http://lod.bco-dmo.org/id/dataset/998990
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
2026-05-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Red seaweed Gracilaria vermiculophylla population genomics (SNP genotype likelihoods) from collections of populations in Asia North America and Europe in 2014 and 2015
2026-05-19
publication
2026-05-19
revision
BCO-DMO Linked Data URI
2026-05-19
creation
http://lod.bco-dmo.org/id/dataset/998990
Erik Sotka
College of Charleston
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: Sotka, E. (2026) Red seaweed Gracilaria vermiculophylla population genomics (SNP genotype likelihoods) from collections of populations in Asia North America and Europe in 2014 and 2015. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-05-19 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/998990 [access date]
Dataset Description: <p>The related BioProject&nbsp;PRJNA700770 aggregates accessions in the Sequence Read Archive (SRA), and related Genbank nucleotide accession JAHNZQ000000000.2, and assembly "ASM1915520v2" (GCA_019155205.2).</p> Methods and Sampling: <p>We collected A. vermiculophyllum thalli at 35 intertidal sites across the Northern Hemisphere. This included 11 Japanese sites, five sites along the western coast of North America, 10 sites on the eastern coast of the United States, and nine sites along the European coast. At each site, we haphazardly collected 100 thalli separated by at least one meter and determined the reproductive state of each thallus (i.e., male gametophyte, female gametophyte, diploid tetrasporophyte, or nonreproductive) using a dissecting microscope. We then preserved 5–10 cm fragments of each thallus in silica gel as vouchers and for DNA extraction. Total gDNA was extracted from approximately 5–10 mg of dried tissue of 560 thalli (n = 16 per site) that were either phenotypically-diploid (i.e., bearing reproductive structures) or when not enough thalli were reproductive from a site, we used nonreproductive thalli. We used the Nucleospin Plant Kit (Macherey-Nagel) and followed the manufacturer's protocol with two exceptions: we performed the lysis step for 1 h at room temperature and eluted in 100 μl of molecular grade water. Briefly, we digested gDNA with two restriction enzymes, EcoRI and MseI, and ligated adaptors containing unique 8–10 bp barcodes to the digested DNA of each individual. The products were&nbsp;then&nbsp;PCR amplified in two independent reactions with standard Illumina primers. All amplicons were pooled and shipped to the University of Texas Genomic Sequencing and Analysis Facility, which used BluePippin Prep to isolate the 300–500 bp fraction. This fraction was then single-read sequenced with one lane each on Illumina HiSeq 2500 and HiSeq 4000 platforms.<br />
<br />
<strong>Name synononyms for&nbsp;"Gracilaria (Agarophyton) vermiculophyllum"</strong><br />
<br />
Accepted name (as of 2026-05-21):<br />
Gracilaria vermiculophylla,&nbsp;LSID(urn:lsid:marinespecies.org:taxname:236157)<br />
NCBI Taxonomy ID:2608709<br />
<br />
Unaccepted synonym (as&nbsp;of 2026-05-21):<br />
Agarophyton vermiculophyllum,&nbsp; LSID(urn:lsid:marinespecies.org:taxname:1327786)</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1357386 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1357386
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924599 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924599
onGoing
Erik Sotka
College of Charleston
843-953-9191
Grice Marine Laboratory 205 Fort Johnson Road
Charleston
SC
29412
USA
sotkae@cofc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_Name
SiteName_short
Run
BioProject
BioSample
Collection_Date
SiteName_long
geo_loc_name_country
geo_loc_name_country_continent
lat
lon
Illumina sequencing machine (HiSeq 2500 and 4000)
384-well Thermocycler (Eppendorf)
theme
None, User defined
sample identification
Site_ID
NCBI SRA run accession (SRR)
NCBI BioProject accession
NCBI BioSample accession
year
No BCO-DMO term
region
latitude
longitude
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
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.
Detecting genetic adaptation during marine invasions
https://osprey.bco-dmo.org/project/472708
Detecting genetic adaptation during marine invasions
<p><em>Description from NSF award abstract:</em><br />
Biological introductions, defined as the establishment of species in geographic regions outside the reach of their natural dispersal mechanisms, have dramatically increased in frequency during the 20th century and are now altering community structure and ecosystem function of virtually all marine habitats. To date, studies on marine invasions focus principally on demographic and ecological processes, and the importance of evolutionary processes has been rarely tested. This knowledge gap has implications for management policies, which attempt to prevent biological introductions and mitigate their impacts. The Asian seaweed <em>Gracilaria vermiculophylla</em> has been introduced to every continental margin in the Northern Hemisphere, and preliminary data indicate that non-native populations are both more resistant to heat stress and resistant to snail herbivory. The project will integrate population genetics, field survey and common-garden laboratory experiments to comprehensively address the role of rapid evolutionary adaptation in the invasion success of this seaweed. Specifically, the PIs will answer the following. What is the consequence of introductions on seaweed demography and mating systems? How many successful introductions have occurred in North America and Europe? Where did introduced propagules originate? Do native, native-source and non-native locations differ in environmental conditions? Do native, native-source and non-native populations differ in phenotype?</p>
<p>The intellectual merit of this project is based on three gaps in the literature. First, while biological invasions are widely recognized as a major component of global change, there are surprisingly few studies that compare native and non-native populations in their biology or ecology. Native and non-native populations will be surveyed in a similar manner, allowing assessment of differences in population dynamics, mating system, epifaunal and epiphytic communities, and the surrounding abiotic and biotic environment. Second, <em>G. vermiculophylla</em> exhibits a life cycle typical of other invasive species (including some benthic invertebrates), yet we still lack data on the effects of decoupling the haploid and diploid stages on genetic structure, and in turn, on the evolvability of their populations. Finally, this project will provide unequivocal evidence of an adaptive shift in a marine invasive. To our knowledge, such evolutionary change has been described previously for only a complex of marine copepod species. <em>G. vermiculophylla</em> will serve as a model for understanding evolution in other nuisance invasions, and perhaps lead to novel methods to counter future invasions or their spread.</p>
Genetic Adaptation Marine Inv
largerWorkCitation
project
The genetic legacy of an Asian oyster introduction and its disease-causing parasite
https://osprey.bco-dmo.org/project/820200
The genetic legacy of an Asian oyster introduction and its disease-causing parasite
<p><em>NSF abstract:</em></p>
<p>During the 20th century, the Pacific oyster <em>Crassostrea gigas</em> was deliberately introduced from its native range of coastal Asia to the estuaries of six continents. While the introduced Pacific oysters are widely aquacultured and thus can generate local economic wealth, they sometimes outcompete native oysters, and can carry microbial, animal and plant hitchhikers that negatively impact local economies and the ecological functioning of local estuaries. This study comprehensively assesses the pathways and sources of Pacific oyster introductions using a worldwide, population genetic survey. Simultaneously, the study also assesses the pathways and source of one hitchhiking protist (<em>Haplosporidium nelsoni</em>) that causes the disease MSX (multinucleated sphere X) in the Virginia oyster (<em>Crassostrea virginica</em>) along the eastern seaboard of the United States. One goal of this research is to generate management strategies that combat the negative impacts of the Pacific oyster and its associated invaders, and minimize future invasions. A second goal is to minimize some uncertainty about the population biology of the devastating Haplosporidium parasite, and thus, increase confidence of policy makers who are managing shellfish health, restoration and commerce. By quantifying the pathways and sources of <em>C. gigas</em>, this project may inform strategies to combat negative impacts of <em>C. gigas</em> and its associated invaders, as well as minimize future invasions. Moreover, quantifying dispersal within and among populations of <em>H. nelsoni</em> along the US East Coast will provide perspective on the effectiveness of regional biosecurity measures in preventing the ongoing dispersal of this destructive pathogen via aquaculture. In addition, the project lends itself well to programs that foster critical thinking and research experience among both undergraduate and K-12 students. The project provides opportunities for 6-9 undergraduates to perform research, includes a 2-day workshop on bioinformatics for the wider undergraduate community, and facilitates ongoing opportunities for K-12 students to participate in citizen-science research.</p>
<p>There is a wealth of information on the source, pathways and vectors of <em>C. gigas</em> based largely on historical documents but no study has comprehensively tested whether these historical accounts are correct using a worldwide, population genetic survey. Using >14K single-nucleotide polymorphisms (SNPs) from 41 populations across five continents a high level of spatial genetic differentiation was found within the native range and differences in source populations among non-native regions. Preliminary genetic data indicated that the parasitic protist, <em>Haplosporidium nelsoni </em>arrived with C. gigas imports to the US Atlantic coastline and then infected the native C. virginica, however the native source populations, the pathways and vector from which <em>H. nelsoni </em>arrived remain unknown. This project couples high-throughput sequencing technologies and Approximate Bayesian Computing (ABC)-based models to answer the following: What are the population genomic patterns among <em>C. gigas</em> from native and non-native regions? What are the population genomic patterns of <em>Haplosporidium nelsoni </em>among Asian and North American Crassostrea gigas and eastern North American <em>C. virginica</em>? What were the source populations and invasion pathways of <em>C. gigas</em> and <em>H. nelsoni</em>? Identifying source locations, pathways and vectors of introduction of C. gigas will provide researchers with a null-model of invasion history for dozens of other non-native species that were transported with <em>C. gigas</em>. Currently, there are no verified 'vector maps' for historical shipments of <em>C. gigas</em> that are similar to those generated from modern-day or historical shipping records.</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>
Oyster historical genetics
largerWorkCitation
project
eng; USA
oceans
-123.055447
144.879657
31.7321
54.486315
2014-05-19
2015-05-19
From projects that focused on the following 2 locations: 1. Estuaries of NW and NE Pacific; estuaries of NW and NE Atlantic 2. Global
0
BCO-DMO catalogue of parameters from Red seaweed Gracilaria vermiculophylla population genomics (SNP genotype likelihoods) from collections of populations in Asia North America and Europe in 2014 and 2015
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/999023.rdf
Name: Sample_Name
Units: unitless
Description: <p>Individuals</p>
http://lod.bco-dmo.org/id/dataset-parameter/999024.rdf
Name: SiteName_short
Units: unitless
Description: <p>Site name identifier (3 characters)</p>
http://lod.bco-dmo.org/id/dataset-parameter/999025.rdf
Name: Run
Units: unitless
Description: <p>The National Center for Biotechnology Information (NCBI) Run accession in the Sequence Read Archive (SRA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/999026.rdf
Name: BioProject
Units: unitless
Description: <p>National Center for Biotechnology Information (NCBI) BioProject identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/999027.rdf
Name: BioSample
Units: unitless
Description: <p>The National Center for Biotechnology Information (NCBI) BioSample accession number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/999028.rdf
Name: Collection_Date
Units: Year
Description: <p>Collection year (yyyy)</p>
http://lod.bco-dmo.org/id/dataset-parameter/999029.rdf
Name: SiteName_long
Units: unitless
Description: <p>Full site name (not truncated)</p>
http://lod.bco-dmo.org/id/dataset-parameter/999030.rdf
Name: geo_loc_name_country
Units: unitless
Description: <p>Country</p>
http://lod.bco-dmo.org/id/dataset-parameter/999031.rdf
Name: geo_loc_name_country_continent
Units: unitless
Description: <p>Continent</p>
http://lod.bco-dmo.org/id/dataset-parameter/999032.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/999033.rdf
Name: lon
Units: decimal degrees
Description: <p>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
https://osprey.bco-dmo.org/dataset/998990/data/download
download
onLine
dataset
<p>We collected A. vermiculophyllum thalli at 35 intertidal sites across the Northern Hemisphere. This included 11 Japanese sites, five sites along the western coast of North America, 10 sites on the eastern coast of the United States, and nine sites along the European coast. At each site, we haphazardly collected 100 thalli separated by at least one meter and determined the reproductive state of each thallus (i.e., male gametophyte, female gametophyte, diploid tetrasporophyte, or nonreproductive) using a dissecting microscope. We then preserved 5–10 cm fragments of each thallus in silica gel as vouchers and for DNA extraction. Total gDNA was extracted from approximately 5–10 mg of dried tissue of 560 thalli (n = 16 per site) that were either phenotypically-diploid (i.e., bearing reproductive structures) or when not enough thalli were reproductive from a site, we used nonreproductive thalli. We used the Nucleospin Plant Kit (Macherey-Nagel) and followed the manufacturer's protocol with two exceptions: we performed the lysis step for 1 h at room temperature and eluted in 100 μl of molecular grade water. Briefly, we digested gDNA with two restriction enzymes, EcoRI and MseI, and ligated adaptors containing unique 8–10 bp barcodes to the digested DNA of each individual. The products were&nbsp;then&nbsp;PCR amplified in two independent reactions with standard Illumina primers. All amplicons were pooled and shipped to the University of Texas Genomic Sequencing and Analysis Facility, which used BluePippin Prep to isolate the 300–500 bp fraction. This fraction was then single-read sequenced with one lane each on Illumina HiSeq 2500 and HiSeq 4000 platforms.<br />
<br />
<strong>Name synononyms for&nbsp;"Gracilaria (Agarophyton) vermiculophyllum"</strong><br />
<br />
Accepted name (as of 2026-05-21):<br />
Gracilaria vermiculophylla,&nbsp;LSID(urn:lsid:marinespecies.org:taxname:236157)<br />
NCBI Taxonomy ID:2608709<br />
<br />
Unaccepted synonym (as&nbsp;of 2026-05-21):<br />
Agarophyton vermiculophyllum,&nbsp; LSID(urn:lsid:marinespecies.org:taxname:1327786)</p>
Specified by the Principal Investigator(s)
<p>The two Illumina sequencing lanes yielded 4.4 × 108 short read fragments after removal of PhiX sequences. Fragments that did not have adapter nor barcode sequences were removed using a custom perl script. All reads were then aligned to the 24 scaffolds to identify variant, multiallelic SNPs and generate genotype likelihoods. We then removed loci with a minor allele frequency less than or equal to 2%. We filtered out poorly sequenced individuals (i.e., reads at &lt;20% of all loci) and loci (i.e., 1+ reads at 50% of individuals). We were left with a set of 62,285 loci and 351 individuals, sequenced to a depth of 19.4 reads per locus</p>
Specified by the Principal Investigator(s)
- Loaded data from "meta_forBCODMO.csv" as table "998990_v1_g-verm-pop-genomics" (CSV format, header row 1, missing values: "", "nd")
- Split column "lat_lon" into "lat", "lon" and converted to decimal degrees. lat_lon column removed after verifying correct parsing.
- Renamed column "Sample Name" to "Sample_Name"
- Set types for all retained columns: "BioProject", "BioSample", "Run", "Sample_Name", "SiteName_long", "SiteName_short", "geo_loc_name_country", "geo_loc_name_country_continent", "lat_lon" as string; "Collection_Date" as integer; "lat" and "lon" as number
- Updated field metadata (descriptions, standard name IDs, units) for all columns including BioProject, BioSample, Run, Sample_Name, SiteName_long, SiteName_short, geo_loc_name_country, geo_loc_name_country_continent, Collection_Date, lat, and lon
- Replaced escape character sequences (backslash followed by spaces) with a single space in "SiteName_long" values
- Output final table as "998990_v1_g-verm-pop-genomics.csv"
Organism name note: the name as provided in the metadata "Gracilaria (Agarophyton) vermiculophyllum" combines genera and species of both the currently accepted and unaccepted synonyms. Both names and life science identifiers were included for discoverability purposes.
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 sequencing machine (HiSeq 2500 and 4000)
Illumina sequencing machine (HiSeq 2500 and 4000)
PI Supplied Instrument Name: Illumina sequencing machine (HiSeq 2500 and 4000) 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.
384-well Thermocycler (Eppendorf)
384-well Thermocycler (Eppendorf)
PI Supplied Instrument Name: 384-well Thermocycler (Eppendorf) Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)