http://lod.bco-dmo.org/id/dataset/854878
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
2021-06-29
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sample information and genetic accession information for raw low-coverage genomic sequence reads from 248 different Atlantic silverside (Menidia menidia) collected along the east coast of North America between 2005 to 2007
2021-06-30
publication
2021-06-30
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-01-02
publication
https://doi.org/10.26008/1912/bco-dmo.854878.1
Nina Overgaard Therkildsen
Cornell University
principalInvestigator
Hannes Baumann
University of Connecticut
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: Therkildsen, N. O., Baumann, H. (2024) Sample information and genetic accession information for raw low-coverage genomic sequence reads from 248 different Atlantic silverside (Menidia menidia) collected along the east coast of North America between 2005 to 2007. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-06-30 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.854878.1 [access date]
Methods and Sampling: <p>The following is an excerpt of the methods used to generate these data. Full details can be found in the associated publication and supplemental material of Wilder et al. (2020).</p>
<p><strong>Data generation:</strong></p>
<p>Atlantic silverside muscle samples collected from Georgia (GA), New York (NY), Gulf of Maine (GoM) and Gulf of St. Lawrence (GSL) were sequenced by Therkildsen &amp; Palumbi (2017) to a final, average depth of 1.5x across the reference transcriptome. All the samples were collected in the spring.&nbsp; See Therkildsen &amp; Palumbi (2017) and Therkildsen et al. (2019) for further detail. We added 47 additional samples from Oregon Inlet, North Carolina (NC) near Cape Hatteras.&nbsp;<br />
<br />
Individually barcoded sample libraries were prepared at Cornells Biotechnology Resource Center using similar methods to Therkildsen &amp; Palumbi (2017), with a few minor modifications. Reagents from the Illumina Nextera kit (96 sample Nextera DNA Library Prep Kit) were used at 1/3 the recommended concentration in 1/10 the recommended volume (5ul instead of 50ul), with 2ng of input DNA. Individual libraries were pooled, and size-selected using a Pippin Prep to remove fragments &lt;286 bp (150 bp insert plus 136 bp of Illumina adapters). Filtered mapped reads for the NC samples had a final average depth of 1.5x.</p>
<p><strong>Sampling and analytical procedures:</strong></p>
<p>Samples were collected directly from the wild as described in Hice et al. (2012).</p>
<p><strong>Locations:</strong><br />
Five locations along the east coast of North America.</p>
<div>USA:Jekyll Island,Georgia 31.02 -81.43<br />
USA:Oregon Inlet,NorthCarolina 35.77 -75.52<br />
USA:Minas Basin,Gulf of Maine 45.2 -64.38<br />
USA:Patchogue,NewYork 40.75 -73.00<br />
Canada:Magdalen Island, Gulf of St. Lawrence 47.4 -61.85<br />
<br />
<strong>Problem report:</strong><br />
<br />
The following samples should be excluded from analysis because of possible errors during library preparation:<br />
JekyllIs_1223, JekyllIs_1224, MagdalenIs_911, MagdalenIs_912, MagdalenIs_913, MagdalenIs_914, MagdalenIs_915, MagdalenIs_916, MagdalenIs_917, MagdalenIs_918, Patchogue_1030</div>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756316 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756316
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756751 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756751
completed
Nina Overgaard Therkildsen
Cornell University
607-255-2014
Department of Natural Resources 208 Fernow Hall
Ithaca
NY
14853
USA
nt246@cornell.edu
pointOfContact
Hannes Baumann
University of Connecticut
860-405-9297
Department of Marine Sciences 1080 Shennecossett Road
Groton
CT
06340-6048
USA
hannes.baumann@uconn.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
SampleID
bioproject_accession
biosample_accession
Population
collection_date
geo_loc_name
lat
lon
Illumina HiSeq 2000
Illumina NextSeq500
theme
None, User defined
sample identification
NCBI BioProject accession
NCBI BioSample accession
site
year
latitude
longitude
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Automated DNA Sequencer
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.
Collaborative research: The genomic underpinnings of local adaptation despite gene flow along a coastal environmental cline
https://befel.marinesciences.uconn.edu/2018/03/07/research-news-new-nsf-grant-to-study-silverside-genes/
Collaborative research: The genomic underpinnings of local adaptation despite gene flow along a coastal environmental cline
<p>NSF Abstract:</p>
<p>Oceans are large, open habitats, and it was previously believed that their lack of obvious barriers to dispersal would result in extensive mixing, preventing organisms from adapting genetically to particular habitats. It has recently become clear, however, that many marine species are subdivided into multiple populations that have evolved to thrive best under contrasting local environmental conditions. Nevertheless, we still know very little about the genomic mechanisms that enable divergent adaptations in the face of ongoing intermixing. This project focuses on the Atlantic silverside (Menidia menidia), a small estuarine fish that exhibits a remarkable degree of local adaptation in growth rates and a suite of other traits tightly associated with a climatic gradient across latitudes. Decades of prior lab and field studies have made Atlantic silverside one of the marine species for which we have the best understanding of evolutionary tradeoffs among traits and drivers of selection causing adaptive divergence. Yet, the underlying genomic basis is so far completely unknown. The investigators will integrate whole genome sequencing data from wild fish sampled across the distribution range with breeding experiments in the laboratory to decipher these genomic underpinnings. This will provide one of the most comprehensive assessments of the genomic basis for local adaptation in the oceans to date, thereby generating insights that are urgently needed for better predictions about how species can respond to rapid environmental change. The project will provide interdisciplinary training for a postdoc as well as two graduate and several undergraduate students from underrepresented minorities. The findings will also be leveraged to develop engaging teaching and outreach materials (e.g. a video documentary and popular science articles) to promote a better understanding of ecology, evolution, and local adaptation among science students and the general public.</p>
<p>The goal of the project is to characterize the genomic basis and architecture underlying local adaptation in M. menidia and examine how the adaptive divergence is shaped by varying levels of gene flow and maintained over ecological time scales. The project is organized into four interconnected components. Part 1 examines fine-scale spatial patterns of genomic differentiation along the adaptive cline to a) characterize the connectivity landscape, b) identify genomic regions under divergent selection, and c) deduce potential drivers and targets of selection by examining how allele frequencies vary in relation to environmental factors and biogeographic features. Part 2 maps key locally adapted traits to the genome to dissect their underlying genomic basis. Part 3 integrates patterns of variation in the wild (part 1) and the mapping of traits under controlled conditions (part 2) to a) examine how genomic architectures underlying local adaptation vary across gene flow regimes and b) elucidating the potential role of chromosomal rearrangements and other tight linkage among adaptive alleles in facilitating adaptation. Finally, part 4 examines dispersal - selection dynamics over seasonal time scales to a) infer how selection against migrants and their offspring maintains local adaptation despite homogenizing connectivity and b) validate candidate loci for local adaptation. Varying levels of gene flow across the species range create a natural experiment for testing general predictions about the genomic mechanisms that enable adaptive divergence in the face of gene flow. The findings will therefore have broad implications and will significantly advance our understanding of the role genomic architecture plays in modifying the gene flow - selection balance within coastal environments.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
GenomAdapt
largerWorkCitation
project
eng; USA
oceans
-81.43
-61.85
31.02
47.4
2005-01-01
2007-01-01
Eastern coastline of North America
0
BCO-DMO catalogue of parameters from Sample information and genetic accession information for raw low-coverage genomic sequence reads from 248 different Atlantic silverside (Menidia menidia) collected along the east coast of North America between 2005 to 2007
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/854960.rdf
Name: SampleID
Units: unitless
Description: <p>Sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/854961.rdf
Name: bioproject_accession
Units: unitless
Description: <p>NCBI BioProject accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/854962.rdf
Name: biosample_accession
Units: unitless
Description: <p>NCBI BioSample accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/854963.rdf
Name: Population
Units: unitless
Description: <p>Description of the population sampled by region name</p>
http://lod.bco-dmo.org/id/dataset-parameter/854964.rdf
Name: collection_date
Units: unitless
Description: <p>Collection year in format yyyy</p>
http://lod.bco-dmo.org/id/dataset-parameter/854965.rdf
Name: geo_loc_name
Units: unitless
Description: <p>Geolocation name of the collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/854966.rdf
Name: lat
Units: decimal degrees
Description: <p>Collection latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/854967.rdf
Name: lon
Units: decimal degrees
Description: <p>Collection longitude</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
26140
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/a58ab9ad-b0ca-48d9-9158-8abe1019f42e/content
download
https://doi.org/10.26008/1912/bco-dmo.854878.1
download
onLine
dataset
<p>The following is an excerpt of the methods used to generate these data. Full details can be found in the associated publication and supplemental material of Wilder et al. (2020).</p>
<p><strong>Data generation:</strong></p>
<p>Atlantic silverside muscle samples collected from Georgia (GA), New York (NY), Gulf of Maine (GoM) and Gulf of St. Lawrence (GSL) were sequenced by Therkildsen &amp; Palumbi (2017) to a final, average depth of 1.5x across the reference transcriptome. All the samples were collected in the spring.&nbsp; See Therkildsen &amp; Palumbi (2017) and Therkildsen et al. (2019) for further detail. We added 47 additional samples from Oregon Inlet, North Carolina (NC) near Cape Hatteras.&nbsp;<br />
<br />
Individually barcoded sample libraries were prepared at Cornells Biotechnology Resource Center using similar methods to Therkildsen &amp; Palumbi (2017), with a few minor modifications. Reagents from the Illumina Nextera kit (96 sample Nextera DNA Library Prep Kit) were used at 1/3 the recommended concentration in 1/10 the recommended volume (5ul instead of 50ul), with 2ng of input DNA. Individual libraries were pooled, and size-selected using a Pippin Prep to remove fragments &lt;286 bp (150 bp insert plus 136 bp of Illumina adapters). Filtered mapped reads for the NC samples had a final average depth of 1.5x.</p>
<p><strong>Sampling and analytical procedures:</strong></p>
<p>Samples were collected directly from the wild as described in Hice et al. (2012).</p>
<p><strong>Locations:</strong><br />
Five locations along the east coast of North America.</p>
<div>USA:Jekyll Island,Georgia 31.02 -81.43<br />
USA:Oregon Inlet,NorthCarolina 35.77 -75.52<br />
USA:Minas Basin,Gulf of Maine 45.2 -64.38<br />
USA:Patchogue,NewYork 40.75 -73.00<br />
Canada:Magdalen Island, Gulf of St. Lawrence 47.4 -61.85<br />
<br />
<strong>Problem report:</strong><br />
<br />
The following samples should be excluded from analysis because of possible errors during library preparation:<br />
JekyllIs_1223, JekyllIs_1224, MagdalenIs_911, MagdalenIs_912, MagdalenIs_913, MagdalenIs_914, MagdalenIs_915, MagdalenIs_916, MagdalenIs_917, MagdalenIs_918, Patchogue_1030</div>
Specified by the Principal Investigator(s)
<p>BCO-DMO Data Manager Processing Notes:<br />
* Converted&nbsp;SampleLocationDetails.xlsx Sheet 1 to csv and imported into the BCO-DMO data system.<br />
* Split latitude and longitude into respective columns from combined string column.<br />
* replaced comma in geolocation name to semicolon for better support for csv exports.</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:Illumina HiSeq 2000 with paired-end 125 bp (for samples from GA, NY, GoM, and GSL) 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.
Illumina NextSeq500
Illumina NextSeq500
PI Supplied Instrument Name: Illumina NextSeq500 PI Supplied Instrument Description:Illumina NextSeq500 paired-end 75 bp (for samples from NC) 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.