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38 results for “ecological quality”
LAGOS-NE-LIMNO v1.087.3: A module for LAGOS-NE, a multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of U.S. Lakes: 1925-2013
This data package, LAGOS-NE-LIMNO v1.087.3, is 1 of 5 data packages associated with the LAGOS-NE database-- the LAke multi-scaled GeOSpatial and temporal database. With this release, only this data package is being updated and users are expected to use prior releases of the other types of data. Please see the attached additional documentation for a full description of the changes that have been made for this new release.The data packages that make up LAGOS-NE include the following information on lakes and reservoirs in 17 lake-rich states in the Northeastern and upper Midwestern U.S. (1) LAGOS-NE-LOCUS v1.01: lake location and physical characteristics for all lakes greater than one hectare. (2) LAGOS-NE-GEO v1.05: ecological context (i.e., the land use, geologic, climatic, and hydrologic setting of lakes) for all lakes and for all spatial resolutions, also called ‘zones’ (i.e., ecoregions, states, counties). These geospatial data were created by processing national-scale and publicly-accessible datasets to quantify numerous metrics at multiple spatial resolutions. (3) LAGOS-NE-LIMNO v1.087.3: in-situ measurements of lake water quality from the past three decades for approximately 2,600-12,000 lakes, depending on the variable. This module was created by harmonizing 87 water quality datasets from federal, state, tribal, and non-profit agencies, university researchers, and citizen scientists. This module includes variables that are most commonly measured by state agencies and researchers for studying eutrophication. For each water quality data value, we also include metadata related to the sampling program, methods, qualifiers with data flags from the original program (qual, not standardized for LAGOS-NE), censor codes from our quality control procedures (censorcode, standardized for LAGOS-NE), and the date of each sample. (4) LAGOS-NE-GIS v1.0: the GIS data layers for lakes, wetlands, and streams, as well as the spatial resolutions that were used to create the LAGOS-N
Interagency Ecological Program: Fish catch and water quality data from the Sacramento River floodplain and tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998-2024.
Largely supported by the Interagency Ecological Program (IEP), California Department of Water Resources (DWR) has operated a fish monitoring program in the Yolo Bypass, a seasonal floodplain and tidal slough, since 1998. The objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to: 1. Collect baseline data on water quality, chlorophyll, lower trophic level biota, and fish in the Yolo Bypass to monitor spatial and temporal changes in trends and abundance. 2. Analyze and communicate Yolo Bypass data with interested parties and the scientific and management communities to address pertinent management-related questions. 3. Provide technical expertise on Yolo Bypass aquatic ecology and monitoring and sampling methods. The YBFMP operates a rotary screw trap and fyke trap and conducts biweekly beach seine and lower trophic surveys in addition to maintaining water quality instrumentation in the bypass. Only juvenile and adult fish catch with associated water quality are presented in this dataset. The rotary screw trap sampling objectives are to: (1) examine species abundance and life stage of juvenile outmigrants and resident small-bodied fishes, (2) identify temporal and spatial patterns in fish abundance and species composition, and (3) examine the effect of physical and environmental conditions on these patterns. The fyke trap sampling objectives are to: (1) examine abundance of migrating and resident adult fishes, (2) identify temporal and spatial patterns in fish abundance and species composition, especially with regard to anadromous species, (3) examine the effect of physical and environmental conditions on these patterns, and (4) provide data on the timing and duration of species captured in the Yolo Bypass for comparison to those captured in other Sacramento Valley tributaries. The beach seine surveys are conducted in the Yolo Bypass’s perennial channel (Toe Drain), inundated floodplain, disconnected inundated ponds, and perennial ponds. The objectives o
Interagency Ecological Program: Zooplankton catch and water quality data from the Sacramento River floodplain and tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998-2018
Largely supported by the Interagency Ecological Program (IEP), the California Department of Water Resources (DWR) has operated a fisheries and invertebrate monitoring program in the Yolo Bypass since 1998. The main objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to collect baseline data on lower trophic levels (phytoplankton, zooplankton and insect drift), juvenile and adult fish, hydrology, and water quality parameters. As the Yolo Bypass has been identified as a high restoration priority by numerous regulatory agencies, these baseline data are critical for evaluating success of future restoration projects. In addition, the data have already served to increase our understanding of the role of the Yolo Bypass in the life history of native fishes, and its ecological function in the San Francisco Estuary. Zooplankton are an important component in the diet of larval, juvenile, and small adult fishes within the San Francisco Estuary, including Delta Smelt, juvenile Chinook Salmon, Striped Bass, and Sacramento Splittail. The YBFMP collects zooplankton year-round from two sites. Since 2011, samples have been collected biweekly (every other week) to weekly (during floodplain inundation) using 150- and 50- micrometer mesh plankton nets. Zooplankton are identified and enumerated by contractors (currently BSA Environmental Services). The goals of the zooplankton monitoring program are to compare the seasonal variation in species densities and trends between (1) the Sacramento River channel, and (2) the Yolo Bypass, the river’s seasonal floodplain. Data on zooplankton catch and associated water quality parameters are presented in this dataset.
Interagency Ecological Program: Water quality, fish, and zooplankton monitoring and modeling to support the 2018 Suisun Marsh Salinity Control Gates Summer Action
In summer 2018 we used a unique water control structure in the San Francisco Estuary (SFE) to direct a managed flow pulse into Suisun Marsh, one of the largest contiguous tidal marshes on the west coast of the United States. The action was designed to increase habitat suitability for the endangered Delta Smelt Hypomesus transpacificus, a small osmerid fish endemic to the upper SFE. The approach was to operate the Suisun Marsh Salinity Control Gates (SMSCG) in conjunction with increased Sacramento River tributary inflow to direct an estimated 160 x 10^6 m3 pulse of low salinity water into Suisun Marsh during August, a critical time period for juvenile Delta Smelt rearing. This dataset includes physical and biological monitoring data collected for the action. Datasets include Delta Smelt catch from the USFWS Enhanced Delta Smelt Monitoring program, zooplankton and Microcystis abundance from the Environmental Monitoring Program, historic Delta Smelt catch from the Summer Townet Survey, Delta Outflow from the Dayflow model, extent of Delta Smelt habitat from the UnTRIM Bay-Delta model, and water quality (Salinity, Temperature, Chlorophyll, and Turibidity) collected at continuous sondes at three locations. These data are associated with the manuscript "Evaluation of a large-scale flow manipulation to the upper San Francisco Estuary: Response of habitat conditions for an endangered native fish," by Dr. Ted Sommer, et al. 2020 PLOS One, in review.
Interagency Ecological Program: Drift invertebrate and ichthyoplankton catch and water quality from the Sacramento River channel, and Sacramento River floodplain and tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998-2022
Largely supported by the Interagency Ecological Program (IEP), California Department of Water Resources (DWR) has operated a fish monitoring program in the Yolo Bypass, a seasonal floodplain and tidal slough, since 1998. The objectives of the Yolo Bypass Fish Monitoring Program (YBFMP) are to: 1. Collect baseline data on water quality, chlorophyll, lower trophic level biota, and fish in the Yolo Bypass to monitor spatial and temporal changes in trends and abundance. 2. Analyze and communicate Yolo Bypass data with interested parties and the scientific and management communities to address pertinent management-related questions. 3. Provide technical expertise on Yolo Bypass aquatic ecology and monitoring and sampling methods. Aquatic and terrestrial insects are an important component in the diet of juvenile and adult fishes within the San Francisco Estuary, including two important native fishes: juvenile Chinook Salmon and Sacramento Splittail. The YBFMP collects drift invertebrates year-round from two sites. Currently, samples are collected biweekly (every other week) to weekly (during floodplain inundation) using a rectangular aquatic drift net that sits at the surface of the water. Invertebrates are identified and enumerated by contractors (currently EcoAnalysts, Inc.). The goals of the monitoring program are to compare the seasonal variations in densities and species trends of aquatic and terrestrial insects/non-insects within the Sacramento River channel and the Yolo Bypass, the river’s seasonal floodplain. Drift invertebrate Key findings to date include: (1) Chinook Salmon sampled in the floodplain had diets comprised of 90% Dipterans and zooplankton, with Chironomidae being the dominant Diptera family (Sommer et al., 2001), (2) The floodplain of the Yolo Bypass contains significantly higher densities of Diptera (Diptera densities being positively associated with flow) and terrestrial invertebrates than the adjacent Sacramento River (Sommer et al. 2001b: Sommer
LAGOS-NE-LOCUS v1.01: A module for LAGOS-NE, a multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of U.S. Lakes: 1925-2013
This data package, LAGOS-NE-LOCUS v1.01, is 1 of 5 data packages associated with the LAGOS-NE database-- the LAke multi-scaled GeOSpatial and temporal database. Three of the data packages each contain different types of data for 51,101 lakes and reservoirs larger than 4 ha in 17 lake-rich U.S. states to support research on thousands of lakes. These three package are: (1) LAGOS-NE-LOCUS v1.01: lake location and physical characteristics for all lakes. (2) LAGOS-NEGEO v1.05: ecological context (i.e., the land use, geologic, climatic, and hydrologic setting of lakes) for all lakes. These geospatial data were created by processing national-scale and publicly-accessible datasets to quantify numerous metrics at multiple spatial resolutions. And, (3) LAGOS-NE-LIMNO v1.087.1: in-situ measurements of lake water quality from the past three decades for approximately 2,600-12,000 lakes, depending on the variable. This module was created by harmonizing 87 water quality datasets from federal, state, tribal, and non-profit agencies, university researchers, and citizen scientists. The other two data packages contain supporting data for the LAGOS-NE database: (4) LAGOS-NE-GIS v1.0: the GIS data layers for lakes, wetlands, and streams, as well as the spatial resolutions that were used to create the LAGOS-NE-GEO module. (5) LAGOS-NE-RAWDATA: the original 87 datasets of lake water quality prior to processing, the R code that converts the original data formats into LAGOS-NE data format, and the log file from this procedure to create LAGOS-NE. This latter data package supports the reproducibility of LAGOS-NE-LIMNO. The LAGOS-NE-LOCUS v1.01 module includes information on the physical location and features of all lakes > 4 ha. The information provided for this population of lakes includes: lake unique identifiers, lake area, perimeter, latitude and longitude, and the zone IDs that the lake is located within (e.g., state, county, the hydrologic unit at each level (4, 8, and 12). Citation for
Interagency Ecological Program: Zooplankton and water quality data in the San Francisco Estuary collected by the Summer Townet and Fall Midwater Trawl monitoring programs.
The Interagency Ecological Program’s (IEP) Summer Townet Survey (STN) and Fall Midwater Trawl (FMWT) are two long-term monitoring projects conducted by the California Department of Fish and Wildlife (CDFW) to monitor fish abundance and distribution trends in the San Francisco Estuary (SFE) since 1959 and 1967, respectively. Starting in 2005, zooplankton monitoring was added and paired with fish tows to investigate food availability for young fishes. Food limitation has been a long-term issue and a focus of the Pelagic Organism Decline (POD) studies that began in 2005. By 2011, STN routinely conducted zooplankton monitoring at 40 stations, and FMWT at 32 stations in the upper SFE from Carquinez Strait to the Sacramento Deep Water Ship Channel and into the South Delta. STN samples every other week from June to August and FMWT samples once monthly from September to December. Both projects collect mesozooplankton samples using a modified Clarke-Bumpus (CB) net to target copepods and cladocerans, and FMWT also samples macrozooplankton (i.e. mysids and amphipods) using a mysid net. Flowmeters are used to measure the volume sampled to determine zooplankton catch per unit effort. Environmental variables such as water temperature, turbidity, secchi, and electrical conductivity are collected with each zooplankton sample. Concurrent fish and zooplankton tows conducted by STN and FMWT have allowed for comparisons of fish diet to the available zooplankton prey at the time of collection.
Interagency Ecological Program: Discrete water quality and phytoplankton data from the Sacramento River floodplain and Yolo Bypass tidal slough, collected by the Yolo Bypass Fish Monitoring Program, 1998 - 2022
The Yolo Bypass Fish Monitoring Program (YBFMP) operates a rotary screw trap and fyke trap and conducts biweekly beach seine and lower trophic surveys in addition to maintaining water quality instrumentation in the bypass. The YBFMP serves to fill information gaps regarding environmental conditions in the bypass that trigger migrations and enhanced survival and growth of native fishes, as well as provide data for IEP synthesis efforts. YBFMP staff also conduct analyses of YBFMP monitoring data to address pertinent management related questions as identified by IEP. The Yolo Bypass has been identified as a high restoration priority by the National Marine Fisheries Service and US Fish and Wildlife Service Biological Opinions for Delta Smelt, Winter and Spring-run Chinook salmon and by California EcoRestore. The YBFMP informs the restoration actions that are mandated or recommended in these plans and provides critical baseline data on the ecology of the bypass and how it interacts with the broader San Francisco Estuary. Program objectives include: Collecting baseline data on water quality, chlorophyll, lower trophic level biota, and fish in the Yolo Bypass to monitor spatial and temporal changes in trends and abundance; Analyzing and communicating Yolo Bypass data with stakeholders and the scientific and management communities to address pertinent management related questions; Providing technical expertise on Yolo Bypass aquatic ecology and monitoring and sampling methods. We collect discrete water quality data using a YSI ProDSS and sample phytoplankton, chlorophyll and nutrients as discrete water grabs taken biweekly (or weekly during Yolo Bypass inundation) along with lower trophic tows. Water is sampled at three sites along the Yolo Bypass and Sacramento River, then processed and analyzed by an internal DWR laboratory.
Interagency Ecological Program: Fish catch and associated water quality for the Fall Midwater Trawl Survey, Sacramento-San Joaquin Delta, 1967-2024
The Interagency Ecological Program’s (IEP) Fall Midwater Trawl Survey (FMWT) is a long-term monitoring survey conducted by the California Department of Fish and Wildlife (CDFW) and has sampled annually since its inception in 1967, with the exceptions of 1974 and 1979, when sampling was not conducted. The FMWT was initiated to determine the relative abundance and distribution of age-0 Striped Bass (Morone saxatilis) in the San Francisco Estuary (California, United States), but the data has also been used for other upper estuary pelagic species, including Delta Smelt (Hypomesus transpacificus), Longfin Smelt (Spirinchus thaleichthys), American Shad (Alosa sapidissima), Splittail (Pogonichthys macrolepidotus), and Threadfin Shad (Dorosoma petenense). The FMWT currently samples 130 stations each month from September to December and a subset of this data is used to calculate an annual abundance index. These 130 stations range from San Pablo Bay upstream to Stockton on the San Joaquin River, and West Sacramento on the Sacramento Deep Water Ship Channel. FMWT sampling data includes 193 unique station locations throughout the San Francisco Estuary; 63 are not currently sampled. Most stations no longer sampled occur in South and Central San Francisco Bay (1968-1979), with others located in San Pablo Bay and upstream into the Delta. There are catch records for stations that were sampled only once. Data users are encouraged to look at station frequency over time to understand when and where sampling occurred. Sampling takes approximately 14 days per month to complete. Historically, FMWT sampling occasionally began as early as July (1972) or August (1968-1973, 1993-1994, 1996-1997) and sometimes continued past December to March (1968-1973, 1978, 1991-2001) or beyond (1992-1995). The Spring Midwater Trawl (SMWT) was a modified survey created to continue sampling January-March to track movements of mature adult delta smelt from 1991-2001. SMWT was replaced in 2002 with the more e
Interagency Ecological Program: Discrete water quality monitoring in the Sacramento-San Joaquin Bay-Delta, collected by the Environmental Monitoring Program, 1975-2023
\<markdown\> The Interagency Ecological Program’s (IEP) Environmental Monitoring Program (EMP) was initiated in compliance with the Water Right Decision D-1379 (now mandated by Water Right Decision D-1641) and has monitored discrete water quality and nutrients in the upper San Francisco Estuary since 1975. The objectives of the EMP are to obtain consistent and accurate monthly data at established monitoring stations, provide and document information necessary to achieve compliance with salinity, flow, and dissolved oxygen standards, and to report this information for the purpose of management and conservation of the upper San Francisco Estuary. While the EMP also collects biological data, this dataset only includes the discrete water quality and nutrient data collected by the EMP from 1975-2021. Links to other EMP datasets can be found [here](https://emp-des.github.io/emp-reports/data-links.html) \</markdown\>
Interagency Ecological Program: Monitoring of water quality, phytoplankton, zooplankton, clams, and Delta Smelt to support the Summer-Fall Suisun Marsh Salinity Control Gates Action 2018-2024
The Suisun Marsh Salinity Control Gates (SMSCG) have the potential to increase low-salinity-zone habitat for endangered Delta Smelt (Hypomesus transpacificus, California Endangered Species Act listed as Endangered, Federal Endangered Species Act listed as Threatened), and to allow them to more frequently occupy Suisun Marsh, especially Montezuma Slough, one of their most important rearing habitats. Operation of the SMSCG in summer and fall to improve Delta Smelt habitat are called for in the Biological Opinion and Incidental Take permit for the Central Valley Project and State Water Project. To support the adaptive management of the action, the California Department of Water Resources and collaborating agencies monitored water quality, phytoplankton, zooplankton, clams, and fishes during the SMSCG management actions in 2018. Monitoring has continued during the summer and fall months of all subsequent years, including both those with and without actions. This data package includes data collected by the Interagency Ecological Program’s (IEP) long-term monitoring programs supplemented with targeted sample collection where existing surveys lacked spatial or temporal coverage. Monitoring during no-action years will be used as a baseline for comparison during action years. This data package will be updated annually.
LAGOS-NE-GEO v1.05: A module for LAGOS-NE, a multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of U.S. Lakes: 1925-2013
This data package, LAGOS-NE-GEO v1.05, is 1 of 5 data packages associated with the LAGOS-NE database-- the LAke multi-scaled GeOSpatial and temporal database. Three of the data packages each contain different types of data for 51,101 lakes and reservoirs larger than 4 ha in 17 lake-rich U.S. states to support research on thousands of lakes. These three package are: (1) LAGOS-NE-LOCUS: lake location and physical characteristics for all lakes. (2) LAGOS-NE-GEO: ecological context (i.e., the land use, geologic, climatic, and hydrologic setting of lakes) for all lakes. These geospatial data were created by processing national-scale and publicly-accessible datasets to quantify numerous metrics at multiple spatial resolutions. And, (3) LAGOS-NE-LIMNO: in-situ measurements of lake water quality from the past three decades for approximately 2,600-12,000 lakes, depending on the variable. This module was created by harmonizing 87 water quality datasets from federal, state, tribal, and non-profit agencies, university researchers, and citizen scientists. The other two data packages contain supporting data for the LAGOS-NE database: (4) LAGOS-NE-GIS v1.0: the GIS data layers for lakes, wetlands, and streams, as well as the spatial resolutions that were used to create the LAGOS-NEGEO module. (5) LAGOS-NE-RAWDATA: the original 87 datasets of lake water quality prior to processing, the R code that converts the original data formats into LAGOS-NE data format, and the log file from this procedure to create LAGOS-NE. This latter data package supports the reproducibility of LAGOS-NE-LIMNO. The LAGOS-NE-GEO v1.05 module includes information on the ecological context of the census lakes, all lakes > 4 ha in the study extent, their watersheds, and their regions. The information provided in the data tables for this module is organized into three main themes: CHAG - climate, hydrology, atmospheric deposition of nitrogen and sulfur, and surficial geology; LULC - land use/cover, impervious co
LakeBeD-US: Ecology Edition - a benchmark dataset of lake water quality time series and vertical profiles
LakeBeD-US: Ecology Edition is a harmonized lake water quality dataset containing time series and vertical profiles of 21 lakes in the United States monitored by long-term monitoring institutions. These institutions include the North Temperate Lakes Long-Term Ecological Research program (NTL-LTER), Niwot Ridge Long-Term Ecological Research program (NWT-LTER), National Ecological Observatory Network (NEON), and the Carey Lab at Virginia Tech as part of the Virginia Reservoirs Long-Term Research in Environmental Biology (LTREB) site in collaboration with the Western Virginia Water Authority. The data include depth-discrete observations of 17 water quality variables including temperature, dissolved oxygen, chemical properties, Secchi depth, and more. Observations are divided into data collected by automated sensors at a relatively high temporal frequency and manually sampled data at a relatively low temporal frequency. All data were collected in situ. The data are available as Apache Parquet files, and the included R scripts give guidance on how to utilize and query the dataset in R. LakeBeD-US: Ecology Edition is an ecological science-oriented companion to LakeBeD-US: Computer Science Edition. The Computer Science Edition is available on the Hugging Face Hub.
LAGOS-NE-GIS v1.0: A module for LAGOS-NE, a multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of U.S. Lakes: 2013-1925
This data package, LAGOS-NE-GIS v1.0, is 1 of 5 data packages associated with the LAGOS-NE database-- the LAke multi-scaled GeOSpatial and temporal database. Three of the data packages each contain different types of data for 51,101 lakes and reservoirs larger than 4 ha in 17 lake-rich U.S. states to support research on thousands of lakes. These three package are: (1) LAGOS-NE-LOCUS v1.01: lake location and physical characteristics for all lakes. (2) LAGOS-NE-GEO v1.05: ecological context (i.e., the land use, geologic, climatic, and hydrologic setting of lakes) for all lakes. These geospatial data were created by processing national-scale and publicly-accessible datasets to quantify numerous metrics at multiple spatial resolutions. And, (3) LAGOS-NE-LIMNO v1.087.1: in-situ measurements of lake water quality from the past three decades for approximately 2,600-12,000 lakes, depending on the variable. This module was created by harmonizing 87 water quality datasets from federal, state, tribal, and non-profit agencies, university researchers, and citizen scientists. The other two data packages contain supporting data for the LAGOS-NE database: (4) LAGOS-NE-GIS v1.0: the GIS data layers for lakes, wetlands, and streams, as well as the spatial resolutions that were used to create the LAGOS-NE-GEO module. (5) LAGOS-NE-RAWDATA: the original 87 datasets of lake water quality prior to processing, the R code that converts the original data formats into LAGOS-NE data format, and the log file from this procedure to create LAGOS-NE. This latter data package supports the reproducibility of LAGOS-NE-LIMNO. The LAGOS-NE GIS v1.0 module includes GIS datasets for: lake polygons and their hydrologic classification; wetland polygons and their classification; streams as a line coverage and their classification by stream order; the zones used for this study (state and county; hydrologic units [at the 4, 8 and 12 scales]); and, lake watersheds (IWS). We also include boundaries of U.S. stat
Data and JAGS-code for "Michel et al 2022 Ecology and Evolution - Reduced habitat quality increases intrinsic but not ecological costs of reproduction"
<p><strong>Abstract</strong></p> <p>Although the costs of reproduction are predicted to vary with the quality of the breeding habitat thereby affecting population dynamics and life-history trade-offs, empirical evidence for this pattern remains sparse and equivocal. Costs of reproduction can operate through immediate ecological mechanisms or through delayed intrinsic mechanisms. Ignoring these separate pathways might hinder the identification of costs and the understanding of their consequences. We experimentally investigated the survival costs of reproduction for adult little owls (<em>Athene noctua</em>) within a gradient of habitat quality. We supplemented food to nestlings, thereby relieving the parents’ effort for brood provisioning. We used radio-tracking and Bayesian multi-state modelling based on marked recapture and dead recovery to estimate survival rates of adult little owls across the year as a function of food supplementation and habitat characteristics. Food supplementation to nestlings during the breeding season increased parental survival not only during the breeding season but also during the rest of the year. Thus, the low survival of parents of unfed broods likely represents both, strong ecological and strong intrinsic costs of reproduction. However, while immediate ecological costs occurred also in high quality habitats, intrinsic costs carrying over to the post-breeding period occurred only in low quality habitats. Our results suggest that immediate costs resulting from ecological mechanisms such as predation, are high also in territories of high habitat quality. Long-term costs resulting from intrinsic trade-offs, however, are only paid in low quality habitats. Consequently, differential effects of habitat quality on immediate ecological and delayed intrinsic mechanisms can mask the increase of costs of reproduction in low quality breeding habitats. Intrinsic costs may represent an underrated mechanism of habitat quality affecting adult survival rate thereby considerably accelerating population decline in degrading habitats. This study therefore highlights the need for a long-term perspective to fully assess the costs of reproduction and the role of habitat quality in modifying these costs.</p>
Fig. 3 in The nematode assemblage as a tool for the assessment of marine ecological quality status: a case-study in the Central Adriatic Sea
Fig. 3: Composition of colonizers-persisters (c-p) at each station and in each period. The c-p1 and c-p5 were excluded because they were not found in the study area.
Fig. 2 in The nematode assemblage as a tool for the assessment of marine ecological quality status: a case-study in the Central Adriatic Sea
Fig. 2: a) Shannon Index; b) Pielou Index; c) Maturity Index; d) Index of Trophic Dominance calculated for the nematode assemblage at each station in the study area.
Data from: Genomics meets applied ecology: characterizing habitat quality for sloths in a tropical agroecosystem
Understanding how habitat quality in heterogeneous landscapes governs the distribution and fitness of individuals is a fundamental aspect of ecology. While mean individual fitness is generally considered a key to assessing habitat quality, a comprehensive understanding of habitat quality in heterogeneous landscapes requires estimates of dispersal rates among habitat types. The increasing accessibility of genomic approaches, combined with field-based demographic methods, provides novel opportunities for incorporating dispersal estimation into assessments of habitat quality. In this study, we integrated genomic kinship approaches with field-based estimates of fitness components and Approximate Bayesian Computation (ABC) procedures to estimate habitat-specific dispersal rates and characterize habitat quality in two-toed sloths (Choloepus hoffmanni) occurring in a Costa Rican agricultural ecosystem. Field-based observations indicated that birth and survival rates were similar in a sparsely-shaded cacao farm and adjacent cattle pasture-forest mosaic. Sloth density was threefold higher in pasture compared to cacao, whereas home range size and overlap were greater in cacao compared to pasture. Dispersal rates were similar between the two habitats, as estimated using ABC procedures applied to the spatial distribution of pairs of related individuals identified using 3,431 SNP and 11 microsatellite locus genotypes. Our results indicate that crops produced under a sparse overstory can, in some cases, constitute lower quality habitat than pasture-forest mosaics for sloths, perhaps because of differences in food resources or predator communities. Finally, our study demonstrates that integrating field-based demographic approaches with genomic methods can provide a powerful means for characterizing habitat quality for animal populations occurring in heterogeneous landscapes.
Data from: Freshwater ecological quality assessment of the gold mining Mashcon watershed, Cajamarca - Peru
<p>These data were generated to investigate the aquatic community gradients across different types of anthropogenic impacts (reference, mining, rural and urban) and Andean environmental gradients (headwaters, midstream and downstream) in the Mashcon watershed. </p> <p>The macroinvertebrates' taxa abundance and abundance of traits modalities serve as biological values. The latter in combination with abiotic measurements of the freshwater habitats (i.e. physicochemical water quality and hydromorphology) constitute the ecological data.</p> <p>The values were obtained from river sediments (macroinvertebrates collection), water samples for laboratory analyses, field protocols and in-situ water quality measurements at 40 sites, wherein 6 were downstream of the gold mine's artificially recharged headwaters, 8 sites at near-pristine headwaters tributary streams, 14 sites at midstream rural areas and 12 sites at downstream urban areas (sample grouping information is shown in the Field_protocol.xlsx file).</p>
Full list of publications dealing with resources nutritional quality in ecology
<p><span>Our understanding of ecosystem functioning is strongly linked to the study of predator-prey relationships and food web structures. However, trophic ecology has often focused on identifying taxonomic relationships and quantifying the biomass or energy ingested by consumers, but has often failed to integrate the importance of the nutritional quality of resources in ecological dynamics. Underlying this gap is the multi-dimensional nature of resource quality which has hampered any consensus on the definition of resource nutritional quality. In this special issue, we aimed at gathering a subset of articles exemplifying the diversity of variables by which resources quality is quantified, the diversity of research topics that can be tackled in ecology - from physiological or evolutionary aspects to ecosystem processes - and propose some perspectives on the integration of nutritional quality within broader ecological concepts. Using a semi-automated literature analysis, we map the current landscape of the "resources nutritional quality" research of the last 30 years. We depict how it has been quantified through physical, biological or chemical indicators, the use of these parameters being largely dependent on the type of ecosystem studied and on the investigated ecological process. We then position t</span><span>he articles published in this special issue of Oikos within this landscape, showing they cover a small but relatively well representative subset of the domains of resources quality-related issues. Articles in this special issue browse a range of individual and population-level approaches (embracing evolutionary questions) to community related questions, include methodological issues and ecosystem-wide approaches using trophic quality indicators as tracers of resources origin. Based on these studies and on the literature review, we identify a non-exhaustive list of challenges and perspectives of research that we consider of highest priority in the large topic of trophic ecology.</span></p>
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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.