Data from: Composition and functional diversity of juvenile groundfish assemblages in the California current
Data files
Feb 20, 2025 version files 839.12 KB
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README.md
4.88 KB
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YOYGroundfishBiodiv_Data.csv
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Abstract
This dataset is a collation of young-of-the year juvenile groundfish data from pelagic trawl surveys operated by NOAA Southwest Fisheries Science Center's Rockfish Recruitment & Ecosystem Assessment Survey and NOAA Northwest Fisheries Science Center's Pre-Recruit survey. These annual surveys respectively cover portions of the California Current Large Marine Ecosystem from 1990-2023 and 2011-2023. These data were used to calculate a suite of compositional and functional biodiversity metrics and test prevailing hypotheses related to biogeography in the California Current. See Gasbarro et al. (2025) for complete description of sampling methods and processing.
Each row of data contains the average catch-per-unit effort (CPUE) of all hauls at a given station in a given year for each species, a suite of compositoinal and functional biodiversity metrics calculated from CPUE data, and associated metadata for each sample. See the README file for a detailed description of the data contained in each column.
https://doi.org/10.5061/dryad.w0vt4b92x
Description of the data and file structure
Files and variables
File: YOYGroundfishBiodiv_Data.csv
Description:
Variables
- YEAR_STATION: Unique identifier for each sample representing year & station of sampling
- YEAR: Sample Year
- STATION: Sample station number
- WOLF_EEL: Taxon CPUE (log + 1)
- SABLEFISH: Taxon CPUE (log + 1)
- ARROWTOOTH_FLOUNDER: Taxon CPUE (log + 1)
- PACIFIC_SANDDAB: Taxon CPUE (log + 1)
- SPECKLED_SANDDAB: Taxon CPUE (log + 1)
- SCULPIN: Taxon CPUE (log + 1)
- REX_SOLE: Taxon CPUE (log + 1)
- GREENLING: Taxon CPUE (log + 1)
- SLENDER_SOLE: Taxon CPUE (log + 1)
- PACIFIC_HAKE: Taxon CPUE (log + 1)
- DOVER_SOLE: Taxon CPUE (log + 1)
- LINGCOD: Taxon CPUE (log + 1)
- PAINTED_GREENLING: Taxon CPUE (log + 1)
- RIGHT_EYED_FLATFISH: Taxon CPUE (log + 1)
- TURBOT: Taxon CPUE (log + 1)
- SAND_SOLE: Taxon CPUE (log + 1)
- CABEZON: Taxon CPUE (log + 1)
- BROWN_ROCKFISH: Taxon CPUE (log + 1)
- DARKBLOTCHED_ROCKFISH: Taxon CPUE (log + 1)
- CALICO_ROCKFISH: Taxon CPUE (log + 1)
- SPLITNOSE_ROCKFISH: Taxon CPUE (log + 1)
- GREENSTRIPED_ROCKFISH: Taxon CPUE (log + 1)
- WIDOW_ROCKFISH: Taxon CPUE (log + 1)
- YELLOWTAIL_ROCKFISH: Taxon CPUE (log + 1)
- CHILIPEPPER: Taxon CPUE (log + 1)
- SQUARESPOT_ROCKFISH: Taxon CPUE (log + 1)
- SHORTBELLY_ROCKFISH: Taxon CPUE (log + 1)
- COWCOD: Taxon CPUE (log + 1)
- BLACK_ROCKFISH: Taxon CPUE (log + 1)
- BLACKGILL_ROCKFISH: Taxon CPUE (log + 1)
- BLUE_ROCKFISH: Taxon CPUE (log + 1)
- BOCACCIO: Taxon CPUE (log + 1)
- CANARY_ROCKFISH: Taxon CPUE (log + 1)
- YELLOWMOUTH_ROCKFISH: Taxon CPUE (log + 1)
- YELLOWEYE_ROCKFISH: Taxon CPUE (log + 1)
- BANK_ROCKFISH: Taxon CPUE (log + 1)
- STRIPETAIL_ROCKFISH: Taxon CPUE (log + 1)
- HALFBANDED_ROCKFISH: Taxon CPUE (log + 1)
- OLIVE_ROCKFISH: Taxon CPUE (log + 1)
- PYGMY_ROCKFISH: Taxon CPUE (log + 1)
- SHARPCHIN_ROCKFISH: Taxon CPUE (log + 1)
- ROCKFISH: Taxon CPUE (log + 1)
- ROSY_ROCKFISH_GROUP: Taxon CPUE (log + 1)
- PACIFIC_TOMCOD: Taxon CPUE (log + 1)
- COPPER_ROCKFISH_GROUP: Taxon CPUE (log + 1)
- IRISH_LORD: Taxon CPUE (log + 1)
- sdiv: Shannon-Weiner Diversity Index
- nspec: Species Richness
- eve: Pielou's Evenness (J); NA values present where <2 taxa are present.
- LCBD: Local Contributions to Beta Diversity
- LONDD: Longitude in decimal degrees
- LATDD: Latitude in decimal degrees
- PROVINCE: California Current biogeographic province (North, Central, or South)
- SURVEY: Survey on which the sample occurred (RREAS or NWFSC)
- CRUISE: Unique cruise identifier
- STATION_BOTTOM_DEPTH: Bottom depth of station
- AREA: Geographic area of station
- ACTIVE: Binary; is station active (1) or not (0)
- clust_6: Assemblage cluster assigned to sample
- core: Binary; is sample inside 'Core' region (1) or not (0)
- cpue: Total CPUE across species
- MDS1: Sample location on first axis of compositional NMDS
- MDS2: Sample location on second axis of compositional NMDS
- MDS3: Sample location on third axis of compositional NMDS
- centroid_distance: Euclidean distance in NMDS space of sample to the regional (by Province) climatological centroid
- rar50: Rarefied (50 individuals) species richness
- fMDS1: Sample location on first axis of functional trait NMDS; NA values present in samples with <5 taxa.
- fMDS2: Sample location on second axis of functional trait NMDS; NA values present in samples with <5 taxa.
- fMDS3: Sample location on third axis of functional trait NMDS; NA values present in samples with <5 taxa.
- centroid_distance_fd: Euclidean distance in functional NMDS space of sample to the regional (by Province) climatological centroid; NA values present in samples with <5 taxa.
- feve: Functional Evenness; NA values present in samples with <5 taxa.
- fric: Functional Richness; NA values present in samples with <5 taxa.
- fdiv: Functional Divergence; NA values present in samples with <5 taxa.
Access information
Raw trawl data from RREAS is available on ERRDAP (https://coastwatch.pfeg.noaa.gov/erddap/tabledap/FED_Rockfish_Catch.html) and can be accessed using the ‘RREAS’ R package (https://github.com/tanyalrogers/RREAS). Raw trawl data from the NOAA Northwest Fisheries Science Center’s pre-recruit survey is available upon reasonable request. Functional trait data from the Pelagic Species Traits database (Glieber et al. 2024a) can be accessed at the following URL: https://borealisdata.ca/dataset.xhtml?persistentId=doi:10.5683/SP3/0YFJED.