BOLD Public Fish Data

Freshwater fishes are regarded as South Africa’s most threatened species group. Long-term distributional data for freshwater fish species can be vital for detecting critical ecosystem changes, such as species range shifts, new records of non-native invasions and loss of ecosystem services or unique biodiversity. Understanding exactly how the abundance and distribution of freshwater fishes (both native and non-native) are changing is pivotal to effectively manage and conserve unique and threatened freshwater biodiversity and ecosystems. In light of this, a comprehensive freshwater fish dataset (freshwaterbiodiversity.org) was built, comprising all available records of formally described freshwater fish species occurring in South Africa. The comprehensive search for data resulted in the accrual of a total of 60 837 records of freshwater fish from South Africa, which includes 35 955 records new records to the Global Biodiversity Information Facility (GBIF). Of the 101 native species occurring in the country, almost half of all assessed species were found to be threatened, with the number of occurrences decreasing in recent years. Conversely, the number of occurrences and distribution ranges of many non-native species were found to be increasing, especially within the past three decades. These data have provided a much-needed update to the known status and distribution of freshwater fishes in the country.

The data set is abundance or presence/absence data collected by species from wadeable stream sites along with water chemistry, including specifically specific conductivity and some other variables that were not used in the analysis. This dataset is associated with the following publication: Griffith, M., L. Zheng, and S. Cormier. Using extirpation to evaluate ionic tolerance of freshwater fish. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 37(3): 871-883, (2018).

Fish Data Without BG

## Overview

Fish Data Without BG is a dataset for object detection tasks - it contains Fish UlaI annotations for 322 images.

## Getting Started

You can download this dataset for use within your own projects, or fork it into a workspace on Roboflow to create your own model.

  ## License

  This dataset is available under the [CC BY 4.0 license](https://creativecommons.org/licenses/CC BY 4.0).

The Living Murray (TLM) Fish data extends from 2007 to 2012. The sampling program monitored species occurrence, age, size and recruitment of fish sampled at two of the six TLM Icon Sites: Barmah?Millewa Forest, and Gunbower?Koondrook?Perricoota Forest.

See http://www.mdba.gov.au/managing-water/environmental-water/delivering-environmental-water/living-murray-program for more information about the Living Murray program.

This historic fish dataset was digitized and standardized by ICES iin the framework of the EMODNet Biology project. It contains data from the Danish Biological Station who collected quantitative fish samples on a yearly basis from a range of stations in the Limjord during more than 3 decades.

Distance matrices for the fish dataset.

More details on the data collection methods can be found in Fourtune, L., Paz‐Vinas, I., Loot, G., Prunier, J. G., & Blanchet, S. (2016). Lessons from the fish: a multi‐species analysis reveals common processes underlying similar species‐genetic diversity correlations. Freshwater Biology, 61(11), 1830-1845.

A commented R script to use these data is provided at https://github.com/franckjabot/metacommunity-analysis-script

This geodatabase contains a comparable set of community fish samples from 12 sources, spanning the conterminous United States. The data were compiled through efforts of Michigan State University for the 2010 National Fish Habitat Action Plan (NFHAP) and with support from the U.S. Fish and Wildlife Service (USFWS) and U.S. Geological Survey (USGS) Aquatic GAP Program. All fish sample locations were verified and linked to flowlines of the National Hydrography Dataset Plus Version 1 (NHDPlusV1) using the COMID identifier. Fish records were provided by the following organizations and agencies: USGS, U.S. Environmental Protection Agency (EPA), Connecticut Department of Environmental Protection, Iowa Department of Natural Resources, Florida Fish and Wildlife Conservation Commission, Kansas Department of Wildlife and Parks, Kentucky Division of Water, Missouri Department of Conservation, New York Department of Environmental Conservation, North Carolina Division of Water Quality, Vermont Fish and Wildlife Department, and Little Tennessee Watershed Association. These datasets met the following criteria: (1) protocols were focused on sampling the entire community; (2) all samples were collected by single-pass electrofishing (3) samples were collected between 1990-2010, (4) samples had sufficient descriptive information to determine location of sample. Please use the following citation: Esselman, P., D.M. Infante, D. Wieferich, A. Cooper, L. Wang, W. Taylor, R. Tingley, D. Thornbrugh, J. Ross, and J. Fenner. (May 2013) National Fish Habitat Action Plan (NFHAP) 2010 Community Fish Data. National Fish Habitat Partnership Data System. http://dx.doi.org/doi:10.5066/F7QN64RG

Data included in this dataset includes: 1) 2016 reach fish data for the Santa Ana Sucker (Catostomus santaanae) and the Arroyo Chub (Gila orcutti) in the upper Santa Ana River.

Fish census data were collected from sites around Micronesia as part of the ongoing Micronesia Challenge. Information on the program can be found at (www.micronesiareefmonitoring.com). Survey sites were selected around each island to be representative of natural environmental gradients, management, and major reef types. Thus, full site designs can be used to evaluate both island trends and site-specific trends. The size and abundance of fishes, which are generally consumed by people (hereinafter food-fish), were collected by four calibrated observers, with individual observers being consistent across jurisdictions. Fish assemblages were estimated from 12 stationary-point counts (SPCs) conducted at equal intervals along the transect lines. At each SPC, the observer recorded the species name and the size of all food-fish within a 5 m circular radius for a period of 3 minutes. Food-fish were defined as acanthurids, scarids, serranids, carangids, labrids, lethrinids, lutjanids, balistids, kyphosids, mullids, holocentrids, and sharks. The data in this submission include fish identification, counts, and sizes obtained during SPC surveys.

Field sampling occurred at locations within Ten Thousand Islands National Wildlife Refuge on three transects along the natural salinity gradient of increasing salinity to the coastal south. We used three replicates per tier (east-west) for a total of nine sampling sites. Sites were approximately 1300 m apart in all directions. Sampling events occurred every 3–4 weeks from January to May for 7 sampling events in 2015 and 5 in 2016. These dates were selected to capture signals of the natural variation in water levels and salinity that occur during the transition from the wet season to the dry season. Fish traps were deployed at each of the nine sites and then retrieved the following day, allowing 24 hours soak time. Two minnow traps (Gee Minnow Trap; 22.9 x 44.5 cm, 0.6 cm mesh, 1.9 cm diameter opening) and two Breder traps (15 cm x 15 cm x 30 cm, 12 mm opening width, 15 cm opening height) were placed at each sampling site because the two trap types have the potential to catch different fish species.

Imputed multiplexed DNA FISH data from the following studies:

1. Huang et al 2021 (DOI: 10.1038/s41588-021-00863-6): 5kb resolution chromatin tracing data of mouse embryonic stem cells
2. Takei et al 2021 (DOI: 10.1038/s41586-020-03126-2): 5kb and 1Mb resolution DNA seqFISH+ data of mouse embryonic stem cells
3. Takei et al 2021 (DOI: 10.1126/science.abj1966): 1Mb resolution DNA seqFISH+ data of mouse brain cells (excitatory neurons not included)

Fish data from the Gdańsk Bay collected between 1985 and 1993 during cruises by MIR-PIB.

The Pre-recruit survey project is collaborative involving researchers from the FE Division based in 3 laboratories (Newport, Seattle and Hammond), scientists from the Southwest Fisheries Science Center (Santa Cruz), along with researchers from several universities (Oregon State University, University of Oregon, University of Washington, University of California, Santa Cruz). In concert with a similar SWFSC survey effort through California, the purpose of this project is to conduct annual surveys within the coastal ecosystem off Oregon and Washington to quantify the environmental conditions and biota found along the California Current and to elucidate ecosystem-level processes affecting managed and protected marine resources. This project currently supports three main efforts: An annual sampling regime of the hydrology, plankton, small fish, and predators along transects over the Continental Shelf from Oregon and Washington. This consistent survey has generated significant information on within- and between-year variability in the California Current Marine Ecosystem and has yielded valuable insights into the food web off our coast. Collection of specimens for diet analysis, growth, containment load, and other studies related to the ecology and production of commercially important taxa and their relationships within the food web. Parameters and ecological processes quantified during this effort are used in forecasts involving species, assemblages, and ecosystems and also to parameterize ecosystem models used to evaluate cumulative risks and managerial strategies. We towed a Cobb Trawl at 30 m at all stations.

The data covers sampling sites over all of the province of Québec, with more data in the southern regions of the province. Data are from Hydro-Québec and the Québec Ministère de l’Environnement, de la Lutte contre les changements climatiques, de la Faune et des Parcs (MELCCFP). These datasets include a heterogeneous mix of standardized and non-standardized fish surveys by government biologists and by environmental consulting firms sub-contracted by Hydro-Québec, collected between 1973 and 2021. Overall, 6498 unique sites (3087 sites in lakes, 3412 sites in rivers; reservoirs excluded), were included in the database. For each site, the data consisted of species counts (adult and juvenile life stages), location (latitude and longitude), sampling date, habitat type (lake or river) and fishing gear (three categories: electrofishing, gillnet, or seine). Climate data (means over 1970 to 2000) and elevation were extracted for each site according to the site’s location from the WorldClim website (https://www.worldclim.org/) in 2023; a site which provides global weather and climate data at high spatial resolution. All 19 ‘bioclimatic variables’ provided by WorldClim were obtained from WorldClim raster files (10-min. resolution) using the function extract from the package raster (Hijmans and van Etten 2012). Five weakly-correlated bioclimatic variables were retained: annual means for temperature and precipitation, mean diurnal temperature range, annual temperature range, and precipitation seasonality (coefficient of variation of monthly total precipitation).

In this study, we hypothesized that seasonal variation in upwelling-favorable winds has differential influences on species of the central California Current pelagic ecosystem. To test this hypothesis, we developed multivariate indicators of upwelling and species’ responses using wind and sea surface temperature (SST) data from buoys and growth and reproductive data for 11 species of fish and seabirds.

This dataset represents fish sampling and habitat measurements (https://data.kingcounty.gov/Environment-Waste-Management/Habitat-data-for-Juvenile-Pacific-salmonid-habitat/mtrd-zgtr/about_data) from the Snoqualmie and Green rivers in the Puget Sound region of Washington State, USA. Using a cataraft mounted with a boat electrofisher, these data were collected between late winter and late spring from 2016 through 2022. Measurements were of 25-m-long transects along six different edge habitat types in the two rivers. The edge habitats represented in this dataset are ‘armored banks’, ‘biorevetment banks’, ‘unarmored banks’, ‘bars’, ‘backwaters’, and ‘side channels’. These data were collected as part of monitoring of eight habitat restoration or bioengineered bank stabilization projects in the Snoqualmie and Green rivers, along with three more general studies of fish-habitat relationships in the two rivers. These data are analyzed and presented in the journal article “Juvenile Pacific salmonid habitat use in two Puget Sound lowland Rivers”, published in the Transactions of the American Fisheries Society (https://afspubs.onlinelibrary.wiley.com/doi/10.1002/tafs.10457). All data were collected by the King County Water and Land Resources Division, Science and Technical Support Section. Habitat data were collected during the day and include measurements of the width of low-velocity habitat (≤ 0.45m/s) and water depth along each transect. Fish sampling occurred after darkness fell the evening following habitat data collection. Fish data include the number of each species sampled at each transect and the number of seconds each transect was electrofished. For additional details on the data and collection methods, please see the associated journal article or contact the article authors: Aaron David (adavid@kingcounty.gov), Christopher Gregersen (chris.gregersen@kingcounty.gov), Joshua Kubo (josh.kubo@kingcounty.gov), Daniel Lantz (dan.lantz@kingcounty.gov), and James Bower (james.bower@kingcounty.gov).

Electrofishing data from streams and rivers in Hesse and NRW. Purope of data collection: variable. a large proportion of the samples were taken to characterize the ecological status of the river according to the EU Water Framework Directive. In a few cases, data are from samples for expert reports / assessments, e.g. effects of a dam, water abstraction, restoration...

During 23 years, 3 institutions sampled fish in the Belgian part of the river Meuse with two distincts methodologies.

Data were provided by the survey of fish passages in fish ladders at Tailfer (upstream Namur) and Lixhe (downstream Liège) over the 1989-2011 period (Matondo & Ovidio 2016). Fish were collected daily in a trap placed in the upper pool of the ladder when the migration peaks occurred, and twice a week outside the major migration period. All the fish species were identified and species abundances were estimated without taking into account the juveniles and the youngs-of-the-year. Annual fish abundances were expressed as monthly averages.

Data from Hastière, Andenne and Visé were provided by electrofishing from a boat along the banks in 1994, 2007, 2008, 2009 and 2010. Abundances were expressed as number of individuals by 100m² of river sampled.

This historic fish dataset was digitized and standardized by ICES iin the framework of the EMODNet Biology project. It contains data from the Danish Biological Station who collected quantitative fish samples on a yearly basis from a range of stations in the Limjord during more than 3 decades.