http://lod.bco-dmo.org/id/dataset/750667
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
2018-12-03
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
GPS waypoints for habitat complexity photos collected along the Northern Central California coast from 2017 to 2021
2024-02-29
publication
2024-02-29
revision
BCO-DMO Linked Data URI
2024-02-29
creation
http://lod.bco-dmo.org/id/dataset/750667
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. N., Schiebelhut, L. (2024) GPS waypoints for habitat complexity photos collected along the Northern Central California coast from 2017 to 2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 3) Version Date 2024-02-29 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/750667 [access date]
Dataset Description: This page serves the "GPS waypoints" dataset. See the "Related Datasets" section for access to the other data types mentioned in the study data description below and the Methods & Sampling section.
Study data description:
Abundances and sizes of target invertebrates in quadrat surveys; photos of habitat complexity and a subset of specimens; and GPS coordinates of quadrats. Methods and Sampling: Sampling and analytical procedures for habitat complexity photos and related datasets:
At each site, we sampled two rocky intertidal areas (usually one on either side of a beach or headland and separated by approximately 100 meters) during low tide (usually less than -0.8 feet), using quadrats to estimate abundances of Pisaster ochraceus, Cryptochiton stelleri, Leptasterias sp., and Henricia pumila. We exhaustively searched 20–32 one-meter square quadrats per site (i.e. 10–16 per each of 2 areas), recording GPS waypoint, time, and abundances and sizes of the target species for each quadrat. Each quadrat was photographed. Quadrat locations were selected by first finding one of the target habitat types—surf grass, low-zone red algae, coralline turf, cobble or boulder field, or urchin pools with pits either empty or occupied—selecting a starting point haphazardly, and then using a random numbers table (range of 1–10 meters) to choose remaining quadrat locations. All quadrats and specimens were georeferenced using a Garmin C60X GPS (±3 m precision). The accuracy of the GPS in meters at the time the waypoint was recorded can be found in column "GPS_Accuracy" of the "Quadrat data" dataset. Tissues samples are preserved in 95% Ethanol and stored at -20 degrees C. A subset of tissue samples are also preserved in RNA Later and stored at -20 degrees C (as indicated in the "Quadrat data" dataset).
Problem report for data between 2018-12-21 and 2019-07-06: In Strongylocentrotus purpuratus were only counted in the first quadrant (0.25 x 0.25m) of each quadrat (1m2), so the total search area for that species is one quarter that of other species and so the density should be calculated accordingly.
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1737381 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1737381
onGoing
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: 3
Unknown
wpt_ID
lat
lon
Date
Site
Area
GPS_name
GPS_ID
time
Garmin C60X GPS
theme
None, User defined
site description
latitude
longitude
date_local
site
Sensor_Id
ISO_DateTime_UTC
featureType
BCO-DMO Standard Parameters
Camera
GPS receiver
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.
Collaborative Proposal: Selection and Genetic Succession in the Intertidal -- Population Genomics of Pisaster ochraceus During a Wasting Disease Outbreak and its Aftermath
https://www.bco-dmo.org/project/704716
Collaborative Proposal: Selection and Genetic Succession in the Intertidal -- Population Genomics of Pisaster ochraceus During a Wasting Disease Outbreak and its Aftermath
<p><strong>NSF abstract:</strong></p>
<p>This project seeks to understand the outcomes of predator-disease dynamics by exploring a recent pandemic that decimated 90% of ochre sea stars (Pisaster ochraceus) in the eastern North Pacific in 2013. The research team will explore how recovery may depend upon often difficult-to-see processes such as the interplay of migration and natural selection in marine species. While the population of sea stars is currently rebounding due to several years of unusually high recruitment, the sea star wasting disease continues to persist at low levels. This project aims to determine the genetic consequences of the pandemic and subsequent recovery. The team will determine whether the majority of susceptible sea stars have died and identify possible refuges where susceptible sea stars survived. They will examine the potential for heritable variation in resistance to this disease in order to assess whether the new recruits are tolerant or susceptible to wasting. Resolving these issues will enable predictions about the trajectory of their recovery and the potential responses to future large scale disease outbreaks. Research findings will be shared with resource managers and scientists at a collaborative workshop that will focus on state-of-the-art methods to advance research on marine diseases. The public will have the opportunity to learn more about sea star wasting disease through a partnership with the UCSC Seymour Marine Discovery Center and can track the incidence of disease using an online interactive map available at <a href="http://www.seastarwasting.org">www.seastarwasting.org</a>. Results will be incorporated into professional development for teachers with CalTeach and adapted for teaching materials up to college-level. This project will train diverse early career scientists - undergraduates, graduates, and a postdoctoral scholar - in integration of ecological and genomic methods.</p>
<p>Understanding the consequences of large-scale pandemics in the broader contexts of geographic heterogeneity and chronic changes in ocean pH and temperature is an emerging contemporary issue. This project employs long-term characterization of population dynamics and genetic consequences of a sea star wasting disease (SSWD) outbreak, which caused median 90% mortality in Pisaster ochraceus populations in the northeastern Pacific, to estimate potential long-term consequences for the species. While the largest recorded influx of new recruits occurred in 2014-2016, it is unknown where they originated from, whether recruits and surviving adults remained susceptible to the disease, which persisted at low levels, and for how long these dynamics might continue. This long-term dataset provides a unique opportunity for exploring the short and long term repercussions of such large-scale disease outbreaks and the population dynamics that they precipitate. This project builds on long-term field studies of wild populations to describe host population dynamics, the disease, and genomic diversity. The goal is to discover genetic variation associated with SSWD and to dissociate that variation from population genomic effects attributable to abiotic environmental variation. Objectives are: (1) Census P. ochraceus at 24 sites throughout its range to describe population dynamics, the prevalence of SSWD, and measure abiotic variables. (2) Conduct laboratory experiments coupled with RNAseq analyses to determine loci differentially regulated during exposure to SSWD, temperature, salinity, and pCO2 anomalies. (3) Map ddRAD, RNAseq, and candidate loci under selection to a P. ochraceus genome. (4) Conduct range-wide population genomic analyses for 3 years to assess genetic (SNP) variation among wild-caught specimens with, versus without, SSWD across a geographic mosaic of abiotic variation. (5) Explore links between SSWD and candidate loci, such as EF1A. These analyses will describe the immediate genomic consequences of the disease outbreak, the population dynamics that the outbreak set in motion, and the interplay of factors and mechanisms - such as disease, temperature, migration, selection - that affected these changes. The results will advance understanding of general processes and interactions that shape population genomic structure in coastal ecosystems, providing resources to inform future research and applications in design of management strategies for coastal living resources.</p>
<p><strong>Proposal abstract</strong></p>
<p>Extreme disturbances are expected to increase in frequency and intensity with climate change; their consequences for marine species will depend upon the often enigmatic interplay of dispersal and selection (and drift). This project seeks to understand the population and genomic consequences of a decimating epizootic of the sea star <em>Pisaster </em><em>ochraceus</em>. Existing collections, which immediately preceded and followed the outbreak and documented >90% mortality of adults and massive subsequent recruitment, will be coupled with continuing annual surveys and population genomic, transcriptomic, and candidate locus analyses. The project aims to determine the extent to which this disease outbreak may (or may not) lead to long-term changes in the frequencies of alleles associated with survival of SSWD.</p>
<p>Understanding the consequences of large perturbations set against a backdrop of geographic heterogeneity and gradual environmental change is an emerging contemporary issue. It requires long-term characterization of population dynamics, genetic consequences, and future implications. In 2013, sea star wasting disease (SSWD) swept through <em>P. </em><em>ochraceus</em><em> </em>populations in the northeastern Pacific. We captured this epizootic in long-term ecological-genetic studies, which documented median 90% mortality coast-wide (site-specific rates 51–96%). In the aftermath of the initial outbreak, we quantified the largest influx of new recruitments on record. The disease currently persists at low-levels among surviving populations, and recruitment continues to be above average. Given heterogeneity in the environment and in mortality rates, and because 2013 recruits may have been spawned by adults pre-outbreak, but 2014-to-current recruits are progeny of adults that survived, the genomic consequences of the outbreak and the implications for future population and disease dynamics are uncertain.</p>
<p>This project builds on long-term field studies of wild populations of <em>P. </em><em>ochraceus</em><em> </em>to describe population dynamics, the disease, and genomic diversity. Goals are to discover genetic variation associated with SSWD and to dissociate that variation from population genomic effects attributable to abiotic environmental variation. Objectives are: (1) Census <em>P. ochraceus </em>at 24 sites throughout its range to describe population dynamics, the prevalence of SSWD, and measure abiotic variables. (2) Conduct laboratory experiments coupled with RNAseq analyses to determine loci differentially regulated during exposure to SSWD, temperature, salinity, and pCO2 anomalies. (3) Map ddRAD, RNAseq, and candidate loci under selection to a <em>P. </em><em>ochraceus</em> genome. (4) Conduct range-wide population genomic analyses for 3 years, including intensive study of a focal region, in which we will assess genetic (RAD) variation among wild-caught specimens with versus without SSWD and experiencing the geographic mosaic of abiotic variation. (5) Explore links between SSWD and candidate loci, such as EF1A.</p>
<p>Preliminary results are consistent with an association between SSWD, very high mortality (90%), and differential susceptibility of<em> P. </em><em>ochraceus</em> linked to variation in ddRAD markers, expression of RNAseq loci, and overdominance at a candidate locus (EF1A). RAD analyses show site-specific differences between <em>P. </em><em>ochraceus</em><em> </em>adults despite high gene flow, and while intertidal juveniles and adults were selected by SSWD in 2013, the subsequent pulse of new recruits was most genetically similar to the pre-outbreak population. The consequences of the SSWD outbreak are still unfurling in a dynamic eco-evolutionary landscape.</p>
<p>Research mentoring</p>
<p>This project trains a postdoc, 3 graduate students, >= 6 undergraduates. The postdoc and graduates will be cross-trained in field, lab, and genomics. Undergraduates will participate in field and laboratory research, have opportunities for internships, and be involved in outreach activities addressing environmental change. UCM and UCSC are designated Hispanic Serving Institutions. Teaching. Collaboration with the CalTeach program at UC Merced, lab research experience for high school students at Cornell, and an interactive web-based instructional exercise at UCSC will draw upon the iconic natures of <em>Pisaster</em>, the rocky intertidal, and keystone predators in education, policy, and management, interweaving project outcomes. Public understanding. Outreach efforts will target general public and marine resource managers using a website and interactive map for tracking sea star wasting (<a href="http://www.seastarwasting.org">www.seastarwasting.org</a>). Scientific understanding. An end-of-project workshop will host several groups working on different aspects of SSWD and its consequences.</p>
PoGOMO
largerWorkCitation
project
eng; USA
oceans
-123.715
-120.672
35.1522
38.9165
2017-12-02
2021-07-25
Northeastern Pacific (32–60 ºN), particularly northern Central California (35–40 ºN)
0
BCO-DMO catalogue of parameters from GPS waypoints for habitat complexity photos collected along the Northern Central California coast from 2017 to 2021
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/863896.rdf
Name: wpt_ID
Units: unitless
Description: The waypoint number logged for a particular GPS Name, Date, Site, and Area; corresponds to "Quadrat_Waypoint" in the "Quadrat data" dataset
http://lod.bco-dmo.org/id/dataset-parameter/863897.rdf
Name: lat
Units: decimal degrees
Description: latitude (accuracy ±3m unless otherwise stated in Quadrat data)
http://lod.bco-dmo.org/id/dataset-parameter/863898.rdf
Name: lon
Units: decimal degrees
Description: longitude (accuracy ±3m unless otherwise stated in Quadrat data)
http://lod.bco-dmo.org/id/dataset-parameter/863899.rdf
Name: Date
Units: unitless
Description: Date the survey was conducted in ISO 8601 format yyyy-mm-dd
http://lod.bco-dmo.org/id/dataset-parameter/863900.rdf
Name: Site
Units: unitless
Description: Survey site location name
http://lod.bco-dmo.org/id/dataset-parameter/863901.rdf
Name: Area
Units: unitless
Description: Area number (1 or 2) within the site
http://lod.bco-dmo.org/id/dataset-parameter/863902.rdf
Name: GPS_name
Units: unitless
Description: GPS name. Assigned name to distinguish GPS units.
http://lod.bco-dmo.org/id/dataset-parameter/863903.rdf
Name: GPS_ID
Units: unitless
Description: GPS unit ID
http://lod.bco-dmo.org/id/dataset-parameter/868837.rdf
Name: time
Units: unitless
Description: Timestamp (UTC) in ISO 8601 format %Y-%m-%dT%H:%M:%SZ
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
https://www.bco-dmo.org/dataset/750667/data/download
download
onLine
dataset
Sampling and analytical procedures for habitat complexity photos and related datasets:
At each site, we sampled two rocky intertidal areas (usually one on either side of a beach or headland and separated by approximately 100 meters) during low tide (usually less than -0.8 feet), using quadrats to estimate abundances of Pisaster ochraceus, Cryptochiton stelleri, Leptasterias sp., and Henricia pumila. We exhaustively searched 20–32 one-meter square quadrats per site (i.e. 10–16 per each of 2 areas), recording GPS waypoint, time, and abundances and sizes of the target species for each quadrat. Each quadrat was photographed. Quadrat locations were selected by first finding one of the target habitat types—surf grass, low-zone red algae, coralline turf, cobble or boulder field, or urchin pools with pits either empty or occupied—selecting a starting point haphazardly, and then using a random numbers table (range of 1–10 meters) to choose remaining quadrat locations. All quadrats and specimens were georeferenced using a Garmin C60X GPS (±3 m precision). The accuracy of the GPS in meters at the time the waypoint was recorded can be found in column "GPS_Accuracy" of the "Quadrat data" dataset. Tissues samples are preserved in 95% Ethanol and stored at -20 degrees C. A subset of tissue samples are also preserved in RNA Later and stored at -20 degrees C (as indicated in the "Quadrat data" dataset).
Problem report for data between 2018-12-21 and 2019-07-06: In Strongylocentrotus purpuratus were only counted in the first quadrant (0.25 x 0.25m) of each quadrat (1m2), so the total search area for that species is one quarter that of other species and so the density should be calculated accordingly.
Specified by the Principal Investigator(s)
* individual csv files concatenated into one data table. Information contained in the file names was added in the following columns (Date,Site,Area,GPS_name,GPS_id).
* Parameters (column names) renamed to comply with BCO-DMO naming conventions. See https://www.bco-dmo.org/page/bco-dmo-data-processing-conventions
* Date format converted to ISO 8601 date format yyyy-mm-dd
* lat and lon rounded to 5 decimal places
Data version 2 replaced data version 1 on 2022-01-26.
* Data version 2 adds additional data from 2019-2020.
* The new data also includes a column called "time" which is the ISO_DateTime_UTC. Parameter section updated to describe the new column.
* Data version 3 adds additional data from 2020-2021.
Specified by BCO-DMO Data Managers
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
PI Supplied Instrument Name: PI Supplied Instrument Description:The vast majority of images were taken on a Panasonic DMC-FT5 or Panasonic DMC-ST4, some were taken from an iPhone. Instrument Name: Camera Instrument Short Name:camera Instrument Description: All types of photographic equipment including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/311/
Garmin C60X GPS
Garmin C60X GPS
PI Supplied Instrument Name: Garmin C60X GPS PI Supplied Instrument Description:Garmin C60X GPS (±3 m precision) Instrument Name: GPS receiver Instrument Short Name: Instrument Description: Acquires satellite signals and tracks your location.
This term has been deprecated. Use instead: https://www.bco-dmo.org/instrument/560