http://lod.bco-dmo.org/id/dataset/629302
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
2015-12-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
The genotypes from 9 microsatellites generated on individuals of the red invasive seaweed Gracilaria vermiculophylla
2015-12-18
publication
2015-12-18
revision
BCO-DMO Linked Data URI
2015-12-18
creation
http://lod.bco-dmo.org/id/dataset/629302
James E. Byers
University of Georgia
principalInvestigator
Erik Sotka
College of Charleston
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: Sotka, E., Byers, J. E. (2015) The genotypes from 9 microsatellites generated on individuals of the red invasive seaweed Gracilaria vermiculophylla. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 18 Dec 2015) Version Date 2015-12-18 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/629302 [access date]
The genotypes from 9 microsatellites generated on individuals of the red invasive seaweed Gracilaria vermiculophylla. Dataset Description: <p>This dataset contains&nbsp;the genotypes from 9 microsatellites generated on individuals of the red invasive seaweed <em>Gracilaria vermiculophylla</em>.&nbsp;</p>
<p>This is a supplemental file (PeerJ_genotype_data.xlsx) of the manuscript:<br />
Kollars, N. M., S. a. Krueger-Hadfield, J. E. Byers, T. W. Greig, A. E. Strand, F. Weinberger, and E. E. Sotka. 2015. Development and characterization of microsatellite loci for the haploid–diploid red seaweed <em>Gracilaria vermiculophylla</em>. PeerJ 3:e1159. doi:&nbsp;<a href="https://dx.doi.org/10.7717/peerj.1159" target="_blank">10.7717/peerj.1159</a></p>
<p>Related supplemental files:<br />
<a href="http://www.bco-dmo.org/dataset/630041" target="_blank">Table S1</a>:&nbsp;Characteristics of 33 microsatellite loci developed for <em>Gracilaria vermiculophylla </em>that showed monomorphism, non-amplification, or multi-locus genetic determinism.</p>
<p><a href="http://dmoserv3.whoi.edu/data_docs/Gracilaria_effects/PeerJ_TableS2.pdf" target="_blank">Table S2</a>: Null allele frequencies for the microsatellite loci developed for&nbsp;<em>Gracilaria vermiculophylla</em>. Frequencies were directly estimated in the haploid subpopulations, whereas frequencies in each of the diploid subpopulations at Akkeshi, Elkhorn Slough, Fort Johnson and Nordstrand were calculated using maximum likelihood and the software MLNullFreq.</p>
<p><a href="http://dmoserv3.whoi.edu/data_docs/Gracilaria_effects/PeerJ_TableS3.pdf" target="_blank">Table S3</a>:&nbsp;Short allele dominance analysis for microsatellite loci developed for&nbsp;<em>Gracilaria vermiculophylla</em>&nbsp;including number of pooled size classes used in regression analysis (following Wattier&nbsp;<em>et al.&nbsp;</em>1998),&nbsp;<em>No. of classes</em>, and linear regression statistics. Loci Gverm_10367 and Gverm_2790 only exhibited two alleles in our sampled populations and consequently, short allele dominance analysis was not applicable (NA).&nbsp;</p>
<p><a href="http://dmoserv3.whoi.edu/data_docs/Gracilaria_effects/PeerJ_TableS4.pdf" target="_blank">Table S4</a>:&nbsp;Linkage disequilibrium analysis for microsatellite loci developed for&nbsp;<em>Gracilaria vermiculophylla</em>. Darkened cells indicate pairs of loci that show significant linkage disequilibrium after Bonferroni correction (<em>p</em>-value threshold &lt; 0.006 at α = 0.05).</p>
<p><a href="http://dmoserv3.whoi.edu/data_docs/Gracilaria_effects/PeerJ_TableS5.pdf" target="_blank">Table S5</a>:&nbsp;Genetic features per locus of four populations of&nbsp;<em>Gracilaria vermiculophylla</em>, including: number of alleles at each locus,&nbsp;<em>NA</em>, + standard error (SE); mean allelic richness,&nbsp;<em>AE</em>, based on the smallest global sample size of 46 alleles (23 diploid individuals) + SE; mean observed heterozygosity,&nbsp;<em>HO</em>, + SE; mean expected heterozygosity,&nbsp;<em>HE</em>, + SE.&nbsp;</p> Methods and Sampling: <p>Data were generated on an ABI genotyper.</p>
<p>Briefly, from <a href="http://dx.doi.org/10.7717/peerj.1159" target="_blank">Kollars et al. (2015)</a>:<br />
A library of contigs for <em>G. vermiculophylla</em> was generated using the 454 next-generation sequencing platform (Cornell University Life Sciences Core Laboratory Center) from a single individual collected fromCharleston, South Carolina, USA. Total genomic DNA was isolated and loci were amplified on a thermocycler (BioRad). Samples were electrophoresed on an ABI 3130xL genetic analyzer equipped with 36 cm capillaries (Applied Biosystems). Alleles were scored manually using GENEMAPPER ver. 4 (Applied Biosystems) and allele sizes were binned with TANDEM ver. 1.08 software.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1057707 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1057707
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1057713 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1057713
completed
James E. Byers
University of Georgia
706-583-0012
Odum School of Ecology 140 E. Green St.
Athens
GA
30602
USA
jebyers@uga.edu
pointOfContact
Erik Sotka
College of Charleston
843-953-9191
Grice Marine Laboratory 205 Fort Johnson Road
Charleston
SC
29412
USA
SotkaE@cofc.edu
pointOfContact
asNeeded
Dataset Version: 18 Dec 2015
Unknown
individual
population
range
Gverm_1203
Gverm_1203b
Gverm_6311
Gverm_6311b
Gverm_8036
Gverm_8036b
Gverm_804
Gverm_804b
Gverm_10367
Gverm_10367b
Gverm_5276
Gverm_5276b
Gverm_2790
Gverm_2790b
Gverm_3003
Gverm_3003b
Gverm_1803
Gverm_1803b
ABI 3130xL genetic analyzer
Thermocycler
theme
None, User defined
individual
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
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.
Cascading effects of an invasive seaweed on estuarine food webs of the southeastern US
https://osprey.bco-dmo.org/project/564687
Cascading effects of an invasive seaweed on estuarine food webs of the southeastern US
<p><em>Description from NSF award abstract:</em><br />
During the last decade, the Asian seaweed, <em>Gracilaria vermiculophylla</em>, has proliferated along high-salinity mudflats in several Georgia and South Carolina estuaries. The invasion is noteworthy because the mudflats in these estuaries were historically devoid of macrophyte-based primary production and structure. <em>Gracilaria</em> has few native analogues in these mudflat environments, and thus represents an opportunity to examine the ecosystem consequences of an invasion within an historically-unexploited niche. In theory, <em>Gracilaria</em> affects populations of species that are directly dependent on the invader for structure and food, as well as altering community- and ecosystem-level processes such as detrital production and food web structure. Through a combination of manipulative field experiments, laboratory assays and stable isotope analysis, the investigators will test three mechanisms by which <em>Gracilaria</em> influences native community structure. The novel structure and primary production generated by <em>Gracilaria vermiculophylla</em> may be 1) increasing rates of secondary production, 2) increasing levels of mudflat microbial production through leeching of dissolved nutrients, and 3) increasing detrital input to microbial and macrobial food webs.</p>
<p>This project will provide a mechanistic understanding of the multiple cascading impacts of an invasive species within the estuarine community. Species invasions that alter ecosystem functions are usually the most profound. These alterations are often generated by a small number of invaders that create physical structure, including important biogenic habitat, de novo. By altering physical structure, these non-native ecosystem engineers alter local abiotic conditions, interactions between species, and species composition. Highly influential invaders may also change food web structure and trophic flow of energy and materials. Such substantive food web changes can occur when an influential invader provides nutrients or resources that are different in quality, quantity or both. An invasive species that both provisions new physical structure and fundamentally alters food web structure could exert an overwhelming influence on native communities when these mechanisms act in synergy.</p>
Gracilaria effects
largerWorkCitation
project
eng; USA
oceans
2015-12-18
Georgia and South Carolina coasts
0
BCO-DMO catalogue of parameters from The genotypes from 9 microsatellites generated on individuals of the red invasive seaweed Gracilaria vermiculophylla
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/629977.rdf
Name: individual
Units: dimensionless
Description: <p>Individual identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/629978.rdf
Name: population
Units: dimensionless
Description: <p>Population.</p>
http://lod.bco-dmo.org/id/dataset-parameter/629979.rdf
Name: range
Units: dimensionless
Description: <p>Range (native or non-native).</p>
http://lod.bco-dmo.org/id/dataset-parameter/629980.rdf
Name: Gverm_1203
Units: dimensionless
Description: <p>Name of loci (with two columns per locus to capture the diploid genotypes).</p>
http://lod.bco-dmo.org/id/dataset-parameter/629981.rdf
Name: Gverm_1203b
Units: dimensionless
Description: <p>Name of loci (with two columns per locus to capture the diploid genotypes).</p>
http://lod.bco-dmo.org/id/dataset-parameter/629982.rdf
Name: Gverm_6311
Units: dimensionless
Description: <p>Name of loci (with two columns per locus to capture the diploid genotypes).</p>
http://lod.bco-dmo.org/id/dataset-parameter/629983.rdf
Name: Gverm_6311b
Units: dimensionless
Description: <p>Name of loci (with two columns per locus to capture the diploid genotypes).</p>
http://lod.bco-dmo.org/id/dataset-parameter/629984.rdf
Name: Gverm_8036
Units: dimensionless
Description: <p>Name of loci (with two columns per locus to capture the diploid genotypes).</p>
http://lod.bco-dmo.org/id/dataset-parameter/629985.rdf
Name: Gverm_8036b
Units: dimensionless
Description: <p>Name of loci (with two columns per locus to capture the diploid genotypes).</p>
http://lod.bco-dmo.org/id/dataset-parameter/629986.rdf
Name: Gverm_804
Units: dimensionless
Description: <p>Name of loci (with two columns per locus to capture the diploid genotypes).</p>
http://lod.bco-dmo.org/id/dataset-parameter/629987.rdf
Name: Gverm_804b
Units: dimensionless
Description: <p>Name of loci (with two columns per locus to capture the diploid genotypes).</p>
http://lod.bco-dmo.org/id/dataset-parameter/629988.rdf
Name: Gverm_10367
Units: dimensionless
Description: <p>Name of loci (with two columns per locus to capture the diploid genotypes).</p>
http://lod.bco-dmo.org/id/dataset-parameter/629989.rdf
Name: Gverm_10367b
Units: dimensionless
Description: <p>Name of loci (with two columns per locus to capture the diploid genotypes).</p>
http://lod.bco-dmo.org/id/dataset-parameter/629990.rdf
Name: Gverm_5276
Units: dimensionless
Description: <p>Name of loci (with two columns per locus to capture the diploid genotypes).</p>
http://lod.bco-dmo.org/id/dataset-parameter/629991.rdf
Name: Gverm_5276b
Units: dimensionless
Description: <p>Name of loci (with two columns per locus to capture the diploid genotypes).</p>
http://lod.bco-dmo.org/id/dataset-parameter/629992.rdf
Name: Gverm_2790
Units: dimensionless
Description: <p>Name of loci (with two columns per locus to capture the diploid genotypes).</p>
http://lod.bco-dmo.org/id/dataset-parameter/629993.rdf
Name: Gverm_2790b
Units: dimensionless
Description: <p>Name of loci (with two columns per locus to capture the diploid genotypes).</p>
http://lod.bco-dmo.org/id/dataset-parameter/629994.rdf
Name: Gverm_3003
Units: dimensionless
Description: <p>Name of loci (with two columns per locus to capture the diploid genotypes).</p>
http://lod.bco-dmo.org/id/dataset-parameter/629995.rdf
Name: Gverm_3003b
Units: dimensionless
Description: <p>Name of loci (with two columns per locus to capture the diploid genotypes).</p>
http://lod.bco-dmo.org/id/dataset-parameter/629996.rdf
Name: Gverm_1803
Units: dimensionless
Description: <p>Name of loci (with two columns per locus to capture the diploid genotypes).</p>
http://lod.bco-dmo.org/id/dataset-parameter/629997.rdf
Name: Gverm_1803b
Units: dimensionless
Description: <p>Name of loci (with two columns per locus to capture the diploid genotypes).</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
15355
https://datadocs.bco-dmo.org/file/A88rLyzilAy0Z2/raw_genotypes.csv
raw_genotypes.csv
Primary data file for dataset ID 629302
download
https://osprey.bco-dmo.org/dataset/629302/data/download
download
onLine
dataset
<p>Data were generated on an ABI genotyper.</p>
<p>Briefly, from <a href="http://dx.doi.org/10.7717/peerj.1159" target="_blank">Kollars et al. (2015)</a>:<br />
A library of contigs for <em>G. vermiculophylla</em> was generated using the 454 next-generation sequencing platform (Cornell University Life Sciences Core Laboratory Center) from a single individual collected fromCharleston, South Carolina, USA. Total genomic DNA was isolated and loci were amplified on a thermocycler (BioRad). Samples were electrophoresed on an ABI 3130xL genetic analyzer equipped with 36 cm capillaries (Applied Biosystems). Alleles were scored manually using GENEMAPPER ver. 4 (Applied Biosystems) and allele sizes were binned with TANDEM ver. 1.08 software.</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 3130xL genetic analyzer
ABI 3130xL genetic analyzer
PI Supplied Instrument Name: ABI 3130xL genetic analyzer PI Supplied Instrument Description:Samples were electrophoresed on an ABI 3130xL genetic analyzer equipped with 36 cm capillaries (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.
Thermocycler
Thermocycler
PI Supplied Instrument Name: Thermocycler PI Supplied Instrument Description:Loci were amplified on a thermocycler (BioRad). The PCR program included 2 min at 95 degrees C, 30 cycles of 30 s at 95 degrees C, 30 s at 55 degrees C and 30 s at 72 degrees C, and a final 5 min at 72 degrees C. 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)