Dataset: Vouchered specimens

Name: Catalog numbers, GenBank accession numbers, and key details for specimens collected during cruises AT37-13 (2017), AT42-03 (2018), and FK190106 (2019) and vouchered in the Scripps Institution of Oceanography Benthic Invertebrate Collection
Published: 2021-01-26
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.838088.1

Spatial Extent: N:9.1193 E:-84.21491667 S:8.80167 W:-85.1893

Temporal Extent: 2017-05-21 - 2018-10-25

Project:

Collaborative research: Quantifying the biological, chemical, and physical linkages between chemosynthetic communities and the surrounding deep sea (Costa Rica Seeps)

Principal Investigator:

Gregory Rouse (University of California-San Diego Scripps, UCSD-SIO)

Co-Principal Investigator:

Erik E. Cordes (Temple University, Temple)

Lisa A. Levin (University of California-San Diego Scripps, UCSD-SIO)

Victoria J. Orphan (California Institute of Technology, Caltech)

Christopher Neil Roman (University of Rhode Island, URI)

Contact:

Charlotte Seid (University of California-San Diego Scripps, UCSD-SIO)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2021-01-26

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Catalog numbers, GenBank accession numbers, and key details for specimens collected during cruises AT37-13 (2017), AT42-03 (2018), and FK190106 (2019) and vouchered in the Scripps Institution of Oceanography Benthic Invertebrate Collection

Abstract:

This dataset includes catalog numbers, GenBank accession numbers, and key details for specimens collected during cruises AT37-13 (2017), AT42-03 (2018), and FK190106 (2019) and vouchered in the Scripps Institution of Oceanography Benthic Invertebrate Collection.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2021-01-26	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.838088.1	2021-01-27

Description

The Scripps Institution of Oceanography Benthic Invertebrate Collection (SIO-BIC) specimen holdings are publicly available in DarwinCore format via GBIF, but please note that this version is updated infrequently: https://www.gbif.org/dataset/a267b6a7-91f9-457c-889a-481e7aa920b6

For the most up-to-date version of this dataset, please use the SIO-BIC searchable database: https://sioapps.ucsd.edu/collections/bi/. This database is updated at least weekly to reflect corrections, updated identifications, new GenBank accession numbers, and newly added specimens.

Methods & Sampling

Samples were collected using the deep-sea submersibles HOV Alvin (cruise AT37-13 in 2017; cruise AT42-03 in 2018) or ROV SuBastian (cruise FK190106 in 2019). Sampling instruments used by the deep-sea submersibles include: manipulator arm, scoops, suction sampler (also known as a "slurp"; suctions material into an enclosed chamber), mussel pot (stainless steel pot with a twistable handle connected to a Kevlar bag insert; used for quantitative sampling of deep-sea mussel beds), and Bushmaster (hydraulic rods surrounding a fine mesh; original instrument developed at Penn State University for quantitative sampling of deep-sea tubeworms).

Live specimens were relaxed with an appropriate agent (e.g. 7% MgCl2 in fresh water, menthol) and photographed. For genetic analysis, specimens were preserved whole or subsampled into 95% ethanol, RNAlater, and/or liquid nitrogen. Whole or partial specimens serving as morphological vouchers were fixed in 10% seawater formalin for at least 24 hours, then rinsed with fresh water and transferred to 50% ethanol for long-term archival. For certain taxa, e.g. echinoderms and crustaceans, vouchers were treated with 95% ethanol instead of formalin. Selected specimens were treated with paraformaldehyde, glutaraldehyde, or osmium tetroxide for histology and electron microscopy.

Data Processing Description

Data Processing:
Data were organized using FileMaker Pro 12.

BCO-DMO Processing:
- replaced commas with semi-colons throughout dataset.

Data Files

File
vouchered_specimens.csv (Comma Separated Values (.csv), 862.27 KB) MD5:296eb335ef03a48f6f2fc17dc872f76f Primary data file for dataset ID 838088

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1634002
NSF Division of Ocean Sciences	OCE-1634172
NSF Division of Ocean Sciences	OCE-1634559
NSF Division of Ocean Sciences	OCE-1635219

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
AT37-13		2017-05-20	R/V Atlantis	Erik E. Cordes (Chief Scientist)	data info
AT37-13_Alvin_Dives		2017-05-21	Alvin	Victoria J. Orphan (Principal Investigator)	data info
AT42-03		2018-10-17	R/V Atlantis	Erik E. Cordes (Chief Scientist)	data info
AT42-03_Alvin_Dives		2018-10-17	Alvin		data info
FK190106	FK 190106	2019-01-06	R/V Falkor	Erik E. Cordes (Chief Scientist)	data info

Instruments

Alvin Slurp Sampler

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Alvin Slurp Sampler

Generic Description:

Small and large capacity vacuum pump samplers. May have single or multiple chambers. See http://www.whoi.edu/main/alvin/subsystems/optional-scientific-samplers

Bushmaster

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Bushmaster

Generic Description:

Bushmaster samplers are original instruments created at Penn State to collect hydrothermal vent and methane seep communities. Hydraulic rods are attached to a very fine mesh that is deployed over the tubeworm patch of interest to collect the tubeworms and associated community. Once the assemblage is enclosed, the net is cinched closed using the submersible or ROV manipulator. This allows for quantitative collections of tubeworm communities.

Mussel Pot

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Mussel Pot

Generic Description:

The mussel pot is a 12-quart aluminium-clad stainless steel pot with a twistable handle connected to a Kevlar bag insert. It is used to sample mussel beds and associated communities. The pot is deployed over the select mussel patch using the submersible or ROV manipulator, then collects the enclosed assemblage by cinching the Kevlar bag closed by turning the handle. This method allows for quantitative analysis of deep-sea mussel bed communities.

ROV SuBastian

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: ROV SuBastian

Generic Description:

ROV SuBastian is operated from the research vessel Falkor and the R/V Falkor(too). The ROV is outfitted with a suite of sensors and scientific equipment to support scientific data and sample collection, as well as interactive research, experimentation, and technology development. More information available at https://schmidtocean.org/technology/robotic-platforms/4500-m-remotely-operated-vehicle-rov/

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
catalogNumber	permanent identifying code for a vouchered specimen at SIO-BIC	unitless	sample
phylum	phylum	unitless	phylum
class	class	unitless	class
order	order	unitless	order
family	family	unitless	family
genus	genus	unitless	genus
species	species	unitless	species
identifiedBy	person(s) responsible for the most recent identification of this specimen	unitless	person
typeStatus	status of this specimen as a name-bearing type for this species, e.g. holotype	unitless	sample_descrip
individualCount	number of individuals represented by this lot	unitless	count
sex	sex(es) of the individual(s) in this lot	unitless	sex
lifeStage	developmental life stage, e.g. larva	unitless	stage
genBankAccessionNumber	NCBI GenBank accession number(s) for DNA sequence(s) derived from this lot	unitless	accession_number
materialPreserved	physical material available, e.g. whole or tissue	unitless	sample_descrip
voucherTreatment	initial chemical treatment of the morphological voucher, e.g. formalin	unitless	sample_descrip
voucherPreservative	long-term preservative of the morphological voucher, e.g. ethanol	unitless	sample_descrip
otherCodes	identifying codes, other than SIO-BIC catalog number; may include temporary field codes and catalog numbers from other institutions	unitless	sample_descrip
diveNumber	submersible dive number; may be followed by a sampling event code or deployment number	unitless	dive_id
locality	name or description of collection location	unitless	site
country	country of collection	unitless	site
ocean	ocean of collection	unitless	site
lat_start	latitude of collection; south is negative; if collection occurred between two points, this point represents the start point	decimal degrees	lat
lon_start	longitude of collection; west is negative; if collection occurred between two points, this point represents the start point	decimal degrees	lon
lat_end	latitude of collection; south is negative; if collection occurred between two points, this point represents the end point	decimal degrees	lat
lon_end	longitude of collection; west is negative; if collection occurred between two points, this point represents the end point	decimal degrees	lon
depth_start	depth of collection; if collection occurred between two depths, this point represents the minimum depth	meters (m)	depth
depth_end	depth of collection; if collection occurred between two depths, this point represents the maximum depth	meters (m)	depth
collectionDate	date of collection; format ISO8601 (YYYY-MM-DD); in local time (UTC-6) Format: %Y-%m-%d	unitless	date
submersible	name of submersible	unitless	instrument
ship	name of support ship	unitless	ship
collectedBy	person(s) who participated in the submersible dive or preserved the specimen	unitless	person
collectionEventRemarks	further details about the submersible dive and sampling event	unitless	comment

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Database

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Dataset: Vouchered specimens