,Whole genome sequence data for Bovidae Bos taurus - beef Angus. The data is in "fastq" format.,The National Animal Germplasm Program has germplasm for this animal, with the repository number 44883.,There are two versions of each file because we did paired end sequencing. There are two reads for each of the 210 data lines (a forward and a reverse read) summing to 420 total. A diagram of this is provided in the Collection Dataset . In the diagram, the two reads would correspond to read 1 and read 3.,Resources in this dataset:,Resource Title: Animal 44883 Sequence Data - SCINet.,File Name: Web Page, url: https://app.globus.org/file-manager?origin_id=904c2108-90cf-11e8-9672-0a6d4e044368&origin_path=/LTS/ADCdatastorage/NAL/published/node32139/,tar file containing 14 files. The files are:,SCINet users: The .tar file can be accessed/retrieved with valid SCINet account at this location: /LTS/ADCdatastorage/NAL/published/node32139/44883.tar,See the SCINet File Transfer guide for more information on moving large files: https://scinet.usda.gov/guides/data/datatransfer,Globus users: The files can also be accessed through Globus by following this data link. The user will need to log in to Globus in order to retrieve this data. User accounts are free of charge with several options for signing on. Instructions for creating an account are on the login page.,,

,Whole genome sequence data for Bovidae Bos taurus - beef Angus. The data is in "fastq" format.,The National Animal Germplasm Program has germplasm for this animal, with the repository number 20544.,There are two versions of each file because we did paired end sequencing. There are two reads for each of the 210 data lines (a forward and a reverse read) summing to 420 total. A diagram of this is provided in the Collection Dataset. In the diagram, the two reads would correspond to read 1 and read 3.,Resources in this dataset:,Resource Title: Animal 20544 Sequence Data - SCINet.File Name: Web Page, url: https://app.globus.org/file-manager?origin_id=904c2108-90cf-11e8-9672-0a6d4e044368&origin_path=/LTS/ADCdatastorage/NAL/published/node32019/,tar file containing 14 files. The files are:,SCINet users: The .tar file can be accessed/retrieved with valid SCINet account at this location: /LTS/ADCdatastorage/NAL/published/node32019/,See the SCINet File Transfer guide for more information on moving large files: https://scinet.usda.gov/guides/data/datatransfer,Globus users: The files can also be accessed through Globus by following this data link. The user will need to log in to Globus in order to retrieve this data. User accounts are free of charge with several options for signing on. Instructions for creating an account are on the login page.,,

,Whole genome sequence data for Bovidae Bos taurus - beef Angus. The data is in "fastq" format.,The National Animal Germplasm Program does not have germplasm for this animal.,There are two versions of each file because we did paired end sequencing. There are two reads for each of the 210 data lines (a forward and a reverse read) summing to 420 total. A diagram of this is provided in the Collection Dataset. In the diagram, the two reads would correspond to read 1 and read 3.,Resources in this dataset:,Resource Title: Animal Dark_Knight Sequence Data - SCINet.,File Name: Web Page, url: https://app.globus.org/file-manager?origin_id=904c2108-90cf-11e8-9672-0a6d4e044368&origin_path=/LTS/ADCdatastorage/NAL/published/node33210/,tar file containing 14 files. The files are:,SCINet users: The .tar file can be accessed/retrieved with valid SCINet account at this location: /LTS/ADCdatastorage/NAL/published/node33210/Dark_Knight.tar,See the SCINet File Transfer guide for more information on moving large files: https://scinet.usda.gov/guides/data/datatransfer,Globus users: The files can also be accessed through Globus by following this data link. The user will need to log in to Globus in order to retrieve this data. User accounts are free of charge with several options for signing on. Instructions for creating an account are on the login page.,,

,Cattle and Sheep Whole Genome Sequence (WGS),USMARC Beef Cattle Diversity Panel (MBCDPv2.9),

The GIS shapefile "bison_locations" provides 132996 locations of 5 adult female bison marked with global positioning system (GPS) collars at Tallgrass Prairie National Preserve during February 2021 to November 2023. We provide locations computed at 15-min and 1-h intervals for individual bison and the date and time of acquisition for each location. Users are advised that ground conditions within the study area may change over time, leading to changes in bison distribution.

This GIS shapefile, "quantile_bands," is derived from a parent shapefile, "density_contours," which describes 1) a bison study area in the North Unit of Theodore Roosevelt National Park, North Dakota and 2) 25%, 50%, 75%, and 99% kernel density contours for locations of bison marked with GPS collars during 2017-2020. Percentages associated with contours describe nominal coverage, i.e., proportions of observations they are expected to encompass, and approximate the distribution of bison activity within the study area. Each contour encompasses lower-coverage contours: the 75% contour, for example, encompasses the 50% and 25% contours but not the 99% contour. Quantile bands correspond with intervals between contours in "density_contours." Each of the first 4 bands encompasses approximately 25% of bison locations. Percentages associated with contours describe nominal coverage, i.e., quantiles the bands are expected to encompass. Bands comprise a partition of the bison study area and do not overlap. Users are advised that ground conditions within the study area may change over time, leading to changes in bison distribution.

This GIS shapefile, "quantile_bands," is derived from a parent shapefile, "density_contours," which describes 1) a bison study area at Badlands National Park, South Dakota, and 2) 25%, 50%, 75%, and 99% kernel density contours for locations of bison marked with GPS collars during 2015-2024. Percentages associated with parent contours describe nominal coverage, i.e., proportions of observations they are expected to encompass, and approximate the distribution of bison activity within the study area. Each contour encompasses lower-coverage contours: the 75% contour, for example, encompasses the 50% and 25% contours but not the 99% contour. Quantile bands correspond with intervals between contours in "density_contours." Each of the first 4 bands encompasses approximately 25% of bison locations. Percentages associated with contours describe nominal coverage, i.e., quantiles the bands are expected to encompass. Bands comprise a partition of the bison study area and do not overlap. Users are advised that ground conditions within the study area may change over time, leading to changes in bison distribution.

We developed and report a microsatellite data set composed of 52 microsatellite loci for 2305 individuals from 20 bison conservation herds (17 US federal, 1 tribal, 2 Canadian) and a single nucleotide polymorphism (SNP) data set composed of 5013 biallic loci for 376 individuals from 16 bison conservation herds that were used as part of a broader study. We also developed an algorithm to select a subset of SNPs that captures the genetic variation present in the full SNP data set. Human expansion is a major driver of both declining wildlife species abundance and the contraction of species’ distributions, increasing the risk of genetic erosion and the need for genetic monitoring. Rapidly advancing technology has expanded the types of genetic data that are available for wildlife conservation. However, the use of different genetic markers could result in different management decisions and, thus, must be considered carefully. Rebounding from near extinction in the early 1900s, the majority of plains bison (Bison bison bison) are managed as small and isolated herds. Microsatellite-based analyses are currently used to inform management of the US federal bison conservation herds. Transitioning from monitoring with tens of multiallelic loci (e.g., microsatellite loci) to thousands of biallelic loci (e.g., SNP loci) could increase genotyping efficiency and improve the precision of population genetic inference but would require an understanding of the inferential differences between genetic marker types.

This data set provides sample data and NCBI accession information for genomic sequencing of ptarmigan and grouse from Alaska.

,Animal genetic resources underpin the livestock sector's production and profitability. As a result livestock industries contribute billions of dollars to national economies. The Animal Germplasm Resources Information Network (A-GRIN) mission is to acquire, evaluate and preserve these strategic resources so that industry and the research community can have access to a broad array of genetic variability for: national security, introduction of genetic variation, corrective breeding, and various research initiatives. There are three major technical components:,In addition this program interacts with a wide range of livestock producers, researchers, and various industry representatives. Users can drill down to explore the germplasm collection by species, breed, line, and individual; compare taxonomies; find animals that meet their criteria to make a germplasm request.,,