ERDDAP > info > bcodmo_dataset_768180

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data			files	public	Marine lakes of Palau barcoded specimens from transect survey with both lab identification number (M0D#) and original tube number		I   M	background			BCO-DMO	bcodmo_dataset_768180

The Dataset's Variables and Attributes

Row Type	Variable Name	Attribute Name	Data Type	Value
attribute	NC_GLOBAL	access_formats	String	.htmlTable,.csv,.json,.mat,.nc,.tsv
attribute	NC_GLOBAL	acquisition_description	String	Sample collection: Each lake was sampled using the point intercept transect method at no less than 10 randomly chosen sites around its perimeter (unless the small size of a lake precluded this number of non-overlapping sites).\u00a0 At each site, three parallel transects approximately were run 5 m apart from the intertidal (0 m) to the deepest depth accessible to SCUBA divers (i.e. the bottom of the lake, or bottom of the epilimnion, or the divers\u2019 maximum certified depth).\u00a0 In lakes 8m or deeper, a line (\u2018the horizontal\u2019) was placed, at eight evenly spaced target depths (1\u20134 m depth intervals, depending on lake), orthogonal to each of the transect lines so that small (2.0 cm diameter) cells fell over four points A\u2013D each at 15 cm increments to the right of the transect line at the same depth.\u00a0 At each depth, from deepest to shallowest, the actual depth was measured in feet with a dive computer, the \u2018horizontal\u2019 was photographed from ~0.5 m distance, the substrate type was recorded, and then each cell photographed in close-up.\u00a0 A tissue sample of the \u2018primary\u2019 organism within each cell, i.e. the organism at the center of the cell, or if no organism in the centre then the first organisms at the periphery going clockwise from noon, or if only sediment visible, the organism within the sediment directly under the Cell was then biopsied for DNA analyses and placed in a container labeled with site, depth, and cell code A\u2013D.\u00a0 Because the benthos may be three dimensional a \u2018primary\u2019 organism might also have many \u2018secondary\u2019 epibionts and/or epiphytes attached.\u00a0 Any organisms in the photographs but not sampled were classified as \u2018tertiary\u2019.\u00a0 After all four cells were sampled at a depth, the diver ascended to the next shallowest depth on his/her transect and repeated the procedure.\u00a0 Thus, at each randomly chosen site, we surveyed a total of 96 points from the deepest to shallowest depths of the lake habitable by macro-invertebrates and macrophytes, with two categories of exception. (1) If a lake was <8 m deep, the number of depths sampled was equivalent to the maximum depth in meters. (2) Lakes with gently sloping sides could lead to adjacent target depths being >10 m apart leading to undersampling of horizontal patchiness; in which case the transect distance between adjacent target depths was estimated and divided in half or in thirds so that no two samples were more than 10 transect meters apart.\u00a0 At the surface, at the end of each dive, samples were transferred to individual tubes of 95% ethanol labeled with a field number composed of lake, site, collector, depth, and cell IDs.\u00a0 Each evening, new samples were stored in a freezer, dive profiles were downloaded, and fieldnotes were transcribed to a standardized electronic data sheet. Error-checking biodiversity transect files Each evening, or as soon thereafter as possible, divers compared specimens to standardize field-identifications and all tissue samples were reconciled to the electronic data sheet for each lake using tube labels, original field notes, photographs of specimens in the field, and visual inspection of tube contents.\u00a0 If necessary, primary and secondary specimens were placed in individually labelled tubes of ethanol.\u00a0 In cases of discrepancy between electronic notes and original field notes, we edited the electronic data sheet to be consistent with original notes and corroborated this by double-checking the original photographs and inspecting tube contents.\u00a0 Significant changes\u2014i.e. samples that could not be reconciled after accounting for tube transpositions, mislabeling, or mis-identification in the field\u2014were logged in a separate file highlighting the specific change and justification.\u00a0 If a specimen was unable to be reconciled with notes it was discarded (this was necessary for only one specimen).\u00a0 Subsequently, every tissue sample was assigned an unique identifying number (M0D#) for curation; during this process, every tenth sample was double-checked for agreement between the original field number and new M0D#.
attribute	NC_GLOBAL	awards_0_award_nid	String	55103
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1241255
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1241255
attribute	NC_GLOBAL	awards_0_funder_name	String	NSF Division of Ocean Sciences
attribute	NC_GLOBAL	awards_0_funding_acronym	String	NSF OCE
attribute	NC_GLOBAL	awards_0_funding_source_nid	String	355
attribute	NC_GLOBAL	awards_0_program_manager	String	David L. Garrison
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	50534
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	PaPaPro Tissue Archive Transect survey barcoded specimens with both lab identification number (M0D#) and original tube number. M. Dawson (UC-Merced) version date: 2019-05-13
attribute	NC_GLOBAL	Conventions	String	COARDS, CF-1.6, ACDD-1.3
attribute	NC_GLOBAL	creator_email	String	info at bco-dmo.org
attribute	NC_GLOBAL	creator_name	String	BCO-DMO
attribute	NC_GLOBAL	creator_type	String	institution
attribute	NC_GLOBAL	creator_url	String	https://www.bco-dmo.org/
attribute	NC_GLOBAL	data_source	String	extract_data_as_tsv version 2.3 19 Dec 2019
attribute	NC_GLOBAL	date_created	String	2019-05-16T19:27:54Z
attribute	NC_GLOBAL	date_modified	String	2019-07-08T13:00:52Z
attribute	NC_GLOBAL	defaultDataQuery	String	&amp;time&lt;now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.768180.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/768180
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	keywords	String	assigned, bco, bco-dmo, biological, chemical, code, data, dataset, dmo, erddap, field, Field_assigned_phylum, instant, Instant_Field_ID, lake, lake_code, M0D, management, number, oceanography, office, phylum, preliminary, tube, Tube_Number
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/768180/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/768180
attribute	NC_GLOBAL	param_mapping	String	{'768180': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/768180/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	University of California-Merced
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	UC Merced
attribute	NC_GLOBAL	people_0_person_name	String	Michael N Dawson
attribute	NC_GLOBAL	people_0_person_nid	String	51577
attribute	NC_GLOBAL	people_0_role	String	Principal Investigator
attribute	NC_GLOBAL	people_0_role_type	String	originator
attribute	NC_GLOBAL	people_1_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_1_affiliation_acronym	String	WHOI BCO-DMO
attribute	NC_GLOBAL	people_1_person_name	String	Nancy Copley
attribute	NC_GLOBAL	people_1_person_nid	String	50396
attribute	NC_GLOBAL	people_1_role	String	BCO-DMO Data Manager
attribute	NC_GLOBAL	people_1_role_type	String	related
attribute	NC_GLOBAL	project	String	PaPaPro
attribute	NC_GLOBAL	projects_0_acronym	String	PaPaPro
attribute	NC_GLOBAL	projects_0_description	String	This project will survey the taxonomic, genetic, and functional diversity of the organisms found in marine lakes, and investigate the processes that cause gains and losses in this biodiversity. Marine lakes formed as melting ice sheets raised sea level after the last glacial maximum and flooded hundreds of inland valleys around the world. Inoculated with marine life from the surrounding sea and then isolated to varying degrees for the next 6,000 to 15,000 years, these marine lakes provide multiple, independent examples of how environments and interactions between species can drive extinction and speciation. Researchers will survey the microbes, algae, invertebrates, and fishes present in 40 marine lakes in Palau and Papua, and study how diversity has changed over time by retrieving the remains of organisms preserved in sediments on the lake bottoms. The project will test whether the number of species, the diversity of functional roles played by organisms, and the genetic diversity within species increase and decrease in parallel; whether certain species can greatly curtail diversity by changing the environment; whether the size of a lake determines its biodiversity; and whether the processes that control diversity in marine organisms are similar to those that operate on land. Because biodiversity underlies the ecosystem services on which society depends, society has a great interest in understanding the processes that generate and retain biodiversity in nature. This project will also help conserve areas of economic importance. Marine lakes in the study region are important for tourism, and researchers will work closely with governmental and non-governmental conservation and education groups and with diving and tourism businesses to raise awareness of the value and threats to marine lakes in Indonesia and Palau.
attribute	NC_GLOBAL	projects_0_end_date	String	2017-12
attribute	NC_GLOBAL	projects_0_geolocation	String	Western Pacific; Palau; Indonesia (West Papua)
attribute	NC_GLOBAL	projects_0_name	String	Do Parallel Patterns Arise from Parallel Processes?
attribute	NC_GLOBAL	projects_0_project_nid	String	2238
attribute	NC_GLOBAL	projects_0_project_website	String	http://marinelakes.ucmerced.edu/
attribute	NC_GLOBAL	projects_0_start_date	String	2013-01
attribute	NC_GLOBAL	publisher_name	String	Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute	NC_GLOBAL	publisher_type	String	institution
attribute	NC_GLOBAL	sourceUrl	String	(local files)
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	summary	String	Marine lakes of Palau barcoded specimens from transect survey with both lab identification number (M0D#) and original tube number. The purpose of this dataset is (1) to link unique identification numbers used in different circumstances and files, specifically tube ID used in the field and the M0D# identifier for the lab\u2019s permanent collection, and (2) to summarize the tissue samples collected during biodiversity surveys under this project.
attribute	NC_GLOBAL	title	String	Marine lakes of Palau barcoded specimens from transect survey with both lab identification number (M0D#) and original tube number
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	M0D		String
attribute	M0D	bcodmo_name	String	sample
attribute	M0D	description	String	Unique lab number assigned to curate specimens and sequences.
attribute	M0D	long_name	String	M0 D
attribute	M0D	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	M0D	units	String	unitless
variable	Tube_Number		String
attribute	Tube_Number	bcodmo_name	String	sample
attribute	Tube_Number	description	String	The tube number assigned in the field and comprised of the location code; transect/site number; the collector's initials; the target depth in meters; and the cell (i.e. A; B; C; or D).
attribute	Tube_Number	long_name	String	Tube Number
attribute	Tube_Number	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	Tube_Number	units	String	unitless
variable	Field_assigned_phylum		String
attribute	Field_assigned_phylum	bcodmo_name	String	phylum
attribute	Field_assigned_phylum	description	String	The phylum of the specimen or high level categorization assigned in the field.
attribute	Field_assigned_phylum	long_name	String	Field Assigned Phylum
attribute	Field_assigned_phylum	units	String	unitless
variable	Instant_Field_ID		String
attribute	Instant_Field_ID	bcodmo_name	String	sample_descrip
attribute	Instant_Field_ID	description	String	Identification assigned in the field; In some cases a single tube can contain multiple species but assigned phylum will only reflect one for specimens that were not separated (i.e. multiple taxa in a single logged tube)
attribute	Instant_Field_ID	long_name	String	Instant Field ID
attribute	Instant_Field_ID	units	String	unitless
variable	lake_code		String
attribute	lake_code	bcodmo_name	String	site
attribute	lake_code	description	String	3-letter code for sampled lake name
attribute	lake_code	long_name	String	Lake Code
attribute	lake_code	units	String	unitless

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.