of variants of a</span><br><span>monomeric</span><span> </span><span>reference</span><span> </span><span>G-quadruplex</span><span> </span><span>for</span><span> </span><span>the</span><span> </span><span>ability</span><span> </span><span>to</span><span> </span><span>bind</span><span> </span><span>GTP,</span><br><span>promote a model peroxidase reaction, generate intrinsic fluorescence,</span><br><span>and to form multimers. Here we used NMR to obtain a broad overview</span><br><span>of the structural features of this library. After determining the</span><span> </span><span>1</span><span>H NMR</span><br><span>spectrum of each of these 496 sequences, spectra were sorted into</span><br><span>multiple classes, most</span><span> </span><span>of</span><span> </span><span>which could be rationalized based on</span><br><span>mutational patterns in the primary sequence. A more detailed screen</span><br><span>using representative sequences provided additional information about</span><br><span>spectral classes, and confirmed that the classes determined based on</span><br><span>analysis of</span><span> </span><span>1</span><span>H NMR spectra are correlated with functional categories</span><br><span>identified in previous studies. These results provide new insights into</span><br><span>the surprising structural diversity of this library. They also show how</span><br><span>NMR can be used to identify classes of sequences with distinct</span><br><span>mutational signatures and functions.</span></p> <p><span>Link to journal article: <a href="https://doi.org/10.1002/chem.202401437"><span>https://doi.org/10.1002/chem.202401437</span></a></span></p>
Dataset for "Holocene hydroclimatic variability in the tropical Pacific explained by changing ENSO diversity."
<p>This repository contains the tropical Pacific sea surface temperature and global precipitation data from the CESM1 time slice experiments, which were used for the analysis presented in Karamperidou & DiNezio (2022), Nature Communications (https://www.nature.com/articles/s41467-022-34880-8)</p> <p> </p> <p>From Karamperidou & DiNezio (2022):</p> <p>“To assess the response of ENSO flavors to orbital forcing over the past 12,000 years (12ka), we use a suite of time-slice experiments in 3ka intervals with version 1 of the Community Earth System Model (CESM1). Each experiment is 400-600 years long and was run until the surface climate and oceanic processes controlling tropical climate, such as the depth of the thermocline in the equatorial Pacific or the Atlantic Meridional Overturning Circulation (AMOC), have reached equilibrium. All simulations exhibit minimal drift in global mean surface temperature (less than 0.05<sup>o</sup>C per century), tropical mean surface temperature (less than 0.04<sup>o</sup>C per century), the depth of the equatorial thermocline in the Pacific (less than 0.3m per century), and the strength of the AMOC (less than 0.25 Sv per century) during the periods used in the analyses. With the exception of the 12 ka BP interval which includes ice sheet changes and lower greenhouse gases, the primary forcing in the 0, 3, 6, and 9 ka BP intervals is changes in Earth's precession, and each simulation branched off its preceding one, starting from 0ka sequentially through the Holocene. The maximum TOA energetic imbalance does not exceed 0.45 Wm<sup>-2</sup>, which is much smaller than the imposed radiative forcing.”</p> <p> </p> <p> </p> <p>Karamperidou, C., DiNezio, P.N. Holocene hydroclimatic variability in the tropical Pacific explained by changing ENSO diversity. <em>Nat Commun</em> <strong>13</strong>, 7244 (2022). https://doi.org/10.1038/s41467-022-34880-8</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.