Dataset: Quadrat counts

Name: Quadrat species counts and measurements along the Northern Central California coast from 2017 to 2021
Published: 2024-02-29
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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Spatial Extent: N:38.9165 E:-120.672 S:35.1522 W:-123.715

Northern Central California coast, ~36–39 N

Temporal Extent: 2017-12-03 - 2021-07-25

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:

2024-02-29

Restricted:

Validated:

Current State:

Under revision

Quadrat species counts and measurements along the Northern Central California coast from 2017 to 2021

Abstract:

Quadrat species counts and measurements collected concurrently with habitat complexity photos along the Northern Central California coast from 2017 to 2021.

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Description

This page serves the "Quadrat counts" dataset. See "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 & 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.

Category in "Species" column and Life Sciences Identifier (LSID):

Cryptochiton stelleri,urn:lsid:marinespecies.org:taxname:240776
Dermasterias,urn:lsid:marinespecies.org:taxname:240770
Dermasterias imbricata,urn:lsid:marinespecies.org:taxname:240771
Henricia leviuscula,urn:lsid:marinespecies.org:taxname:369117
Henricia pumila,urn:lsid:marinespecies.org:taxname:467966
Henricia sp,urn:lsid:marinespecies.org:taxname:123276
Leptasterias sp.,urn:lsid:marinespecies.org:taxname:123222
Patiria miniata,urn:lsid:marinespecies.org:taxname:382131
Pink sponge,
Pisaster ochraceus,urn:lsid:marinespecies.org:taxname:240755
Strongylocentrotus franciscanus,urn:lsid:marinespecies.org:taxname:240762
Strongylocentrotus purpuratus,urn:lsid:marinespecies.org:taxname:240747

* Strongylocentrotus franciscanus (urn:lsid:marinespecies.org:taxname:240762) is currently the unaccepted synonym. The matching accepted name as of 2022-02-01 is Mesocentrotus franciscanus (urn:lsid:marinespecies.org:taxname:591102).

Problems/Issues

For 2018-12-21 and 2019-07-06: 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. For 2020-2021: Strongylocentrotus purpuratus were not counted or measured this field year.

Data Processing Description

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

BCO-DMO Processing

Data version 1:
* Data submitted in 75 Excel files (e.g. Quadrat_181221_MCM_Area1_LMS.xlsx) with sheets named "Counts" was exported as csv and imported into the BCO-DMO data system. All data concatenated into one table.
* Columns Date, Site_Code, Area_Number from information in the source file names.
* 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
* Commas in "Notes" changed to semicolons to support csv export from the BCO-DMO data system.
* Columns named "Area" renamed to Quadrat_Area (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.
* Species column was a mix of taxonomic names and species codes. Definition of column was "species identification shorthand: S = Strongylocentrotus purpuratus, P = Pisaster ochraceus, C = Cryptochiton stelleri, L = Leptasterias sp., H = Henricia pumila; if other species were recorded their full name is written out". These codes were replaced with the full name in the dataset.
* Taxonomic names checked using the World Register of Marine Species Taxa Match tool on 2022-02-01. All names matched a known name exactly. Though one matched an unaccepted synonym. Details added to metadata.

Dataset version 3 adds data for 2020-2021.
* Dataset imported the same way as v1 and v2. lat lon was added from related "GPS waypoints" version 3.
* Taxonomic names checked using the World Register of Marine Species Taxa Match tool on 2024-02-24. Taxon ids for names used added to metadata. One name correction was made in the data from "Patria miniata" to "Patiria miniata" (LSID: urn:lsid:marinespecies.org:taxname:382131)

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	The specific sector within the quadrat in which this specimen was observed. 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	The area of a sector	square meters (m^2)	area_measured
Species	Species identification. (Genus species, Genus sp., or common name).	per individual	taxon
n	Number of individuals of a particular species observed; separated into separate lines if extra details are recorded for each individual	per individual	abundance
Tube_Number	A unique field number assigned to each tube containing a tissue sample	unitless	sample_descrip
Primary_Measurement_Size	The primary size measurement in mm; usually to the nearest mm unless otherwised stated in the Notes	millimeters (mm)	length
Primary_Measurement_description	A description of the primary size measurement	unitless	comment
Secondary_Measurement_Size	The secondary size measurement in mm; usually to the nearest mm unless otherwised stated in the Notes	millimeters (mm)	length
Secondary_Measurement_description	A description of the secondary size measurement	unitless	comment
Notes	Any notes about the specimen (e.g. health status, malformation, feeding, etc.)	unitless	comment
Photo_ID	The name of the photo(s) taken of this specimen. (See "Habitat complexity photos" Dataset for access to the images)	unitless	file_name

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Dataset: Quadrat counts