http://lod.bco-dmo.org/id/dataset/684944
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
2017-03-20
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Rockfish microhaplotype sequence accessions from samples near Carmel and Monterey Bays, CA, 2013-2016 (Larval Dispersal in Kelp Rockfish project)
2018-02-27
publication
2018-02-27
revision
BCO-DMO Linked Data URI
2018-02-27
creation
http://lod.bco-dmo.org/id/dataset/684944
Mark Carr
University of California-Santa Cruz
principalInvestigator
Christopher Edwards
principalInvestigator
Dr John Carlos Garza
University of California-Santa Cruz
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: Carr, M., Garza, J. C., Edwards, C. (2018) Rockfish microhaplotype sequence accessions from samples near Carmel and Monterey Bays, CA, 2013-2016 (Larval Dispersal in Kelp Rockfish project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-02-27 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/684944 [access date]
Links to sequence files associated with this project Dataset Description: <p>2018-02-21: The data are currently stored in the Dryad repository as the following two packages. The files may also be accessed here via the 'Get Data' button (above).</p>
<p>Dryad package: <strong>Kelp-rockfish genotypes</strong>, DOI: <a href="https://datadryad.org/stash/dataset/doi:10.5061/dryad.6cp14g8" target="_blank">10.5061/dryad.6cp14g8</a><br />
Data from: "Larval dispersal connects marine reserves and replenishes fished populations along the central California coast." Baetscher DS, Anderson EC, Saarman E, Malone D, Carr MH, Garza JC (2018?) Molecular Ecology (in press).<br />
NOTE: not all files are publicly available until the associated publication is published.</p>
<p>This data repository contains the following:&nbsp; Genotypes for 96 microhaplotypes - this file contains the genotypes for 6,108 kelp rockfish sequenced at 96 amplicon loci using paired-end Illumina sequencing. Genotypes were filtered for read depth (minimum 20 reads total per locus/individual) and allele balance (0.4 ratio of read depth for allele 1:allele 2 in a heterozygote). Samples with missing data at more than 10 percent of loci were excluded from this data set. Variant call format file generated using Freebayes software from 2,293 rockfish samples sequenced at 96 microhaplotype loci. Samples include four species of rockfishes: kelp (Sebastes atrovirens), copper (S. caurinus), black-and-yellow (S. chrysomelas), and gopher (S. carnatus). This file contains 1,495 variant sites across the 96 loci.</p>
<p>Dryad package:&nbsp;<strong>Rockfish microhaplotype sequences,</strong> DOI:&nbsp;<a href="https://doi.org/10.5061/dryad.5863d" target="_blank">10.5061/dryad.5863d</a><br />
Data from: Baetscher DS, Clemento AJ, Ng TC, Anderson EC, Garza JC (2017) Microhaplotypes provide increased power from short-read DNA sequences for relationship inference. Molecular Ecology Resources, <a href="https://doi.org/10.1111/1755-0998.12737" target="_blank">https://doi.org/10.1111/1755-0998.12737</a><br />
Consensus sequences and primer information for 192 targeted amplicons, the Binary Alignment/Map (BAM) files and variant call format (VCF) files for all retained regions genotype files for 144 kelp rockfish species and an R Notebook documenting all statistical analyses.</p> Methods and Sampling: <p>Haplotype data from 150bp amplicon sequencing on an Illumina MiSeq. All loci used in the generation of haplotype sequence data will be submitted to GenBank (National Center for Biotechnology Information).</p>
<p>Genotype data are generated with high-throughput DNA sequencing on an Illumina MiSeq instrument. Amplicons are prepared through polymerase chain reaction with primers designed from either expressed sequence tags in publicly available databases (e.g., Cyverse) or from sequences generated by double digest Restriction-Site Associated DNA (RAD) sequencing. Amplicon sequencing is using the procedure described in Campbell et al. 2015 (Molecular Ecology Resources 15: 855-867) termed genotyping in thousands by sequencing (GT-seq). Data are filtered by quality score and genotypes called for all locus by individual combinations with read depth ≥20. Genotyping accuracy is evaluated by confirmation of Mendelian segregation in known families. Haplotypes are called from constituent SNPs using FreeBayes software.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1260693 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1260693
completed
Mark Carr
University of California-Santa Cruz
(831) 459-3958
Long Marine Laboratory University of California, Santa Cruz
Santa Cruz
CA
95060
USA
mhcarr@ucsc.edu
pointOfContact
Christopher Edwards
(831) 459-3734
UC Santa Cruz / OCEAN SCIENCES 1156 High Street
Santa Cruz
CA
95064
USA
cedwards@ucsc.edu
pointOfContact
Dr John Carlos Garza
University of California-Santa Cruz
831-420-3903
Southwest Fisheries Science Center 110 Shaffer Road
Santa Cruz
CA
95060
USA
carlos.garza@noaa.gov
pointOfContact
asNeeded
Dataset Version: 1
Unknown
file_link
file_size
publication
Dryad_DOI
description
file_name
Illumina MiSeq
theme
None, User defined
file_link
file_size
reference_paper
No BCO-DMO term
brief description
file_name
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
Carr_1999
service
Deployment Activity
Monterey and Carmel nearshore
place
Locations
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.
Partnership for Interdisciplinary Studies of Coastal Oceans
http://www.piscoweb.org/
Partnership for Interdisciplinary Studies of Coastal Oceans
The Partnership for Interdisciplinary Studies of Coastal Oceans is a long-term ecosystem research and monitoring program established with the goals of:
understanding dynamics of the coastal ocean ecosystem along the U.S. west coast
sharing that knowledge so ocean managers and policy makers can make science based decisions regarding coastal and marine stewardship
producing a new generation of scientists trained in interdisciplinary collaborative approaches
Over the last 10 years, PISCO has successfully built a unique research program that combines complementary disciplines to answer critical environmental questions and inform management and policy. Activities are conducted at the latitudinal scale of the California Current Large Marine Ecosystem along the west coast of North America, but anchored around the dynamics of coastal, hardbottom habitats and the oceanography of the nearshore ocean – among the most productive and diverse components of this ecosystem. The program integrates studies of changes in the ocean environment through ecological monitoring and experiments. Scientists examine the causes and consequences of ecosystem changes over spatial scales that are the most relevant to marine species and management, but largely unstudied elsewhere.
Findings are linked to solutions through a growing portfolio of tools for policy and management decisions. The time from scientific discovery to policy change is greatly reduced by coordinated, efficient links between scientists and key decision makers.
Core elements of PISCO are:
Interdisciplinary ecosystem science
Data archiving and sharing
Outreach to public and decision-making user groups
Interdisciplinary training
Coordination of distributed research team
Established in 1999 with funding from The David and Lucile Packard Foundation, PISCO is led by scientists from core campuses Oregon State University (OSU); Stanford University’s Hopkins Marine Station; University of California, Santa Cruz (UCSC); and University of California, Santa Barbara (UCSB). Collaborators from other institutions also contribute to leadership and development of PISCO programs. As of 2005, core PISCO activities are funded by collaborative grants from The David and Lucile Packard Foundation and the Gordon and Betty Moore Foundation. Core support, along with additional funding from diverse public and private sources, make this unique partnership possible.
PISCO
largerWorkCitation
program
Integrative evaluation of larval dispersal and delivery in kelp rockfish using inter-generational genetic tagging, demography and oceanography
http://research.pbsci.ucsc.edu/eeb/rclab/kelp-rockfish-pbt-project/
Integrative evaluation of larval dispersal and delivery in kelp rockfish using inter-generational genetic tagging, demography and oceanography
<p><em>Description from NSF award abstract:</em><br />
The spatial structure and dynamics of coastal marine fish populations are strongly influenced by the transport and recruitment of larvae. However, the scale and patterns of larval dispersal are among the most difficult demographic parameters to quantify in marine systems, due to the inability to tag and track the movement of larvae. In particular, the extent of local retention of larvae versus regional dispersal to other locations and populations is currently a hotly debated topic in the field of marine ecology and has profound implications for the design and effectiveness of Marine Protected Areas (MPAs). The research will identify patterns of larval dispersal and use those patterns to test predictions of dispersal generated by state-of-the-art circulation models.</p>
<p>The PI team brings together ecologists, geneticists, statisticians, and oceanographers with expertise in population demography and field sampling, mark/recapture data from genetic tags, and empirical and model-based evaluation of oceanographic processes to answer the following questions:<br />
1. Do observed patterns of dispersal and connectivity of larval kelp rockfish correspond to patterns predicted by high spatial resolution regional ocean circulation models? Model predictions will be tested empirically using larval settlement samples. Parentage analysis will be used to verify the occurrence of larvae derived from genetically tagged source populations.<br />
2. Is there evidence for local retention of larval kelp rockfish within the study area? To test the hypothesis that local retention of juvenile kelp rockfish from source populations is greater than expected by existing larval transport models, the PIs will compare the proportion of recruits that are genetically identified to have been produced from within three focal sites with the proportion of larval production that was tagged in those sites.<br />
3. Is the relative recruitment of recently settled kelp rockfish to focal sites in the study region proportionate to the relative larval production of those focal sites? The PIs will compare the proportion of tagged recruits with the proportion of larval production generated from tagged adults at varying spatial scales. They will use goodness of fit models to compare expected and observed connectivity matrices under varying hypotheses of larval dispersal. Alternatively, if the relative contribution of focal sites to larval replenishment of themselves, one another, and more distant populations is disproportionate to their relative production, can this discrepancy be explained by oceanographic processes that could facilitate particular trajectories of larval dispersal?</p>
<p>To determine if differences in self recruitment and connectivity can be attributed to local oceanographic features, the PIs will examine spatial and temporal correlations between these features and the spatial distribution and timing of recruitment.</p>
<p><em>Related websites:</em><br />
<a href="http://piscoweb.org" target="_blank">http://piscoweb.org</a><br />
<a href="http://research.pbsci.ucsc.edu/eeb/rclab/kelp-rockfish-pbt-project/" target="_blank">http://research.pbsci.ucsc.edu/eeb/rclab/kelp-rockfish-pbt-project/</a> (broken link)<br />
<a href="http://rockfish.ucsc.edu/" target="_blank">http://rockfish.ucsc.edu/</a><br />
<a href="http://oceanmodeling.ucsc.edu" target="_blank">http://oceanmodeling.ucsc.edu</a></p>
Larval Dispersal in Kelp Rockfish
largerWorkCitation
project
eng; USA
biota
oceans
Monterey and Carmel nearshore
-121.9825
-121.8946
36.3977
36.6405
2013-07-19
2015-10-01
Monterey Bay and vicinity
0
BCO-DMO catalogue of parameters from Rockfish microhaplotype sequence accessions from samples near Carmel and Monterey Bays, CA, 2013-2016 (Larval Dispersal in Kelp Rockfish 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
http://lod.bco-dmo.org/id/dataset-parameter/728580.rdf
Name: file_link
Units: unitless
Description: <p>hyperlink to downloadable file</p>
http://lod.bco-dmo.org/id/dataset-parameter/728581.rdf
Name: file_size
Units: kilobytes to gigabytes
Description: <p>file size</p>
http://lod.bco-dmo.org/id/dataset-parameter/728582.rdf
Name: publication
Units: unitless
Description: <p>publication that used the data</p>
http://lod.bco-dmo.org/id/dataset-parameter/728583.rdf
Name: Dryad_DOI
Units: unitless
Description: <p>dryad.org DOI</p>
http://lod.bco-dmo.org/id/dataset-parameter/728584.rdf
Name: description
Units: unitless
Description: <p>description of file contents</p>
http://lod.bco-dmo.org/id/dataset-parameter/728585.rdf
Name: file_name
Units: unitless
Description: <p>file name</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
49857599
https://datadocs.bco-dmo.org/docs/302/Kelp_Rockfish/data_docs/doi_10.5061_dryad.vq3rg55__v1.zip
Dryad package: Kelp-rockfish genotypes, DOI: 10.5061/dryad.6cp14g8
Zip file containing two files: Genotype data (CSV) and the variant call format (VCF) file used to generate genotypes for all kelp rockfish.
download
4509
https://datadocs.bco-dmo.org/file/k66gk5mUXGqKgM/rockfish_microhaplotype_dryad.csv
rockfish_microhaplotype_dryad.csv
Primary data file for dataset ID 684944
download
https://osprey.bco-dmo.org/dataset/684944/data/download
download
onLine
dataset
<p>Haplotype data from 150bp amplicon sequencing on an Illumina MiSeq. All loci used in the generation of haplotype sequence data will be submitted to GenBank (National Center for Biotechnology Information).</p>
<p>Genotype data are generated with high-throughput DNA sequencing on an Illumina MiSeq instrument. Amplicons are prepared through polymerase chain reaction with primers designed from either expressed sequence tags in publicly available databases (e.g., Cyverse) or from sequences generated by double digest Restriction-Site Associated DNA (RAD) sequencing. Amplicon sequencing is using the procedure described in Campbell et al. 2015 (Molecular Ecology Resources 15: 855-867) termed genotyping in thousands by sequencing (GT-seq). Data are filtered by quality score and genotypes called for all locus by individual combinations with read depth ≥20. Genotyping accuracy is evaluated by confirmation of Mendelian segregation in known families. Haplotypes are called from constituent SNPs using FreeBayes software.</p>
Specified by the Principal Investigator(s)
<p>Standard filtering for quality scores and read depth have been applied to the raw instrument output to call haplotypes.</p>
<p><strong>BCO-DMO Processing Notes:</strong><br />
- created table of files downloaded from Dryad<br />
- added conventional header with dataset name, PI name, version date</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 MiSeq
Illumina MiSeq
PI Supplied Instrument Name: Illumina MiSeq PI Supplied Instrument Description:Used to sequence genomes 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.
PI Supplied Instrument Name: 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)
Deployment: Carr_1999
Carr_1999
Long Marine Lab UCSC
Long Marine Lab UCSC
laboratory
Carr_1999
Mark Carr
University of California-Santa Cruz
Long Marine Lab UCSC
Long Marine Lab UCSC
laboratory