http://lod.bco-dmo.org/id/dataset/768180
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
2019-05-16
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Marine lakes of Palau barcoded specimens from transect survey with both lab identification number (M0D#) and original tube number
2019-05-13
publication
2019-05-13
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-07-08
publication
https://doi.org/10.1575/1912/bco-dmo.768180.1
Michael N. Dawson
University of California-Merced
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: Dawson, M. (2019) Marine lakes of Palau barcoded specimens from transect survey with both lab identification number (M0D#) and original tube number. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2019-05-13 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.768180.1 [access date]
Palau lakes: tissue archive Dataset Description: <p>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’s permanent collection, and (2) to summarize the tissue samples collected during biodiversity surveys under this project.</p>
<p>* NOTE:&nbsp;The P.I.'s are using this dataset to write papers. Please contact them before using these data to make sure you are not duplicating efforts.</p> Methods and Sampling: <p><strong>Sample collection:</strong></p>
<p>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).&nbsp; 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’ maximum certified depth).&nbsp; In lakes 8m or deeper, a line (‘the horizontal’) was placed, at eight evenly spaced target depths (1–4 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–D each at 15 cm increments to the right of the transect line at the same depth.&nbsp; At each depth, from deepest to shallowest, the actual depth was measured in feet with a dive computer, the ‘horizontal’ was photographed from ~0.5 m distance, the substrate type was recorded, and then each cell photographed in close-up.&nbsp; A tissue sample of the ‘primary’ 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–D.&nbsp; Because the benthos may be three dimensional a ‘primary’ organism might also have many ‘secondary’ epibionts and/or epiphytes attached.&nbsp; Any organisms in the photographs but not sampled were classified as ‘tertiary’.&nbsp; 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.&nbsp; 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 &lt;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 &gt;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.&nbsp; 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.&nbsp; Each evening, new samples were stored in a freezer, dive profiles were downloaded, and fieldnotes were transcribed to a standardized electronic data sheet.</p>
<p><strong>Error-checking biodiversity transect files</strong></p>
<p>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.&nbsp; If necessary, primary and secondary specimens were placed in individually labelled tubes of ethanol.&nbsp; 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.&nbsp; Significant changes—i.e. samples that could not be reconciled after accounting for tube transpositions, mislabeling, or mis-identification in the field—were logged in a separate file highlighting the specific change and justification.&nbsp; If a specimen was unable to be reconciled with notes it was discarded (this was necessary for only one specimen).&nbsp; 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#.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1241255 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1241255
completed
Michael N. Dawson
University of California-Merced
209-228-4056
School of Natural Sciences 5200 North Lake Road
Merced
CA
95343
United States
mdawson@ucmerced.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
M0D
Tube_Number
Field_assigned_phylum
Instant_Field_ID
lake_code
theme
None, User defined
sample identification
phylum
sample description
site
featureType
BCO-DMO Standard Parameters
Palau_lakes
service
Deployment Activity
NW Pacific
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.
Dimensions of Biodiversity
http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503446
Dimensions of Biodiversity
(adapted from the NSF Synopsis of Program)
Dimensions of Biodiversity is a program solicitation from the NSF Directorate for Biological Sciences. FY 2010 was year one of the program. [MORE from NSF]
The NSF Dimensions of Biodiversity program seeks to characterize biodiversity on Earth by using integrative, innovative approaches to fill rapidly the most substantial gaps in our understanding. The program will take a broad view of biodiversity, and in its initial phase will focus on the integration of genetic, taxonomic, and functional dimensions of biodiversity. Project investigators are encouraged to integrate these three dimensions to understand the interactions and feedbacks among them. While this focus complements several core NSF programs, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, to understand the roles of biodiversity in critical ecological and evolutionary processes.
Dimensions of Biodiversity
largerWorkCitation
program
Do Parallel Patterns Arise from Parallel Processes?
http://marinelakes.ucmerced.edu/
Do Parallel Patterns Arise from Parallel Processes?
<p>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.</p>
<p>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.</p>
PaPaPro
largerWorkCitation
project
eng; USA
biota
oceans
NW Pacific
134.3447
134.5089
7.1506
7.3237
2011-06-04
2015-07-02
Western Pacific; Palau; Indonesia (West Papua)
0
BCO-DMO catalogue of parameters from Marine lakes of Palau barcoded specimens from transect survey with both lab identification number (M0D#) and original tube number
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/768191.rdf
Name: M0D
Units: unitless
Description: <p>Unique lab number assigned to curate specimens and sequences.</p>
http://lod.bco-dmo.org/id/dataset-parameter/768192.rdf
Name: Tube_Number
Units: unitless
Description: <p>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).</p>
http://lod.bco-dmo.org/id/dataset-parameter/768193.rdf
Name: Field_assigned_phylum
Units: unitless
Description: <p>The phylum of the specimen or high level categorization assigned in the field.</p>
http://lod.bco-dmo.org/id/dataset-parameter/768194.rdf
Name: Instant_Field_ID
Units: unitless
Description: <p>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)</p>
http://lod.bco-dmo.org/id/dataset-parameter/768195.rdf
Name: lake_code
Units: unitless
Description: <p>3-letter code for sampled lake name</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
647465
https://darchive.mblwhoilibrary.org/bitstream/1912/24324/1/dataset-768180_palau-lakes-tissue-archive__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.768180.1
download
onLine
dataset
<p><strong>Sample collection:</strong></p>
<p>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).&nbsp; 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’ maximum certified depth).&nbsp; In lakes 8m or deeper, a line (‘the horizontal’) was placed, at eight evenly spaced target depths (1–4 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–D each at 15 cm increments to the right of the transect line at the same depth.&nbsp; At each depth, from deepest to shallowest, the actual depth was measured in feet with a dive computer, the ‘horizontal’ was photographed from ~0.5 m distance, the substrate type was recorded, and then each cell photographed in close-up.&nbsp; A tissue sample of the ‘primary’ 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–D.&nbsp; Because the benthos may be three dimensional a ‘primary’ organism might also have many ‘secondary’ epibionts and/or epiphytes attached.&nbsp; Any organisms in the photographs but not sampled were classified as ‘tertiary’.&nbsp; 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.&nbsp; 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 &lt;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 &gt;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.&nbsp; 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.&nbsp; Each evening, new samples were stored in a freezer, dive profiles were downloaded, and fieldnotes were transcribed to a standardized electronic data sheet.</p>
<p><strong>Error-checking biodiversity transect files</strong></p>
<p>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.&nbsp; If necessary, primary and secondary specimens were placed in individually labelled tubes of ethanol.&nbsp; 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.&nbsp; Significant changes—i.e. samples that could not be reconciled after accounting for tube transpositions, mislabeling, or mis-identification in the field—were logged in a separate file highlighting the specific change and justification.&nbsp; If a specimen was unable to be reconciled with notes it was discarded (this was necessary for only one specimen).&nbsp; 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#.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- replaced blanks cells with nd</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: Palau_lakes
Palau_lakes
Small boats - CRRF
vessel
Palau_lakes
Michael N. Dawson
University of California-Merced
Small boats - CRRF
vessel