Dataset: Pool-seq data from wild populations of copepods in the Baltic Sea from May 2018 through August 2019

Final no updates expectedDOI: 10.26008/1912/bco-dmo.878322.1Version 1 (2022-08-11)Dataset Type:Other Field Results

Principal Investigator: Carol E. Lee (University of Wisconsin)

Contact: David B. Stern (University of Wisconsin)

BCO-DMO Data Manager: Taylor Heyl (Woods Hole Oceanographic Institution)

BCO-DMO Data Manager: Shannon Rauch (Woods Hole Oceanographic Institution)

Project: Evolutionary Responses to Global Changes in Salinity and Temperature (Evolutionary genomics of a copepod)

Abstract

This dataset was generated from studies of wild populations of Eurytemora affinis (E. affinis). Copepod populations were collected from eight locations in the Baltic Sea using bongo and WP2 nets with 100 micrometer (μm) mesh and stored in RNAlater. Sampling locations spanned a range of mean annual salinities from low (~3 PSU) to higher (~19 PSU). Individual copepods (ranging from 50 to 200 in number) were pooled and their DNA was extracted. Paired-end whole-genome sequencing libraries were prepa...

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Sampling and analytical procedures:
Wild Eurytemora affinis populations were collected from eight locations in the Baltic Sea using bongo and WP2 nets with 100 micrometer (μm) mesh. Copepods were stored in RNAlater. Sampling locations spanned a range of mean annual salinities from low (~3 PSU) to higher (~19 PSU). From each population, individual copepods (ranging from 50 to 200 in number) were pooled and their DNA was extracted using the DNeasy Blood and Tissue Extraction kit (Qiagen, Inc.). Paired-end whole-genome sequencing libraries were prepared using the Illumina Nextera DNA kit (Illumina, Inc.) and sequenced on five lanes of an Illumina HiSeq 4000 sequencer at the University of Chicago Genomics Facility, generating an average of approximately 176 million paired-end (100 bp) reads per pool.

Related Datasets

IsRelatedTo
Dataset: Evolve and re-sequence experiment - laboratory selection lines
Lee, C. E., Stern, D. B. (2022) Pool-seq data from laboratory selection lines of copepods collected from Kiel Canal in Germany in 2017 and 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-08-29 doi:10.26008/1912/bco-dmo.878335.1
IsRelatedTo
Dataset: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA844002
University of Wisconsin - Madison. Genome-wide signatures of synergistic epistasis during parallel adaptation in a Baltic Sea copepod. 2022/05. In: BioProject [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; 2011-. Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA844002. NCBI:BioProject: PRJNA844002.

Related Publications

Results
Stern, D. B., Anderson, N. W., Diaz, J. A., & Lee, C. E. (2022). Genome-wide signatures of synergistic epistasis during parallel adaptation in a Baltic Sea copepod. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-31622-8
Software
Juanitadiaz, & Stern, D. B. (2022). TheDBStern/Baltic_Lab_Wild: First release (Version v0.0.1) [Computer software]. Zenodo. https://doi.org/10.5281/ZENODO.6615047

Lee, C. E., Stern, D. B. (2022) Pool-seq data from wild populations of copepods in the Baltic Sea from May 2018 through August 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-08-11 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.878322.1 [access date]

Terms of Use

This dataset is licensed under Creative Commons Attribution 4.0.


If you wish to use this dataset, it is highly recommended that you contact the original principal investigators (PI). Should the relevant PI be unavailable, please contact BCO-DMO (info@bco-dmo.org) for additional guidance. For general guidance please see the BCO-DMO Terms of Use document.

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Funded by the U.S. National Science Foundation