http://lod.bco-dmo.org/id/dataset/995189
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
2026-03-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
GTseq DNA sequencing of Kelletia kelletii collected in California, USA and Baja, Mexico from 2015 to 2017
2026-03-19
publication
2026-03-19
revision
BCO-DMO Linked Data URI
2026-03-19
creation
http://lod.bco-dmo.org/id/dataset/995189
Crow White
California Polytechnic State University
principalInvestigator
Mark Christie
Purdue University
principalInvestigator
Robert J. Toonen
University of Hawaiʻi at Mānoa
principalInvestigator
Jean Davidson
California Polytechnic 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: White, C., Toonen, R. J., Christie, M., Daniels, B., Davidson, J., Lee, A., López, C. (2026) GTseq DNA sequencing of Kelletia kelletii collected in California, USA and Baja, Mexico from 2015 to 2017. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-03-19 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/995189 [access date]
Dataset Description: <p>"KW" or "kw" in this dataset's files, sample IDs,&nbsp;or metadata&nbsp;indicate&nbsp;the organism of interest:<br />
<strong>K</strong>ellet’s <strong>w</strong>helk, gastropod,&nbsp;<em>Kelletia kelletii</em>, LSID&nbsp;(urn:lsid:marinespecies.org:taxname:491054)</p> Methods and Sampling: <p><em>Field Collections&nbsp;</em></p>
<p>Using SCUBA, we collected adult and recruit Kellet's whelks by hand from sub-tidal (approximately 15 m depth) locations across Kellet’s whelk’s entire biogeographic range, from Isla San Roque in Baja California, Mexico to Monterey Bay in California, USA. Collections occurred across three years, from 2015 to 2017. We used Kellet’s whelk’s growth function to classify the ages of recruit whelks based on length (White et al., 2025).</p>
<p><em>DNA extraction</em></p>
<p>DNA was extracted from whelk tissue using a Salting-out protocol (described in detail by Daniels, et al., 2023), cleaned using the ZR-96 DNA Clean-Up Kit (Zymo Research, USA), and sequenced using the generated GT-Seq panel.&nbsp;</p>
<p><em>Sequencing</em></p>
<p>We developed a novel GT-Seq panel (Campbell et al., 2015) using SNPs found on differentially expressed genes between Kellet’s whelks’ expanded and historical range sites (MON and NAP respectively) (Lee et al., 2024). Individuals were genotyped by GTSeek (Twin Falls, ID).&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924537 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924537
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924505 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924505
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924604 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924604
onGoing
Crow White
California Polytechnic State University
805-756-2954
California Polytechnic State University 1 Grand Avenue
San Luis Obispo
CA
93407
US
cwhite31@calpoly.edu
pointOfContact
Mark Christie
Purdue University
christ99@purdue.edu
pointOfContact
Robert J. Toonen
University of Hawaiʻi at Mānoa
808-236-7401
Hawaii Institute of Marine Biology 46-007 Lilipuna Rd
Kaneohe
HI
96744
USA
rjtoonen@gmail.com
pointOfContact
Jean Davidson
California Polytechnic State University
jdavid06@calpoly.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
CLNo
CapLabel
SiteDescription
SiteCode
Lat
Lon
SiteCodeLetter_cap
Whelk_ID
TissueType
Year
ExtractionCap
DateOfExtraction
PerformedBy
OriginalCalculatedConcentration
Elution_TEBuffer
DNAYield_ug
Measurement_mm
GTseq_Sample
GTseq_Raw_Reads
GTseq_On_Target_Reads
GTseq_Percent_On_Target
GTseq_Percent_GT
GTseq_IFI
GTseq_Sample_reprep
GTseq_Raw_Reads_reprep
GTseq_On_Target_Reads_reprep
GTseq_Percent_On_Target_reprep
GTseq_Percent_GT_reprep
GTseq_IFI_reprep
GTseq_Run_reprep
PoolRADseq
Recruit_label
SL_mm
Age_year
SurveyDate
tfert_date
thatch_date
tmiddisp_date
tsettle_date
Cohort_year
Region
Recruit_type
Lee_etal
theme
None, User defined
sample description
site
Site_ID
latitude
longitude
sample identification
year
date
person name
genetic material concentration
length
age
region
featureType
BCO-DMO Standard Parameters
Self-Contained Underwater Breathing Apparatus
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: RUI: Combined spatial and temporal analyses of population connectivity during a northern range expansion
https://osprey.bco-dmo.org/project/851109
Collaborative Research: RUI: Combined spatial and temporal analyses of population connectivity during a northern range expansion
<p><em>NSF Award Abstract:</em><br />
Where do young marine fish and shellfish come from? This project aims to improve our understanding of how coastal marine populations are connected in space and time. Coastal populations are replenished through the arrival of minuscule larvae that have been dispersed for weeks to months in the open ocean after spawning at remote sites. The combination of the long dispersal period of marine fish and shellfish larvae and the varying ocean currents results in complex patterns of "connectivity" among populations near and far. Identifying these patterns of connectivity is fundamental to marine science and critical for effective fisheries management and conservation, yet it remains an unresolved component of marine ecology. The study species is currently expanding its biogeographic range up the U.S. west coast. By genetically analyzing individuals from across the species' range, including offspring spawned in the laboratory by experimentally-crossed individuals collected in the field from throughout the species historical and expanded range, certain genes can serve to differentiate populations along the coast. The team leverages the statistical power of these geographically-informative genes to assign thousands of young collected in the field to the source populations that spawned them (across the species' range and over multiple years). The team then quantifies patterns of connectivity over multiple years, and tests fundamental hypotheses on the spatial scale, temporal variability, biogeographic patterns, and biophysical drivers of population connectivity. The project trains approximately two dozen U.S. university students in molecular ecology and marine science, as well as creating intellectual linkages among Ph.D.-granting and non-Ph.D.-granting universities. The project also supports further development of a K-12 education program that uses SCUBA diving and videography to teach elementary school students Next Generation Science Standards and train them for careers in science, technology, engineering and mathematics.</p>
<p>Using a kelp forest gastropod and fisheries species (Kellet's whelk, Kelletia kelletii), this project combines genome-wide Restriction site Associated DNA (RAD) loci with transcriptomic loci identified from common-garden laboratory crosses of individuals from the species' historical and expanded range to identify geographically-informative loci that maximize power for individual assignment testing. Leveraging the combined power of these loci, genetic assignment of approximately three thousand recruit samples to 20 putative source populations allows the team to construct three independent years of connectivity matrices and test some of the most fundamental questions in marine ecology, including: 1) Are marine populations open or closed and at what scales? 2) To what degree is the evolutionary pattern of gene flow represented by single versus multiple generations of connectivity events? And, 3) How spatially heterogeneous and temporally variable is population connectivity? Can one year of connectivity data predict anything about the next? Additionally, by focusing on a range-expanding species with common life history traits, the team addresses a number of questions with broad applicability and significant ecological and societal implications: 4) How much is population connectivity influenced by post-recruitment demographic and evolutionary processes? 5) How well-connected are historic- and expanded-range populations? And, of particular relevance to climate change, 6) Are El Nino oceanographic conditions, which are predicted to increase in frequency and intensity this century, driving the poleward range expansion of this coastal marine species? By coupling common-garden experimental crosses to identify maximally-informative transcriptomic loci with genomic RAD analysis of field samples, this project aims to accurately and precisely quantify marine population connectivity in high gene flow species with large population sizes.</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>
KW connectivity
largerWorkCitation
project
eng; USA
oceans
-121.939167
-114.36197
27.15326
36.618167
2015-06-19
2017-08-19
California, USA and Baja, Mexico coast
0
BCO-DMO catalogue of parameters from GTseq DNA sequencing of Kelletia kelletii collected in California, USA and Baja, Mexico from 2015 to 2017
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/996876.rdf
Name: CLNo
Units: unitless
Description: <p>DNA extraction cap label number</p>
http://lod.bco-dmo.org/id/dataset-parameter/996877.rdf
Name: CapLabel
Units: unitless
Description: <p>DNA extraction cap label</p>
http://lod.bco-dmo.org/id/dataset-parameter/996878.rdf
Name: SiteDescription
Units: unitless
Description: <p>Name of Kelletia kelletii tissue sample collection site</p>
http://lod.bco-dmo.org/id/dataset-parameter/996879.rdf
Name: SiteCode
Units: unitless
Description: <p>Code name of Kelletia kelletii tissue sample collection site</p>
http://lod.bco-dmo.org/id/dataset-parameter/996880.rdf
Name: Lat
Units: decimal degrees
Description: <p>Latitude of Kelletia kelletii tissue sample collection site, North is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/996882.rdf
Name: Lon
Units: decimal degrees
Description: <p>Longitude of Kelletia kelletii tissue sample collection site, West is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/996884.rdf
Name: SiteCodeLetter_cap
Units: unitless
Description: <p>DNA extraction cap label letter</p>
http://lod.bco-dmo.org/id/dataset-parameter/996885.rdf
Name: Whelk_ID
Units: unitless
Description: <p>Unique sample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/996886.rdf
Name: TissueType
Units: unitless
Description: <p>Sample tissue type (adult or recruit)</p>
http://lod.bco-dmo.org/id/dataset-parameter/996887.rdf
Name: Year
Units: unitless
Description: <p>Year of Kelletia kelletii tissue sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/996888.rdf
Name: ExtractionCap
Units: unitless
Description: <p>DNA extraction cap label number</p>
http://lod.bco-dmo.org/id/dataset-parameter/996889.rdf
Name: DateOfExtraction
Units: unitless
Description: <p>Date DNA extraction was performed</p>
http://lod.bco-dmo.org/id/dataset-parameter/996890.rdf
Name: PerformedBy
Units: unitless
Description: <p>Researcher number who performed DNA extraction</p>
http://lod.bco-dmo.org/id/dataset-parameter/996891.rdf
Name: OriginalCalculatedConcentration
Units: ug/ul or ng/ul (conflicting units description)
Description: <p>DNA extraction concentration (ng/ul) if measured</p>
http://lod.bco-dmo.org/id/dataset-parameter/996892.rdf
Name: Elution_TEBuffer
Units: microliters (uL)
Description: <p>TE elution buffer used in DNA extraction protocol</p>
http://lod.bco-dmo.org/id/dataset-parameter/996893.rdf
Name: DNAYield_ug
Units: micrograms (ug)
Description: <p>DNA extraction yield (ug), if measured</p>
http://lod.bco-dmo.org/id/dataset-parameter/996894.rdf
Name: Measurement_mm
Units: millimeters (mm)
Description: <p>Kelletia kelletii maximum shell length (mm), if measured (recruits only)</p>
http://lod.bco-dmo.org/id/dataset-parameter/996895.rdf
Name: GTseq_Sample
Units: unitless
Description: <p>Unique sample ID used by GTSeek for sequencing (same meaning in GTseq_Sample in supplemental kw_gtseq_genotypes.csv)</p>
http://lod.bco-dmo.org/id/dataset-parameter/996896.rdf
Name: GTseq_Raw_Reads
Units: unitless
Description: <p>Raw number of reads sequenced</p>
http://lod.bco-dmo.org/id/dataset-parameter/996897.rdf
Name: GTseq_On_Target_Reads
Units: unitless
Description: <p>Number of reads containing in-silico probe sequences</p>
http://lod.bco-dmo.org/id/dataset-parameter/996898.rdf
Name: GTseq_Percent_On_Target
Units: percent (%)
Description: <p>Percentage of raw reads containing in-silico probe sequences.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996899.rdf
Name: GTseq_Percent_GT
Units: percent (%)
Description: <p>Percentage of loci that was genotyped</p>
http://lod.bco-dmo.org/id/dataset-parameter/996900.rdf
Name: GTseq_IFI
Units: unitless
Description: <p>Individual fuzziness index of each sample. This is a measure of DNA cross-contamination and is calculated using read counts from the background signal at homozygous and No-Call loci. Low scores are better than high scores</p>
http://lod.bco-dmo.org/id/dataset-parameter/996901.rdf
Name: GTseq_Sample_reprep
Units: unitless
Description: <p>Unique sample ID for resequenced individuals</p>
http://lod.bco-dmo.org/id/dataset-parameter/996902.rdf
Name: GTseq_Raw_Reads_reprep
Units: count
Description: <p>Raw number of reads sequenced for resequenced individuals</p>
http://lod.bco-dmo.org/id/dataset-parameter/996903.rdf
Name: GTseq_On_Target_Reads_reprep
Units: count
Description: <p>Number of reads containing in-silico probe sequences for resequenced individuals</p>
http://lod.bco-dmo.org/id/dataset-parameter/996904.rdf
Name: GTseq_Percent_On_Target_reprep
Units: percent (%)
Description: <p>Percentage of raw reads containing in-silico probe sequences for resequenced individuals</p>
http://lod.bco-dmo.org/id/dataset-parameter/996905.rdf
Name: GTseq_Percent_GT_reprep
Units: percent (%)
Description: <p>Percentage of loci that was genotyped for resequenced individuals</p>
http://lod.bco-dmo.org/id/dataset-parameter/996906.rdf
Name: GTseq_IFI_reprep
Units: unitless
Description: <p>Individual fuzziness index of each sample for resequenced individuals. This is a measure of DNA cross-contamination and is calculated using read counts from the background signal at homozygous and No-Call loci. Low scores are better than high scores</p>
http://lod.bco-dmo.org/id/dataset-parameter/996907.rdf
Name: GTseq_Run_reprep
Units: unitless
Description: <p>Whether or not a sample was re-run, 0 = no, 2 = yes.</p>
http://lod.bco-dmo.org/id/dataset-parameter/996908.rdf
Name: PoolRADseq
Units: unitless
Description: <p>Flag if sample used in Pooled RADseq (1=yes, 0=no)</p>
http://lod.bco-dmo.org/id/dataset-parameter/996909.rdf
Name: Recruit_label
Units: unitless
Description: <p>CLNo for just recruits</p>
http://lod.bco-dmo.org/id/dataset-parameter/996910.rdf
Name: SL_mm
Units: millimeters (mm)
Description: <p>Recruit shell length</p>
http://lod.bco-dmo.org/id/dataset-parameter/996911.rdf
Name: Age_year
Units: years
Description: <p>Recruit age calculated using growth function from White et al. (2025)</p>
http://lod.bco-dmo.org/id/dataset-parameter/996912.rdf
Name: SurveyDate
Units: unitless
Description: <p>Date sample was collected in the wild</p>
http://lod.bco-dmo.org/id/dataset-parameter/996913.rdf
Name: tfert_date
Units: unitless
Description: <p>Date recruit was estimated to have been fertilized</p>
http://lod.bco-dmo.org/id/dataset-parameter/996914.rdf
Name: thatch_date
Units: unitless
Description: <p>Date recruit was estimated to have hatched from its egg capsule</p>
http://lod.bco-dmo.org/id/dataset-parameter/996915.rdf
Name: tmiddisp_date
Units: unitless
Description: <p>Date recruit was estimated to be midpoint in its dispersal period</p>
http://lod.bco-dmo.org/id/dataset-parameter/996916.rdf
Name: tsettle_date
Units: unitless
Description: <p>Date recruit was estimated to have settled post-dispersal</p>
http://lod.bco-dmo.org/id/dataset-parameter/996917.rdf
Name: Cohort_year
Units: unitless
Description: <p>Year recruit was estimated to be midpoint in its dispersal period</p>
http://lod.bco-dmo.org/id/dataset-parameter/996918.rdf
Name: Region
Units: unitless
Description: <p>Region recruit was collected (species' historical or expanded range region)</p>
http://lod.bco-dmo.org/id/dataset-parameter/996919.rdf
Name: Recruit_type
Units: unitless
Description: <p>Categorical age group of recruits</p>
http://lod.bco-dmo.org/id/dataset-parameter/996920.rdf
Name: Lee_etal
Units: unitless
Description: <p>Flag if sample used in GTseq (included=yes, excluded=no)</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/995189/data/download
download
onLine
dataset
<p><em>Field Collections&nbsp;</em></p>
<p>Using SCUBA, we collected adult and recruit Kellet's whelks by hand from sub-tidal (approximately 15 m depth) locations across Kellet’s whelk’s entire biogeographic range, from Isla San Roque in Baja California, Mexico to Monterey Bay in California, USA. Collections occurred across three years, from 2015 to 2017. We used Kellet’s whelk’s growth function to classify the ages of recruit whelks based on length (White et al., 2025).</p>
<p><em>DNA extraction</em></p>
<p>DNA was extracted from whelk tissue using a Salting-out protocol (described in detail by Daniels, et al., 2023), cleaned using the ZR-96 DNA Clean-Up Kit (Zymo Research, USA), and sequenced using the generated GT-Seq panel.&nbsp;</p>
<p><em>Sequencing</em></p>
<p>We developed a novel GT-Seq panel (Campbell et al., 2015) using SNPs found on differentially expressed genes between Kellet’s whelks’ expanded and historical range sites (MON and NAP respectively) (Lee et al., 2024). Individuals were genotyped by GTSeek (Twin Falls, ID).&nbsp;</p>
Specified by the Principal Investigator(s)
<p>Briefly, RNA reads from the expanded and historical ranges were aligned to a de novo reference transcriptome (Daniels, et al., 2023) using bowtie2/2.4.2 (Langmead &amp; Salzberg, 2012), sorted using samtools/1.9 (Li et al., 2009), and merged using stringtie2/2.1.1 (Kovaka et al., 2019). The count matrix was created using the featureCounts tool of subread/2.0.1 (Liao et al., 2014). Differentially expressed genes (DEGs) were identified using the R package DESeq2/1.34 (Love et al., 2014) using a minimum significance threshold of 0.05 after false discovery rate correction via the Benjamini–Hochberg method (Benjamini &amp; Hochberg, 1995). SNPs were identified on DEG contigs using the GATK pipeline (Van der Auwera &amp; O’Connor, 2020), following best practices for RNA-Seq. We then selected 1,000 SNPs with the highest pairwise <em>F<sub>ST </sub></em>values for GT-Seq multi-plex primer design by GTSeek (Twin Falls, ID).&nbsp;</p>
Specified by the Principal Investigator(s)
- Loaded two CSV files: "kw_gtseq_allinds_samplemeta v3.csv" as resource "995189_v1_kw_gtseq_allinds_samplemeta" and "kw_gtseq_genotypes_combined v3.csv" as resource "kw_gtseq_genotypes"; both with missing values defined as empty strings and "NA"
- Applied extensive field-level metadata (descriptions, standard name IDs, supplied units) to all fields in the sample metadata resource
- Renamed four columns in the sample metadata resource: "OriginalCalculatedConcentration_ng_ul_" → "OriginalCalculatedConcentration_ng_ul", "ExtractionCap_" → "ExtractionCap", "Elution_TEBuffer_" → "Elution_TEBuffer", "DNAYield_ug_" → "DNAYield_ug"
- Time was not provided so removed trailing " 0:00" time padding from six date fields (DateOfExtraction, SurveyDate, tfert_date, thatch_date, tmiddisp_date, tsettle_date).
- Converted all six date fields from "%m/%d/%Y" format to ISO 8601 "%Y-%m-%d" format
- Set data types for all columns in the sample metadata resource: numeric fields (Age_year, Lat, Lon, etc.), integer fields (CLNo, Cohort_year, GTseq_On_Target_Reads, etc.), string fields (CapLabel, GTseq_Sample, Region, etc.), and date fields with "%Y-%m-%d" format
- Fixed longitude values in the sample metadata resource by prepending a negative sign, as these decimal degree locations should be negative (West)
- Output two CSV files: "995189_v1_kw_gtseq_allinds_samplemeta.csv" and supplemental table "kw_gtseq_genotypes.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
PI Supplied Instrument Name: PI Supplied Instrument Description:Tissue samples collected via SCUBA and small vessel Instrument Name: Self-Contained Underwater Breathing Apparatus Instrument Short Name:SCUBA Instrument Description: The self-contained underwater breathing apparatus or scuba diving system is the result of technological developments and innovations that began almost 300 years ago. Scuba diving is the most extensively used system for breathing underwater by recreational divers throughout the world and in various forms is also widely used to perform underwater work for military, scientific, and commercial purposes.
Reference: https://oceanexplorer.noaa.gov/technology/technical/technical.html