Dataset: Pooled sequencing data of field-collected Eurytemora affinis copepods from nine locations in North America collected October 2012 to March 2014

Final no updates expectedDOI: 10.26008/1912/bco-dmo.883227.1Version 1 (2022-11-12)Dataset Type:Other Field Results

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

Scientist: David B. Stern (University of Wisconsin)

BCO-DMO Data Manager: Dana Stuart Gerlach (Woods Hole Oceanographic Institution)

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

Abstract

This dataset consists of pooled whole-genome sequencing data (Pool-seq) of Eurytemora affinis complex copepods collected from nine locations across North America. Each sample consists of 100 pooled individuals with an approximate 1:1 sex ratio, sequenced using the Nextera DNA library preparation kit and Illumina HiSeq platform. Population sampling targeted nine wild populations of the E. affinis complex from two genetically distinct lineages (the Gulf and Atlantic clades) including both native ...

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Copepods were collected by Drs. Martin Bontrager, David B. Stern, and Carol E. Lee of the University of Wisconsin-Madison using plankton tows from nine locations across North America:

  • Braddock Bay, Lake Ontario, NY            (43.307, -77.706)
  • Milwaukee, Lake Michigan, WI               (43.051, -87.882)
  • Montmagny, St. Lawrence Estuary, QC  (46.99, -70.55)
  • L’Isle Verte, St. Lawrence Estuary, QC   (48.002, -69.423)
  • Lake Texoma, Red. River, OK                 (33.882, -96.797)
  • Lake Eufaula, Arkansas River, OK          (35.146, -95.627)
  • Louisville, Ohio River, KY                        (38.26, -85.747)
  • Cocodrie Bayou, Gulf of Mexico, LA       (29.254, -90.664)
  • Taylor Bayou, Gulf of Mexico, TX            (29.883, -94.051)

Population sampling targeted nine wild populations of the Eurytemora affinis complex (copepods) from two genetically distinct lineages (the Gulf and Atlantic clades) including both native saline and invaded freshwater locations. Salinity measurements from each sampling site were collected using a handheld refractometer.

Plankton was brought back to the lab and sorted.  Eurytemora affinis complex copepods were pooled into samples consisting of 100 individuals with an approximate 1:1 sex ratio, and subjected to DNA extraction. DNA sequencing data were collected using the Nextera DNA library preparation kit (Illumina, Inc., San Diego, CA, USA). Libraries were sequenced on an Illumina HiSeq platform at the University of Maryland, School of Medicine, Institute for Genome Sciences. The data were generated to investigate evolutionary genomic factors underlying successful invasion of freshwater habitats. Patterns of genetic diversity within and among populations were analyzed to detect signatures of natural selection.

Additional methods and results can be found in Stern & Lee (2020).
Scripts to process allele frequency files used in the PoolSeq analyses available in Stern (2022).
Sequence data is archived under NCBI BioProject PRJNA610547 (see Related Datasets below)

Related Datasets

IsSupplementedBy
Dataset: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA610547
University of Wisconsin - Madison. Eurytemora affinis pooled whole-genome sequencing. 2020/03. 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/PRJNA610547. NCBI:BioProject: PRJNA610547.

Related Publications

Results
Stern, D. B., & Lee, C. E. (2020). Evolutionary origins of genomic adaptations in an invasive copepod. Nature Ecology & Evolution, 4(8), 1084–1094. https://doi.org/10.1038/s41559-020-1201-y
Methods
Stern, D. B. (2022). TheDBStern/poolseq_utils: First release(Version v0.0.1) [Computer software]. Zenodo. https://doi.org/10.5281/ZENODO.7300110
Methods, Software
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., … Homer, N. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078–2079. doi:10.1093/bioinformatics/btp352
Software
Bushnell, B. (2014). BBTools software package. http://bbtools.jgi.doe.gov
Software
Foll, M., & Gaggiotti, O. (2008). A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective. Genetics, 180(2), 977–993. https://doi.org/10.1534/genetics.108.092221

Stern, D. B., Lee, C. E. (2022) Pooled sequencing data of field-collected Eurytemora affinis copepods from nine locations in North America collected October 2012 to March 2014. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-11-12 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.883227.1 [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