DOI: 10.5061/dryad.hmgqnk9s0
title: Processed EK60 acoustics data used to examine changes in vertical distribution of mesopelagic fish

description: Marine heatwaves can impact the distribution and abundance of epipelagic
 organisms, but their effect on deep pelagic communities is unclear. Using
 fisheries acoustics data collected in the Central California current from
 2013-2018, we found that during the warmest years of a large marine
 heatwave (2015-2016), the estimated center of mass depth of mesopelagic
 fishes deepened by up to 100 m compared to pre-heatwave conditions. Using
 a generalized additive model, we evaluated which biophysical factors may
 have driven these changes and found that light, dynamic height anomaly,
 and acoustic backscatter explained 81% of the variability in depth. We
 attribute the vertical shift by mesopelagic fishes into deeper waters to
 heatwave driven compression of upwelling habitat that indirectly increased
 the amount of light reaching mesopelagic depths. Our results suggest that
 mesopelagic fishes are interconnected with and thus sensitive to changes
 in near-surface oceanographic conditions, which could lead to cascading
 effects on vertical carbon export and the availability of mesopelagic
 fishes as prey for top predators under future climate conditions.
description: Examining the effects of the 2015-2016 marine heatwave on
 mesopelagic fishes in the California Current Ecosystem
 The project includes the following data:
 -Processed EK60 Acoustics Data from central California: daytime
 acoustics data (2 hours before/after sunrise/sunset, when ship speed
 &gt; 5knots, bottom depths &gt;725 m). These data were 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. 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.  This
 project R code is available at:
 https://github.com/ilyiglesias/Meso_acoustics
description: # Processed EK60 acoustics data used to examine changes in vertical
 distribution of mesopelagic fishes in the California Current
 [https://doi.org/10.5061/dryad.hmgqnk9s0](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](https://doi.org/10.1093/icesjms/fsae129)). Code for our analysis is publicly available at [https://github.com/ilyiglesias/Meso_acoustics](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 &gt; 5knots, bottom depths &gt;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](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](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](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](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](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](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](https://github.com/ilyiglesias/Meso_acoustics)