Zooplankton research in the US AMLR Program focuses on the link between prey production, availability, and climate variability in relation to predator and fishery demands. Annual studies include estimates of krill abundance, and experiments to develop and enhance hydro-acoustic methodologies. Long-term objectives include quantifying the inter-annual and decadal mesoscale (10's to 100's of kilometers) variability in water mass structure, phytoplankton biomass and productivity, and zooplankton (especially krill) associated with potential basin scale climate forcing. Conversely, the microscale (1 to 10's of kilometers) features of the distribution and abundance of krill within the foraging range of krill predators breeding at Cape Shirreff and Admiralty Bay is also studied to resolve local and remote forcing effects on predator foraging success.

The integrated modeling framework for Antarctic krill (Euphausia superba) has been extended to include estimates of krill growth consistent with survey data and to use multi-nation survey data collected from 1981 to 2014 near the Antarctic Peninsula. Four models of the population dynamics of Antarctic krill in Subarea 48.1 based on different aggregations of the data are described to illustrate the capabilities of the framework.

An integrated, age-structured model was fitted to different combinations of survey data using two forms of selectivity (logistic or double-logistic) with time-constant or annually varying selectivity to investigate the population dynamics of Antarctic krill (Euphausia superba) near the Antarctic Peninsula. The data were from surveys conducted by the U.S. Antarctic Marine Living Resources Program around the South Shetland Islands from 1992 to 2011. Two indices of krill biomass based on (1) trawl-net samples and (2) hydroacoustic sampling were combined with length-compositions from the nets. Sixteen model configurations using different combinations of the two biomass surveys with the various options for modeling selectivities were examined.

Dataset contains continuous underway measurements of ship’s position, sea surface temperature, salinity, turbidity, fluorescence, air temperature, barometric pressure, relative humidity, plus wind speed and direction. These data are part of a long term ecosystem project centered on the South Shetland Islands of the Antarctic Peninsula, Antarctica. The datasets incorporated into this archive have been collected by researchers affiliated with the U.S. Antarctic Marine Living Resources (AMLR) Program under the National Marine Fisheries Service (NMFS); funding for this project was from the NMFS AMLR Program. Actual data collected any given year varies, dependent on funding availability for resources, staging and sea days.

The attached file details the workflow for the processing and analysis of active acoustic data (Simrad EK60; 12, 38, 120 and 200 kHz) collected from RSV Aurora Australis during the 2006 BROKE-West voyage. The attached file is in Echoview(R) (https://www.echoview.com/) version 8 format. The Echoview file is suitable for working with fisheries acoustics, i.e. water column backscatter, data collected using a Simrad EK60 and the file is set-up to read 38, 120 and 200 kHz split-beam data. The file has operators to remove acoustic noise, e.g. spikes and dropped pings, and operators for removing surface noise and seabed echoes. Echoes arising from krill are isolated using the ‘dB-difference’ method recommended by CCAMLR. The Echoview file is set-up to export the results of krill echo integration as both intervals and swarms. Full details of the method are available in Jarvis et al. (2010) and the krill swarms methods are described in Bestley et al. (2017).

Data Acquisition: DIFAR (DIrectional Fixing And Ranging) 53D sonobuoys were deployed every 30 minutes of longitude during each of the north-south sampling transects as part of the acoustic survey for marine mammals. Sonobuoys were also deployed opportunistically when large numbers of whales (in particular minke whales) were sighted. Additionally, on the initial E-W transect (#12) sonobouys were deployed prior to the majority of CTD stations. The VHF receiving system for the sonobuoys aboard the ship began with a 6 element YAGI antenna mounted atop the ship's mast. The sonobuoy's VHF signal output from the YAGI was amplified through an Advanced Receiver Research VHF amplifier and received on ICOM PCR-1000 VHF receivers modified to improve low frequency audio output. The audio signal passed through a low pass anti-alias filter (National Instruments analogue bessel SCXI module) and was recorded onto a laptop through a National Instruments E-series (model 6062E) sound card at a sampling rate of 48kHz. Difar sonobuoys have an effective audio response up to 2.5kHz before the low-pass filter roll-off starts. DIFAR bearing information is carried on 7.5 and 15kHz carrier frequencies. Once sonobuoys were deployed, recordings were made for at least 70 minutes unless the sonobuoy failed or the signal was lost. During recordings at CTD stations, recordings were typically made for the length of time it took to complete the CTD (4 or more hours). Data Processing: Signals were monitored in real-time during acquisition using Ishmael software (Dave Mellinger, http://www.bioacoustics.us/ishmael.html). A scrolling spectrogram (FFT size: 16384 samples, overlap: 50%, frequency range displayed: 0-1000 Hz, time scaling: 5 sec/cm) was monitored in real-time. Sounds of interest were clipped and the time and description were logged in the sonobuoy deployment data logs. Bearings to sounds were attained with a modified version of DiFarV (Mark McDonald, http://www.whaleacoustics.com ). Note that bearings to the ship noise given by DifarV are ~180 degrees off for an as yet undetermined reason (potentially deep cold water propagation effects), but the bearings to whale sounds and other sounds of interest are thought to be correct. This appears to be the case with a series of light bulb calibration tests I did, suggesting that bearings to other sounds are in fact, correct. After acquisition, recordings were also post-processed in Ishmael with two further passes, one examining 0-2.5kHz, and another monitoring 0-1kHz again, to ensure as many marine mammal sounds as possible were identified. Clips were also re-examined when necessary to ensure species were correctly identified. In instances when apparently multiple whales were calling, calculated bearings were used to determine whether the sounds came from different bearings, and hence, different whales. Dataset Format: The dataset description is in an excel workbook, with a summary sheet at the front. The summary sheet has a single line summarising each sonobuoy deployment. The sonobuoy deployment data log sheets are separated by days when the deployment began. Each is marked by date - eg 01.10 is the 10th of January. Each deployment has an initial entry and the following rows are a running log of the sonobuoy recording session. The data sheets and the summary sheet are in the following format with column headers from left to right: Observer(real time/post-processing)Summary of the sounds that occurred within the sample (70 minutes) Total recording length (in minutes) Date UTC time of deployment Initial latitude (decimal degrees) Initial Longitude (decimal degrees) Depth setting of sonobuoy hydrophone (90, 120, or 300m) National Instruments sound card gain (0, 5, or 10 times) Ship heading (true degrees) Ship speed (knots) Distance of deployment from CTD location (if applicable) UTC time of events (applies mainly to log of events in sonobuoy deployment data log) Species or sound description (applies mainly to

Acoustic densities of Antarctic krill in Scotia Sea from 01162001 to 03032011. Data were collected from research vessels using either Simrad EK500 (years 2001-2004) or Simrad EK60 (2005-2011) echosounders operating at 3 different frequencies (38, 120, and 200 kHz). Raw acoustic data were collected from calibrated echosounders and archived on the vessel and later on shore-based servers. The datasets were ultimately returned to the SWFSC for QA/QC, archiving and review. Krill were identified from these acoustic data using the distorted-wave Born approximation. (Reiss et al., 2008; Fielding et al., 2011). Data were exported using Echoview into gridded bins 5 m deep by 100 m horizontal over a total depth range of 5 m to a maximum of 505 m below the hulls of survey vessels.

Bathymetry data was collected using a Simrad EK60 echosounder. The sample data have been corrected for the relative locations of GPS antenna, transducers and waterline. A sound-speed value of 1500 m/s was applied when calculating depth. The seafloor depth itself was defined firstly as the depth of the sounder-detected bottom minus 10m (contact Simrad for more information about their bottom-detection algorithm), and then modified manually where necessary to ensure that the line followed the seafloor as perceived by eye from the echogram. This is therefore a subjective process, and the true seafloor depth may vary from the perceived depth by several hundred metres in the worst cases. The greatest uncertainties are typically at greater depths, e.g. greater than 1000 m. This seafloor depth line therefore refers to the approximate depth (not range from transducer) of the seafloor less 10 m, i.e. 10 m should be added to the 'depth' values in the *.CSV file to give the 'true' seafloor depth. Depths greater than 5000 m are not available due to the 12 kHz data not being logged any deeper than this. These data are preliminary and subject to change. Bathymetry data was exported during the voyage by Belinda Ronai. Post voyage enquiries however should be directed to Toby Jarvis.

Readme - Bathymetry Files Data for BROKE-WEST 2006 1) Zipped folder contains .csv files created from each acoustics ev file for Transects 1 to 11. 2) These files contain subsections of each transect of variable length (usually between 50 and 100 km). 3) No data exists for files; Transect01_01 and 01_02 as the sea floor was greater than 5000m deep in these areas and was below the range set for the sounder. 4) Each file contains 11 columns of data; Ping_date, Ping_time, Ping_milliseconds, Latitude, Longitude, Position_status, Depth, Line_Status, Ping_status, Altitude, GPS_UTC time. 5) For practical purposes, the columns of interest will be Ping_date, Ping_time, Latitude, Longitude and Depth. Other columns are ancillary acoustics information and can be ignored. Line status should be 1 (meaning good) as sea floor was only picked when it could be easily defined. If the sea floor could not be visually defined or was deemed to uncertain, it was not picked in the echogram. Hence sea floor may not be totally contiguous. 6) Depth of the sea floor was only defined for those areas deemed to be 'on transect', i.e. straight transects for acoustics survey purposes. Deviations from the transect, i.e. to pick up moorings, conduct target or routine trawls or visit nice looking bergs were deemed 'off transect' and were excluded from the analysis. 7) Sea floor depth was primarly defined for the purposes of the acoustics analysis, i.e. exclusion from the echograms. Hence the values in the files are for the 'sea floor exclusion line' that is set above the true sea floor in order to exclude noise from the analysis. This means the sea floor depths in these files are likely to be an underestimate of the true depth. The uncertainty is likely to be of the order of 2 to 10m. 8) Another source of error is that depth was calculated with values of absorption coefficient and sound speed set to default values derived from pre-cruise hydrographic data. One value for each parameter was applied to the whole data set. These values were; 0.028 dB/m (120 KhZ), 0.010 dB/m (38kHz), 0.041 dB/m (200 kHz), 0.0017 dB/m (12kHz - bathy sounder) for absorption coefficient and 1456 m/s for sound speed. 9) These values will be recalculated from the oceanographic data derived during the voyage and applied to the data set during post-processing (forthcoming analyses for May-June 2006). Revision of these parameters may cause a slight shift in the calculated depths, although this is likely to be small. 10) Reprocessing of the data may also result in more accurate bottom detection. This data should be available post June 2006 and will be sent to interested parties as soon as it is completed. 11) Dataset was created by Esmee van Wijk.

This dataset contains long-term underwater acoustic recordings made under Australian Antarctic Science Projects 4101 and 4102, and the International Whaling Commission’s Southern Ocean Research Partnership (IWC-SORP) Southern Ocean Hydrophone Network (SOHN). Calibrated measurements of sound pressure were made at several sites across several years using custom moored acoustic recorders (MARs) designed and manufactured by the Science Technical Support group of the Australian Antarctic Division. These moored acoustic recorders were designed to operate for year-long, deep-water, Antarctic deployments. Each moored acoustic recorder included a factory calibrated HTI 90-U hydrophone and workshop-calibrated frontend electronics (hydrophone preamplifier, bandpass filter, and analog-digital converter), and used solid state digital storage (SDHC) to reduce power consumption and mechanical self-noise (e.g. from hard-drives with motors and rotating disks). Electronics were placed in a glass instrumentation sphere rated to a depth of 6000 m, and the sphere was attached to a short mooring with nylon straps to decouple recorder and hydrophone from sea-bed. The hydrophone was mounted above the glass sphere with elastic connections to the mooring frame to reduce mechanical self-noise from movement of the hydrophone. The target noise floor of each recorder was below that expected for a quiet ocean at sea state zero. The analog-digital converter, based on an AD7683B chip, provides 100 dB of spurious free dynamic range, but a total signal-to-noise and distortion of 86 dB which yields 14 effective bits of dynamic range at a 1 kHz input frequency. The data for each recording site comprise a folder of 16-bit WAV audio files recorded at a nominal sample rate of 12 kHz. The names of each WAV file correspond to a deployment code followed by the start time (in UTC) of the file as determined by the microprocessor’s real-time clock e.g. 201_2013-12-25_13-00-00.wav would correspond to a wav file with deployment code 201 that starts at 1 pm on December 25th 2013 (UTC). Recording locations were chosen to correspond to sites used during AAS Project 2683. These sites were along the resupply routes for Australia’s Antarctic stations, and typically there was only one opportunity to recover and redeploy MARs each year.