http://lod.bco-dmo.org/id/dataset/851773
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
2021-05-11
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
DNA microsatellite alleles from flowering shoots and seeds collected Curlew Beach in Nahant, MA and Niles Beach in Gloucester, MA in 2014
2021-05-11
publication
2021-05-11
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-05-14
publication
https://doi.org/10.26008/1912/bco-dmo.851773.1
Cynthia Hays
Keene State College
principalInvestigator
Torrance C. Hanley
Northeastern University
principalInvestigator
A. Randall Hughes
Northeastern 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: Hays, C., Hanley, T., Hughes, A. R. (2021) DNA microsatellite alleles from flowering shoots and seeds collected Curlew Beach in Nahant, MA and Niles Beach in Gloucester, MA in 2014. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-05-11 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.851773.1 [access date]
DNA microsatellite alleles from flowering shoots and seeds Dataset Description: Methods and Sampling: <p>SCUBA was used to sample <em>Zostera marina</em> in late summer 2014 from two coastal eelgrass meadows in the Gulf of Maine, USA, separated by approximately 48 km: Curlew Beach in Nahant, MA (hereafter CB) and Niles Beach in Gloucester, MA (hereafter NI). Samples were collected from three depths at each site: the center of the meadow (mid), and approximately 5 m from the inshore and offshore edges (shallow and deep, respectively); depth of our shallow, mid and deep samples was approximately 1, 3 and 5 m MLLW, respectively.&nbsp;At each depth, 8-10 flowering shoots. separated by at least 2 meters, were collected; from each of these focal flowering shoots, a leaf tissue sample was harvested along with ~8-15 developing seeds from within a single spathe on the highest and youngest rhipidia, or cluster of inflorescences (n = ~250 seeds per site). Leaf tissue was preserved in silica or frozen until DNA extraction; seeds were frozen at -80C.</p>
<p><strong>Molecular methods:</strong><br />
DNA was extracted from leaf tissue by grinding each sample with a Retsch mixer mill MM400 and using the Omega Bio-Tek E.Z.N.A.® Plant DNA Kit. DNA from seeds was extracted with Chelex 100 (Bio-Rad). Individual seeds were ground by hand in microfuge tubes with micropestles after removing the seed coat; samples were then incubated at 55<span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">°</span>C for 8-24 h, gently mixed, heated to 98<span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">°</span>C for 10 min, vortexed, centrifuged at 14,000 rpm for 5 min, and the supernatant stored at -20<span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">°</span>C until PCR.</p>
<p>Each leaf sample was genotyped using 12 microsatellite loci developed for <em>Zostera marina</em>, multiplexed in three 11 ul PCR reactions. Each reaction consisted of 1 ul DNA template, 5 μl 2X Type-It multiplex master mix (Qiagen), and 0.25 ul of each 10 uM primer. PCR cycling conditions included initial activation/denaturation at 95<span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">°</span>C for 5 min, followed by 28 cycles of 95<span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">°</span>C for 30 sec, 60<span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">°</span>C for 90 sec, and 72<span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">°</span>C for 30 sec, and final extension at 60<span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">°</span>C for 30 min. PCR products were separated on a 3730xl Genetic Analyzer (Applied Biosystems) at the Yale University DNA Analysis Facility, and fragment analysis was performed using GeneMarker version 2.6 (SoftGenetics). Nine of the 12 markers used for adult shoots proved useful for analyzing seed diversity. ZMC-12075 was eliminated due to a pattern of stutter around peaks that made scoring paternal alleles unreliable; two other markers (GA-3, CT-12) showed low allelic diversity in the adult populations and thus low power to discriminate among fathers.&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851432 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851432
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851043 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851043
completed
Cynthia Hays
Keene State College
603-358-2527
229 Main Street
Keene
NH
03435
USA
chays@keene.edu
pointOfContact
Torrance C. Hanley
Northeastern University
4000 Mayflower Hill Diamond 204
Waterville
ME
04901
USA
hanleyt2@sacredheart.edu
pointOfContact
A. Randall Hughes
Northeastern University
781-581-7370
430 Nahant Rd.
Nahant
MA
01908
USA
ann.hughes@northeastern.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
date
lat
lon
site
type
family
quad
sample_code
CT3_a
CT3_b
GA2_a
GA2_b
CT19_a
CT19_b
CL412_a
CL412_b
ZMC13053_a
ZMC13053_b
CL32_a
CL32_b
ZMC19017_a
ZMC19017_b
CL172_a
CL172_b
GA35_a
GA35_b
3730xl Genetic Analyzer (Applied Biosystems)
SCUBA
theme
None, User defined
date
latitude
longitude
site
sample description
family
sample identification
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Self-Contained Underwater Breathing Apparatus
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.
RUI: Collaborative Research: Trait differentiation and local adaptation to depth within meadows of the foundation seagrass Zostera marina
https://osprey.bco-dmo.org/project/792405
RUI: Collaborative Research: Trait differentiation and local adaptation to depth within meadows of the foundation seagrass Zostera marina
<p><em>NSF Award Abstract:</em><br />
Understanding how species cope with spatial variation in their environment (e.g. gradients in light and temperature) is necessary for informed management as well as for predicting how they may respond to change. This project will examine how key traits vary with depth in common eelgrass (Zostera marina), one of the most important foundation species in temperate nearshore ecosystems worldwide. The investigators will use a combination of experiments in the field and lab, paired with fine-scale molecular analyses, to determine the genetic and environmental components of seagrass trait variation. This work will provide important information on the microevolutionary mechanisms that allow a foundation species to persist in a variable environment, and thus to drive the ecological function of whole nearshore communities. The Northeastern University graduate and Keene State College (KSC) undergraduate students supported by this project will receive training in state-of-the-art molecular techniques, as well as mentorship and experience in scientific communication and outreach. A significant portion of KSC students are from groups under-represented in science. Key findings of the research will be incorporated into undergraduate courses and outreach programs for high school students from under-represented groups, and presented at local and national meetings of scientists and stakeholders.</p>
<p>Local adaptation, the superior performance of "home" versus "foreign" genotypes in a local environment, is a powerful demonstration of how natural selection can overcome gene flow and drift to shape phenotypes to match their environment. The classic test for local adaptation is a reciprocal transplant. However, such experiments often fail to capture critical aspects of the immigration process that may mediate realized gene flow in natural systems. For example, reciprocal transplant experiments typically test local and non-local phenotypes at the same (often adult) life history stage, and at the same abundance or density, which does not mirror how dispersal actually occurs for most species. In real populations, migrants (non-local) often arrive at low numbers compared to residents (local), and relative frequency itself can impact fitness. In particular, rare phenotypes may experience reduced competition for resources, or relative release from specialized pathogens. Such negative frequency dependent selection can reduce fitness differences between migrants and residents due to local adaptation, and magnify effective gene flow, thus maintaining greater within-population genetic diversity. The investigators will combine spatially paired sampling and fine-scale molecular analyses to link seed/seedling trait variation across the depth gradient at six meadows to key factors that may drive these patterns: local environmental conditions, population demography, and gene flow across depths. The team will then experimentally test the outcome of cross-gradient dispersal in an ecologically relevant context, by reciprocally out-planting seeds from different depths and manipulating relative frequency in relation to both adults and other seedling lineages. The possible interaction between local adaptation and frequency-dependence is particularly relevant for Zostera marina, which represents one of the best documented examples of the ecological effects of genetic diversity and identity. Further, a better understanding of seagrass trait differentiation is not simply a matter of academic interest, but critical to successful seagrass restoration and conservation.</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>
ZosMarLA
largerWorkCitation
project
eng; USA
oceans
-70.915
-70.655
42.42
42.597
2014-07-14
2014-08-03
Massachusetts, USA
0
BCO-DMO catalogue of parameters from DNA microsatellite alleles from flowering shoots and seeds collected Curlew Beach in Nahant, MA and Niles Beach in Gloucester, MA in 2014
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/851787.rdf
Name: date
Units: unitless
Description: <p>Sampling date; format: YYYY-MM-DD</p>
http://lod.bco-dmo.org/id/dataset-parameter/851788.rdf
Name: lat
Units: degrees North
Description: <p>Latitude of sampling site</p>
http://lod.bco-dmo.org/id/dataset-parameter/851789.rdf
Name: lon
Units: degrees East
Description: <p>Longitude of sampling site</p>
http://lod.bco-dmo.org/id/dataset-parameter/851790.rdf
Name: site
Units: unitless
Description: <p>Site: CB = Curlew Beach; NI = Niles Beach.</p>
http://lod.bco-dmo.org/id/dataset-parameter/851791.rdf
Name: type
Units: unitless
Description: <p>mom or seed</p>
http://lod.bco-dmo.org/id/dataset-parameter/851792.rdf
Name: family
Units: unitless
Description: <p>unique identifier for the maternal family</p>
http://lod.bco-dmo.org/id/dataset-parameter/851793.rdf
Name: quad
Units: unitless
Description: <p>Quadrat number</p>
http://lod.bco-dmo.org/id/dataset-parameter/851794.rdf
Name: sample_code
Units: unitless
Description: <p>Unique identifier for the genetic sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/851795.rdf
Name: CT3_a
Units: bp (base pairs)
Description: <p>allele 1 for locus ZosmarCT-3</p>
http://lod.bco-dmo.org/id/dataset-parameter/851796.rdf
Name: CT3_b
Units: bp (base pairs)
Description: <p>allele 2 for locus ZosmarCT-3</p>
http://lod.bco-dmo.org/id/dataset-parameter/851797.rdf
Name: GA2_a
Units: bp (base pairs)
Description: <p>allele 1 for locus ZosmarGA-2</p>
http://lod.bco-dmo.org/id/dataset-parameter/851798.rdf
Name: GA2_b
Units: bp (base pairs)
Description: <p>allele 2 for locus ZosmarGA-2</p>
http://lod.bco-dmo.org/id/dataset-parameter/851799.rdf
Name: CT19_a
Units: bp (base pairs)
Description: <p>allele 1 for locus ZosmarCT-19</p>
http://lod.bco-dmo.org/id/dataset-parameter/851800.rdf
Name: CT19_b
Units: bp (base pairs)
Description: <p>allele 2 for locus ZosmarCT-19</p>
http://lod.bco-dmo.org/id/dataset-parameter/851801.rdf
Name: CL412_a
Units: bp (base pairs)
Description: <p>allele 1 for locus CL412Contig1</p>
http://lod.bco-dmo.org/id/dataset-parameter/851802.rdf
Name: CL412_b
Units: bp (base pairs)
Description: <p>allele 2 for locus CL412Contig1</p>
http://lod.bco-dmo.org/id/dataset-parameter/851803.rdf
Name: ZMC13053_a
Units: bp (base pairs)
Description: <p>allele 1 for locus ZMC13053</p>
http://lod.bco-dmo.org/id/dataset-parameter/851804.rdf
Name: ZMC13053_b
Units: bp (base pairs)
Description: <p>allele 2 for locus ZMC13053</p>
http://lod.bco-dmo.org/id/dataset-parameter/851805.rdf
Name: CL32_a
Units: bp (base pairs)
Description: <p>allele 1 for locus CL32Contig2</p>
http://lod.bco-dmo.org/id/dataset-parameter/851806.rdf
Name: CL32_b
Units: bp (base pairs)
Description: <p>allele 2 for locus CL32Contig2</p>
http://lod.bco-dmo.org/id/dataset-parameter/851807.rdf
Name: ZMC19017_a
Units: bp (base pairs)
Description: <p>allele 1 for locus ZMC19017</p>
http://lod.bco-dmo.org/id/dataset-parameter/851808.rdf
Name: ZMC19017_b
Units: bp (base pairs)
Description: <p>allele 2 for locus ZMC19017</p>
http://lod.bco-dmo.org/id/dataset-parameter/851809.rdf
Name: CL172_a
Units: bp (base pairs)
Description: <p>allele 1 for locus CL172Contig1</p>
http://lod.bco-dmo.org/id/dataset-parameter/851810.rdf
Name: CL172_b
Units: bp (base pairs)
Description: <p>allele 2 for locus CL172Contig1</p>
http://lod.bco-dmo.org/id/dataset-parameter/851811.rdf
Name: GA35_a
Units: bp (base pairs)
Description: <p>allele 1 for locus ZosmarGA-35</p>
http://lod.bco-dmo.org/id/dataset-parameter/851812.rdf
Name: GA35_b
Units: bp (base pairs)
Description: <p>allele 2 for locus ZosmarGA-35</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
63884
https://darchive.mblwhoilibrary.org/bitstream/1912/27117/1/dataset-851773_dna-microsatellite-alleles-flowering-shoots-and-seeds__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.851773.1
download
onLine
dataset
<p>SCUBA was used to sample <em>Zostera marina</em> in late summer 2014 from two coastal eelgrass meadows in the Gulf of Maine, USA, separated by approximately 48 km: Curlew Beach in Nahant, MA (hereafter CB) and Niles Beach in Gloucester, MA (hereafter NI). Samples were collected from three depths at each site: the center of the meadow (mid), and approximately 5 m from the inshore and offshore edges (shallow and deep, respectively); depth of our shallow, mid and deep samples was approximately 1, 3 and 5 m MLLW, respectively.&nbsp;At each depth, 8-10 flowering shoots. separated by at least 2 meters, were collected; from each of these focal flowering shoots, a leaf tissue sample was harvested along with ~8-15 developing seeds from within a single spathe on the highest and youngest rhipidia, or cluster of inflorescences (n = ~250 seeds per site). Leaf tissue was preserved in silica or frozen until DNA extraction; seeds were frozen at -80C.</p>
<p><strong>Molecular methods:</strong><br />
DNA was extracted from leaf tissue by grinding each sample with a Retsch mixer mill MM400 and using the Omega Bio-Tek E.Z.N.A.® Plant DNA Kit. DNA from seeds was extracted with Chelex 100 (Bio-Rad). Individual seeds were ground by hand in microfuge tubes with micropestles after removing the seed coat; samples were then incubated at 55<span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">°</span>C for 8-24 h, gently mixed, heated to 98<span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">°</span>C for 10 min, vortexed, centrifuged at 14,000 rpm for 5 min, and the supernatant stored at -20<span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">°</span>C until PCR.</p>
<p>Each leaf sample was genotyped using 12 microsatellite loci developed for <em>Zostera marina</em>, multiplexed in three 11 ul PCR reactions. Each reaction consisted of 1 ul DNA template, 5 μl 2X Type-It multiplex master mix (Qiagen), and 0.25 ul of each 10 uM primer. PCR cycling conditions included initial activation/denaturation at 95<span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">°</span>C for 5 min, followed by 28 cycles of 95<span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">°</span>C for 30 sec, 60<span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">°</span>C for 90 sec, and 72<span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">°</span>C for 30 sec, and final extension at 60<span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">°</span>C for 30 min. PCR products were separated on a 3730xl Genetic Analyzer (Applied Biosystems) at the Yale University DNA Analysis Facility, and fragment analysis was performed using GeneMarker version 2.6 (SoftGenetics). Nine of the 12 markers used for adult shoots proved useful for analyzing seed diversity. ZMC-12075 was eliminated due to a pattern of stutter around peaks that made scoring paternal alleles unreliable; two other markers (GA-3, CT-12) showed low allelic diversity in the adult populations and thus low power to discriminate among fathers.&nbsp;</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- changed date format to YYYY-MM-DD.</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
3730xl Genetic Analyzer (Applied Biosystems)
3730xl Genetic Analyzer (Applied Biosystems)
PI Supplied Instrument Name: 3730xl Genetic Analyzer (Applied Biosystems) 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.
SCUBA
SCUBA
PI Supplied Instrument Name: SCUBA 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
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)