http://lod.bco-dmo.org/id/dataset/883227
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
2022-11-03
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Pooled sequencing data of field-collected Eurytemora affinis copepods from nine locations in North America collected October 2012 to March 2014
2022-11-12
publication
2022-11-12
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-11-14
publication
https://doi.org/10.26008/1912/bco-dmo.883227.1
Carol E. Lee
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: Stern, D. B., Lee, C. E. (2022) Pooled sequencing data of field-collected Eurytemora affinis copepods from nine locations in North America collected October 2012 to March 2014. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-11-12 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.883227.1 [access date]
Methods and Sampling: <p>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:</p>
<ul>
<li>Braddock Bay, Lake&nbsp;Ontario, NY&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (43.307, -77.706)</li>
<li>Milwaukee, Lake&nbsp;Michigan, WI&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;(43.051, -87.882)</li>
<li>Montmagny, St. Lawrence Estuary, QC&nbsp; (46.99, -70.55)</li>
<li>L’Isle Verte, St. Lawrence Estuary, QC&nbsp; &nbsp;(48.002, -69.423)</li>
<li>Lake Texoma, Red. River, OK&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;(33.882, -96.797)</li>
<li>Lake Eufaula, Arkansas River, OK&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (35.146, -95.627)</li>
<li>Louisville, Ohio River, KY&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (38.26, -85.747)</li>
<li>Cocodrie Bayou, Gulf of Mexico, LA&nbsp; &nbsp; &nbsp; &nbsp;(29.254, -90.664)</li>
<li>Taylor Bayou, Gulf of Mexico, TX&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (29.883, -94.051)</li>
</ul>
<p>Population sampling targeted nine wild populations of the&nbsp;<em>Eurytemora affinis</em>&nbsp;complex (copepods)&nbsp;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.</p>
<p>Plankton was brought back to the lab and sorted. &nbsp;<em>Eurytemora affinis</em> 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.</p>
<p>Additional methods and results can be found in Stern &amp; Lee (2020).<br />
Scripts to process allele frequency files used in the PoolSeq analyses available in Stern (2022).<br />
Sequence data is archived under NCBI BioProject PRJNA610547 (see Related Datasets below)</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
completed
Carol E. Lee
University of Wisconsin
Department of Integrative BIology, Birge Hall 430 Lincoln Drive
Madison
WI
53706
USA
carollee@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
BioProject
Collection_Date
Latitude
Longitude
geo_loc_name
Salinity
Origin
Run
Bases
BioSample
Experiment
Library_Name
Instrument
Illumina HiSeq 2000
handheld refractometer
theme
None, User defined
NCBI BioProject accession
date
latitude
longitude
site
salinity
sample description
NCBI SRA run accession (SRR)
genetic material concentration
NCBI BioSample accession
NCBI SRA experiment accession (SRX)
sample identification
instrument
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Plankton Net
Refractometer
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
biota
oceans
-96.797
-69.423
29.254
48.002
2012-10-14
2014-03-21
St. Lawrence estuary, Gulf of Mexico, Great Lakes, Baltic Sea
0
BCO-DMO catalogue of parameters from Pooled sequencing data of field-collected Eurytemora affinis copepods from nine locations in North America collected October 2012 to March 2014
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/883649.rdf
Name: BioProject
Units: unitless
Description: <p>NCBI BioProject identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/883650.rdf
Name: Collection_Date
Units: unitless
Description: <p>Date of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/883651.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of copepod sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/883652.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of copepod sample collection (West is negative)</p>
http://lod.bco-dmo.org/id/dataset-parameter/883653.rdf
Name: geo_loc_name
Units: unitless
Description: <p>Country and location of copepod sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/883654.rdf
Name: Salinity
Units: PSU
Description: <p>Water salinity of collected sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/883655.rdf
Name: Origin
Units: unitless
Description: <p>Copepod origin indicating whether the population was native or invasive</p>
http://lod.bco-dmo.org/id/dataset-parameter/883656.rdf
Name: Run
Units: unitless
Description: <p>NCBI SRA run number</p>
http://lod.bco-dmo.org/id/dataset-parameter/883657.rdf
Name: Bases
Units: unitless
Description: <p>Total sequenced DNA bases</p>
http://lod.bco-dmo.org/id/dataset-parameter/883658.rdf
Name: BioSample
Units: unitless
Description: <p>NCBI BioSample number</p>
http://lod.bco-dmo.org/id/dataset-parameter/883659.rdf
Name: Experiment
Units: unitless
Description: <p>NCBI SRA experiment number</p>
http://lod.bco-dmo.org/id/dataset-parameter/883660.rdf
Name: Library_Name
Units: unitless
Description: <p>Sample code</p>
http://lod.bco-dmo.org/id/dataset-parameter/883661.rdf
Name: Instrument
Units: unitless
Description: <p>Illumina sequencing instrument used to generate the data</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
1557
https://darchive.mblwhoilibrary.org/bitstream/1912/29502/1/dataset-883227_pooled-sequencing-data-field-collected-eurytemora-affinis__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.883227.1
download
onLine
dataset
<p>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:</p>
<ul>
<li>Braddock Bay, Lake&nbsp;Ontario, NY&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (43.307, -77.706)</li>
<li>Milwaukee, Lake&nbsp;Michigan, WI&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;(43.051, -87.882)</li>
<li>Montmagny, St. Lawrence Estuary, QC&nbsp; (46.99, -70.55)</li>
<li>L’Isle Verte, St. Lawrence Estuary, QC&nbsp; &nbsp;(48.002, -69.423)</li>
<li>Lake Texoma, Red. River, OK&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;(33.882, -96.797)</li>
<li>Lake Eufaula, Arkansas River, OK&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (35.146, -95.627)</li>
<li>Louisville, Ohio River, KY&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (38.26, -85.747)</li>
<li>Cocodrie Bayou, Gulf of Mexico, LA&nbsp; &nbsp; &nbsp; &nbsp;(29.254, -90.664)</li>
<li>Taylor Bayou, Gulf of Mexico, TX&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; (29.883, -94.051)</li>
</ul>
<p>Population sampling targeted nine wild populations of the&nbsp;<em>Eurytemora affinis</em>&nbsp;complex (copepods)&nbsp;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.</p>
<p>Plankton was brought back to the lab and sorted. &nbsp;<em>Eurytemora affinis</em> 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.</p>
<p>Additional methods and results can be found in Stern &amp; Lee (2020).<br />
Scripts to process allele frequency files used in the PoolSeq analyses available in Stern (2022).<br />
Sequence data is archived under NCBI BioProject PRJNA610547 (see Related Datasets below)</p>
Specified by the Principal Investigator(s)
<p><strong>Raw reads</strong> were trimmed and filtered of adapter sequences, low-complexity sequences and low-quality (Q&lt;15) bases using BBDuk in the BBTools package (Bushnell, 2014). <strong>Processed read</strong>s were mapped to the repeat-masked <em>E. affinis</em> complex (Atlantic clade) draft reference genome using BWA-MEM v.0.7.17 (Li, 2013). <strong>Paired-end read</strong>s that did not align concordantly with BWA-MEM were aligned as single-end reads using NextGenMap v.0.5.5 (Sedlazeck et al., 2013)&nbsp;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 &amp; 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&lt;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,&nbsp;2011). The R package poolfstat v.1.0 (Gautier et al., 2021)&nbsp;was used to detect bi-allelic SNPs with a global minor allele frequency &gt;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.</p>
<p><strong>Software</strong><br />
(See also&nbsp;Related Publications section below)</p>
<ul>
<li>BBTools v38.33&nbsp;&nbsp;(Bushnell, 2014)</li>
<li>BWA-MEM v0.7.17&nbsp; (Li, 2013)</li>
<li>NextGenMap v0.5.5&nbsp; (Sedlazeck, 2013)</li>
<li>Picard v2.18.27&nbsp; (Soifer, 2022)</li>
<li>GATK v3.8&nbsp; (Van der Auwera &amp; O'Connor, 2020)</li>
<li>SAMtools v1.3.1&nbsp; (Li et al., 2009)&nbsp;</li>
<li>PoPoolation v1.2.2&nbsp;&nbsp;(Kofler et al., 2011)</li>
<li>PoPoolation2 v1.013&nbsp; (Kofler, Pandey, Schlotterer, 2011)</li>
<li>poolfstat v.1.0&nbsp; (Gautier et al., 2021)</li>
<li>TreeMix v1.13&nbsp; (Pickrell &amp; Pritchard, 2012)</li>
<li>phytools v.0.6&nbsp; (Revell, 2011)</li>
<li>BayeScan 2, BayeScan 3&nbsp; (Foll &amp; Gaggiotti, 2008)</li>
<li>BayPass v2.1&nbsp; (Gautier, 2015)</li>
<li>BetaScan2&nbsp; (Siewert &amp; Voight, 2020)</li>
<li>GenMap&nbsp; (Pockrandt et al., 2020)&nbsp;</li>
<li>edgeR&nbsp; (Robinson et al, 2010)</li>
<li>BedTools v2.28&nbsp; (Quinlan &amp; Hall, 2010)</li>
<li>BEDOPS&nbsp; (Neph et al., 2012)</li>
<li>Gowinda&nbsp; (Kofler &amp; Schlotterer, 2012)</li>
<li>custom code&nbsp; (Stern, 2022 for https://github.com/TheDBStern/poolseq_utils)</li>
</ul>
<p><strong>BCO-DMO Processing</strong><br />
- Converted date to Y-M-D format<br />
-&nbsp;Separated latitude and longitude into separate columns and converted to decimal degrees<br />
- Added a column for BioProject<br />
- Added dates of collection based on Supplemental File information<br />
- Sorted by Collection_Date<br />
&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
Illumina HiSeq 2000
PI Supplied Instrument Name: Illumina HiSeq 2000 PI Supplied Instrument Description:Libraries were sequenced on an Illumina HiSeq platform at the University of Maryland, School of Medicine, Institute for Genome Sciences. 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.
PI Supplied Instrument Name: Instrument Name: Plankton Net Instrument Short Name:Plankton Net Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/22/
handheld refractometer
handheld refractometer
PI Supplied Instrument Name: handheld refractometer PI Supplied Instrument Description:Salinity measurements from each sampling site were collected using a handheld refractometer. Instrument Name: Refractometer Instrument Short Name:Refractometer Instrument 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.