Dataset: Wild copepod pool-seq data

Name: Pool-seq data from wild populations of copepods in the North Sea from May 2014 (Evolutionary genomics of a copepod project)
Published: 2023-06-27
Keywords: oceans

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Spatial Extent: N:52.699 E:5.29 S:51.302 W:4.286

Temporal Extent: 2014-05 - 2014-05

Project:

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

Principal Investigator:

Carol E. Lee (University of Wisconsin, UW-Madison)

Scientist:

Juanita A. Diaz (University of Wisconsin, UW-Madison)

David B. Stern (University of Wisconsin, UW-Madison)

Contact:

Juanita A. Diaz (University of Wisconsin, UW-Madison)

Carol E. Lee (University of Wisconsin, UW-Madison)

BCO-DMO Data Manager:

Sawyer Newman (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2023-06-27

Restricted:

Validated:

Current State:

Preliminary and in progress

Pool-seq data from wild populations of copepods in the North Sea from May 2014 (Evolutionary genomics of a copepod project)

Abstract:

This dataset was generated from studies of wild populations of Eurytemora affinis (E. affinis). Copepod populations were collected from three locations in the North Sea using bongo nets with 100 micrometer (μm) mesh and stored in RNAlater. Sampling locations included two freshwater lakes and one brackish estuary. Individual copepods (100 individuals, 50:50 male:female) were pooled and their DNA was extracted. Paired-end whole-genome sequencing libraries were prepared using the Illumina Nextera DNA kit (Illumina, Inc.) and sequenced on three lanes of an Illumina HiSeq 2000 sequencer, generating an average of approximately 158 million paired-end (100 bp) reads per pool. These data have been deposited in the National Center for Biotechnology Information (NCBI) under BioProject number PRJNA923656.

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Description

These data have been deposited in NCBI under BioProject number PRJNA923656.

Methods & Sampling

Methods and Sampling:

Wild Eurytemora affinis populations were collected from three locations in the North Sea using bongo nets with 100 micrometer (μm) mesh. Copepods were stored in RNAlater. Sampling locations included two fresh water lakes and one brackish estuary. From each population, individual copepods (100 individuals, 50:50 male:female) 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 Illumina Nextera DNA kit (Illumina, Inc.) and sequenced on three lanes of an Illumina HiSeq 2000 sequencer at the Maryland Institute of Genome Science, generating an average of approximately 158 million paired-end (100 bp) reads per pool.

Data Processing Description

Processing notes from researcher:

Raw sequence reads were mapped to a reference genome to call SNPs. We then detected SNPs with significant signatures of selection across temperature and salinity gradients. Signatures of selection were detected using an outlier approach and an association with an environmental variable (i.e., temperature or salinity) approach.

The following software was used:
BayPass v.2.2, BEDOPS v.2.4.39, BITE v.1.2.8, BLAST 2.7.1+, BWA-MEM v.0.7.17, GATK v.3.8, Gowinda v.1.12, ggplot2 v.3.3.5, gplots v.3.1.3, OptM v.0.1.6, PHYLIP v.3.697, Picard v. 2.18.27, poolfstat v.1.0, poolfstat v.2.1.1, PoPoolation v.1.2.2, PoPoolation2 v.1.201, SAMtools v.1.3.1, stats v.4.1.2, TreeMix v.1.13, Trimmomatic v.0.39, VarScan v.2.4.3, vegan v.2.6-2, https://github.com/TheDBStern/Baltic_Lab_Wild (DOI:10.5281/zenodo.6615047), https://github.com/juanitadiaz/Europe_Wild_LocalAdaptation_GeneFlow (DOI:10.5281/zenodo.7819560), https://github.com/carolindahms/TreeMix

BCO-DMO Processing Notes:

The submitted data file (named jdiaz_04.23_bco-dmo_metadatasheet-1.xlsx changed to 897977_v1_wild_pool-seq_data.csv post-processing

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1658517

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Illumina HiSeq 2000 sequencer

Supplied Description:

Used to sequence pooled E. affinis samples.

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Bongo Net

Supplied Name: Bongo net

Supplied Description:

E. affinis samples were collected using a Bongo net with 100 μm mesh.

Instrument Type

Generic Name: Bongo Net

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/NETT0009/

Generic Description:

A Bongo Net consists of paired plankton nets, typically with a 60 cm diameter mouth opening and varying mesh sizes, 10 to 1000 micron. The Bongo Frame was designed by the National Marine Fisheries Service for use in the MARMAP program. It consists of two cylindrical collars connected with a yoke so that replicate samples are collected at the same time. Variations in models are designed for either vertical hauls (OI-2500 = NMFS Pairovet-Style, MARMAP Bongo, CalVET) or both oblique and vertical hauls (Aquatic Research). The OI-1200 has an opening and closing mechanism that allows discrete "known-depth" sampling. This model is large enough to filter water at the rate of 47.5 m3/minute when towing at a speed of two knots. More information: Ocean Instruments, Aquatic Research, Sea-Gear

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Location	Location of sample site	unitless	site
Collection_Date	Date of sample collection in format YYYY-MM-DD Format: %Y-%m-%d	unitless	date
Sample_Code	Unique identifier for sample	unitless	sample
Sample_Salinity	Sea surface salnity measured by refractometer	Practical salinity units (PSU)	sal
Sample_Temperature	Sea surface temperature measured by thermometer	degrees Celsius	temp
Latitude	Latitude of collection location in decimal degrees. A positive value indicates a Northern coordinate.	decimal degrees	lat
Longitude	Longitude of collection location in decimal degrees. A positive value indicates an Eastern coordinate.	decimal degrees	lon
BioSample	NCBI BioSample ID	unitless	BioSample
SRA_Run	NCBI SRA Run number	unitless	SRA_run

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Dataset: Wild copepod pool-seq data