AndreaBozzo/ceres-open-data-index huggingface dataset:
Angus Sequence Data: Animal 20841

<p dir="ltr">Whole genome sequence data for Bovidae Bos taurus - beef Angus. The data is in "fastq" format.</p><p dir="ltr">The National Animal Germplasm Program has germplasm for this animal, with the repository number 20841.</p><p dir="ltr">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 <a href="https://data.nal.usda.gov/dataset/angus-sequence-dataset-collection">Collection Dataset</a>. In the diagram, the two reads would correspond to read 1 and read 3.</p><p dir="ltr">Resources in this dataset:</p><p dir="ltr">tar file containing 14 files. The files are:</p><ul><li>RAPiD-Genomics_F112_CSU_136201_P001_WB07_i5-515_i7-115_S19_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics_F112_CSU_136201_P001_WB07_i5-515_i7-115_S19_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WB07-i5-515-i7-115_S155_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WB07-i5-515-i7-115_S155_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WB07-i5-515-i7-115_S19_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WB07-i5-515-i7-115_S19_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WB07-i5-515-i7-115_S19_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WB07-i5-515-i7-115_S19_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WB07_i5-515_i7-115_S19_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WB07_i5-515_i7-115_S19_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WB07_i5-515_i7-115_S19_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WB07_i5-515_i7-115_S19_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WB07_i5-515_i7-115_S374_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WB07_i5-515_i7-115_S374_L002_R2_001.fastq.gz</li></ul><p><br></p>

Tags: animals, ars, cryopreservation, data-gov, dna-sequence, genetic-diversity, germplasm, grin, np101
Organization: Department of Agriculture
Angus Sequence Data: Animal 29443

<p dir="ltr">Whole genome sequence data for Bovidae Bos taurus - beef Angus. The data is in "fastq" format.</p><p dir="ltr">The National Animal Germplasm Program has germplasm for this animal, with the repository number 29443.</p><p dir="ltr">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 <a href="https://data.nal.usda.gov/dataset/angus-sequence-dataset-collection">Collection Dataset</a>. In the diagram, the two reads would correspond to read 1 and read 3.</p><p dir="ltr">Resources in this dataset:</p><p dir="ltr">tar file containing 14 files. The files are:</p><ul><li>RAPiD-Genomics_F112_CSU_136201_P001_WB09_i5-515_i7-117_S21_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics_F112_CSU_136201_P001_WB09_i5-515_i7-117_S21_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WB09-i5-515-i7-117_S157_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WB09-i5-515-i7-117_S157_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WB09-i5-515-i7-117_S21_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WB09-i5-515-i7-117_S21_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WB09-i5-515-i7-117_S21_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WB09-i5-515-i7-117_S21_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WB09_i5-515_i7-117_S21_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WB09_i5-515_i7-117_S21_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WB09_i5-515_i7-117_S21_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WB09_i5-515_i7-117_S21_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WB09_i5-515_i7-117_S376_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WB09_i5-515_i7-117_S376_L002_R2_001.fastq.gz</li></ul><p dir="ltr"><br></p>

Tags: animals, ars, cryopreservation, data-gov, dna-sequence, genetic-diversity, germplasm, grin, np101
Organization: Department of Agriculture
Angus Sequence Data: Animal 45052

<p dir="ltr">Whole genome sequence data for Bovidae Bos taurus - beef Angus. The data is in "fastq" format.</p><p dir="ltr">The National Animal Germplasm Program has germplasm for this animal, with the repository number 45052.</p><p dir="ltr">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 <a href="https://data.nal.usda.gov/dataset/angus-sequence-dataset-collection">Collection Dataset</a>. In the diagram, the two reads would correspond to read 1 and read 3.</p><p dir="ltr">Resources in this dataset:</p><p dir="ltr">tar file containing 14 files. The files are:</p><ul><li>RAPiD-Genomics_F112_CSU_136201_P001_WC05_i5-515_i7-125_S29_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics_F112_CSU_136201_P001_WC05_i5-515_i7-125_S29_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WC05-i5-515-i7-125_S165_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WC05-i5-515-i7-125_S165_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WC05-i5-515-i7-125_S29_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WC05-i5-515-i7-125_S29_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WC05-i5-515-i7-125_S29_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WC05-i5-515-i7-125_S29_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WC05_i5-515_i7-125_S29_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WC05_i5-515_i7-125_S29_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WC05_i5-515_i7-125_S29_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WC05_i5-515_i7-125_S29_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WC05_i5-515_i7-125_S384_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WC05_i5-515_i7-125_S384_L002_R2_001.fastq.gz</li></ul><p><br></p>

Tags: animals, ars, cryopreservation, data-gov, dna-sequence, genetic-diversity, germplasm, grin, np101
Organization: Department of Agriculture
Angus Sequence Data: Animal 29451

<p dir="ltr">Whole genome sequence data for Bovidae Bos taurus - beef Angus. The data is in "fastq" format.</p><p dir="ltr">The National Animal Germplasm Program has germplasm for this animal, with the repository number 29451.</p><p dir="ltr">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 <a href="https://data.nal.usda.gov/dataset/angus-sequence-dataset-collection">Collection Dataset</a>. In the diagram, the two reads would correspond to read 1 and read 3.</p><p dir="ltr">Resources in this dataset:</p><p dir="ltr">tar file containing 14 files. The files are:</p><ul><li>RAPiD-Genomics_F112_CSU_136201_P001_WB10_i5-515_i7-118_S22_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics_F112_CSU_136201_P001_WB10_i5-515_i7-118_S22_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WB10-i5-515-i7-118_S158_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WB10-i5-515-i7-118_S158_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WB10-i5-515-i7-118_S22_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WB10-i5-515-i7-118_S22_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WB10-i5-515-i7-118_S22_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WB10-i5-515-i7-118_S22_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WB10_i5-515_i7-118_S22_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WB10_i5-515_i7-118_S22_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WB10_i5-515_i7-118_S22_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WB10_i5-515_i7-118_S22_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WB10_i5-515_i7-118_S377_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WB10_i5-515_i7-118_S377_L002_R2_001.fastq.gz</li></ul><p dir="ltr"><br></p>

Tags: animals, ars, cryopreservation, data-gov, dna-sequence, genetic-diversity, germplasm, grin, np101
Organization: Department of Agriculture
Angus Sequence Data: Animal Donnie

<p dir="ltr">Whole genome sequence data for Bovidae Bos taurus - beef Angus. The data is in "fastq" format.</p><p dir="ltr">The National Animal Germplasm Program does not have germplasm for this animal.</p><p dir="ltr">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 <a href="https://data.nal.usda.gov/dataset/angus-sequence-dataset-collection">Collection Dataset</a>. In the diagram, the two reads would correspond to read 1 and read 3.</p><p dir="ltr">Resources in this dataset:</p><p dir="ltr">Resource Title: Animal Donnie Sequence Data - SCINet .</p><p dir="ltr">tar file containing 14 files. The files are:</p><ul><li>RAPiD-Genomics_F112_CSU_136201_P001_WA02_i5-515_i7-98_S2_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics_F112_CSU_136201_P001_WA02_i5-515_i7-98_S2_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA02-i5-515-i7-98_S138_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA02-i5-515-i7-98_S138_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA02-i5-515-i7-98_S2_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA02-i5-515-i7-98_S2_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WA02-i5-515-i7-98_S2_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WA02-i5-515-i7-98_S2_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA02_i5-515_i7-98_S2_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA02_i5-515_i7-98_S2_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA02_i5-515_i7-98_S2_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA02_i5-515_i7-98_S2_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WA02_i5-515_i7-98_S357_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WA02_i5-515_i7-98_S357_L002_R2_001.fastq.gz</li></ul><p dir="ltr"><br></p>

Tags: animals, ars, cryopreservation, data-gov, dna-sequence, genetic-diversity, germplasm, grin, np101
Organization: Department of Agriculture
Angus Sequence Data: Animal 103-3

<p dir="ltr">Whole genome sequence data for Bovidae Bos taurus - beef Angus. The data is in "fastq" format.</p><p dir="ltr">The National Animal Germplasm Program does not have germplasm for this animal.</p><p dir="ltr">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 <a href="https://data.nal.usda.gov/dataset/angus-sequence-dataset-collection">Collection Dataset</a> . In the diagram, the two reads would correspond to read 1 and read 3.</p><p dir="ltr">Resources in this dataset:</p><p dir="ltr">tar file containing 14 files. The files are:</p><ul><li>RAPiD-Genomics_F112_CSU_136201_P001_WA03_i5-515_i7-99_S3_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics_F112_CSU_136201_P001_WA03_i5-515_i7-99_S3_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA03-i5-515-i7-99_S139_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA03-i5-515-i7-99_S139_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA03-i5-515-i7-99_S3_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA03-i5-515-i7-99_S3_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WA03-i5-515-i7-99_S3_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WA03-i5-515-i7-99_S3_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA03_i5-515_i7-99_S3_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA03_i5-515_i7-99_S3_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA03_i5-515_i7-99_S3_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA03_i5-515_i7-99_S3_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WA03_i5-515_i7-99_S358_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WA03_i5-515_i7-99_S358_L002_R2_001.fastq.gz</li></ul><p><br></p>

Tags: animals, ars, cryopreservation, data-gov, dna-sequence, genetic-diversity, germplasm, grin, np101
Organization: Department of Agriculture
Angus Sequence Data: Animal 20544

<p dir="ltr">Whole genome sequence data for Bovidae Bos taurus - beef Angus. The data is in "fastq" format.</p><p dir="ltr">The National Animal Germplasm Program has germplasm for this animal, with the repository number 20544.</p><p dir="ltr">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 <a href="https://data.nal.usda.gov/dataset/angus-sequence-dataset-collection">Collection Dataset</a>. In the diagram, the two reads would correspond to read 1 and read 3.</p><p dir="ltr">Resources in this dataset:</p><p dir="ltr">tar file containing 14 files. The files are:</p><ul><li>RAPiD-Genomics_F112_CSU_136201_P001_WA08_i5-515_i7-104_S8_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics_F112_CSU_136201_P001_WA08_i5-515_i7-104_S8_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA08-i5-515-i7-104_S144_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA08-i5-515-i7-104_S144_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA08-i5-515-i7-104_S8_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA08-i5-515-i7-104_S8_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WA08-i5-515-i7-104_S8_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WA08-i5-515-i7-104_S8_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA08_i5-515_i7-104_S8_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA08_i5-515_i7-104_S8_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA08_i5-515_i7-104_S8_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA08_i5-515_i7-104_S8_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WA08_i5-515_i7-104_S363_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WA08_i5-515_i7-104_S363_L002_R2_001.fastq.gz</li></ul><p><br></p>

Tags: animals, ars, cryopreservation, data-gov, dna-sequence, genetic-diversity, germplasm, grin, np101
Organization: Department of Agriculture
Angus Sequence Data: Animal 400-1

<p dir="ltr">Whole genome sequence data for Bovidae Bos taurus - beef Angus. The data is in "fastq" format.</p><p dir="ltr">The National Animal Germplasm Program does not have germplasm for this animal.</p><p dir="ltr">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 <a href="https://data.nal.usda.gov/dataset/angus-sequence-dataset-collection">Collection Dataset</a>. In the diagram, the two reads would correspond to read 1 and read 3.</p><p dir="ltr">Resources in this dataset:</p><p dir="ltr">tar file containing 14 files. The files are:</p><ul><li>RAPiD-Genomics_F112_CSU_136201_P001_WA05_i5-515_i7-101_S5_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics_F112_CSU_136201_P001_WA05_i5-515_i7-101_S5_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA05-i5-515-i7-101_S141_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA05-i5-515-i7-101_S141_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA05-i5-515-i7-101_S5_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics-F113-CSU-136201-P001-WA05-i5-515-i7-101_S5_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WA05-i5-515-i7-101_S5_L003_R1_001.fastq.gz</li><li>RAPiD-Genomics-F114-CSU-136201-P001-WA05-i5-515-i7-101_S5_L003_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA05_i5-515_i7-101_S5_L001_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA05_i5-515_i7-101_S5_L001_R2_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA05_i5-515_i7-101_S5_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F115_CSU_136201_P001_WA05_i5-515_i7-101_S5_L002_R2_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WA05_i5-515_i7-101_S360_L002_R1_001.fastq.gz</li><li>RAPiD-Genomics_F116_CSU_136201_P001_WA05_i5-515_i7-101_S360_L002_R2_001.fastq.gz</li></ul><p dir="ltr"><br></p>

Tags: animals, ars, cryopreservation, data-gov, dna-sequence, genetic-diversity, germplasm, grin, np101
Organization: Department of Agriculture
Data from: Pathogenesis and transmission of reassorted H1 influenza A viruses detected in North American swine

<p dir="ltr">Changes in influenza viruses that infect pigs have been observed for over two decades. The evolution of these viruses has led to several new strains. For instance, one such strain known as H1N2 emerged to infect pigs in the United States in 2015. This virus recently gained prevalence after acquiring a new N1 gene. Our study aimed to determine if the new N1 gene was responsible for increased transmission of the virus among pigs. To investigate this hypothesis, we analyzed four different strains of H1N1 or H1N2 influenza A virus. Each strain had different combinations of N1 and N2 genes. We infected pigs with these viruses and observed their clinical signs as well as transmission to other pigs. Regardless of the viral genes present, all variants of the virus were transmitted from one infected pig to another at the same levels. Therefore, the new N1 gene did not seem to have direct importance in increasing the transmission of the virus. These results suggest that the increase in detection may be associated with less protection from previous vaccines or infections due to the change in N1 or N2, or changes related to pig management or movement. Understanding how influenza A viruses spread provides important insights for the swine industry for disease prevention and vaccine developers for vaccine strain selection.</p>

Tags: animal-health, bioinformatics, influenza-a-virus, pathogenesis, swine, transmission
Organization: Department of Agriculture
Data from: The importance of vertically stratified, multi-year sampling for understanding native bee assemblages in southeastern temperate deciduous forests

<p dir="ltr">We sampled and compared the bee assemblages of a temperate deciduous forest (Tuskegee National Forest, Tuskegee, Macon County, Alabama, USA) in both canopy and understory from April-October 2021 and March-October 2022. Blue vane traps were deployed at four sites across Tuskegee National Forest with four replicates per site. Each replicate had a blue vane in the understory (1m) and in the upper canopy (20 m average). In total, we captured 1,494 bees representing 38 taxa belonging to 15 genera and 5 families (Andrenidae, Apidae, Colletidae, Halictidae, and Megachilidae). Abundance varied seasonally and by year. The canopy traps produced 70% of all captures and there were almost three times as many bees in the canopy as in the understory. The four most commonly captured species (Lasioglossum bruneri, Melissodes bimaculatus, Augochlora pura, and Bombus impatiens) were present in significantly higher abundances in the canopy. We found no significant differences in species richness between the canopy and understory, but found that Simpson diversity was significantly different between strata. Interestingly, while overall and in 2021 Simpson diversity was higher in the canopy, in 2022 it was higher in the understory. </p>

Tags: blue-vane-trap, forest-canopy, native-bees, pollinators, temperate-forest, vertical-strata
Organization: Department of Agriculture
Data from: Tillage in southeastern U.S. row crops reduces ground-nesting bee incidence and diversity compared to field edges

<p dir="ltr">This dataset was collected to assess the response of ground-nesting bees to different agricultural management treatments while documenting key environmental variables. Data were collected from March 2021 to November 2022 at the E.V. Smith Research Center in Shorter, Alabama. The study site consisted of 96 experimental subplots arranged in a randomized block design within a long-established agricultural field. It provides valuable insights into the interactions between soil management practices, soil conditions, vegetation cover, and ground-nesting bee populations in agricultural landscapes. It may be useful for ecological modeling, particularly in understanding how management actions influence bee emergence. However, caution should be used in interpreting emergence trap data, as it does not represent floral visitation behavior.</p>

Tags: agricultural-methods, agricultural-sciences, agroecology, ground-nesting-bees, land-use, native-bees, pollinator-conservation, tillage, tillage-practices-included
Organization: Department of Agriculture
Data from: How you start matters: Density, resource size, and life stage impact population levels for pest insects

<p dir="ltr"><i>Tribolium castaneum</i>, the red flour beetle, is a key pest of cereal grains and products that routinely infests food processing facilities. Such facilities represent dynamic environments comprising patches of resources of variable size and quality. To understand the influence of resource availability, insect density, and initial life stage on population regulation in <i>T. castaneum</i>, this study assessed the carrying capacity and population growth rates of <i>T. castaneum </i>populations<i> </i>kept for 20 weeks in a closed environment on four different amounts of diet at four starting population levels, then compared <i>T. castaneum</i> attraction to, reproductive output on, and the volatile profiles of previously-infested (e.g., conditioned) flour. Resource availability (e.g. the amount of flour) interacted with founding population density and life stage to influence <i>T. castaneum </i>population dynamics. In resource-limited patches, carrying capacity estimates were similar across founding densities, but the effect of founding population density on carrying capacity increased with flour availability. The opposite was observed for population growth rate, which tended to be more variable for small patches but stabilized as resource availability increased. Interestingly, both effects were reduced for populations founded as larvae compared to those founded as adults. The volatile profile of conditioned flour was also influenced by the interaction of patch size, density, and life stage. The relative abundance of 1-pentadecene and benzoquinones tended to be reduced in the volatile profiles of large patches, whereas 4,8-dimethyldecanal comprised a higher proportion of the total volatile emissions. Conditioned flour from large patches tended to be more attractive to <i>T. castaneum </i>adults, although this effect decreased as founding density increased. By contrast, when populations were founded as larvae, the volatile profiles of <i>T. castaneum </i>attraction to, and <i>T. castaneum </i>fecundity on conditioned flours were similar. These findings expand our understanding of how resource limitation and density-dependent effects influence <i>T. castaneum </i>population regulation and behavior, with implications for long-term trap monitoring and population thresholds in stored products.</p>

Tags: anemotaxis, carrying-capacity-limitations, density-regulation, red-flour-beetle, semiochemicals, triboliiu-castaneum
Organization: Department of Agriculture