http://lod.bco-dmo.org/id/dataset/661446
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
2016-10-12
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
A re-sampling of historical population genetic surveys of Zostera marina from Bodega, Tomales, and San Francisco Bays USA; study performed at Bodega Marine Laboratory in 2014-15
2016-10-12
publication
2016-10-12
revision
BCO-DMO Linked Data URI
2016-10-12
creation
http://lod.bco-dmo.org/id/dataset/661446
John J. Stachowicz
University of California-Davis
principalInvestigator
Richard K. Grosberg
University of California-Davis
principalInvestigator
Susan L. Williams
University of California - Davis: Bodega Marine Laboratory
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: Stachowicz, J. J., Grosberg, R. K., Williams, S. L. (2016) A re-sampling of historical population genetic surveys of Zostera marina from Bodega, Tomales, and San Francisco Bays USA; study performed at Bodega Marine Laboratory in 2014-15. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 12 October 2016) Version Date 2016-10-12 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/661446 [access date]
A re-sampling of historical population genetic surveys of Zostera marina from Bodega, Tomales, and San Francisco Bays USA Dataset Description: <p>A re-sampling of historical population genetic surveys of <em>Zostera marina </em>from Bodega (BB), Tomales (TB), and San Francisco Bays (SFB) USA.&nbsp;Plant (<em>Zostera marina</em>) samples were collected from Bodega Bay, Tomales Bay, and San Francisco Bay in 2013. DNA was extracted and amplified in the Stachowicz and Grosberg labs at UCDavis, and fragments were analyzed at the UCDavis core facility during 2014-2015. Data are presented as number of base pairs.</p> Methods and Sampling: <p>Both sampling and analyses are&nbsp;described in the manuscript in press in the journal <em>Heredity,&nbsp;</em>titled "Temporal stability in patterns of genetic diversity and structure of a marine foundation species (<em>Zostera marina</em>)".</p>
<p>Briefly, we re-sampled <em>Z. marina</em> populations previously described genetically in the literature. Because the goal of sampling these populations was to compare changes over time within each region, we designed the re-sampling to match the previously published studies as closely as possible. Consequently, sampling schemes (haphazard collection (SFB) vs. quadrat sampling (TB and BB)) differed between regions. DNA from all samples was analyzed at 12 microsatellite loci.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1234345 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1234345
completed
John J. Stachowicz
University of California-Davis
530-752-1113
Department of Evolution and Ecology 1 Shields Ave
Davis
CA
95616
USA
jjstachowicz@ucdavis.edu
pointOfContact
Richard K. Grosberg
University of California-Davis
Department of Ecology and Evolution 1 Shields Ave
Davis
CA
95616
USA
rkgrosberg@ucdavis.edu
pointOfContact
Susan L. Williams
University of California - Davis: Bodega Marine Laboratory
707-875-1950
Bodega Marine Laboratory P.O. Box 247
Bodega Bay
CA
94923
USA
slwilliams@ucdavis.edu
pointOfContact
asNeeded
Dataset Version: 12 October 2016
Unknown
region_code
region
meadow_code
meadow
tidal_height_code
tidal_height
CL32_Con2_a1
CL32_Con2_a2
CL559_Con1_a1
CL559_Con1_a2
ZMC12075_a1
ZMC12075_a2
ZMC13053_a1
ZMC13053_a2
CL172_Con1_a1
CL172_Con1_a2
ZMC19017_a1
ZMC19017_a2
ZMC19062_a1
ZMC19062_a2
CT12_a1
CT12_a2
CT19_a1
CT19_a2
CT3_a1
CT3_a2
GA2_a1
GA2_a2
GA3_a1
GA3_a2
ABI 3010XL
theme
None, User defined
site
site description
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
BML_Stachowicz
service
Deployment Activity
Bodega Marine Lab
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.
Connecting genetic diversity to ecosystem functioning: links between genetic diversity, relatedness and trait variation in a seagrass community
https://osprey.bco-dmo.org/project/564447
Connecting genetic diversity to ecosystem functioning: links between genetic diversity, relatedness and trait variation in a seagrass community
<p>There is growing evidence that genetic variation within and among populations of key species plays an important role in marine ecosystem processes. Several experiments provide compelling evidence that the number of genotypes in an assemblage (genotypic richness) can influence critical ecosystem functions including productivity, resistance to disturbance and invasion or colonization success. However, these studies use only the number of genotypes as a measure of genetic diversity. Recent analyses of species diversity experiments show that phylogenetic diversity may be a more reliable predictor of ecosystem functioning than simply the number of species. However, such approaches have not yet been applied to understanding the effects of genetics on ecosystem functioning. While genetic relatedness within a species holds the potential to predict the outcome of intraspecific interactions, and the functioning of ecosystems that depend on those species, we currently have few data to assess the shape or strength of this relationship. The investigators will build on their own previous work, and that of others, in eelgrass (<em>Zostera marina</em>) ecosystems showing strong effects of genotypic richness on a spectrum of critical ecosystem processes. The investigators will ask whether genotypic richness, or - as in studies at the level of species diversity - genetic relatedness/distance better predicts ecosystem functioning? If genetic relatedness measures are better predictors, then what mechanisms underlie this relationship? Can genetic relatedness predict ecological relatedness?</p>
<p>Although the current focus is on eelgrass, the research should be applicable to many systems. The project will assess the relationship between genetic relatedness and phenotypic distinctiveness of a key marine foundation species and use manipulative experiments to test the relative importance of the number of genotypes in an assemblage vs. their genetic relatedness and trait diversity for ecosystem functioning. Specifically, experiments will:<br />
(1) characterize the relationship between genetic relatedness and trait similarity among individual genotypes of eelgrass, including responses to experimental warming;<br />
(2) compare the effects of genetic relatedness and trait similarity among genotypes on the outcome of intraspecific competitive interactions; and<br />
(3) test the relative effect of genetic relatedness vs. number of genotypes of eelgrass on the growth of eelgrass, its associated ecosystem functions it (e.g., primary production, nutrient dynamics, trophic transfer, habitat provision, and detrital production and decomposition).</p>
<p>Seagrass ecosystems provide important services to coastal regions including primary production, nutrient cycling, habitat for fisheries species, and erosion control. Previous studies have shown these services can be compromised by reduction in the numbers of species of grazers or genotypes, but this study will allow a more predictive approach to diversity loss by integrating the effects of multiple components of diversity and clarifying the extent to which diversity effects can be predicted by the genetic or ecological uniqueness of component genotypes.</p>
Genetic Div to Ecosys Functioning
largerWorkCitation
project
eng; USA
oceans
Bodega Marine Lab
2016-10-12
0
BCO-DMO catalogue of parameters from A re-sampling of historical population genetic surveys of Zostera marina from Bodega, Tomales, and San Francisco Bays USA; study performed at Bodega Marine Laboratory in 2014-15
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/661499.rdf
Name: region_code
Units: unitless
Description: <p>Code assigned to region where samples were collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/661500.rdf
Name: region
Units: unitless
Description: <p>Region where samples were collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/661501.rdf
Name: meadow_code
Units: unitless
Description: <p>Code assigned to meadow within the region where samples were collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/661502.rdf
Name: meadow
Units: unitless
Description: <p>Meadow within the region where samples were collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/661503.rdf
Name: tidal_height_code
Units: unitless
Description: <p>Code assigned to tidal height. NA = Not applicable because samples were collected over a gradient</p>
http://lod.bco-dmo.org/id/dataset-parameter/661504.rdf
Name: tidal_height
Units: unitless
Description: <p>Description of tidal height of area sampled</p>
http://lod.bco-dmo.org/id/dataset-parameter/661505.rdf
Name: CL32_Con2_a1
Units: unitless
Description: <p>Locus CL32 Contig 2 (Oetjen & Reusch 2007 Molecular Ecology); allele 1; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661506.rdf
Name: CL32_Con2_a2
Units: unitless
Description: <p>Locus CL32 Contig 2 (Oetjen & Reusch 2007 Molecular Ecology); allele 2; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661507.rdf
Name: CL559_Con1_a1
Units: unitless
Description: <p>Locus CL 559 Contig 1 (Oetjen et al. 2010 Marine Biology); allele 1; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661508.rdf
Name: CL559_Con1_a2
Units: unitless
Description: <p>Locus CL 559 Contig 1 (Oetjen et al. 2010 Marine Biology); allele 2; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661509.rdf
Name: ZMC12075_a1
Units: unitless
Description: <p>Locus ZMC 12075 (Oetjen & Reusch 2007 Molecular Ecology); allele 1; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661510.rdf
Name: ZMC12075_a2
Units: unitless
Description: <p>Locus ZMC 12075 (Oetjen & Reusch 2007 Molecular Ecology); allele 2; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661511.rdf
Name: ZMC13053_a1
Units: unitless
Description: <p>Locus ZMC 13053 (Oetjen & Reusch 2007 Molecular Ecology); allele 1; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661512.rdf
Name: ZMC13053_a2
Units: unitless
Description: <p>Locus ZMC 13053 (Oetjen & Reusch 2007 Molecular Ecology); allele 2; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661513.rdf
Name: CL172_Con1_a1
Units: unitless
Description: <p>Locus CL172 Contig 1 (Oetjen et al. 2010 Marine Biology); allele 1; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661514.rdf
Name: CL172_Con1_a2
Units: unitless
Description: <p>Locus CL172 Contig 1 (Oetjen et al. 2010 Marine Biology); allele 2; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661515.rdf
Name: ZMC19017_a1
Units: unitless
Description: <p>Locus ZMC 19017 (Oetjen & Reusch 2007 Molecular Ecology); allele 1; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661516.rdf
Name: ZMC19017_a2
Units: unitless
Description: <p>Locus ZMC 19017 (Oetjen & Reusch 2007 Molecular Ecology); allele 2; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661517.rdf
Name: ZMC19062_a1
Units: unitless
Description: <p>Locus ZMC 19062 (Oetjen et al. 2010 Marine Biology); allele 1; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661518.rdf
Name: ZMC19062_a2
Units: unitless
Description: <p>Locus ZMC 19062 (Oetjen et al. 2010 Marine Biology); allele 2; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661519.rdf
Name: CT12_a1
Units: unitless
Description: <p>Locus CT12 (Reusch 2000 Molecular Ecology); allele 1; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661520.rdf
Name: CT12_a2
Units: unitless
Description: <p>Locus CT12 (Reusch 2000 Molecular Ecology); allele 2; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661521.rdf
Name: CT19_a1
Units: unitless
Description: <p>Locus CT19 (Reusch 2000 Molecular Ecology); allele 1; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661522.rdf
Name: CT19_a2
Units: unitless
Description: <p>Locus CT19 (Reusch 2000 Molecular Ecology); allele 2; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661523.rdf
Name: CT3_a1
Units: unitless
Description: <p>Locus CT3 (Reusch et al. 1999 Marine Biology); allele 1; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661524.rdf
Name: CT3_a2
Units: unitless
Description: <p>Locus CT3 (Reusch et al. 1999 Marine Biology); allele 2; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661525.rdf
Name: GA2_a1
Units: unitless
Description: <p>Locus GA2 (Reusch et al. 1999 Marine Biology); allele 1; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661526.rdf
Name: GA2_a2
Units: unitless
Description: <p>Locus GA2 (Reusch et al. 1999 Marine Biology); allele 2; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661527.rdf
Name: GA3_a1
Units: unitless
Description: <p>Locus GA3 (Reusch et al. 1999 Marine Biology); allele 1; reported in number of base pairs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/661528.rdf
Name: GA3_a2
Units: unitless
Description: <p>Locus GA3 (Reusch et al. 1999 Marine Biology); allele 2; reported in number of base pairs.</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
46790
https://datadocs.bco-dmo.org/file/vmmwyqMFEG0VWN/heredity.csv
heredity.csv
Primary data file for dataset ID 661446
download
https://osprey.bco-dmo.org/dataset/661446/data/download
download
onLine
dataset
<p>Both sampling and analyses are&nbsp;described in the manuscript in press in the journal <em>Heredity,&nbsp;</em>titled "Temporal stability in patterns of genetic diversity and structure of a marine foundation species (<em>Zostera marina</em>)".</p>
<p>Briefly, we re-sampled <em>Z. marina</em> populations previously described genetically in the literature. Because the goal of sampling these populations was to compare changes over time within each region, we designed the re-sampling to match the previously published studies as closely as possible. Consequently, sampling schemes (haphazard collection (SFB) vs. quadrat sampling (TB and BB)) differed between regions. DNA from all samples was analyzed at 12 microsatellite loci.</p>
Specified by the Principal Investigator(s)
<p>We amplified 12 previously characterized microsatellite loci (CT12, CT19 (Reusch 2000), CT3, GA2, GA3 (Reusch et al. 1999), CL32 Contig 2, ZMC 12075, ZMC 13053, ZMC 19017, (Oetjen &amp; Reusch 2007), CL 559 Contig 1, CL172 Contig 1, ZMC 19062 (Oetjen et al. 2010)). We analyzed fragments on an ABI 3010XL at the UC Davis DNA sequencing facility, and visualized the fragments using STRand software (Toonen &amp; Hughes 2001).&nbsp;</p>
<p>BCO-DMO Processing:<br />
- modified parameter names to conform with BCO-DMO naming conventions; appended "a1" (allele 1) or "a2" (allele 2).<br />
- added columns containing the full name/meaning for region, meadow, and tidal height codes.</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
ABI 3010XL
ABI 3010XL
PI Supplied Instrument Name: ABI 3010XL PI Supplied Instrument Description:We analyzed fragments on an ABI 3010XL at the UC Davis DNA sequencing facility, and visualized the fragments using STRand software (Toonen & Hughes 2001). 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.
Deployment: BML_Stachowicz
BML_Stachowicz
lab Bodega Marine Laboratory
laboratory
BML_Stachowicz
John J. Stachowicz
University of California-Davis
lab Bodega Marine Laboratory
laboratory