Dataset: Evolve and re-sequence experiment - wild populations

Name: Pool-seq data from wild populations of copepods in the Baltic Sea from May 2018 through August 2019
Published: 2022-08-11
Keywords: epistasis, parallel evolution, evolve, resequence, biota, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.878322.1

Spatial Extent: N:65.3836 E:23.7097 S:54.3333 W:10.15

Temporal Extent: 2018-05 - 2019-08

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)

Contact:

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

BCO-DMO Data Manager:

Taylor Heyl (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-08-11

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Pool-seq data from wild populations of copepods in the Baltic Sea from May 2018 through August 2019

Abstract:

This dataset was generated from studies of wild populations of Eurytemora affinis (E. affinis). Copepod populations were collected from eight locations in the Baltic Sea using bongo and WP2 nets with 100 micrometer (μm) mesh and stored in RNAlater. Sampling locations spanned a range of mean annual salinities from low (~3 PSU) to higher (~19 PSU). Individual copepods (ranging from 50 to 200 in number) 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 five lanes of an Illumina HiSeq 4000 sequencer, generating an average of approximately 176 million paired-end (100 bp) reads per pool. These data have been deposited in the National Center for Biotechnology Information (NCBI) under BioProject number PRJNA844002.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2022-08-11	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.878322.1	2022-09-08

Methods & Sampling

Sampling and analytical procedures:
Wild Eurytemora affinis populations were collected from eight locations in the Baltic Sea using bongo and WP2 nets with 100 micrometer (μm) mesh. Copepods were stored in RNAlater. Sampling locations spanned a range of mean annual salinities from low (~3 PSU) to higher (~19 PSU). From each population, individual copepods (ranging from 50 to 200 in number) 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 five lanes of an Illumina HiSeq 4000 sequencer at the University of Chicago Genomics Facility, generating an average of approximately 176 million paired-end (100 bp) reads per pool.

Data Processing Description

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;
- Replaced commas with semicolons in the "Location" column.

Data Files

File
wild_samples-1.csv (Comma Separated Values (.csv), 839 bytes) MD5:a0b3735148c7e931c72ea850f3bdc54e Primary data file for dataset ID 878322

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 4000 sequencer

Supplied Description:

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:

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

CTD - fixed

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: CTD - fixed

Generic Description:

A reusable instrument that always simultaneously measures conductivity and temperature (for salinity) and pressure (for depth).

This term applies to CTDs that are fixed and do not measure by profiling through the water column. For profiling CTDs, see https://www.bco-dmo.org/instrument/417.

WP-2 Plankton Net

Supplied Name: WP-2 Net

Supplied Description:

WP2 net with 100 μm mesh

Instrument Type

Generic Name: WP-2 Plankton Net

Acronym: WP-2

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/NETT0168/

Generic Description:

The WP-2 net is a variety of Ring Net for zooplankton but which is capable of being closed by means of a Nansen bottle-type release messenger weighing 0.8 kg and which can be equipped with a digital flow meter for determining the amount of water passing through the plankton net. The rings may have a variety of sizes (57cm, 70cm, 75 cm, or 1m internal diameter) and the nets which make up this device are in two parts, a cylindrical upper part and a conical lower part. The closing ring is between the two net segments. (more at KC Denmark)

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Location	Location of site, station ID	unitless	region
Collection_Date	Date of sample collection in format YYYY-MM Format: %Y-%m	unitless	date
Sample_Code	unique identifier for sample	unitless	sample
Sample_Salinity	Average water column salinity measured by CTD	Practical salinity units (PSU)	sal
Latitude	Latitude North of collection location	decimal degrees	lat
Longitude	Longitude East (West is negative) of collection location	decimal degrees	lon
BioSample	NCBI BioSample	unitless	BioSample
SRA_Run	NCBI SRA Run number	unitless	SRA_sample

Status message

Database

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Dataset: Evolve and re-sequence experiment - wild populations