Echosounder data were collected on a multidisciplinary research voyage conducted from the RV Tangaroa, operated by New Zealand’s National Institute of Water and Atmospheric Research Limited (NIWA). The voyage lasted 42 days, departing from Wellington, New Zealand on January 29th , 2015 and returning to the same port on 11th March 2015. Active acoustic data were obtained continuously using a calibrated scientific echosounder (Simrad EK60, Horten, Norway). The echosounder operated at 38 and 120 kHz for the duration of the voyage with a pulse duration of 1.024 ms, a pulse repetition rate of one ping per second and a 7° beam width. The echosounder data here are a subset of that collected throughout the voyage and include only data from south of 65°S. This subset of data focuses on research questions pertaining to Antarctic blue whales and krill.

This dataset contains acoustic recordings from Directional Frequency Analysis and Recording (DIFAR) sonobuoys that were deployed from 22 January – 18 March 2017 during the Antarctic Circumnavigation Expedition. During the 52 days at sea 301 sonobuoys were deployed yielding 492 hours of acoustic recordings. Two models of sonobuoys were used during the voyage: 1 was a bespoke reusable DIFAR buoy based on a sensor and radio from an AN/SSQ-53F sonobuoy (Ultra Electronics: SonobuoyTechSystems, USA) and 300 were re-lifed AN/SSQ-955-HIDAR (deployed in DIFAR compatibility mode; Ultra Electronics Sonar Systems, UK). Two dedicated acousticians monitored round-the-clock for blue, fin, sperm, humpback, minke, killer, and sei whales, and crabeater, leopard, Ross, and weddell seals and in all weather conditions. During ACE, we conducted a broad-scale, passing-mode passive acoustic survey for marine mammals in the Southern Ocean. Listening stations were conducted by deploying SSQ955 HIDAR sonobuoys in DIFAR (standard) mode to monitor for and measure bearings to vocalising whales while the ship was underway (Gedamke and Robinson 2010, Miller et al. 2015). During transit, listening stations were conducted every 30-60 nmi in water depths greater than 200 m. Sonobuoys were occasionally deployed with spacing less than 30 nmi in an attempt to more precisely determine spatial extent and vocal characteristics of calls that were believed to be coming from animals relatively close to the ship’s track. During terrestrial stopovers and marine science stations, sonobuoys were deployed approximately 2-4 nmi prior to stopping in order to attempt to monitor them for the full six-hour duration of their operational life. This distance ensured good radio signal while minimising acoustic interference from the vessel. The sampling regime was chosen to balance spatial resolution with the finite number of sonobuoys available for this study. Instrumentation, software, and data collection At each listening station, a HIDAR sonobuoy was deployed with the hydrophone set to a depth of 140 m. Sonobuoys transmitted underwater acoustic signals from the hydrophone and directional sensors back to the ship via a VHF radio transmitter. Radio signals from the sonobuoy were received using an omnidirectional VHF antenna (PCTel Inc. MFB1443; 3 dB gain tuned to 144 MHz centre frequency) and a Yagi antenna (Broadband Propagation Pty Ltd, Sydney Australia) mounted on the top of the helicopter control room at a height of 23.0 m. The antennas were each directly connected to a WiNRADiO G39WSBe sonobuoy receiver via low-loss LMR400 coaxial cable. The radio reception range on the Yagi antenna was similar to previous Antarctic voyages, and was adequate for monitoring and localisation typically out to a range of 12-14 nmi, provided that the direction to the sonobuoy was close (i.e. within around 30o) to the main axis of the antenna. The radio reception on the omnidirectional antenna typically provided 5-8 nmi of omnidirectional reception from sonobuoys. At transit speed (14-15 knots), the Yagi antenna provided about 55 minutes of acoustic recording time per sonobuoy Using both antennas together were able obtain radio reception for up to six hours (i.e. the maximum life of a 955 sonobuoy) when sonobuoys were deployed within 5 nmi of a marine science station. Received signals were digitised via the instrument inputs of a Fireface UFX sound board (RME Fireface; RME Inc.). Digitised signals were recorded on a personal computer as 48 kHz 24-bit WAV audio files using the software program PAMGuard (Gillespie et al. 2008). Data from both the Yagi and Omnidirectional antenna were recorded simultaneously as WAV audio channels 0 (left) and 1 (right). Each recorded WAV file therefore contains a substantial amount of duplication since both antennas and receivers were usually receiving the same signals from the same sonobuoy. Directional calibration The magnetic compass in each sonobuoy was calibrated/validated upon deployment as described by Miller et al. (2015, 2016). Calibration procedure involved measuring the mean bearing error and standard deviation of errors between the GPS-derived bearing from the sonobuoy to the ship and the magnetic bearing to the ship noise detected by the sonobuoy. 15-20 bearings were used for each calibration as the ship steamed directly away from the deployment location. Intensity calibration Obtaining calibrated intensity measurements from sonobuoys not only requires knowledge of the sensitivity of the hydrophone, but also the calibration parameters of the radio transmitter and radio receiver. Throughout the voyage, a hydrophone sensitivity of -122 dB re 1 V/micro Pa was applied to recordings via the Hydrophone Array Manager in PAMGuard. This value is defined in the DIFAR specification as the reference intensity at 100 Hz that will generate a frequency deviation of 25 kHz (Maranda 2001), thus the specification combines the hydrophone sensitivity and transmitter calibration. In line with manufacturers specifications, the WiNRADiO G39 WSB had a measured voltage response of 1 V-peak–peak (approximately -3 dB) at 25 kHz frequency deviation (Miller et al. 2014), and this was subtracted from the hydrophone sensitivity to yield an total combined factor of 125 dB re 1 V/µPa. The gain of the instrument input on the Fireface UFX was set to 20 dB, yielding a maximum voltage input voltage range of 8.36 V peak–peak. These calibration settings, along with the shaped filter response provided by Greene et al. (2004) make it possible to obtain calibrated pressure amplitude from the recorded WAV audio files. Sonobuoy deployment metadata The PAMGuard DIFAR Module (Miller et al. 2016) was used to record the sonobuoy deployment metadata such as location, sonobuoy deployment number, and audio channel in the HydrophoneStreamers table of the PAMGuard database (PamguardBlueWhale-2015-02-03.mdb). A written sonobuoy deployment log (Sonobuoy deployment logbook - 2015 Tangaroa.pdf) was also kept during the voyage, and this includes additional notes and additional information not included in the PAMGuard Database such as sonobuoy type, and sonobuoy end-time. Real-time monitoring and analysis (Acoustic event log) Aural and visual monitoring of audio and spectrograms from each sonobuoy was conducted using PAMGuard for at least an hour at each listening station. Two different spectrograms were typically viewed, one for low-frequency sounds with the following parameters: 250 Hz sample rate; 256 sample FFT; 32 sample advance between time slices. The other spectrogram was used to view mid-frequency sounds with the following parameters: 8000 Hz sample rate; 1024 sample FFT; 128 sample advance between time slices. Monitoring was conducted in real-time as data were being acquired, and the intensity scale of the spectrogram was adjusted by the operator to suit the ambient noise conditions. When detections from marine mammals, ice, and other sources were detected, they were classified manually, and their time and frequency bounds marked on the spectrogram. The PAMGuard DIFAR module (Miller, Calderan, et al. 2016) was then used to measure the direction of arrival and intensity of suitable calls such as tonal, frequency-modulated, and pulsed calls of baleen whales, whistles and trills from pinniped, and some whistles from toothed whales. Echolocation clicks from sperm whales (Physeter macrocephalus) were noted in the PAMGuard UserInput (free form notes stored in the PAMGuard Sqlite database), but could not be localised with the DIFAR module due to limitations inherent in directional sensors in the sonobuoy. Detection, bearing, and intensity measurements were saved both within a PAMGuard binary file and within the DIFAR_Localisation table of the PAMGuard database. In addition to PAMGuard binary files and audio files, the PAMGuard settings and metadata were saved to the PAMGuard Sqlite database. During Leg 3, some experimental trials were conducted with sonobuoys deployed in pairs with one hydrophone set to a depth of 140m and the other set to either 300m or 30m (the other two depth options available in the sonobuoy settings). The aim of these experiments was to investigate any differences with received level and the depth of the receiver. Recordings collected over a range of received levels as the vessel headed away from vocalising whales can also allow estimates of bearing accuracy for weak calls (by comparing bearings to the same call from different buoys) and the relative detection probability for calls under different noise conditions (by using the signals from each buoy in a similar way to independent observer experiments). References Greene, C.R.J. et al., 2004. Directional frequency and recording ( DIFAR ) sensors in seafloor recorders to locate calling bowhead whales during their fall migration. Journal of the Acoustical Society of America, 116(2), pp.799–813. Maranda, B.H., 2001. Calibration Factors for DIFAR Processing, Miller, B.S. et al., 2014. Accuracy and precision of DIFAR localisation systems: Calibrations and comparative measurements from three SORP voyages. Submitted to the Scientific Committee 65b of the International Whaling Commission, Bled, Slovenia. SC/65b/SH08, p.14. Miller, B.S. et al., 2016. Software for real-time localization of baleen whale calls using directional sonobuoys: A case study on Antarctic blue whales. The Journal of the Acoustical Society of America, 139(3), p.EL83-EL89. Available at: http://scitation.aip.org/content/asa/journal/jasa/139/3/10.1121/1.4943627. Miller, B.S. et al., 2015. Validating the reliability of passive acoustic localisation: a novel method for encountering rare and remote Antarctic blue whales. Endangered Species Research, 26(3), pp.257–269. Available at: http://www.int-res.com/abstracts/esr/v26/n3/p257-269/.

Metadata record for data collected as part of Australian Antarctic Science project 3010 in the Australian Antarctic program. From the abstract of the referenced paper: The evolutionary history of Antarctic organisms is becoming increasingly important to understand and manage population trajectories under rapid environmental change. The Antarctic sea spider Nymphon australe, with an apparently large population size compared with other sea spider species, is an ideal target to look for molecular signatures of past climatic events. We analysed mitochondrial DNA of specimens collected from the Antarctic continent and two Antarctic islands (AI) to infer past population processes and understand current genetic structure. Demographic history analyses suggest populations survived in refugia during the Last Glacial Maximum. The high genetic diversity found in the Antarctic Peninsula and East Antarctic (EA) seems related to multiple demographic contraction-expansion events associated with deep-sea refugia, while the low genetic diversity in the Weddell Sea points to a more recent expansion from a shelf refugium. We suggest the genetic structure of N. australe from AI reflects recent colonization from the continent. At a local level, EA populations reveal generally low genetic differentiation, geographically and bathymetrically, suggesting limited restrictions to dispersal. Results highlight regional differences in demographic histories and how these relate to the variation in intensity of glaciation-deglaciation events around Antarctica, critical for the study of local evolutionary processes. These are valuable data for understanding the remarkable success of Antarctic pycnogonids, and how environmental changes have shaped the evolution and diversification of Southern Ocean benthic biodiversity.

The ‘Logger’ data entry system was developed by the International Fund for Animal Welfare (IFAW) and is a flexible system to record information during a voyage. All events occurring during daylight operations such as sightings, biopsy attempts and sonobuoy deployments were recorded in a customized data entry program Logger along with weather and effort data. The logger access database contains all data collected throughout theNZ/Aus Antarctic Ecosystems Voyage 2015 related to: Biopsy events (date/time in UTC, success, sample number, reaction, attempts, dart recovery, notes) Comments - time stamped (UTC) with GPS index providing additional detail Observer effort (effort status, event, number of observers and locations, ship guide and data logger) Environmental observations (sightability, sea state, swell, weather, cloud cover, visibility, intensity, glare, ice, sea surface temperature) GPS data - time indexed NMEA feed, also containing heading and ship speed Lookup - table containing topic codes describing the codes that appear in all other tables Cetacean sightings and resightings (date/time in UTC), sighting number, sighting platform, estimate distance, binocular reticles, angle, species, sighting cue, heading, estimate of number of individuals, observer of sighting, behaviour, pod compaction, comments) Sonobuoy deployments (date/time in UTC, sonobuoy number, notes)

Biopsy samples were collected from humpback (n=10) and blue whales (n=1) during the NZ/Aus Antarctic Ecosystems Voyage 2015. Biopsy collection from humpback and blue whales was attempted from the bow of the ship using Larsen rifles. Biopsying blue whales from the bow of the RV Tangaroa proved challenging due to the ship’s manoeuvrability and the limited capacity to change speed rapidly. Biopsy samples were split between All Protect (Qiagen), 70% ethanol, and freezing at -20C. . This dataset consists of an excel spreadsheet (biopsy_events.xlsx) summarising biopsy events containing the fields: Date_taken (in UTC) Location (general) where sample collected Latitude Longitude Individual ID Sample ID Name of sampler Sample type Preservative used Species sampled An excel spreadsheet (Biopsy sample info datasheet AEV 2015.xlsx) details the biopsy processing that occurred upon collection of a sample. Where possible, each sample was split and preserved in 2 x All Protect, 1 x EtOH and 1 x -80 degrees Celsius. Samples preserved in All Protect and 70% ethanol are stored at the Australian Antarctic Division and samples preserved at -80C are stored at NIWA Wellington. A subsample of the Antarctic blue whale biopsy was submitted to the IWC-recognised genetic repository for Antarctic blue whale at NOAA Southwest Fisheries, La Jolla. Biopsy samples were processed to determine sex and the results are held in: TAN1502_Whale biopsy samples.xls

During the 2015 New Zealand-Australia Antarctic Ecosystem Voyage a digital photogrammetric video tracking system was used to collect precise surfacing locations during encounters with some Antarctic blue whales. The photogrammetric video tracking system is a modern digital video version based on the same operating principle as the that described by Leaper and Gordon 2001, and enables determination of the range and bearing to tracked objects relative to the ship. Around 15 hours of video tracking were recorded of which 8 hours were classified as good quality of a single animal or in one case a pair of animals that stayed close together. Focal follows were aborted when it was no longer possible to follow the focal animal due to ice or when the presence of other animals meant it was no longer possible to be sure which was the focal animal. This resulted in 7 tracks of longer than 45 minutes with the longest around 2 hours. Leaper, R. and Gordon, J. 2001. Application of photogrammetric methods for locating and tracking cetacean movements at sea. Journal of Cetacean Research and Management, 3: 131-141.

This dataset contains acoustic recordings from Directional Frequency Analysis and Recording (DIFAR) sonobuoys that were deployed throughout the 2015 NZ-Aus Antarctic Ecosystems Voyage. During the 42 day voyage 310 sonobuoys were deployed yielding 520 hours of acoustic recordings. Two models of sonobuoys were used during the voyage: 2 were AN/SSQ-53F (Ultra Electronics: SonobuoyTechSystems, USA) and 308 were re-lifed AN/SSQ-955-HIDAR (deployed in DIFAR compatibility mode; Ultra Electronics Sonar Systems, UK). A total team of four dedicated acousticians monitored round-the-clock for blue whales and in all weather conditions. After deployment, sonobuoys sent acoustic and directional data to the ship via a VHF radio transmitter. Radio signals from the sonobuoy were received using an omnidirectional VHF antenna (PCTel Inc. MFB1443; 3 dB gain tuned to 144 MHz centre frequency) and pre-amplifier (Minicircuits Inc. ZX60-33LN-S+) mounted on the mast of the ship at a height of 21 m. The preamplifier was connected to a power splitter via LMR400 cable and signals were received with two WiNRaDiO G39WSBe sonobuoy receivers. The radio signal from sonobuoys was adequate for monitoring and localization out to a typical range of 12-15 nmi. Received signals were digitised via the instrument inputs of a Fireface UFX sound board (RME Fireface; RME Inc.) with a gain set to 20 dB (8.396 V peak-peak voltage limits). Digitised signals were recorded on a personal computer as two-channel 48 kHz 24-bit WAV audio files using the software program PAMGuard (Gillespie et al. 2008). Directional calibration The magnetic compass in each sonobuoy was calibrated/validated upon deployment as described by Miller et al. (2015, 2016). Calibration procedure involved measuring the mean bearing error and standard deviation of errors between the GPS-derived bearing from the sonobuoy to the ship and the magnetic bearing to the ship noise detected by the sonobuoy. 15-20 bearings were used for each calibration as the ship steamed directly away from the deployment location. Intensity calibration Obtaining calibrated intensity measurements from sonobuoys not only requires knowledge of the sensitivity of the hydrophone, but also the calibration parameters of the radio transmitter and radio receiver. Throughout the voyage, a hydrophone sensitivity of -122 dB re 1 V/micro Pa was applied to recordings via the Hydrophone Array Manager in PAMGuard. This value is defined in the DIFAR specification as the reference intensity at 100 Hz that will generate a frequency deviation of 25 kHz (Maranda 2001), thus the specification combines the hydrophone sensitivity and transmitter calibration. In line with manufacturers specifications, the WiNRADiO G39 WSB had a measured voltage response of 1 V-peak–peak (approximately -3 dB) at 25 kHz frequency deviation (Miller et al. 2014), and this was subtracted from the hydrophone sensitivity to yield an total combined factor of 125 dB re 1 V/µPa. The gain of the instrument input on the Fireface UFX was set to 20 dB, yielding a maximum voltage input voltage range of 8.36 V peak–peak. These calibration settings, along with the shaped filter response provided by Greene et al. (2004) make it possible to obtain calibrated pressure amplitude from the recorded WAV audio files. Sonobuoy deployment metadata The PAMGuard DIFAR Module (Miller et al. 2016) was used to record the sonobuoy deployment metadata such as location, sonobuoy deployment number, and audio channel in the HydrophoneStreamers table of the PAMGuard database (PamguardBlueWhale-2015-02-03.mdb). A written sonobuoy deployment log (Sonobuoy deployment logbook - 2015 Tangaroa.pdf) was also kept during the voyage, and this includes additional notes and additional information not included in the PAMGuard Database such as sonobuoy type, and sonobuoy end-time. Real-time monitoring and analysis (Acoustic event log) Aural and visual monitoring of audio and spectrograms from each sonobuoy was conducted for each sonobuoy deployment. Two different spectrograms were typically viewed, one for low-frequency sounds with the following parameters: 250 Hz sample rate; 256 sample FFT; 32 sample advance between time slices. The other spectrogram was used to view mid-frequency sounds with the following parameters: 8000 Hz sample rate; 1024 sample FFT; 128 sample advance between time slices. Monitoring was typically conducted in real-time as data were being acquired, and the intensity scale of the spectrogram was adjusted by the operator to suit the ambient noise conditions. Detections from marine mammals, ice, and other sources and were detected and classified manually, and their time and frequency bounds were marked on the PAMGuard spectrogram. The PAMGuard DIFAR module (Miller et al. 2016) was then used to measure the direction of arrival and intensity of suitable calls from a variety of species such as tonal, frequency-modulated, and pulsed calls of baleen whales; and also some whistles from toothed whales. Echolocation clicks from sperm whales and any other short broadband sounds were noted in the PAMGuard UserInput (free form notes stored in the PAMGuard Microsoft Access database), but were not able to be localised with the DIFAR module due to limitations inherent in directional sensors in the sonobuoy. Each detection, bearing, and intensity measurement were saved within PAMGuard binaryStorage files in addition to the DIFAR_Localisation table of the PAMGuard database. In addition to PAMGuard binary files and audio files, the PAMGuard settings and metadata were saved inside the PAMGuard Sqlite database. Parameters for monitoring, recording, directional analysis, and other PAMGuard modules were stored within the PAMGuard database and as stand-alone Pamguard Settings Files (PSF). In addition to recording of Antarctic blue whale song, New Zealand type blue whale song, and blue whale 'D-call' vocalisations, these recordings also contain vocalisations from fin whales, humpback whales, killer whales, sperm whales, as well as low frequency sounds from Antarctic sea ice. Whale tracking log (Written Whale Acoustic Tracking Log - Tangaroa 2015.pdf) During the 2015 Voyage Acousticians also created a written summary of the event log at irregular intervals, typically between 30-60 minutes and this summary comprises the Whale Tracking Log. The acoustician on-duty recorded the average bearings or locations of each calling whale/group in the written Whale Tracking Log when the situation regarding the relative position of tracked whale groups was deemed to have changed. Entries in the written Sonobuoy Tracking Log (on the bench in the acoustics workstation) included the location of different whale groups and total number of different whale groups heard during that time interval. References Greene, C.R.J. et al., 2004. Directional frequency and recording ( DIFAR ) sensors in seafloor recorders to locate calling bowhead whales during their fall migration. Journal of the Acoustical Society of America, 116(2), pp.799–813. Maranda, B.H., 2001. Calibration Factors for DIFAR Processing, Miller, B.S. et al., 2014. Accuracy and precision of DIFAR localisation systems: Calibrations and comparative measurements from three SORP voyages. Submitted to the Scientific Committee 65b of the International Whaling Commission, Bled, Slovenia. SC/65b/SH08, p.14. Miller, B.S. et al., 2016. Software for real-time localization of baleen whale calls using directional sonobuoys: A case study on Antarctic blue whales. The Journal of the Acoustical Society of America, 139(3), p.EL83-EL89. Available at: http://scitation.aip.org/content/asa/journal/jasa/139/3/10.1121/1.4943627. Miller, B.S. et al., 2015. Validating the reliability of passive acoustic localisation: a novel method for encountering rare and remote Antarctic blue whales. Endangered Species Research, 26(3), pp.257–269. Available at: http://www.int-res.com/abstracts/esr/v26/n3/p257-269/. Raw Audio Files: DS05_Sonobuoy_audio Sonobuoy deployment log: DS07_Sonobuoy_deployment_log Acoustic event log: DS08_Acoustic_event_log Whale tracking log: DS09_Whale_tracking_log

All photos taken during the NZ-Australia Antarctic Ecosystems Voyage to the Ross Sea 2015 in an attempt to get a best photo identification image of blue whales, killer whales, humpback whales and minke whales. Image collection location and other details such as photographer, species, date (UTC) can be found in excel spreadsheet.