Dataset: Pooled sequencing data from field-collected Eurytemora affinis

Name: Pooled sequencing data of field-collected Eurytemora affinis copepods from nine locations in North America collected October 2012 to March 2014
Published: 2022-11-12
Keywords: genomics, salinity adaptation, Marine invasion, selection, biota, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.883227.1

Spatial Extent: N:48.002 E:-69.423 S:29.254 W:-96.797

Temporal Extent: 2012 - 2014

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:

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

BCO-DMO Data Manager:

Dana Stuart Gerlach (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-11-12

Restricted:

Validated:

Yes

Current State:

Final no updates expected

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

Abstract:

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.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2022-11-12	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.883227.1	2022-11-14

Methods & Sampling

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)

Data Processing Description

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

Data Files

File
pooled_sequence.csv (Comma Separated Values (.csv), 1.52 KB) MD5:49100700996893c40ca155f9302e8355 Primary data file for dataset ID 883227

Supplemental Files

File
Copepod sampling dates and locations filename: Copepod_sampling_dates_locations.pdf (Portable Document Format (.pdf), 26.09 KB) MD5:8e8166ef7edf9de0ae86600e091af9d0 Copepod sampling dates and locations

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

Supplied Description:

Libraries were sequenced on an Illumina HiSeq platform at the University of Maryland, School of Medicine, Institute for Genome Sciences.

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.

Plankton Net

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Plankton Net

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/22/

Generic Description:

A Plankton Net is a generic term for a sampling net that is used to collect plankton. It is used only when detailed instrument documentation is not available.

Refractometer

Supplied Name: handheld refractometer

Supplied Description:

Salinity measurements from each sampling site were collected using a handheld refractometer.

Instrument Type

Generic Name: Refractometer

Generic Description:

A refractometer is a laboratory or field device for the measurement of an index of refraction (refractometry). The index of refraction is calculated from Snell's law and can be calculated from the composition of the material using the Gladstone-Dale relation.

In optics the refractive index (or index of refraction) n of a substance (optical medium) is a dimensionless number that describes how light, or any other radiation, propagates through that medium.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
BioProject	NCBI BioProject identifier	unitless	BioProject
Collection_Date	Date of sample collection Format: %Y-%m-%d	unitless	date
Latitude	Latitude of copepod sample collection	decimal degrees	lat
Longitude	Longitude of copepod sample collection (West is negative)	decimal degrees	lon
geo_loc_name	Country and location of copepod sample collection	unitless	site
Salinity	Water salinity of collected sample	PSU	sal
Origin	Copepod origin indicating whether the population was native or invasive	unitless	sample_descrip
Run	NCBI SRA run number	unitless	SRA_run
Bases	Total sequenced DNA bases	unitless	genetic_conc
BioSample	NCBI BioSample number	unitless	BioSample
Experiment	NCBI SRA experiment number	unitless	SRA_experiment
Library_Name	Sample code	unitless	sample
Instrument	Illumina sequencing instrument used to generate the data	unitless	instrument

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Database

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Dataset: Pooled sequencing data from field-collected Eurytemora affinis