Dataset: Pool-seq data from laboratory selection lines of copepods collected from Kiel Canal in Germany in 2017 and 2018

ValidatedFinal no updates expectedDOI: 10.26008/1912/bco-dmo.878335.1Version 1 (2022-08-29)Dataset Type:experimental

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

The dataset contains pool-seq data from a laboratory natural selection experiment conducted on Eurytemora affinis. The E. affinis copepods used in the experiment were collected from Kiel Canal in Kiel, Germany in 2017 (approximately 1000 copepods) and on May 30, 2018 (85 gravid females and 40 juveniles). Individual adult copepods (N = 50; 25 male and 25 female) were collected for sequencing from each laboratory selection line at generations six (after one generation at 0 PSU in the treatment lin...

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Sampling and analytical procedures:
The Eurytemora affinis copepods used in the laboratory natural selection experiment were collected from Kiel Canal in Kiel, Germany (latitude = 54° 19' 59.88"N, longitude = 10° 9' 0"W) in 2017 (approximately 1000 copepods) and on May 30, 2018 (85 gravid females and 40 juveniles). Wild E. affinis populations were collected from eight locations in the Baltic Sea using bongo and WP2 nets with 100 μm mesh in 2019 (see related dataset 878322). The two collections of copepods were mixed and maintained at 15 PSU to increase population size and acclimate to laboratory conditions. Two samples of adult copepods (25 male and 25 female each) from the mixed culture were collected for pooled whole-genome sequencing (Pool-seq) to represent the starting population for the laboratory natural selection experiment and capture variance in starting SNP frequency. The culture was then split into 14 equally sized beakers. Control lines (N = 4) were maintained for the duration of the experiment in 15 PSU water made with Instant Ocean, along with Primaxin (20 milligrams per liter) to avoid bacterial infection. The control lines were fed the marine alga Rhodomonas salina every three to four days with the water changed weekly. The ten treatment lines were exposed to decreasing salinity over the first six generations until they reached 0 PSU (Lake Michigan water, ~300 µS/cm conductivity), and then maintained at 0 PSU for four additional generations.

Beginning at generation two, salinity declination proceeded at each generation as follows: 5 PSU, 1 PSU, 0.1 PSU, 0.01 PSU, 0 PSU. The generation number was monitored by assuming a generation time of approximately three weeks. Treatment lines were fed a 50:50 mixture of R. salina and the freshwater alga R. minuta at 5 PSU and only R. minuta at 1 PSU and below.

Individual adult copepods (N = 50; 25 male and 25 female) were collected for sequencing from each laboratory selection line at generations six (after one generation at 0 PSU in the treatment lines) and ten (after five generations at 0 PSU in the treatment lines). Sampled copepods from each line 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 Nextera DNA kit (Illumina Inc.) and sequenced on four lanes of Illumina Hi-Seq 4000 and one lane of Illumina NovaSeq 6000 at the University of Chicago Genomics Facility, generating an average of approximately 117 million paired-end (100 bp) reads per pool.


Related Datasets

IsRelatedTo

Dataset: Wild copepod pool-seq data
Lee, C. E., Diaz, J. A., Stern, D. B. (2023) Pool-seq data from wild populations of copepods in the North Sea from May 2014 (Evolutionary genomics of a copepod project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-06-27 http://lod.bco-dmo.org/id/dataset/897977
IsRelatedTo

Dataset: Evolve and re-sequence experiment - wild populations
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 doi:10.26008/1912/bco-dmo.878322.1
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