http://lod.bco-dmo.org/id/dataset/924808
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
2024-04-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Shoot measurements (sheath length and width) for the eelgrass (Zostera marina) shoots sampled for whole genome sequencing collected from Bodega and Tomales Bay, CA, USA from July to September 2019
2024-04-10
publication
2024-04-10
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-07-02
publication
https://doi.org/10.26008/1912/bco-dmo.924808.1
John J. Stachowicz
University of California-Davis
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. (2024) Shoot measurements (sheath length and width) for the eelgrass (Zostera marina) shoots sampled for whole genome sequencing collected from Bodega and Tomales Bay, CA, USA from July to September 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-04-10 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.924808.1 [access date]
Shoots sampled for whole genome sequencing Dataset Description: Methods and Sampling: <p>We collected 2 to 3 shoots attached by a rhizome from fifteen putative genets (separated by approximately 5 to 10 meters) at 14 sites across Tomales Bay and Bodega Harbor from a height below 0.0 mean lower low water (MLLW) (i.e., not sampling the uppermost or lowermost vertical distribution of <em>Zostera marina</em>). For two of the sites sampled in Bodega Harbor (Mason's Marina and Westside Park), we also collected a deeper set of specimens (at least -0.6 meters below MLLW) to test for differences between shallower versus deeper plants. We transported plants back to the University of California, Davis in a cooler with ice packs, and stored them for no more than 1 day in a recirculating seawater table before measuring the terminal shoot sheath width using calipers and sheath length using a ruler. The sheath width was measured at the abscission point and the length from the abscission point to the base of the shoot. Once measurements were made, we dissected out the tissue from within the leaf sheath and flash-froze them in liquid nitrogen and stored at -80 degrees Celsius (°C).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1829976 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1829976
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
asNeeded
Dataset Version: 1
Unknown
INDV
SITE
collection_date
Latitude
Longitude
sheath_length
sheath_width
depth
mean_temp_C
calipers
ruler
theme
None, User defined
sample identification
site
date
latitude
longitude
length
width
site description
water temperature at measurement depth
featureType
BCO-DMO Standard Parameters
calipers
ruler
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.
Using genomics to link traits to ecosystem function in the eelgrass Zostera marina
https://osprey.bco-dmo.org/project/777102
Using genomics to link traits to ecosystem function in the eelgrass Zostera marina
<p><em>NSF Award Abstract:</em><br />
Seagrass ecosystems provide important services to coastal regions, including primary production, carbon storage, nutrient cycling, habitat for fisheries species, and erosion control. At the same time, eelgrass is threatened by direct destruction, pollution, and other human impacts on the environment. We know that genetic diversity in eelgrass enhances seagrass bed growth and persistence, but application of this knowledge to restoration and conservation is limited. This work will guide restoration programs by considering what specific aspects of diversity are important to conservation and restoration of seagrass ecosystems, helping to guide the selection of source material to improve restoration success (which is often low). The project integrates the effects of multiple components of diversity and clarifies the extent to which genetic and ecological uniqueness can predict ecosystem functions.</p>
<p>Intellectual Merit: Genetic diversity as measured by the number of genetically distinct individuals (genets) in an assemblage influences critical ecosystem functions in a wide range of ecosystems. Functional diversity, the presence of key traits, or population flexibility to respond to environmental change are all potential mechanisms underlying these patterns, but distinguishing among them requires a clear link between genetic diversity and the phenotypes present in an assemblage. The investigators, and others, have previously demonstrated that genet diversity in eelgrass (Zostera marina) increases stand productivity, animal community diversity, and resilience to environmental change. These genet diversity effects are associated with increases in genetically determined trait diversity. Predicting trait diversity without having to measure traits of every genet remains a major barrier to wider application of functional diversity approaches in restoration and management. In this project, the investigators assess the association between Single Nucleotide Polymorphisms (SNPs) across the genome and performance-related traits that we will measure at the individual, population, and seascape-scale. They also assess environmental correlates of trait differentiation from field sampling. Finally, the research team will compare the predictive power of genomic SNP diversity versus other metrics of intraspecific diversity for the functioning (productivity, invertebrate abundance) of field planted eelgrass assemblages. If genomic variation can reliably be used to predict functional traits, then the value of genomic sequencing efforts for informing management will be greatly enhanced. Broader Impacts: Seagrass restoration and mitigation is currently of major interest in California and elsewhere and the project results will inform current initiatives regarding eelgrass management in California through the state's Ocean Protection Council. In addition to recruiting individual students from diverse backgrounds to work on the project, the project broadens participation of students in STEM fields through its partnership with three existing outreach/training programs at UC Davis.</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>
ZosteraEcoGenomics
largerWorkCitation
project
eng; USA
oceans
-123.06
-122.846
38.105
38.3334
2019-07-16
2019-09-30
In Zostera marina beds worldwide, including western and eastern margins of both the Atlantic and Pacific Oceans. Project centered in Bodega Bay, CA 38.31 N; 123.059 W
0
BCO-DMO catalogue of parameters from Shoot measurements (sheath length and width) for the eelgrass (Zostera marina) shoots sampled for whole genome sequencing collected from Bodega and Tomales Bay, CA, USA from July to September 2019
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/924816.rdf
Name: INDV
Units: unitless
Description: <p>sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/924817.rdf
Name: SITE
Units: unitless
Description: <p>B=Bodega Bay; T= Tomales Bay; two letter code indicates site within each Bay from Schiebelhut et al 2023.</p>
http://lod.bco-dmo.org/id/dataset-parameter/924818.rdf
Name: collection_date
Units: unitless
Description: <p>Date of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/924819.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/924820.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/924821.rdf
Name: sheath_length
Units: millimeters (mm)
Description: <p>length of the seagrass sheath from the base to the abscission point</p>
http://lod.bco-dmo.org/id/dataset-parameter/924822.rdf
Name: sheath_width
Units: millimeters (mm)
Description: <p>width of the sheath at the abcission point</p>
http://lod.bco-dmo.org/id/dataset-parameter/924823.rdf
Name: depth
Units: unitless
Description: <p>intertidal (0 to - 0.5m below mllw) or subtidal (deeper than 0.5 m below MLLW)</p>
http://lod.bco-dmo.org/id/dataset-parameter/924824.rdf
Name: mean_temp_C
Units: degrees Celsius
Description: <p>mean temperature at the site during the day of sampling</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
12109
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/1b016e1a-8d0e-47c5-840f-b749fb7479f7/content
download
https://doi.org/10.26008/1912/bco-dmo.924808.1
download
onLine
dataset
<p>We collected 2 to 3 shoots attached by a rhizome from fifteen putative genets (separated by approximately 5 to 10 meters) at 14 sites across Tomales Bay and Bodega Harbor from a height below 0.0 mean lower low water (MLLW) (i.e., not sampling the uppermost or lowermost vertical distribution of <em>Zostera marina</em>). For two of the sites sampled in Bodega Harbor (Mason's Marina and Westside Park), we also collected a deeper set of specimens (at least -0.6 meters below MLLW) to test for differences between shallower versus deeper plants. We transported plants back to the University of California, Davis in a cooler with ice packs, and stored them for no more than 1 day in a recirculating seawater table before measuring the terminal shoot sheath width using calipers and sheath length using a ruler. The sheath width was measured at the abscission point and the length from the abscission point to the base of the shoot. Once measurements were made, we dissected out the tissue from within the leaf sheath and flash-froze them in liquid nitrogen and stored at -80 degrees Celsius (°C).</p>
Specified by the Principal Investigator(s)
- Imported original file "Zm_TomBod_morpohmetrics.xlsx" into the BCO-DMO system.
- Imported original file "WGS_LS_TomalesBodega.xlsx" into the BCO-DMO system.
- Added the "collection_date" column from "WGS_LS_TomalesBodega.xlsx" to the shoot morphometrics file, matching on individual sample ID number
- Converted date field to YYYY-MM-DD format.
- Saved final file as "924808_v1_shoots_sampled_for_sequencing.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
calipers
calipers
PI Supplied Instrument Name: calipers Instrument Name: calipers Instrument Short Name: Instrument Description: A caliper (or "pair of calipers") is a device used to measure the distance between two opposite sides of an object. Many types of calipers permit reading out a measurement on a ruled scale, a dial, or a digital display.
ruler
ruler
PI Supplied Instrument Name: ruler Instrument Name: ruler Instrument Short Name: Instrument Description: A device used for measuring or for drawing straight lines, consisting of an elongated piece of rigid or semi-rigid material marked with units for measurement. Device that allows one or more physical dimensions of a sample or specimen to be determined by visible comparison against marked graduations in units of measurement of dimension length.