http://lod.bco-dmo.org/id/dataset/897977
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2023-06-27
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Pool-seq data from wild populations of copepods in the North Sea from May 2014 (Evolutionary genomics of a copepod project)
2023-06-27
publication
2023-06-27
revision
BCO-DMO Linked Data URI
2023-06-27
creation
http://lod.bco-dmo.org/id/dataset/897977
Carol E. Lee
University of Wisconsin
principalInvestigator
Juanita A. Diaz
University of Wisconsin
principalInvestigator
David B. Stern
University of Wisconsin
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Lee, C. E., Diaz, J. A., Stern, D. B. (2023) Pool-seq data from wild populations of copepods in the North Sea from May 2014 (Evolutionary genomics of a copepod project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-06-27 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/897977 [access date]
Pool-seq data from wild populations of copepods in the North Sea Dataset Description: <p>These data have been deposited in NCBI under BioProject number PRJNA923656.</p> Methods and Sampling: <p><strong>Methods and Sampling:</strong></p>
<p>Wild&nbsp;<em>Eurytemora affinis</em>&nbsp;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.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1658517 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1658517
onGoing
Carol E. Lee
University of Wisconsin
Department of Integrative BIology, Birge Hall 430 Lincoln Drive
Madison
WI
53706
USA
carollee@wisc.edu
pointOfContact
Juanita A. Diaz
University of Wisconsin
jdiaz22@wisc.edu
pointOfContact
David B. Stern
University of Wisconsin
862-703-6074
National Biodefense Analysis and Countermeasures Center 8300 Research Plaza
Frederick
Maryland
21702
USA
dstern7760@gmail.com
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Location
Collection_Date
Sample_Code
Sample_Salinity
Sample_Temperature
Latitude
Longitude
BioSample
SRA_Run
Illumina HiSeq 2000 sequencer
Bongo net
theme
None, User defined
site
date
sample identification
salinity
water temperature at measurement depth
latitude
longitude
NCBI BioSample accession
NCBI SRA run accession (SRR)
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Bongo Net
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Evolutionary Responses to Global Changes in Salinity and Temperature
https://osprey.bco-dmo.org/project/816918
Evolutionary Responses to Global Changes in Salinity and Temperature
<p>NSF Award Abstract:</p>
<p>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.</p>
<p>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.</p>
Evolutionary genomics of a copepod
largerWorkCitation
project
eng; USA
oceans
4.286
5.29
51.302
52.699
2014-05-01
2014-05-31
St. Lawrence estuary, Gulf of Mexico, Great Lakes, Baltic Sea
0
BCO-DMO catalogue of parameters from Pool-seq data from wild populations of copepods in the North Sea from May 2014 (Evolutionary genomics of a copepod project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/898362.rdf
Name: Location
Units: unitless
Description: <p>Location of sample site</p>
http://lod.bco-dmo.org/id/dataset-parameter/898363.rdf
Name: Collection_Date
Units: unitless
Description: <p>Date of sample collection in format YYYY-MM-DD</p>
http://lod.bco-dmo.org/id/dataset-parameter/898364.rdf
Name: Sample_Code
Units: unitless
Description: <p>Unique identifier for sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/898365.rdf
Name: Sample_Salinity
Units: Practical salinity units (PSU)
Description: <p>Sea surface salnity measured by refractometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/898366.rdf
Name: Sample_Temperature
Units: degrees Celsius
Description: <p>Sea surface temperature measured by thermometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/898367.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of collection location in decimal degrees. A positive value indicates a Northern coordinate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/898368.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of collection location in decimal degrees. A positive value indicates an Eastern coordinate.</p>
http://lod.bco-dmo.org/id/dataset-parameter/898369.rdf
Name: BioSample
Units: unitless
Description: <p>NCBI BioSample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/898370.rdf
Name: SRA_Run
Units: unitless
Description: <p>NCBI SRA Run number</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
https://osprey.bco-dmo.org/dataset/897977/data/download
download
onLine
dataset
<p><strong>Methods and Sampling:</strong></p>
<p>Wild&nbsp;<em>Eurytemora affinis</em>&nbsp;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.</p>
Specified by the Principal Investigator(s)
<p><strong>Processing notes from researcher:</strong></p>
<p>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.</p>
<p>The following software was&nbsp;used:<br />
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,&nbsp;<a href="https://github.com/TheDBStern/Baltic_Lab_Wild" target="_blank">https://github.com/TheDBStern/Baltic_Lab_Wild</a>&nbsp;(DOI:<a href="https://dx.doi.org/10.5281/zenodo.6615047" target="_blank">10.5281/zenodo.6615047</a>), https://github.com/juanitadiaz/Europe_Wild_LocalAdaptation_GeneFlow (DOI:10.5281/zenodo.7819560), https://github.com/carolindahms/TreeMix</p>
<p><strong>BCO-DMO Processing Notes</strong>:</p>
<ul>
<li>The submitted data file (named jdiaz_04.23_bco-dmo_metadatasheet-1.xlsx changed to 897977_v1_wild_pool-seq_data.csv post-processing&nbsp;</li>
</ul>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Illumina HiSeq 2000 sequencer
Illumina HiSeq 2000 sequencer
PI Supplied Instrument Name: Illumina HiSeq 2000 sequencer PI Supplied Instrument Description:Used to sequence pooled E. affinis samples. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Bongo net
Bongo net
PI Supplied Instrument Name: Bongo net PI Supplied Instrument Description:E. affinis samples were collected using a Bongo net with 100 μm mesh. Instrument Name: Bongo Net Instrument Short Name:Bongo Net Instrument 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 Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/NETT0009/