https://doi.org/10.5061/dryad.hmgqnk9s0

We explored the effect of a large marine heatwave on the vertical distribution of mesopelagic fishes as estimated from acoustic backscatter. We also examined the oceanographic conditions that may have contributed to observed shifts in this vertical distribution, using a combination of CTD and satellite data. The dataset contained herein are the processed EK60 acoustics data from the central California Current region from 2013-2018 used in our analysis (for processing details please see article: https://doi.org/10.1093/icesjms/fsae129). Code for our analysis is publicly available at https://github.com/ilyiglesias/Meso_acoustics.

Description of the data and file structure

Processed EK60 Acoustics Data: daytime acoustics data (2 hours before/after sunrise/sunset) when ship speed > 5knots, bottom depths >725 m collected as part of the Rockfish Recruitment and Ecosystem Assessment Survey, an annual spring survey by the NOAA National Marine Fisheries Service, Southwest Fisheries Science Center. We focused on the region of Central California between ~Point Reyes and ~Big Sur. Acoustics data were processed in Echoview Software (Version 10): noise removed, a -75 dB threshold applied and gridded into 100 m horizontal, by 5 m vertical grid cells. For details on acoustics processing, please see manuscript. 

File naming conventions: each file is labeled according to its year and day of collection. For example, 2013_0510_deep_725.csv represents data collected in the year 2013, on May 10th, with bottom depths greater than 725 m. Each file is a CSV (comma separated) of acoustics data binned in 100 m horizontal by 5 m vertical cells.

The main metrics we were interested in for our analysis include:

Sv_mean: mean volume backscattering strength [dB re 1m-1]

Lat_M/Lon_M: latitude/longitude of center of cell [decimal degrees]

Depth_mean: depth [m] of center of cell

Note that "Interval" is an identifier in the horizontal direction, while "Layer" identifies the vertical position

Other variables (column names) included in the .csv files (but not directly used) are listed below and were generated on export from Echoview. For fuller descriptions of variables and how they were calculated see: https://support.echoview.com/WebHelp/Reference/Glossary.htm):

Process_ID: assigned identifier from Echoview

NASC: Area Backscattering Coefficient [m2nmi-2]

Sv_max: maximum Sv in the domain analyzed [dB re 1m-1]

Sv_min: minimum Sv in the domain analyzed [dB re 1m-1]

Sv_noise: see https://support.echoview.com/WebHelp/Reference/Algorithms/Background_Noise/Background_noise_calculation.htm

NASC_noise: see https://support.echoview.com/WebHelp/Reference/Algorithms/Background_Noise/Background_noise_calculation.htm

Height_mean: Cell height mean (~5 m)

Good_samples: number of samples retained after processing (cleaning)

Layer_depth: depth of vertical cell [m]

Dist_M: Distance from the start of the GPS source of the acoustic variable to the middle ping in the analysis domain

Date_M: Date in YYYYMMDD

Time_M: acoustic data collection time in HH:MM:SS

Exclude_line depth mean: mean depth of the exclude below line [m]

Noise_Sv_1m: estimated noise at 1m depth [dB re 1m-1]

Minimum_Sv_threshold applied: 1 (we applied a threshold of -75 dB)

Maximum_Sv_threshold applied: 0 (we did not apply a maximum value)

Exclude_above_line_applied: 1 (10 m from echo sounder)

Exclude_above_line_depth _mean: 10 [m]

Exclude_below_line_applied: 1 (bottom depth)

Standard_deviation: standard deviation of all samples values in the domain which was analyzed

Skewness: statistic used to measure the symmetry of the distribution 

Kurtosis: numerical measure for the tails (outliers) of the distribution of a data set

ABC: Area Backscattering Coefficient [m2m-2]

ABC_noise: https://support.echoview.com/WebHelp/Reference/Algorithms/Background_Noise/Background_noise_in_Echoview.htm

Area_Backscatter_Strength: Area backscatter strength for the domain analyzed [dB re 2m-2]

Thickness_mean: Mean thickness of an analysis domain (5 m) [m]

Range_mean: mean range of samples in the domain [m]

Samples_in_domain: number of samples in the analysis domain subject to analysis

Center_of_mass: center of "mass" in [m] of the domain calculated by considering the average of all sample depths weighted by sample sv

Inertia: spread as the sum of squared distances from the center of mass, weighted by the sv at each distance and normalized by the total sa of the main.

Proportion_occupied: proportion of the water column with Sv above a threshold; considers all samples of the domain

Equivalent_area: area [m] that would be occupied if all the samples had the mean Sv of the domain

Aggregation_index: aggregation index [m-1] of the domain, calculated by evaluating the reciprocal of the equivalent area for the samples of the domain.

CTD data: CTD data also come from the Rockfish Recruitment and Ecosystem Assessment survey (RREAS) conducted by the NOAA National Marine Fisheries Service, Southwest Fisheries Science Center and include two files: dbo_CTD_HEADER.txt and dbo_CTD_cast.txt. 

Variables (columns) for dbo_CTD_HEADER.txt:

CRUISE: a unique identifier for each spring survey of the Rockfish Recruitment and Ecosystem Assessment Survey (a concatenation of the year- first two digits and cruise order per vessel)

CTD_INDEX: For each year a numerical cast number 

CTD_NO: this corresponds to the specific Seabird equipment deployed

STATION: long term station id for trawl or ctd station locations (from RREAS)

CTD_DATE: date CTD cast conducted in the format MM/DD/YYYY\
CTD_LAT: latitude of CTD position [degrees minutes]

CTD_LON: longitude of CTD position [degrees minutes]

CTD_BOTTOM_DEPTH: Underlying bottom depth at station location (from nautical charts)

BUCKET_TEMP/BUCKET_SAL: surface temperature, salinity (gathered over the side of the boat)

TS_TEMP/TS_SAL: surface temperature and salinity (from boat flow-through system)

Variables (columns) for dbo_CTD_CAST.txt:

CRUISE: a unique identifier for each spring survey of the Rockfish Recruitment and Ecosystem Assessment Survey (RREAS)

CTD_INDEX: For each year a numerical cast number

CTD_DEPTH: Depth of CTD (in 2 m averaged bins) [m]

TEMPERATURE: water temperature measured by the CTD [C]

SALINITY: Water salinity measured by the CTD [PSU]

DENSITY: water density (sigma-theta) measured by the CTD [kg/m3]

DYN_HGT: Dynamic height measured by the CTD [m]

IRRAD: irradiance of the water as measured by the CTD [microEinsteins/S/m2]

FLUOR_VOLT: voltage of fluorometer measured by the CTD [voltage]

TRANSMISSIVITY: Water transparency measured by the CTD [percent]

CHLOROPHYLL: Calibrate concentration of chlorine-a based on water bottle samples processed back at the laboratory compared to the CTD [ug/L]

OXYGEN_VOLT: Oxygen sensor voltage measured by CTD [voltage]

OXYGEN: Dissolved oxygen concentration measured by CTD [ml/l]

Additional sharing/access information

This analysis utilizes CTD data from the Rockfish Recruitment and Ecosystem Assessment Survey, and while we provide txt files of these data, they are also publicly available at:

https://oceanview.pfeg.noaa.gov/erddap/tabledap/FED_Rockfish_CTD.html

Satellite data describing light is also publicly available from the Aqua Modis satellite (NASA):

https://coastwatch.pfeg.noaa.gov/erddap/search/index.html?page=1&itemsPerPage=1000&searchFor=kd490

Code/Software

Code (R) from our analysis is available publicly at: https://github.com/ilyiglesias/Meso_acoustics