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 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. These data have been deposited in NCBI under BioProject number PRJNA844002.

Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Related Publications
• Related Datasets
• Parameters
• Instruments
• Project Information
• Funding

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.

Raw sequence reads were mapped to a reference genome to call SNPs. We then detected SNPs and genomic regions under natural selection in response to salinity change.

The following software was used:
BLAST 2.7.1+, BWA-MEM v0.7.17, CD-HIT v4.7, PoPoolation2, SAMBLASTER v0.1.26, Samtools v1.3.1, Trinity v2.6.6, VarScan v2.4.3, BioPython v1.78, numpy v1.15.2, lme4 v1.1.21, poolfstat v1.1.1, qvalue v2.14.1, ACER v1.0.2, haplovalidate v0.1.4, BBTools v38, BEDOPS v2.4.39, Bowtie v2.3.5, Gowinda v1.12, HMMER v3.2.1, SLiM v3.7, RSEM v1.3.1, Transdecoder v5.5, Trimmomatic v0.39, TreeMix v1.13, https://github.com/jjberg2/PolygenicAdaptationCode, wtdbg v2.5, Racon v1.4.3, LiftOff v1.6.1, https://github.com/TheDBStern/Baltic_Lab_Wild (DOI:10.5281/zenodo.6615047)

These data have been deposited in NCBI under BioProject number PRJNA844002.

BCO-DMO Processing Description:
- Adjusted field/parameter names to comply with BCO-DMO naming conventions;
- Added a conventional header with dataset name, PI names, version date.

Coverage: St. Lawrence estuary, Gulf of Mexico, Great Lakes, Baltic Sea

NSF Award Abstract:

Drastic changes in the global water cycle and increases in ice melt are causing the freshening of Northern coastal seas. The combination of both reduced salinity and increased temperature will likely act in concert to reduce populations of estuarine and marine organisms. Data indicate that reduced salinity and high temperature would each increase the energy costs as well as reduce survival and reproduction of the common copepod Eurytemora affinis. This project will examine the joint effects of salinity reduction and temperature increase on the evolutionary responses of populations of E. affinis in the wild, as well as in selection experiments in the laboratory. This study will provide novel insights into responses of organisms to climate change, as no study has analyzed the joint impacts of salinity and temperature on evolutionary responses, and relatively few studies have examined the impacts of declining salinity. In general, how selection acts at the whole genome level is not well understood, particularly for non-model organisms. As a dominant estuarine copepod, E. affinis is among the most important species sustaining coastal food webs and fisheries in the Northern Hemisphere, such as salmon, herring, and anchovy. Thus, insights into its evolutionary responses with changing climate have important implications for sustainability of fisheries and food security. Two graduate students from historically underrepresented groups will be trained during this project. The project will have additional societal benefits, including development of educational modules for K-12 students and international collaboration.

This study will address the following questions: (1) To what extent could populations evolve in response to salinity and temperature change, and what are the fitness and physiological costs? (2) How will populations respond to the impacts of salinity-temperature interactions? (3) Do wild populations show evidence of natural selection in response to salinity and temperature? To analyze the evolutionary responses of E. affinis populations to the coupled impacts of salinity and temperature, the investigator will perform laboratory selection experiments and population genomic surveys of wild populations. Selection experiments constitute powerful tools for determining the rate, trajectory, and limits of adaptation. During laboratory selection, evolutionary shifts in fitness-related traits and genomic expression will be examined, as well as genomic signatures of selection in response to low salinity and high temperature selection regimes. The investigator will also conduct population genomic sequencing of E. affinis populations that reside along salinity and temperature gradients in the St. Lawrence and Baltic Sea, and identify genes that show signatures of selection. The project will determine whether the loci that show signatures of selection in the wild populations are the same as those favored during laboratory selection. This reproducibility will provide greater confidence that the genes involved in adaptation to salinity and/or temperature have been captured.