http://lod.bco-dmo.org/id/dataset/878322
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
2022-08-11
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 Baltic Sea from May 2018 through August 2019
2022-08-11
publication
2022-08-11
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-09-08
publication
https://doi.org/10.26008/1912/bco-dmo.878322.1
Carol E. Lee
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
documentDigital
Cite this dataset as: Lee, C. E., Stern, D. B. (2022) Pool-seq data from wild populations of copepods in the Baltic Sea from May 2018 through August 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-08-11 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.878322.1 [access date]
Acquisition Description: <p><strong>Sampling and analytical procedures: </strong><br />
Wild <em>E. affinis</em> 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 salinity (~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.</p>
<p>&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1658517 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=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
asNeeded
Dataset Version: 1
Unknown
Location
Collection_Date
Sample_Code
Sample_Salinity
Latitude
Longitude
BioSample
SRA_Run
Bongo net
WP-2 Net
Illumina HiSeq 4000 sequencer
theme
None, User defined
region
date
sample identification
salinity
latitude
longitude
NCBI BioSample accession
NCBI SRA Sample accession
featureType
BCO-DMO Standard Parameters
Bongo Net
WP-2 Plankton Net
Automated DNA Sequencer
CTD
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://www.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
10.15
23.7097
54.3333
65.3836
2018-05-01
2019-08-31
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 Baltic Sea from May 2018 through August 2019
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/878373.rdf
Name: Location
Units: unitless
Description: Location of site, station ID
http://lod.bco-dmo.org/id/dataset-parameter/878374.rdf
Name: Collection_Date
Units: unitless
Description: Date of sample collection in format YYYY-MM
http://lod.bco-dmo.org/id/dataset-parameter/878375.rdf
Name: Sample_Code
Units: unitless
Description: unique identifier for sample
http://lod.bco-dmo.org/id/dataset-parameter/878376.rdf
Name: Sample_Salinity
Units: Practical salinity units (PSU)
Description: Average water column salinity measured by CTD
http://lod.bco-dmo.org/id/dataset-parameter/878377.rdf
Name: Latitude
Units: decimal degrees
Description: Latitude North of collection location
http://lod.bco-dmo.org/id/dataset-parameter/878378.rdf
Name: Longitude
Units: decimal degrees
Description: Longitude East (West is negative) of collection location
http://lod.bco-dmo.org/id/dataset-parameter/878379.rdf
Name: BioSample
Units: unitless
Description: NCBI BioSample
http://lod.bco-dmo.org/id/dataset-parameter/878380.rdf
Name: SRA_Run
Units: unitless
Description: SRA Run number
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://www.bco-dmo.org/dataset/878322/data/download
download
onLine
dataset
<p><strong>Sampling and analytical procedures: </strong><br />
Wild <em>E. affinis</em> 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 salinity (~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.</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
<p>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.</p>
<p>The following software were used:<br />
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</p>
<p>These genomic data have been deposited in NCBI under BioProject number PRJNA844002.</p>
<p><strong>BCO-DMO Processing Description:</strong><br />
- Adjusted field/parameter names to comply with BCO-DMO naming conventions<br />
- Added a conventional header with dataset name, PI names, version date<br />
- Replaced commas with semicolons in the "Location" column</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
Bongo net
Bongo net
PI Supplied Instrument Name: Bongo net PI Supplied Instrument Description: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/
WP-2 Net
WP-2 Net
PI Supplied Instrument Name: WP-2 Net PI Supplied Instrument Description:WP2 net with 100 μm mesh Instrument Name: WP-2 Plankton Net Instrument Short Name:WP-2 Instrument 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) Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/NETT0168/
Illumina HiSeq 4000 sequencer
Illumina HiSeq 4000 sequencer
PI Supplied Instrument Name: Illumina HiSeq 4000 sequencer Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument 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.
PI Supplied Instrument Name: Instrument Name: CTD Instrument Short Name:CTD Instrument Description: A reusable instrument that always simultaneously measures conductivity and temperature (for salinity) and pressure (for depth).