Pooled sequencing data of field-collected Eurytemora affinis copepods from nine locations in North America collected October 2012 to March 2014 (NCEI Accession 0291553)

This dataset contains biological and physical data collected in the Great Lakes from 2012-10-14 to 2014-03-21. These data include genetic material concentration and salinity. The instruments used to collect these data include Automated DNA Sequencer, Plankton Net, and Refractometer. These data were collected by Carol E. Lee and David B. Stern of University of Wisconsin as part of the "Evolutionary Responses to Global Changes in Salinity and Temperature (Evolutionary genomics of a copepod)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2022-11-14.

The following is the text of the dataset description provided by BCO-DMO:

Acquisition Description:
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)