Dataset: Quadrat data

Name: Quadrat sampling information along the Northern Central California coast from 2017 to 2020
Published: 2022-02-01
Keywords: abundance, California, demography, echinoderm, gene flow, genetic drift, intertidal, invertebrate, mass mortality, population genetics, population genomics, sea star wasting disease, selection, oceans

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Cite This Dataset

Spatial Extent: N:38.9165 E:-120.672 S:35.1522 W:-123.715

Temporal Extent: 2017-12-02 - 2020-07-22

Project:

Collaborative Proposal: Selection and Genetic Succession in the Intertidal -- Population Genomics of Pisaster ochraceus During a Wasting Disease Outbreak and its Aftermath (PoGOMO)

Principal Investigator:

Michael N. Dawson (University of California-Merced, UC Merced)

Contact:

Lauren Schiebelhut (University of California-Merced, UC Merced)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-02-01

Restricted:

Validated:

Current State:

Under revision

Quadrat sampling information along the Northern Central California coast from 2017 to 2020

Abstract:

Quadrat sampling information collected concurrently with habitat complexity photos along the Northern Central California coast from 2017 to 2020.

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Description

This page serves data for only the "Quadrat data" dataset. See "Related Datasets" section for access to the other data types mentioned in the study data description below and the Acquisition Description 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.

The "Quadrat_Photo" column in this "Quadrat data" dataset matches the Habitat complexity photo image names.

Acquisition Description

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.

Processing Description

Data were transcribed from field notes, error-checked, and verified that tissue collections matched up to notes.

BCO-DMO Data Manager Processing Notes:
* Data submitted in 75 Excel files (e.g. Quadrat_181221_MCM_Area1_LMS.xlsx) with sheets named "QuadratData" was exported as csv and imported into the BCO-DMO data system. All data concatenated into one table.
* 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
* Time format converted to ISO 8601 time format HH:MM
* DateTime (UTC) column added in ISO 8601 format yyyy-mm-ddTHH:MMZ from local dates and times "Start_Time" and "Date" in US/Pacific Time to form column "Quadrat_Start_DateTime_UTC."
* Commas in "Person" and "Site" changed to semicolons to support csv export from the BCO-DMO data system.
* Column with blank values "End_Time" was removed from the dataset.
* Columns named "Area" renamed to Quadrat_Area and Area_Number (see parameter descriptions).
* lat and lon columns for the waypoints added to this the dataset from the "GPS waypoints" data using the waypoint ID, date, and area number to join the data tables.

Data version 2 replaced data version 1 on 2022-02-01.
* Data version 2 adds additional data from 2019-2020. Processed the same way as v1.
* value "?" in Start_Time and GPS_Accuracy changed to missing data value. Note added to the Quadrat_Notes column "Start time unknown" and "GPS accuracy unknown" respectively.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1737381

Deployments

None available yet

Instruments

Camera

Supplied Name:

Supplied Description:

The vast majority of images were taken on a Panasonic DMC-FT5 or Panasonic DMC-ST4, some were taken from an iPhone.

Instrument Type

Generic Name: Camera

Acronym: camera

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/311/

Generic Description:

All types of photographic equipment including stills, video, film and digital systems.

GPS receiver

Supplied Name: Garmin C60X GPS

Supplied Description:

Garmin C60X GPS (±3 m precision)

Instrument Type

Generic Name: GPS receiver

Generic Description:

Acquires satellite signals and tracks your location.

This term has been deprecated. Use instead: https://www.bco-dmo.org/instrument/560

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Date	Date the survey was conducted in ISO 8601 format YYYY-MM-DD. Format: %Y-%m-%d	unitless	date_local
Site_Code	The 3 letter code for the survey location	unitless	site
Area_Number	Area number (1 or 2) within the site	unitless	site_descrip
Sector	One of four 0.25m^2 quadrants within a full quadrat; the first is 'NL" and is the sector at which the Waypoint is recorded; an additional 3 sectors are layed out linearly side-by-side, named 'FL', 'FFL', and 'FFFL'; together 4 sectors make up 1m^2 quadrat unless otherwise noted	unitless	site_descrip
Quadrat_Waypoint	The waypoint number logged for a particular GPS Name, Date, Site, and Area; corresponds to "wpt_ID" in the "GPS waypoints" dataset. The quadrat itself is 1 square meter made up of 4 0.25m^2 quadrants (4 sectors)	unitless	site_descrip
lat	Latitude (accuracy ±3m unless otherwise stated in Quadrat data)	decimal degrees	lat
lon	Longitude (accuracy ±3m unless otherwise stated in Quadrat data)	decimal degrees	lon
Quadrat_Area	Area of the sector	square meters (m^2)	area_measured
GPS_Name	GPS Name (e.g. MNDGPS1). Assigned name to distinguish GPS units	unitless	unknown
Site	The name of the survey location	unitless	site
Start_Time	The time (local US/Pacific time zone) the search begin within a particular quadrat Format: %H:%M	unitless	time_local
Quadrat_Notes	Extra notes about quadrats (e.g. description of other; other observations).	unitless	comment
Most_common_substrate	The most common substrate in the quadrat sector	unitless	site_descrip
Second_most_common_substrate	The second most common substrate in the quadrat sector	unitless	site_descrip
Quadrat_Photo	The name of the photo taken of this quadrat sector. (See "Habitat complexity photos" Dataset for accees to the images)	unitless	file_name
GPS_Accuracy	The accuracy of the GPS in meters at the time the waypoint was recorded (+- m)	meters (m)	site_descrip
Person	The person or people doing the quadrat survey (full name).	unitless	person
Quadrat_Start_DateTime_UTC	The DateTime (UTC) the search begin within a particular quadrat in ISO 8601 format YYYY-MM-DDThh:mmZ. Format: %Y-%m-%dT%H:%MZ	unitless	ISO_DateTime_UTC

Database

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Dataset: Quadrat data