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 saline and invaded freshwater locations. The data were generated to investigate evolutionary genomic factors underlying successful invasion of freshwater habitats and were collected by Drs. Martin Bontrager, David B. Stern, and Carol E. Lee of the University of Wisconsin-Madison.

Table of Contents

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

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)

Raw reads were trimmed and filtered of adapter sequences, low-complexity sequences and low-quality (Q<15) bases using BBDuk in the BBTools package (Bushnell, 2014). Processed reads were mapped to the repeat-masked E. affinis complex (Atlantic clade) draft reference genome using BWA-MEM v.0.7.17 (Li, 2013). Paired-end reads that did not align concordantly with BWA-MEM were aligned as single-end reads using NextGenMap v.0.5.5 (Sedlazeck et al., 2013) to aid in the alignment of diverged sequences. The combined read-mapping procedure achieved a mean mapping rate of 95.09 ± 1.42%. Duplicate reads were removed using Picard v.2.18.27 (Soifer, 2022) and regions around insertions or deletions were realigned using GATK v.3.8 (Van der Auwera & O'Connor, 2020). SAMtools v.1.3.1(Li et al., 2009) was used to convert BAM files into mpileup format after removing low-quality alignments and bases (Q<20). Sites within 3 bp (base pair) of an insertion or deletion were removed and the filtered mpileup was converted to sync format using PoPoolation2 (Kofler, Pandey, Schlotterer, 2011). The R package poolfstat v.1.0 (Gautier et al., 2021) was used to detect bi-allelic SNPs with a global minor allele frequency >0.05, at least four reads were required for a base call, and a minimum of 20 and a maximum of 200 total read counts were required for all populations. In total, 6,635,765 SNPs passed these filters when considering all nine populations. A total of 7,565,621 and 5,323,780 SNPs were called for the Atlantic and Gulf clades, respectively.

Software
(See also Related Publications section below)

• BBTools v38.33  (Bushnell, 2014)
• BWA-MEM v0.7.17  (Li, 2013)
• NextGenMap v0.5.5  (Sedlazeck, 2013)
• Picard v2.18.27  (Soifer, 2022)
• GATK v3.8  (Van der Auwera & O'Connor, 2020)
• SAMtools v1.3.1  (Li et al., 2009) 
• PoPoolation v1.2.2  (Kofler et al., 2011)
• PoPoolation2 v1.013  (Kofler, Pandey, Schlotterer, 2011)
• poolfstat v.1.0  (Gautier et al., 2021)
• TreeMix v1.13  (Pickrell & Pritchard, 2012)
• phytools v.0.6  (Revell, 2011)
• BayeScan 2, BayeScan 3  (Foll & Gaggiotti, 2008)
• BayPass v2.1  (Gautier, 2015)
• BetaScan2  (Siewert & Voight, 2020)
• GenMap  (Pockrandt et al., 2020) 
• edgeR  (Robinson et al, 2010)
• BedTools v2.28  (Quinlan & Hall, 2010)
• BEDOPS  (Neph et al., 2012)
• Gowinda  (Kofler & Schlotterer, 2012)
• custom code  (Stern, 2022 for https://github.com/TheDBStern/poolseq_utils)

BCO-DMO Processing
- Converted date to Y-M-D format
- Separated latitude and longitude into separate columns and converted to decimal degrees
- Added a column for BioProject
- Added dates of collection based on Supplemental File information
- Sorted by Collection_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.