Find research datasets worth reusing

openCC (other)May 2025View details →

SBC LTER: Reef: Seasonal Kelp Forest Community Dynamics: Invertebrate and algal density

These data describe the abundance of common reef associated species of macro invertebrates and macroalgae within permanent plots of SBCLTER's seasonal kelp forest monitoring program to track long-term patterns in species abundance and diversity. The number of individuals of approximately 50 taxa were recorded by divers along 40 m transects within each plot. Small species of macroalgae and macinvertebrates were counted within six permanent 1 m2 quadrats positioned uniformly along the 40 m transect, while larger species were counted within four contiguous 20 m2 sub-sections of each 40 m x 2 m transect. Also included at the quadrat scale are estimates of an average size-related measurement of each species, which was developed specifically for each species for the purpose of estimating its biomass. The experiment was initiated in 2008 at five reef sites along the mainland coast of the Santa Barbara Channel.

openCC (other)Oct 2025View details →

SBC LTER: Reef: Kelp Forest Community Dynamics: Invertebrate and algal density

These data describe the density and size of a select group of about 50 species of benthic invertebrates and understory algae in fixed plots (either 1m x 1m or 20m x 1m) along permanent transects. These data are part of SBCLTER’s kelp forest monitoring program to track long-term patterns in species abundance and diversity of reef-associated organisms in the Santa Barbara Channel, California, USA. The sampling locations in this dataset are at nine reef sites along the mainland coast of the Santa Barbara Channel and at two sites on the north side of Santa Cruz Island. These sites reflect several oceanographic regimes in the channel and vary in distance from sources of terrestrial runoff. Sampling began in 2000, and these data are updated annually. The time period of data collection varied among the 11 kelp forest sites. Sampling at BULL, CARP, and NAPL began in 2000, sampling at the other 6 mainland sites (AHND, AQUE, IVEE, GOLB, ABUR, MOHK) began in 2001 (transects 3, 5, 6, 7, 8 at IVEE were added in 2011). Data collection at the two Santa Cruz Island sites (SCTW and SCDI) began in 2004. See Methods for more information. See Methods for more information.

openCC (other)Nov 2024View details →

SBC LTER: Reef: Long-term experiment: Kelp removal: Invertebrate and algal density

These data describe the abundance of common reef associated species of macro invertebrates and macroalgae within permanent plots of a long-term experiment designed to examine trajectories of change in the structure and productivity of kelp forest communities in response to changes in the frequency and severity of disturbance to giant kelp. The number of individuals of approximately 50 taxa were recorded by divers along 40 m transects within each plot. Small species of macroalgae and macinvertebrates were counted within six permanent 1 m2 quadrats positioned uniformly along the 40 m transect, while larger species were counted within four contiguous 20 m2 sub-sections of each 40 m x 2 m transect. Also included at the quadrat scale are estimates of an average size-related measurement of each species, which was developed specifically for each species for the purpose of estimating its biomass. The experiment was initiated in 2008 at five reef sites along the mainland coast of the Santa Barbara Channel and included an annual kelp removal treatment designed to simulate increases in the frequency and severity of winter wave disturbance and a continual kelp removal treatment that allowed the effects of giant kelp on the community to be evaluated. The last experimental removals of giant kelp occurred in winter 2016 or winter 2017, depending on the site. Data collection continued in all plots until spring 2023 to document the recovery trajectory of the reef fish community following the cessation of experimental kelp removal.

openCC (other)Aug 2025View details →

SBC LTER: Settlement of urchins and other invertebrates, ongoing since 1990

The dataset comprises weekly to biweekly data on invertebrate settlement on artificial substrates at six sites in Southern California, and one site in Northern California. The study began in early 1990 and is ongoing. The study’s main focus is on urchins (Strongylocentrotus purpuratus and Mesocentrotus franciscanus), but was expanded to include selected bivalves, gastropods and crabs during the period 1994-1997. The purpose of the study is to compare and contrast patterns of settlement supply across a large geographical gradient to explore the possible influence of oceanographic features on these patterns. Both of these goals are facilitated by the long duration of the dataset, its large geographical range and the high temporal frequency of collection. See Methods for more information.

opencc-by-4.0Nov 2023View details →

Modelled distributions of fish and epibenthic invertebrates in the southern North Sea

These data include distribution maps of fish and invertabrate species in the southern North Sea from 2014 until 2023. The maps are modelled using point data of presence/absence and biomass (per trawled km²) from scientific fisheries surveys to estimate the distribution of the probability of occurrence (POC) or biomass (kg per km²), respectively. Also included are forecasts of species' distributions assuming increasing water temperatures in the southern North Sea according to the ICCP scenario RCP8.5. Each files contains a raster stack with layers for each species. The data can be read into the R using the 'stack'-command from the 'raster'-package. The raster stacks contain layers with headers, which code the species and size group. For some species of relevance to fisheries managment, Numbers behind the latin names of the species give information on the included size classes in cm with 'no' indicating no size class information was available. The file names are composed of the follwing elements: 'bio' = biomass 'poc' = probability of occurrence 'emp' = observed occurrence/abundance data from fisheries surveys with employed spatial smoother 'sdm' = modelled distributin data from random forests 'fc' = forecast distributions based on temperature predictors according to RCP8.5 'rel.ca2' = core areas (CA) of distribution representing values > then the mid-point of modelled POC value range Year numbers give the time frame of empirical data or model predictions.    You can access the .tiff-files with the following R-commands using the directory path where you have stored the files: library(raster) poc<-stack("your_path/poc.sdm.2014_2023.tiff") poc$gadus.morhua_5_113 # Plots distribution of Atlantic cod as probability of occurrence observed at a size range from 5 - 113 cm tail length

opencc-by-4.0Jun 2024View details →

Statistical analysis and dataset for: Three-dimensional body reconstruction enables quantification of liquid consumption in small invertebrates

Linked to the journal article published in bioRxiv (https://doi.org/10.1101/2024.06.14.599002). Abstract Quantifying feeding patterns provides valuable insights into animal behaviour. However, small invertebrates often consume incredibly small amounts of food. This renders traditional methods, such as weighing individuals before and after food acquisition, either inaccurate or prohibitively expensive. Here, we present a non-invasive method to quantify food consumption of small invertebrates whose body expands during feeding. Using the markerless pose estimation software DeepLabCut, we three-dimensionally track the body of Argentine ants, Linepithema humile. Using these extracted markers, we developed an algorithm which computationally reconstructs the ant’s body, directly measuring volumetric change over time. Moreover, we provide measures of accuracy and quantify the ant’s feeding response to a range of sucrose concentrations, as well as a gradient of caffeine-laced sucrose solutions. Small invertebrates are often prolific invasive species and disease vectors, causing significant ecological and economical damage. Understanding their feeding behaviour could be an important step towards effective control strategies.   <ul> <li>VolEst_C1_volume_calculation_multiprocessing.py: Takes as input H5 3D DeepLabCut files, calculates the gaster volume at every frame using seven different methods and outputs these as CSV files.</li> <li>VolEst_C2_interactive_GUI.py: Given a folder with Volume CSV files, interactively plots the volume over time, 3D coordinates tracked by DeepLabCut and the frame of interest for both cameras.</li> <li>VolEst_C3_linear_regression.py: Applies a linear regression to each feeding event tracked and provides measures of interest such as crop load and consumption rate.</li> <li>VolEst_C4_statistical_analysis: Complete statistical analysis and code for the manuscript.</li> <li>VolEst_D1_sucrose_density.csv: Data obtained to quantify the density of sucrose solutions of varying molarity.</li> <li>VolEst_D2_accuracy_weight_metadata.csv: Manually collected metadata pertaining to experimental conditions, subjects, and treatments for the weight-volume accuracy measurements.</li> <li>VolEst_D3_accuracy_weight.zip: Folder containing the raw points tracked using DeepLabCut, all relevant data obtained from the algorithms created, and a sample video of the experiment for the weight-volume accuracy measurements.</li> <li>VolEst_D4_accuracy_nanoliter_metadata.csv: Manually collected metadata pertaining to experimental conditions, subjects, and treatments for the volume-volume accuracy measurements.</li> <li>VolEst_D5_accuracy_nanoliter.zip: Folder containing the raw points tracked using DeepLabCut, all relevant data obtained from the algorithms created, and a sample video of the experiment for the volume-volume accuracy measurements.</li> <li>VolEst_D6_sucrose_caffeine_consumption_metadata.csv: Manually collected metadata pertaining to experimental conditions, subjects, and treatments for the sucrose and caffeine dilutions application measurements.</li> <li>VolEst_D7_sucrose_caffeine_consumption.zip: Folder containing the raw points tracked using DeepLabCut, all relevant data obtained from the algorithms created, and a sample video of the experiment for the sucrose and caffeine dilutions application measurements.</li> <li>VolEst_Camera_A-Henrique-2023-09-20.zip: DeepLabCut labels and trained network for camera A.</li> <li>VolEst_Camera_B-Henrique-2023-09-20.zip: DeepLabCut labels and trained network for camera B.</li> <li>VolEst_base.stl: 3D file for the resin platform used in the experimental validation of the setup.</li> <li>VolEst_platform.stl: 3D file for the resin platform used in the experimental validation of the setup.</li> </ul>

opencc-by-4.0Nov 2024View details →

Datasets for phylogenetic analyses and phylogenetic trees for: Genetic barcodes for species identification and phylogenetic estimation in ghost spiders (Araneae: Anyphaenidae: Amaurobioidinae). Invertebrate Systematics, 2024

We combined the COI sequence data with legacy multigene sequence data to create a new, taxon-rich phylogeny for the Amaurobioidinae. We used sequences for four loci that have been used in previous studies on the subfamily: two mitochondrial loci, COI (658bp) and ribosomal subunit 16S (16S, 410bp); and two nuclear loci, Histone H3 (H3, 327bp) and ribosomal subunit 28S (28S, 839bp). We complemented the Amaurobioidinae data with sequences from several non-amaurobioidine anyphaenids and two clubionids as outgroups. Sequence alignment was performed using the MAFFT (ver. 7.308) plugin in Geneious, allowing MAFFT to automatically select an appropriate alignment strategy based on the properties of each locus, or with the online MAFFT server (https://mafft.cbrc.jp), which consistently selected the L-INS-i algorithm. Finally, alignments of the four loci were concatenated to construct a 2234 bp multigene sequence matrix containing 692 taxa, with about 55% missing/gap data (“full” matrix henceforth). To ensure that excessive missing data did not affect the resulting topology, we also constructed a reduced matrix by removing additional COI-only specimens so that each species and morphotype was represented by just one or two specimens for which all loci were available (where possible). After realignment, this reduced matrix was 2235 bp long, included 167 taxa, and had about 22% missing/gap data (“reduced” matrix henceforth). Phylogenetic analyses under maximum likelihood, including model selection, were then conducted with IQ-TREE 2. We performed phylogenetic analyses on both concatenated matrices (the full matrix and the reduced matrix) and on each individual locus. For model selection, we provided an initial scheme that partitioned the matrix by locus, and further partitioned the protein-coding loci (COI and H3) by codon position. We used ModelFinder and searched for the best partition scheme, all in IQ-TREE. The best models (partitions) for the full dataset were: GTR+F+I+G4 (16S), GTR+F+I+I+R4 (28S), TVM+F+I+I+R2 (COI-1), TIM2+F+R4 (COI-2), GTR+F+R5 (COI-3), TVMe+G4 (H3-1-H3-2), SYM+G4 (H3-3); and for the reduced dataset: GTR+F+I+G4 (16S), GTR+F+I+G4: (28S), GTR+F+I+G4: (COI-2), GTR+F+I+G4: (COI-3), TVM+F+I+G4: (COI-1, H3-2), GTR+F+I+G4: (H3-1), GTR+F+I+G4: (H3-3). For each dataset, once the best models and partitions were defined, we executed 10 independent replicates of tree calculations followed by 1000 ultrafast bootstrap replicates, and the replicate reaching the maximum likelihood was chosen. Phylogenetic analyses under parsimony were made with TNT, under equal weights, using the “new technology” search with default values, asking for 10 independent hits to the minimal length, and submitting the resulting trees to a round of TBR branch swapping.

opencc-by-4.0Mar 2023View details →

Sampled and simulated benthic invertebrate body-mass data from the Porcupine Abyssal Plain Sustained Observatory (4850 m, 48.83° N 16.50 °W, NE Atlantic)

A dataset of sampled and simulated benthic invertebrate body-mass data from the Porcupine Abyssal Plain Sustained Observatory (4850 m, 48.83° N 16.50 °W, NE Atlantic) has been produced. It includes data on macro- and megabenthos derived from a randomly sampled power law distribution, seabed core samples, large-scale seabed photography, and seabed trawls.

openCC (other)Jun 2025View details →

Interagency Ecological Program: Benthic invertebrate monitoring in the Sacramento-San Joaquin Bay-Delta, collected by the Environmental Monitoring Program, 1975-2024.

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 benthic invertebrate macrofauna in the upper San Francisco Estuary (SFE) since 1975. The objectives of the EMP are to obtain consistent and accurate monthly data at established monitoring stations and to report this information for the purpose of management and conservation of the upper San Francisco Estuary. While the EMP also collects discrete and continuous water quality data, along with phytoplankton and zooplankton data, this dataset only includes the benthic invertebrate data collected by the EMP from 1975-2024. EMP monitors invertebrate communities in the benthos of the SFE by collecting dredge samples with a Ponar sampler. Sediment and particles smaller than 0.5mm are removed from the sample using a sieve table. The invertebrates present are preserved in formalin, identified to the lowest possible taxonomic level, and enumerated. Currently, samples are collected monthly at 10 sites across the range of salinities found in the SFE. Four replicate dredge samples are collected at each site. The frequency of sampling, number and identity of sampling sites, and number of replicate samples has changed through the 45+ years of monitoring effort, in response to changes in perceived need for data. Links to other EMP datasets can be found on the EMP website: https://emp-des.github.io/emp-reports/data-links.html, or can be found on EDI for searching for "Environmental Monitoring Program" and "San Francisco".

openCC (other)May 2021View details →

Benthic algae and sessile invertebrate survey data from LTER and other reef ecosystems

Understanding factors that influence ecological stability is a key question in ecology. Population ecology has highlighted that synchrony within a species across locations is an important indicator of species stability. Community ecology, in contrast, has highlighted that asynchrony between species within a location may enhance the stability of aggregate properties (such as total productivity). We compiled LTER and other data across 20 metacommunities in grassland and coastal marine biomes to integrate population and community approaches to synchrony to understand drivers of ecosystem stability at different scales. All datasets feature long-term (10-34 years) measurements of the primary producer community across multiple (6-49) discrete plots, with taxonomic identifications to species in most or all cases. This data package contains data from coastal marine sites: Santa Barbara Coastal LTER; Moorea Coral Reef; US Virgin Islands; Maui, Hawaii; and the Florida Keys.

openCC (other)Aug 2025View details →

UCSB SONGS Mitigation Monitoring: Wetland Performance Standard - Invertebrate Abundance and Richness

These data contain annual estimates of the density of wetland macroinvertebrates (all species combined) and species richness (as a species density) in six main channel and six tidal creek locations at four coastal wetlands as part of the SONGS San Dieguito Wetland Restoration monitoring program to track long-term patterns in species abundance and diversity. This study began in 2012 in the San Dieguito Wetland and Tijuana Estuary in San Diego County, CA, Carpinteria Salt Marsh in Santa Barbara County, CA, and Mugu Lagoon in Ventura County, CA. Beginning in 2024, Tijuana Estuary was replaced with Los Penasquitos Lagoon in San Diego County, CA.

openCC (other)Jun 2019View details →

Riparian controls on light availability, primary producers, invertebrates, fish and salamanders in streams in and near the Andrews Experimental Forest, 2014-2018

The goal of this data collection effort was to determine how the age, stage, and structure of the riparian forest relates to stream primary producers and stream biota. Data were collected on stream habitat, benthic algal, biota (fish, salamanders and macroinvertebrates), and riparian forest cover across a total of 9 streams: 7 streams in the HJ Andrews basin/Lookout Creek stream network; one stream in the westward adjacent Blue River basin, and one stream in the eastward adjacent Deer Creek river basin. In each stream there were 2 study reaches – one bordered by old-growth riparian forest and the other bordered by regenerated second-growth riparian forest on at least one bank (with a stand ages that generally ranged between 30 and 60 years). In each study reach (80 – 150 m), we collected the following data: pool habitat, wetted and bankfull widths, large wood abundance and volume, riparian forest canopy cover, benthic algae accrual on tiles, stream macroinvertebrate abundances (from 6 replicate surber samplers, which were pooled and then sub-sampled, identified and measured), age 1+ cutthroat trout (Oncorhynchus clarkii clarkii) abundance and biomass, age 0+ (young-of-year) trout abundance and biomass, coastal giant salamander (Dicamptodon tenebrosus) abundance and biomass. Fish and salamander abundances were calculated by either mark-recapture or multiple pass depletion methods.

Vegetation and invertebrate communities in 500 plots in the Duplin and Dean Creek watersheds: ground truth data for matching hyperspectral imagery

We measured characteristics of vegetation (Aster tenuifolius, Batis maritima, Borrichia frutescens, Distichlis spicata, Iva frutescens, Juncus roemerianus, Limonium carolinianum, Salicornia biglovii, Salicornia virginica, Spartina alterniflora, Spartina patens, Sporobolus virginicus), soil (salinity, proportion organic and proportion water) and densities of common gastropods and bivalves in 500 plots in the Duplin and Dean Creek watersheds on Sapelo Island on June 20-26, 2006. Plot locations were determined using a high precision hand-held GPS. These data were used to help ground-truth hyperspectral aerial images collected at the same time by Dr. John Schalles.

Comparative transect surveys of invertebrate abundance, plant cover, and sediment characteristics in Atlantic and Gulf of Mexico salt marshes from April 2009 to September 2010

Understanding the relative strengths of top-down and bottom-up forces is an important key to predicting the structure of biological communities. The strength of these effects can be regulated in part by predator abundance and nutrient availability. In 2009, we hypothesized that the importance of these factors varies geographically between the southeastern Atlantic Coast and the Gulf Coast due to differences in tidal regime, and began to study this variation using a biogeographic, manipulative field experiment. Although our original purpose was to understand the structure of salt marsh arthropod food webs, BP's Deepwater Horizon spill in the Gulf Coast presented an opportunity to understand how stress from an oil spill might affect the variables that we were measuring. The fact that we had plots and transect sampling in place at multiple sites along the Gulf and East Coasts put us in a position to evaluate any impacts that might occur if oil hit some of the sites. The study was conducted at 11 sites across the Gulf Coast, from Texas to Florida, and 11 sites along the Atlantic Coast, from Florida to Maine. At each site, experimental plots were sampled and a 100m transect was sampled near the plots within 5m of the high marsh boundary. Sampling was conducted in May 2009, August 2009, and August 2010. In 2010, four extra sites were added to the existing experimental sites because of known oil contamination, and another site was added as an extra control. Only the transect sampling was conducted at these sites. This dataset contains all the transect data; data from experimental plots will be reported in a companion dataset.

Experimental plots studies comparing the impact of fertilization and wrack addition on invertebrate abundance and plant cover in Atlantic and Gulf of Mexico salt marshes from April 2009 to September 2010

Understanding the relative strengths of top-down and bottom-up forces is an important key to predicting the structure of biological communities. The strength of these effects can be regulated in part by predator abundance and nutrient availability. In 2009, we hypothesized that the importance of these factors varies geographically between the southeastern Atlantic Coast and the Gulf Coast due to differences in tidal regime, and began to study this variation using a biogeographic, manipulative field experiment. Although our original purpose was to understand the structure of salt marsh arthropod food webs, BP's Deepwater Horizon spill in the Gulf Coast presented an opportunity to understand how stress from an oil spill might affect the variables that we were measuring. The fact that we had plots and transect sampling in place at multiple sites along the Gulf and East Coasts put us in a position to evaluate any impacts that might occur if oil hit some of the sites. The study was conducted at 11 sites across the Gulf Coast, from Texas to Florida, and 11 sites along the Atlantic Coast, from Florida to Maine. At each site, experimental plots were sampled and a 100m transect was sampled near the plots within 5m of the high marsh boundary. Sampling was conducted in May 2009, August 2009, and August 2010. In 2010, four extra sites were added to the existing experimental sites because of known oil contamination, and another site was added as an extra control. Only the transect sampling was conducted at these sites. This dataset contains all the data from experimental plots; experimental treatments of fertilizer addition, wrack addition, fertilizer & wrack addition, and no addition (control) were randomly applied to the plots. The plot treatments were maintained in August 2009 and May 2010.

GCE-LTER Hammock Well Vegetation and Invertebrate Monitoring - July 2008

In July 2008 the GCE LTER program selected two hammocks for intensive study: HN_i_1 and PC_i_29. HN_i_1 is of Holocene origin and is located adjacent to Blackbeard Island to the north of Sapelo Island, Georgia. PC_i_29 is also of Holocene origin and is located adjacent to the south end of Sapelo Island. These hammocks are of similar size, with similar vegetation zones in the high marsh environment. Groundwater well transects were established that run from the upland, through the marsh, and up and over the upland area of each hammock. Two permanent plots were established at each well in order to characterize the plant and invertebrate diversity and abundance by surveying plots once a year. This data set includes the results of July 2008 monitoring studies.