The fathead minnow (Pimephales promelas) is a key model of vertebrate toxicity. Standardized tests of toxicity in fathead minnow have been developed to support regulatory science, and much is known about the response of the species to various environmental pollutants. However, there is little data on genetic variation within the species, despite the potential influence of genetic background on toxicological outcomes. Furthermore, the phylogenetic relationships among Pimephales species are not fully established and rates of evolutionary divergence within the species and genus have not been investigated. This study examined patterns of genetic variation across the genome within a single wild population of fathead minnow from the San Juan River of the southwestern U.S. These patterns were contrasted with variation in an inbred, captive population reared by the U.S. Environmental Protection Agency. The study also examined variation in two specimens each of the congeners bluntnose minnow (P. notatus), slim minnow (P. tenellus), and the bullhead minnow (P. vigilax). This data release describes the availability of the raw sequence data, the methods for identifying genetic polymorphisms among the samples, and provides the called polymorphisms in a standardized format (the variant call format, or VCF).

The fathead minnow (Pimephales promelas) is a laboratory model organism widely used in regulatory toxicity testing and ecotoxicology research. Despite, the wealth of toxicological data for this organism, until recently genome scale information was lacking for the species, which limited the utility of the species for pathway-based toxicity testing and research. As part of a EPA Pathfinder Innovation Project, next generation sequencing was applied to generate a draft genome assembly, which was published in 2016. However, application of those genome-scale sequencing resources was still limited by the lack of available gene annotations for fathead minnow. Here we report on development of a first generation genome annotation for fathead minnow and the dissemination of that information through a web-based browser that makes it easy to search for genes of interest, extract the corresponding sequence, identify intron and exon boundaries and regulatory regions, and align the computationally predicted genes with other supporting evidence. This work greatly enhances the utility of the genome assemblies that were developed and makes it accessible to the ecotoxicology community world-wide, opening up a wide array of new research opportunities with the species. The URL associated with this data set provides access to the genome browser that was developed as well as the current gene models and evidence tracks. This dataset is associated with the following publication: Saari, T., A. Schroeder, G. Ankley, and D. Villeneuve. First generation annotations for the fathead minnow (Pimephales promelas) genome. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 36(12): 3436-3442, (2017).

This dataset contains single nucleotide polymorphism (SNP) information for aquatic insect species collected in tributaries of the Colorado River in Grand Canyon (Arizona, USA), as well as SNP information for individuals collected from reference reaches of the Upper Colorado River Basin in Utah. This dataset focuses specifically on three species that were common and widely distributed throughout tributary streams in Grand Canyon: a mayfly (Fallceon quilleri), a caddisfly (Hydrospyche oslari), and a water strider (Rhagovelia distincta).

This dataset contains single nucleotide polymorphism (SNP) information for aquatic insect species collected in tributaries of the Colorado River in Grand Canyon (Arizona, USA), as well as SNP information for individuals collected from reference reaches of the Upper Colorado River Basin in Utah. This dataset focuses specifically on three species that were common and widely distributed throughout tributary streams in Grand Canyon: a mayfly (Fallceon quilleri), a caddisfly (Hydrospyche oslari), and a water strider (Rhagovelia distincta).

This data release comprises a dataset that contains sample collection information and microsatellite genotypes, and another dataset that contains single nucleotide polymorphism (SNP) genotypes with sample collection information for populations of white-tailed ptarmigan across the species' range. There is also an additional file (accession numbers.xlsx) linking samples to accession numbers in Genbank. This data was collected in order to address the following: The delineation of intraspecific units that are evolutionarily and demographically distinct is an important step in the development of species-specific management plans. Neutral genetic variation has served as the primary data source for delineating units for conservation, but with recent advances in genomic technology, we now have an unprecedented ability to utilize information about neutral and adaptive variation across the entire genome. Here, we use traditional genetic markers (microsatellites) and a newer reduced-representation genomic approach (single nucleotide polymorphisms) to delineate distinct groups of white-tailed ptarmigan (Lagopus leucura), an alpine-obligate species that is distributed in naturally fragmented habitats from Alaska to New Mexico.

This data release comprises a dataset that contains sample collection information and microsatellite genotypes, and another dataset that contains single nucleotide polymorphism (SNP) genotypes with sample collection information for populations of white-tailed ptarmigan across the species' range. There is also an additional file (accession numbers.xlsx) linking samples to accession numbers in Genbank. This data was collected in order to address the following: The delineation of intraspecific units that are evolutionarily and demographically distinct is an important step in the development of species-specific management plans. Neutral genetic variation has served as the primary data source for delineating units for conservation, but with recent advances in genomic technology, we now have an unprecedented ability to utilize information about neutral and adaptive variation across the entire genome. Here, we use traditional genetic markers (microsatellites) and a newer reduced-representation genomic approach (single nucleotide polymorphisms) to delineate distinct groups of white-tailed ptarmigan (Lagopus leucura), an alpine-obligate species that is distributed in naturally fragmented habitats from Alaska to New Mexico.

We provide genetic and distribution data for the Louisiana Pigtoe, Pleurobema riddellii, to guide decisions related to federal protection for the species under the U.S. Endangered Species Act. Our final dataset includes 125 COI sequences generated as part of our study representing P. riddellii from eight North American river basins. This includes the COI sequence we generated from a museum specimen collected from the Trinity River in the late 1900s, which is the first genetic confirmation of P. riddellii in the Trinity River basin. Also included are sequences from specimens initially identified as Fusconaia cerina (n=3) Fusconaia flava (n=1), Fusconaia sp. (n=5), Pleurobema sintoxia (n=10), and Pustulosa pustulosa (n=1) that were genetically confirmed to be P. riddellii. Additionally, we provide distribution data from freshwater mussel surveys, museum records, and field notes representing 467 records of P. riddellii collected from pre-1900 - 2022. The occurrence data includes records from 9 river basins (Amite, Calcasieu, Neches, Ouachita, Pearl, Red, Sabine, San Jacinto, Trinity), 54 HUC-10 watersheds, and 5 states (Arkansas, Louisiana, Mississippi, Oklahoma, Texas).

We provide genetic and distribution data for the Louisiana Pigtoe, Pleurobema riddellii, to guide decisions related to federal protection for the species under the U.S. Endangered Species Act. Our final dataset includes 125 COI sequences generated as part of our study representing P. riddellii from eight North American river basins. This includes the COI sequence we generated from a museum specimen collected from the Trinity River in the late 1900s, which is the first genetic confirmation of P. riddellii in the Trinity River basin. Also included are sequences from specimens initially identified as Fusconaia cerina (n=3) Fusconaia flava (n=1), Fusconaia sp. (n=5), Pleurobema sintoxia (n=10), and Pustulosa pustulosa (n=1) that were genetically confirmed to be P. riddellii. Additionally, we provide distribution data from freshwater mussel surveys, museum records, and field notes representing 467 records of P. riddellii collected from pre-1900 - 2022. The occurrence data includes records from 9 river basins (Amite, Calcasieu, Neches, Ouachita, Pearl, Red, Sabine, San Jacinto, Trinity), 54 HUC-10 watersheds, and 5 states (Arkansas, Louisiana, Mississippi, Oklahoma, Texas).

Macroinvertebrate samples were collected from streams tributary to Honnedaga Lake and from the Middle Branch of the Black River during 2012-2016 and analyzed for methylmercury concentrations and for stable isotope ratios of nitrogen and carbon. Macroinvertebrates were identified in the field, and the level of taxonomic resolution varied from order to species; most taxa were identified to the family level. Specimens were field-processed into composite samples, field-frozen, and submitted to the mercury laboratory for freeze-drying and analysis. Subsamples were then submitted to the stable isotope laboratory for analysis of nitrogen and carbon isotope ratios. This database contains the resulting data and associated information for these composite samples of whole macroinvertebrates.