http://lod.bco-dmo.org/id/dataset/949610
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
2025-01-24
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Metadata for targeted genotyping of green crabs collected in the northeast Pacific from Aug 2016 to Oct 2022
2025-01-27
publication
2025-01-27
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-02-10
publication
https://doi.org/10.26008/1912/bco-dmo.949610.1
Carolyn Tepolt
Woods Hole Oceanographic Institution
principalInvestigator
Emily Grason
Washington Sea Grant
principalInvestigator
P. Sean McDonald
University of Washington
principalInvestigator
Adrianne Akmajian
Makah Tribe
principalInvestigator
Shon Schooler
South Slough National Estuarine Research Reserve
principalInvestigator
Sylvia Behrens Yamada
Oregon State University
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: Tepolt, C., Grason, E., McDonald, P., Akmajian, A., Yamada, S. B., Schooler, S. (2025) Metadata for targeted genotyping of green crabs collected in the northeast Pacific from Aug 2016 to Oct 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-01-27 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.949610.1 [access date]
Metadata for targeted genotyping of green crabs in the northeast Pacific Dataset Description: Methods and Sampling: <p>Samples of&nbsp;<em>Carcinus maenas</em>&nbsp;(urn:lsid:marinespecies.org:taxname:107381) were collected by large network of collaborators, usually by trapping but approaches vary. Crabs were first frozen at -20C, then muscle or gill tissue was dissected out, preserved in 95% ethanol, and archived at -80C. Genomic DNA was extracted with Chelex 100 resin. Targeted genotyping of ~200 SNPs was conducted following the approach of Campbell et al. 2015; target SNPs were identified in prior population genomics analysis in the region based on RNA-Seq data. Samples were prepared in two groups, with overlapping but not identical targets; some samples were normalized using SequalPrep plates and others were not, following results of replicate sequencing with ("norm" in sequence names) and without normalization showing that this step did not improve genotyping success. Libraries were individually dual-indexed with plate and well barcodes, and multiplexed 800-1500 / lane on two lanes of 150 bp paired-end Illumina NovaSeq X 10B sequencing at the University of California at Berkeley's QB3 Genomics Core lab. Some samples were re-run across multiple plates / lanes as technical replicates ("repA" and "repB" in sequence names).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1850996 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1850996
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1850945 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1850945
completed
Carolyn Tepolt
Woods Hole Oceanographic Institution
5082893542
266 Woods Hole Road
Woods Hole
MA
025431535
US
ctepolt@whoi.edu
pointOfContact
Emily Grason
Washington Sea Grant
egrason@uw.edu
pointOfContact
P. Sean McDonald
University of Washington
2066162186
WA
981955672
US
psean@uw.edu
pointOfContact
Adrianne Akmajian
Makah Tribe
marine.ecologist@makah.com
pointOfContact
Shon Schooler
South Slough National Estuarine Research Reserve
Shon.SCHOOLER@dsl.oregon.gov
pointOfContact
Sylvia Behrens Yamada
Oregon State University
Sylvia.Yamada@oregonstate.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sample_name
SRA_accession
biosample_accession
embayment
site
state
sex
size_CW
color
collection_date
latitude
longitude
collector
collector_affiliation
Illumina NovaSeq X 10B
theme
None, User defined
sample identification
NCBI SRA run accession (SRR)
NCBI BioSample accession
site
region
sex
width
sample description
date
latitude
longitude
person name
featureType
BCO-DMO Standard Parameters
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: Tracking fine-scale selection to temperature at the invasion front of a highly dispersive marine predator
https://osprey.bco-dmo.org/project/811534
Collaborative Research: Tracking fine-scale selection to temperature at the invasion front of a highly dispersive marine predator
<p><em><strong>NSF Award Abstract: </strong></em><br />
Marine invasive species pose a serious and ongoing risk to ocean ecosystems and the economies that rely on them. Understanding how such species adapt rapidly to new environments is key to preventing and managing invasions. Traditionally, the focus has been on inherent traits and flexibility of an invasive species, ignoring the potential for evolutionary change after introduction. However, recent research has shown that some marine species may evolve specific genomic features which allow highly efficient selection over as little as a single generation. This project tests the importance of genomic traits in allowing marine invasive species to survive and thrive on new shores. Its focus is on the high-impact invasive European green crab, which has spread over 1,500 km of the West Coast of North America since 1989 and has very recently begun expanding into the Salish Sea. This project tracks the earliest stages of green crab invasion into a new environment where the species is predicted to have substantial ecological and economic impacts. Genetic differences are followed over time and space across the entire West Coast, with a focus on crabs found in the Salish Sea where the species is currently expanding. Genetic data is complemented by oceanographic modeling to predict the spread of green crabs into the Salish Sea and across the West Coast. Finally, targeted sequencing and prior sampling are used to probe the genomic traits underlying these changes and determine if the same traits have played a role in the species' invasive success on other shores. Sampling for this project is conducted by Washington Sea Grant's Crab Team, an expansive outreach and monitoring program powered largely by hundreds of volunteers who monitor green crabs across 3,000 miles of coastline in the Salish Sea. The results of this project are shared with these volunteers and other stakeholders and is used to inform trans-boundary green crab management and spread prediction on the West Coast.</p>
<p>Recent work has hypothesized that genomic architecture, which has been increasingly discovered to play a role in local adaptation, may also be key to a species' ability to adapt quickly when gene flow is high. This project integrates multiple approaches to track the speed and dynamics of adaptation-with-gene flow across a thermal gradient in an explicit oceanographic context using the invasive European green crab (Carcinus maenas). Prior work in this system identified a suite of genes that appear to constitute balanced polymorphisms whose allele frequencies correlate strongly with site temperature against a homogeneous neutral genetic background. This project has three main goals: 1) To examine fine-scale selection to temperature over a comprehensive spatial and temporal data set comprising most of the species' history on the West Coast, 2) To track the expanding range front in the Salish Sea, comparing the genetic trajectory of individuals at the range edge with oceanographic modeling of dispersal, and 3) To characterize the genomic regions surrounding putative balanced polymorphisms and examine the ubiquity of their association with temperature across globally replicated populations. This coupled evolutionary oceanography approach represents an unprecedented test of the speed and nature of rapid adaptation in a highly dynamic natural marine environment.</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>
West Coast Carcinus
largerWorkCitation
project
eng; USA
biota
oceans
-124.323273
-122.422437
43.347281
49.606306
2016-08-17
2022-10-12
North American west coast: 36 N to 51 N. Emphasis on the Salish Sea
0
BCO-DMO catalogue of parameters from Metadata for targeted genotyping of green crabs collected in the northeast Pacific from Aug 2016 to Oct 2022
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/949858.rdf
Name: sample_name
Units: unitless
Description: <p>Individual sample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/949859.rdf
Name: SRA_accession
Units: unitless
Description: <p>SRA accession number for individual sequence files</p>
http://lod.bco-dmo.org/id/dataset-parameter/949860.rdf
Name: biosample_accession
Units: unitless
Description: <p>Individual NCBI BioSample code</p>
http://lod.bco-dmo.org/id/dataset-parameter/949861.rdf
Name: embayment
Units: unitless
Description: <p>General coastal water body from which sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/949862.rdf
Name: site
Units: unitless
Description: <p>More specific data on collection location provided by collector</p>
http://lod.bco-dmo.org/id/dataset-parameter/949863.rdf
Name: state
Units: unitless
Description: <p>US state or Canadian province where samples was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/949864.rdf
Name: sex
Units: unitless
Description: <p>Sex (M=Male, F=Female, or U=Unknown)</p>
http://lod.bco-dmo.org/id/dataset-parameter/949865.rdf
Name: size_CW
Units: Millimeters (mm)
Description: <p>Carapace width of crab in mm</p>
http://lod.bco-dmo.org/id/dataset-parameter/949866.rdf
Name: color
Units: unitless
Description: <p>Color of ventral side of cephalothorax, as determined by collector</p>
http://lod.bco-dmo.org/id/dataset-parameter/949867.rdf
Name: collection_date
Units: unitless
Description: <p>Date of collection to the level of specificity available</p>
http://lod.bco-dmo.org/id/dataset-parameter/949868.rdf
Name: latitude
Units: decimal degrees
Description: <p>Latitude of collection; positive values = North</p>
http://lod.bco-dmo.org/id/dataset-parameter/949869.rdf
Name: longitude
Units: decimal degrees
Description: <p>Longitude of collection; positive values = East</p>
http://lod.bco-dmo.org/id/dataset-parameter/949870.rdf
Name: collector
Units: unitless
Description: <p>Person who collected the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/949871.rdf
Name: collector_affiliation
Units: unitless
Description: <p>Organization through which the sample was collected</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
243338
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/8d68520a-24a2-4873-b1be-43699f40b749/content
download
https://doi.org/10.26008/1912/bco-dmo.949610.1
download
onLine
dataset
<p>Samples of&nbsp;<em>Carcinus maenas</em>&nbsp;(urn:lsid:marinespecies.org:taxname:107381) were collected by large network of collaborators, usually by trapping but approaches vary. Crabs were first frozen at -20C, then muscle or gill tissue was dissected out, preserved in 95% ethanol, and archived at -80C. Genomic DNA was extracted with Chelex 100 resin. Targeted genotyping of ~200 SNPs was conducted following the approach of Campbell et al. 2015; target SNPs were identified in prior population genomics analysis in the region based on RNA-Seq data. Samples were prepared in two groups, with overlapping but not identical targets; some samples were normalized using SequalPrep plates and others were not, following results of replicate sequencing with ("norm" in sequence names) and without normalization showing that this step did not improve genotyping success. Libraries were individually dual-indexed with plate and well barcodes, and multiplexed 800-1500 / lane on two lanes of 150 bp paired-end Illumina NovaSeq X 10B sequencing at the University of California at Berkeley's QB3 Genomics Core lab. Some samples were re-run across multiple plates / lanes as technical replicates ("repA" and "repB" in sequence names).</p>
Specified by the Principal Investigator(s)
<p>Samples were demultiplexed by UC Berkeley's QB3 Genomics Core lab, and are provided raw with no further processing.</p>
Specified by the Principal Investigator(s)
- Imported "BCO-DMO_GTSeq_metadata_NSF-1850996.csv" into BCO-DMO system
- Replaced "’" with "'" in collector_affiliation field
- Replaced "10-2018-11" with "2018-11" in collection_date field
- Exported file as "949610_v1_green_crab_collection"
Accepted species identifier confirmed on 2025-01-29.
Specified by BCO-DMO Data Managers
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 NovaSeq X 10B
Illumina NovaSeq X 10B
PI Supplied Instrument Name: Illumina NovaSeq X 10B PI Supplied Instrument Description:Illumina NovaSeq X 10B sequencing (150 bp paired-end), conducted at University of California at Berkeley's QB3 Genomics Core lab 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.