http://lod.bco-dmo.org/id/dataset/998972
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)
Population genomics (RADseq-derived SNP genotypes) of the amphipod Ampithoe valida from collections in Japan, North America, and South America in 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/998972
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) Population genomics (RADseq-derived SNP genotypes) of the amphipod Ampithoe valida from collections in Japan, North America, and South America in 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/998972 [access date]
Methods and Sampling: <p>Individuals were collected by hand from eelgrass beds and from algae (primarily <em>Ulva lactuca</em>, <em>Gracilaria vermiculophylla</em> and <em>Fucus vesiculosus)</em> on docks, mudflats, and sandy/rocky shores. They were immediately euthanized and stored in 95% ethanol until use. Genomic DNA was extracted from amphipod tissue using either a Qiagen DNeasy spin-column kit following the manufacturer’s protocol for animal tissues or a Macherey-Nagel Nucleospin Tissue kit. For individuals that were less than approximately one centimeter in length or severely degraded, the entire individual was used; otherwise only half of the individual was used in the extraction. We genotyped single nucleotide polymorphisms (SNPs) using a restriction-site associated genotype-by-sequencing on DNA extractions from 350 individuals. Eleven individuals sampled for mtDNA, but not included in the RADseq library did not have a sufficient amount of DNA extraction product to be included. Genomic DNA was digested with two restriction enzymes, EcoRI and MseI. Pooled fragments for each individual were ligated with customized adaptor sequences containing the Illumina adaptors and primer sequences and unique 8–10&nbsp;bp barcodes to allow for the in silico identification of individuals. DNA fragments were amplified by PCR twice and size selected (300–450&nbsp;bp) using a Blue Pippin. The final library was sequenced using a single-end 100&nbsp;bp protocol within a lane of an Illumina HiSeq 2500 sequencer at the University of Texas at Austin Genome Sequencing and Analysis Facility (GSAF).<br />
<br />
Organism name, Life Science Identifier (LSID):<br />
&nbsp;Ampithoe valida, urn:lsid:marinespecies.org:taxname:102005</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
BioProject
BioSample
sample_name
strain
isolate
collection_date
geo_loc_name
Accession
latitude
longitude
Illumina HiSeq 2500
96-well thermocycler (Eppendorf)
theme
None, User defined
NCBI BioProject accession
NCBI BioSample accession
individual
sample description
year
region
NCBI SRA run accession (SRR)
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
-124.216667
142.5
-43.37
46.66667
2015-01-01
2015-01-01
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 Population genomics (RADseq-derived SNP genotypes) of the amphipod Ampithoe valida from collections in Japan, North America, and South America in 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/999011.rdf
Name: BioProject
Units: unitless
Description: <p>National Center for Biotechnology Information (NCBI) BioProject identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/999012.rdf
Name: BioSample
Units: unitless
Description: <p>BioSample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/999013.rdf
Name: sample_name
Units: unitless
Description: <p>individual ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/999014.rdf
Name: strain
Units: unitless
Description: <p>individual ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/999015.rdf
Name: isolate
Units: unitless
Description: <p>Population ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/999016.rdf
Name: collection_date
Units: unitless
Description: <p>Year of collection (yyyy)</p>
http://lod.bco-dmo.org/id/dataset-parameter/999017.rdf
Name: geo_loc_name
Units: unitless
Description: <p>Country</p>
http://lod.bco-dmo.org/id/dataset-parameter/999018.rdf
Name: Accession
Units: unitless
Description: <p>Sequence Read Archive (at NCBI) Run ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/999019.rdf
Name: latitude
Units: decimal degrees
Description: <p>latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/999021.rdf
Name: longitude
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/998972/data/download
download
onLine
dataset
<p>Individuals were collected by hand from eelgrass beds and from algae (primarily <em>Ulva lactuca</em>, <em>Gracilaria vermiculophylla</em> and <em>Fucus vesiculosus)</em> on docks, mudflats, and sandy/rocky shores. They were immediately euthanized and stored in 95% ethanol until use. Genomic DNA was extracted from amphipod tissue using either a Qiagen DNeasy spin-column kit following the manufacturer’s protocol for animal tissues or a Macherey-Nagel Nucleospin Tissue kit. For individuals that were less than approximately one centimeter in length or severely degraded, the entire individual was used; otherwise only half of the individual was used in the extraction. We genotyped single nucleotide polymorphisms (SNPs) using a restriction-site associated genotype-by-sequencing on DNA extractions from 350 individuals. Eleven individuals sampled for mtDNA, but not included in the RADseq library did not have a sufficient amount of DNA extraction product to be included. Genomic DNA was digested with two restriction enzymes, EcoRI and MseI. Pooled fragments for each individual were ligated with customized adaptor sequences containing the Illumina adaptors and primer sequences and unique 8–10&nbsp;bp barcodes to allow for the in silico identification of individuals. DNA fragments were amplified by PCR twice and size selected (300–450&nbsp;bp) using a Blue Pippin. The final library was sequenced using a single-end 100&nbsp;bp protocol within a lane of an Illumina HiSeq 2500 sequencer at the University of Texas at Austin Genome Sequencing and Analysis Facility (GSAF).<br />
<br />
Organism name, Life Science Identifier (LSID):<br />
&nbsp;Ampithoe valida, urn:lsid:marinespecies.org:taxname:102005</p>
Specified by the Principal Investigator(s)
<p>PhiX sequences present in the raw reads were identified and removed (13% was phiX). Cut sites and adaptors were removed from the remaining reads (256,667,215) and then parsed using barcodes into a single FASTQ file per individual using custom <em>Perl</em> scripts. A subset of 15&nbsp;million raw reads was used to create a de novo assembly. Contigs were assembled with a minimum match percent set to 92% and pruned with a minimum sequence length of 50&nbsp;bp. To remove potential paralogs, consensus sequences obtained for each contig were assembled de novo to each other with a minimum match percent set to 83%. Parsed reads were then assembled, with a maximum edit distance set to 6&nbsp;bp, to the pruned contigs coming out of the de novo assembly. These alignments were then used to call variant SNP sites. We analyzed a single SNP per contig to reduce the effects of physical linkage on population genetic parameters and filtered out SNPs that were recorded in fewer than 50% of individuals, had greater than two alleles per individual and possessed a minor allele frequency &lt; 5%. We generated a set of genotype likelihoods that combine the uncertainty generated by sequence coverage, sequencing error, and alignment error. We converted the phred-scale genotype likelihoods (from samtools/bcftools) per SNP-sample combination into probabilities that summed to 1, and then converted these to a single value that ranges from 0 to 2, where 0, 1 and 2 represent the highest probability of a homozygote, heterozygote, and alternative homozygote, respectively.</p>
Specified by the Principal Investigator(s)
- Loaded "attributes_final.csv" as table "998972_v1_a-valida-pop-genomics" (CSV format, header row 1), treating empty strings and "nd" as missing values
- Applied metadata (descriptions, standard name IDs, units) to columns: Accession, BioSample, collection_date, geo_loc_name, isolate, sample_name, strain
- Split column "lat_lon" (format: decimal degrees + direction, e.g. "12.345 N 67.890 W") into lat,lon column
- Set lat and lon set to number type
- Deleted original lat_lon column after verifying coordinate parsing was correct
- Rounded latitude to 5 decimal places. The coordinates were provided with varying levels of precision from degree to degree with several decimal places. Integers were not padded with decimal 0000s.
- Added constant column "BioProject" with value "PRJNA825556"
- Reordered columns to: BioProject, BioSample, sample_name, strain, isolate, collection_date, geo_loc_name, Accession, latitude, longitude
- Updated metadata (descriptions, standard name IDs, units) for all columns, including latitude and longitude marked as primary parameters with units of decimal degrees
- Output saved as "998972_v1_a-valida-pop-genomics.csv"
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 HiSeq 2500
Illumina HiSeq 2500
PI Supplied Instrument Name: Illumina HiSeq 2500 PI Supplied Instrument Description:Illumina HiSeq 2500 - next-generation sequencing 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.
96-well thermocycler (Eppendorf)
96-well thermocycler (Eppendorf)
PI Supplied Instrument Name: 96-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)