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Genomic variation in the genus Pimephales: raw sequence data and single-nucleotide polymorphisms.

Metadata Updated: October 29, 2023

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).

Access & Use Information

Public: This dataset is intended for public access and use. License: No license information was provided. If this work was prepared by an officer or employee of the United States government as part of that person's official duties it is considered a U.S. Government Work.

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Dates

Metadata Created Date June 1, 2023
Metadata Updated Date October 29, 2023

Metadata Source

Harvested from DOI EDI

Additional Metadata

Resource Type Dataset
Metadata Created Date June 1, 2023
Metadata Updated Date October 29, 2023
Publisher U.S. Geological Survey
Maintainer
@Id http://datainventory.doi.gov/id/dataset/1452a13ac49ddeacc8ab48c1b6044eb7
Identifier USGS:62bc76c5d34ec421d4e12add
Data Last Modified 20220829
Category geospatial
Public Access Level public
Bureau Code 010:12
Metadata Context https://project-open-data.cio.gov/v1.1/schema/catalog.jsonld
Metadata Catalog ID https://datainventory.doi.gov/data.json
Schema Version https://project-open-data.cio.gov/v1.1/schema
Catalog Describedby https://project-open-data.cio.gov/v1.1/schema/catalog.json
Harvest Object Id 5505c503-5d7e-42f2-ae68-991112c99c65
Harvest Source Id 52bfcc16-6e15-478f-809a-b1bc76f1aeda
Harvest Source Title DOI EDI
Metadata Type geospatial
Old Spatial -124.6289,24.3671,-64.1602,48.8069
Publisher Hierarchy White House > U.S. Department of the Interior > U.S. Geological Survey
Source Datajson Identifier True
Source Hash b2848b5abf23f4985744f3d43bc95a942f6f4409032ba6f74b6e1cd5ef612252
Source Schema Version 1.1
Spatial {"type": "Polygon", "coordinates": -124.6289, 24.3671, -124.6289, 48.8069, -64.1602, 48.8069, -64.1602, 24.3671, -124.6289, 24.3671}

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