http://lod.bco-dmo.org/id/dataset/542665
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
2014-12-15
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
GenBank accession numbers for sequences from deep-sea protobranch bivalves collected on R/V Endeavor cruise EN447 in the Western North Atlantic (34-39N, 68-70W) in 2008 (Ev Deep Sea Molluscs II project)
2016-09-23
publication
2016-09-23
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-05-16
publication
https://doi.org/10.26008/1912/bco-dmo.542665.2
Ron J. Etter
University of Massachusetts Boston
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: Etter, R. J. (2022) GenBank accession numbers for sequences from deep-sea protobranch bivalves collected on R/V Endeavor cruise EN447 in the Western North Atlantic (34-39N, 68-70W) in 2008 (Ev Deep Sea Molluscs II project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2016-09-23 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.542665.2 [access date]
GenBank accession numbers for sequences from deep-sea protobranch bivalves. Dataset Description: <p>Sequence data from this research are available on Genbank with metadata (sample location, depth, date, etc.) and&nbsp; accession numbers listed in the publications given below. Details of molecular work are also described in the various publications listed below.</p>
<p>Refer to publications:<br />
Glazier, A.E., and Etter, R.J. 2014. Cryptic speciation along a bathymetric gradient. Biological Journal of the Linnean Society, 113:897-913. doi:<a href="http://dx.doi.org/10.1111/bij.12389" target="_blank">10.1111/bij.12389</a><br />
<strong>Sequences were deposited in GenBank under accession numbers KM102340-KM102448.</strong></p>
<p>Jennings R.M., and Etter, R.J. 2014. Phylogeographic estimates of colonization of the deep Atlantic by the protobranch bivalve <em>Nucula atacellana. </em>Polish Polar Research, 35: 261-278. Invited Paper. doi:<a href="http://dx.doi.org/10.2478/popore-2014-0017" target="_blank">10.2478/popore-2014-0017</a><br />
<strong>New sequences generated in this work were deposited in GenBank under Accessions KJ950184–KJ950282 (Table 1).</strong></p>
<p>Boyle, E.E. and Etter, R.J. 2013. Heteroplasmy in a deep-sea protobranch bivalve suggests an ancient origin of doubly uniparental inheritance of mitochondria in Bivalvia. Marine Biology, 160:413-422. doi:<a href="http://dx.doi.org/10.1007/s00227-012-2099-y" target="_blank">10.1007/s00227-012-2099-y</a><br />
<strong>Sequences from this study are available from GenBank (Accession numbers 16S HQ907887–HQ907914; cytb JX435273–JX435297).</strong></p>
<p>Jennings R.M., Etter, R.J. and Ficarra,L. 2013. Population differentiation and species formation in the deep sea: the potential role of environmental gradients and depth. PLoS ONE<em>, </em>8(10): e77594. doi:<a href="http://dx.doi.org/10.1371/journal.pone.0077594" target="_blank">10.1371/journal.pone.0077594</a><br />
<strong>All sequences were deposited in GenBank (Accessions KC563091-KC563901, Table 2).</strong></p>
<p>Sharma, P.P., Zardus, J.D., Boyle, E.E., González, V.L., Jennings, R.M., McIntyre, E., Bouchet, P., Wheeler, W.C., Etter, R.J., and Giribet, G. 2013. Into the deep: A phylogenetic approach to the bivalve subclass Protobranchia. Molecular Phylogenetics and Evolution, 69:188-204. doi:<a href="http://dx.doi.org/10.1016/j.ympev.2013.05.018" target="_blank">10.1016/j.ympev.2013.05.018</a><br />
<strong>Sequences from this study are available from GenBank (Accession numbers given in Table 2).</strong></p>
<p>Etter, R.J., Boyle, E.E., Glazier, A., Jennings, R.M., Dutra, E., and Chase, M.R. 2011. Phylogeography of a pan-Atlantic abyssal protobranch bivalve: Implications for evolution in the deep Atlantic. Molecular Ecology,<em> </em>20:829-843. doi:<a href="http://dx.doi.org/10.1111/j.1365-294X.2010.04978.x" target="_blank">10.1111/j.1365-294X.2010.04978.x</a><br />
<strong>Sequences from this study are available from GenBank - accession numbers are HQ452629–HQ452677.</strong></p>
<p>Jennings, R.M., and Etter, R.J. 2011. Exon-Primed, Intron-Crossing (EPIC) loci for five nuclear genes in deep-sea protobranch bivalves: primer design, PCR protocols, and locus utility. Molecular Ecology Resources, 11:1102-1112. doi:<a href="http://dx.doi.org/10.1111/j.1755-0998.2011.03038.x" target="_blank">10.1111/j.1755-0998.2011.03038.x</a><br />
<strong>DNA Sequences from this study are available from GenBank - Accessions JF410881– JF411003.</strong></p> Methods and Sampling:
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1130541 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1130541
completed
Ron J. Etter
University of Massachusetts Boston
617-287-6613
Biology Department 100 Morrissey Boulevard
Boston
MA
02125
USA
ron.etter@umb.edu
pointOfContact
asNeeded
Dataset Version: 2
Unknown
reference
Genbank_accession_number
popset_id
organism
description
accession_link
theme
None, User defined
reference_paper
accession number
absorbance
taxon
sample description
featureType
BCO-DMO Standard Parameters
EN447
service
Deployment Activity
Western North Atlantic (34-39N, 68-70W)
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.
Evolution of Deep Sea Molluscs II
http://www.etterlab.umb.edu/Evolution.html
Evolution of Deep Sea Molluscs II
<p><em>Description from NSF award abstract:</em><br />
The first explicit model of population differentiation and speciation in the deep-sea fauna, the depth-differentiation hypothesis, was formulated in the early 1990s. According to this theory, the potential for population differentiation decreases with depth because the bathyal zone (200- 4000 m) has stronger selective gradients and more opportunity for geographic isolation to impede gene flow than does the more extensive and environmentally uniform abyssal plain (>4000 m). To determine whether depth-related variation is genetic, and therefore a consequence of evolutionary change, the PI has developed new methods to extract and sequence mitochondrial DNA from archived deep-sea molluscan species collected in earlier expeditions that had been fixed in formalin and preserved in alcohol. These preliminary studies supported the depth-differentiation hypothesis. They also revealed the limitations of using preserved material. For this project, the PI describes 2 hypotheses about evolution in the deep sea that emerged from the previous work: 1) The depth differentiation hypothesis suggests population divergence decreases with depth; and 2) A strong break in population structure at 3300 m might represent an unrecognized phylogeographic barrier.</p>
<p>The PI will test each of these hypotheses with multiple independent loci using deep-sea protobranch bivalves and recently developed statistical phylogeographic and phylogenetic models. The aforementioned work relied on formalin-fixed tissues, restricting analyses to a single locus (mtDNA). Nuclear loci are essential as independent measures of population structure, gene flow and historical influences, but are also critical to establish whether some of the remarkable divergences the PI documented represent cryptic species. The new material collected during the previous round of funding allowed the PI to develop the necessary nuclear loci and assess their utility for this work. The primary focus of this proposal is to use these new markers to test each of these hypotheses and distinguish intra- versus inter-specific variation.</p>
<p>The deep-sea supports one of the most diverse and unique marine communities, the evolutionary and historical development of which is virtually unknown. The proposed research will contribute very significantly to answering the two most basic questions about evolutionary diversification in this vast and remote environment: Where does it occur, and how? Analysis of the strong bathymetric divergence in Deminucula atacellana will provide the first detailed investigation of potential incipient speciation in a deep-sea organism (apart from reducing environments) and possibly identify the scales and mechanisms involved. It will also create a solid conceptual and methodological context for future evolutionary studies in the deep sea and lay the groundwork for understanding bathymetric and geographic variation at much larger scales (e.g., among ocean basins or pan-Atlantic).</p>
<p><strong>Related Publications:</strong><br />
Baco, AR, RJ Etter, PA Ribeiro, S von der Heyden, P Beerli, BP Kinlan. 2016. A synthesis of genetic connectivity in deep-sea fauna and implications for connectivity and marine reserve design. Molecular Ecology 25:3276-3298. doi:<a href="http://dx.doi.org/10.1111/mec.13689" target="_blank">10.1111/mec.13689</a></p>
<p>Etter, R.J., and A.S. Bower. 2015. Dispersal and population connectivity in the deep North Atlantic estimated from physical transport processes. Deep Sea Research I<em> </em>104:159-172. doi:<a class="S_C_ddDoi" href="http://dx.doi.org/10.1016/j.dsr.2015.06.009" id="ddDoi" style="color: rgb(49, 108, 157); text-decoration: none; border: 0px; margin: 0px; padding: 0px; vertical-align: baseline; font-family: Arial, Helvetica, 'Lucida Sans Unicode', 'Microsoft Sans Serif', 'Segoe UI Symbol', STIXGeneral, 'Cambria Math', 'Arial Unicode MS', sans-serif; line-height: 19.24px;" target="_blank">10.1016/j.dsr.2015.06.009</a></p>
<p>Glazier, AE, and RJ Etter. 2017. Genetic divergence across an oxygen minimum zone. Marine Ecology Progress Series 577: 79–91. doi:<a href="http://dx.doi.org/10.3354/meps12239" target="_blank">10.3354/meps12239</a></p>
Ev Deep Sea Molluscs II
largerWorkCitation
project
eng; USA
biota
oceans
Western North Atlantic (34-39N, 68-70W)
2016-09-23
Western North Atlantic (34 to 39N, 68 to 70W), Depths 1000-5200m
0
BCO-DMO catalogue of parameters from GenBank accession numbers for sequences from deep-sea protobranch bivalves collected on R/V Endeavor cruise EN447 in the Western North Atlantic (34-39N, 68-70W) in 2008 (Ev Deep Sea Molluscs II 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/542987.rdf
Name: reference
Units: text
Description: <p>Name of the reference paper in which the accession numbers were published. Full citation information is provided in the Supplemental File "<a href="https://datadocs.bco-dmo.org/docs/302/etter/Ev_Deep_Sea_Molluscs_II/data_docs/reference_list_v2.csv" target="_blank">reference_list_v2.csv</a>"</p>
http://lod.bco-dmo.org/id/dataset-parameter/542988.rdf
Name: Genbank_accession_number
Units: unitless
Description: <p>GenBank accession number for the sequence.<br />
</p>
http://lod.bco-dmo.org/id/dataset-parameter/542989.rdf
Name: popset_id
Units: unitless
Description: <p>NCBI PopSet ID number (if applicable). (A <a href="http://www.ncbi.nlm.nih.gov/popset" target="_blank">PopSet</a> is a set of DNA sequences that have been collected to analyse the evolutionary relatedness of a population.)</p>
http://lod.bco-dmo.org/id/dataset-parameter/542990.rdf
Name: organism
Units: text
Description: <p>Name of the organism.</p>
http://lod.bco-dmo.org/id/dataset-parameter/542991.rdf
Name: description
Units: text
Description: <p>Description of the type of sequence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/542992.rdf
Name: accession_link
Units: unitless
Description: <p>Hyperlink to GenBank for the accession number.</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
221949
https://darchive.mblwhoilibrary.org/bitstream/1912/28742/1/dataset-542665_sequence-accession-numbers__v2.tsv
download
https://doi.org/10.26008/1912/bco-dmo.542665.2
download
onLine
dataset
<p><strong>Version History:</strong><br />
2019-09-23 (v2) - added links to GenBank for the Jennings 2014 accession numbers (current version)<br />
2014-12-17 (v1) - original version</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
Cruise: EN447
EN447
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN447
Ron J. Etter
University of Massachusetts Boston
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel