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.

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)

Satellite derived tracks of humpback whales tagged on their Antarctic feeding grounds. Data can be found here: https://data.aad.gov.au/aadc/argos/display_campaign.cfm?campaign_id=83 Satellite tags were deployed on adult humpback whales with a modified version of the Air Rocket Transmitter System (ARTS, Restech) and a purpose-designed projectile carrier at a pressure of 7.5 – 10 bar. A custom-designed, 80mm anchor section is attached to a stainless steel cylindrical housing containing a location-only transmitter (SPOT-5 by Wildlife Computers, Redmond, Washington, USA and Kiwisat 202 Cricket by Sirtrack, Havelock North, New Zealand). This superseded anchor design resulted in the anchor section disarticulating upon deployment in order to achieve improved tag retention times while minimising impact. The tags were sterilised with ethylene oxide prior to deployment and implanted up to 290mm into the skin, blubber, interfacial layers and outer muscle mass of the whale. Tags were programmed to transmit to the Argos satellite system at various duty cycles and repetition rates for a maximum of 720 transmissions per day. These transmissions are relayed to processing centres which calculate the transmitter’s location by measuring the Doppler Effect on transmission frequency.

A spreadsheet detailing the filenames of the best left and/or right photos of blue whales photographed and individually identified during the New Zealand Australia Antarctic Ecosystems Voyage 2015. See http://www.marinemammals.gov.au/sorp/antarctic-blue-whale-project for further detail regarding the Antarctic blue whale voyage.

This dataset contains the underway data collected during the Tangaroa Voyage 5.1 1999-2000. This voyage carried out marine science studies off the Antarctic coast between the Dibble ice tongue and Ninnis glacier, departing from and returning to Wellington, NZ. Underway data were received from NIWA (PO Box 14-901, Kilburnie, Wellington, New Zealand) and can be accessed via the Australian Antarctic Division Data Centre web page (or via the Related URL section). For further information, see the Marine Science Support Data Quality Report at the Related URL section.

This dataset contains the underway data collected during Tangaroa Voyage VY1 - AWE - Australia-New Zealand Antarctic Whale Expedition - 2009/10 Track and Underway Data Voyage Objectives: Antarctic Whale Expedition (AWE). Voyage Leader: Anthony Hull Deputy Voyage Leader: Sarah Robinson

Sampling sites with a list of activities at each site for the Tangaroa cruise - March to April 2004. Tangaroa Tube Label our use Sample#our use Date(UTC) Time(UTC)Shorthand entry code - ignore Time(UTC)Formatted Use this Long Degdegrees Long Minminutes Long Decdecimaldegrees Lat Degdegrees Lat Minminutes Lat Decdecimaldegrees Local time (dec hrs)actual solar local time (decimal hours) calc from longitude DOES NOT EQUAL TIME ZONE Sea Temp Ice present/absent Lugol's#microscope sample number for phytoplankton ID (Our use only) HPLC Volvolume filtered for HPLC pigment analysis (Our use only) Cocco Volvolume filtered for coccolithophorid counts (Our use only) Cocco tray No.(Our use only) Location:DCM: Deep chlorophyll maximum Thermo: Thermocline

This is the CTD and Niskin bottle data set from the RV Tangaroa cruise tan0704, 7th Mar 2007 to 29th Mar 2007, along the Macquarie Ridge. This was the deployment cruise for the Macquarie Ridge mooring array. Dissolved oxygen data have been removed from this data set (oxygen bottle data never analysed). There were a total of 75 CTD casts on this cruise.

Metadata record for data from AAS (ASAC) project 2926. Public Summary DNA based approaches will be used to study key features of the ecology of whales, penguins and krill. Standard methods cannot accurately estimate what prey species these predators consume, how old they are, or how they are related to the rest of their species. This project will apply novel DNA based methods to biopsy or scat samples as a non-invasive means of improving our understanding of the diet, age and population structure of these important predators. Project objectives: The overall objective of this project is to use molecular biology to study aspects of the ecology of key Southern Ocean predators that cannot be addressed with other methodologies. The organisms that the project would focus upon have been chosen because they are large biomass components of the Southern Ocean food web and because they are important to the Australian Governments commitments to the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) and the International Whaling Commission (IWC). This project is integral to the work of the Australian Centre for Applied Marine Mammal Science (ACAMMS) that has recently been formed within the Science Branch of the AAD. The focus predators are baleen whales (primarily Minke whales, Balaenoptera edeni and Humpback whales, Megaptera novaengliae), Antarctic krill (Euphausia superba) and Adelie penguins (Pygoscelis adeliae). Within this overall goal, there are three major objectives: 1. To characterise and monitor predation by key Southern Ocean organisms with dietary DNA analysis. 2. To use population genetics to study the stock structure and population size of baleen whales and Antarctic krill. 3. To develop and validate DNA-based age estimation methods for whales. 1. DNA Based Dietary Research A major objective of this project is to apply DNA based methods for dietary analysis to large sample sets taken to address specific ecological questions. My group at the Australian Antarctic Division has been at the forefront of developing DNA based methods to study animal diet. We have been especially active in researching DNA as a non-invasive means of studying the diet of large mammals and birds by reconstructing diet with prey DNA that we can identify in scats from predators. Our development of new DNA-based methodologies (Jarman et al., 2002; Jarman et al., 2004; Deagle et al., 2005; Jarman et al., 2006a) and accompanying software tools (Jarman 2004; Jarman 2006) have led to more efficient dietary analysis methods and has produced a substantial volume of good quality published research and stimulated international interest in these methodologies, which are now being pursued by several overseas laboratories. We have completed short descriptive studies of the diet of Antarctic krill (Passmore et al., 2006), whales (Jarman et al., 2002; Jarman et al., 2004; Jarman et al., 2006b), fur seals (Casper et al., in prep) and macaroni penguins (Deagle et al., in prep) with these methods, but have not had comprehensive sets of samples with which we can address broader ecological questions. The ecological questions that the dietary component of this project will address are: 1a. What is the diversity and identity of prey species consumed by populations of the key predators? 1b. What are the relative biomass proportions of prey species consumed by key predator populations? 1c. What temporal variation is there in diversity, identity and abundance of prey consumed by each key predator population? 1d. What spatial variation is there in diversity, identity and abundance of prey consumed by each key predator population? The focus species cover three trophic levels of the Southern Ocean food web. Krill are thought to feed predominately on primary producers with some heterotrophic prey taken as well. Adelie penguins feed on krill and other small nekton and plankton, as well as being prey of leopard seals and killer whales, making them a mid-to-high level predator. Baleen whales feed on diverse planktonic and nektonic organisms, preferring crustaceans and small fish that tend to form high-concentration swarms and are top predators. By studying krill and their most abundant predators (Adelie penguins) and their largest predators (baleen whales) we get an assessment of trophic flow from primary production to both a mid-level predator and a top-level predator. It is clearly not possible to study all components of the Southern Ocean food web, so by targeting these three key groups it is hoped that we will not only gather information that is most directly relevant to the objectives of the science program, but that this information will also be an efficient means of assaying some of the most important trophic interactions in the Southern Ocean food web as a whole. Krill are highly abundant and quite easy to sample. They are generalist feeders, which makes them a good organism for monitoring changes in populations of primary producers and small heterotrophs. Furthermore, they are the target organism of the world's largest crustacean fishery (Nicol and Endo, 1997). This makes them a species of major interest to CCAMLR. Our scientific objective in studying krill diet with DNA based methods is to improve our understanding of this critically important organism. This research should contribute to Australia's role in CCAMLR and consequent influence within the Antarctic treaty system. Adelie penguins are the only land-based predators in this study. They are the most abundant penguin and can be found in high concentrations at breeding colonies at many points along the Antarctic coastline. This makes their population size and condition relatively easy to estimate when compared to completely marine organisms. These features make them an excellent animal to survey for ecosystem monitoring purposes and they have been selected by CCAMLR as their main organism for the CEMP (CCAMLR Ecosystem Monitoring Program). The objective of the Adelie penguin DNA based diet research is to develop non-invasive diet analysis methods that can rapidly and cheaply analyse large numbers of scat samples for prey DNA. This technology would allow us to monitor penguin diet without stomach flushing and would also enable the generation of much finer-scale temporal and spatial information on Adelie penguin diet. It is hoped that the development of these methods to the point where they become practical and cheap to apply on a large scale may eventually allow them to be recommended to CEMP as a replacement for stomach flushing as a dietary analysis method. Baleen whales are highly visible components of the Southern Ocean ecosystem and despite their relative scarcity, they are very well studied because of their charisma and being the focus of a prominent international fishery and conservation organisation, the IWC. The diet of baleen whales is difficult to study with any methodology, so our previous development of DNA based methods to analyse prey DNA found in whale scats as part of AAS project 2301 was scientifically quite a useful advance. It was also a useful political advance for Australia as we can now argue that lethal whaling for 'scientific' studies is less necessary than previously claimed. The objective of the baleen whale diet work is to continue our previous research in this area to maintain our position as the only country within the IWC that is capable of doing truly non-invasive dietary research on whales. 2. Population Genetics Research This project would also include studies of the population genetics of humpback whales, minke whales and Antarctic krill. These studies have two goals. The first is to study genetic differentiation within each of these species. For humpback whales this work would focus on attempts to link whales found in Australian Antarctic waters during the summer feeding season with the whales that migrate past the west and east coasts of Australia and which breed near south Pacific islands. For Antarctic krill, the genetic differentiation work aims to identify genetic 'stocks' of krill to assist in policy decisions for managing the krill fishery, as well as potentially providing a tool for measuring flux of krill between different regions of the Southern Ocean. The second goal of the population genetics work is to use genetic data to estimate population size. Simple methods for estimating the size of an animal breeding population (the 'effective population') have been available for some time. We would apply these methods and also work on newer genetic 'mark and recapture' type methods that estimate overall population size, rather than just the size of the proportion of the population that reproduces. Another aspect of this goal is the estimation of past population sizes, which would give us a better idea of pre-exploitation stocks of whales and their relative recovery from exploitation to date. 3. DNA-Based Age Estimation Another major goal of the project is to develop genetic methods for estimating the age of whales. This would be a major advance for cetacean science as the methods could be performed on DNA collected through biopsy samples, or potentially even from the 'sloughed' skin that a whale leaves behind when diving. There are currently no validated, non-lethal methods for estimating cetacean age in adults. The only alternative methods for age estimation involve lethal sampling for collection of ear bones in which growth rings can be counted. One of the main claims promulgated by the Japanese scientific whaling program is that lethal sampling of whales is necessary for aging them. The political objective of this research would be to neutralise this claim in the same way that our DNA based dietary research has previously neutralised the claim that lethal sampling is necessary for dietary analysis. Alongside this political objective is the scientific objective that the development of a widely applicable, non-lethal aging method for whales would provide a wealth of information on the age structure of whale populations. This is an especially important feature of their ecology as most of the great whales are still recovering from human exploitation, which should have led to skewed age distributions in these populations when compared to the natural age distribution. Better knowledge of their population age structure will greatly improve our understanding of the recovery process and the current status of whale populations. Taken from the 2009-2010 Progress Report: Progress against objectives: 1. DNA based diet work. We converted our DNA based diet analysis work to next-generation sequencing based methodologies and refined blocking primer approaches for eliminating predator DNA in the libraries that we sequence. This approach was published as Deagle et al (2009) as listed in the papers below. 2. Population genetics research. A microsatellite and mitochondrial sequence dataset for humpback whale population samples in eastern Australian waters, West Australian waters and Antarctic waters in the Ross Sea has been generated, analysed and a paper written. 3. DNA based age estimation. Libraries of cDNA from juvenile, sub Adult and Adult humpback whales have been analysed. ~1.2 gb data was produced for each library. We are currently analysing these to identify genes that are differentially expressed among the three age classes.

This is the CTD data set from RV Tangaroa cruise tan0803, 26th March to 26th April 2008, along the Macquarie Ridge. This was the recovery cruise for the Macquarie Ridge mooring array. The primary aims of the oceanographic program were: 1. recovery of a New Zealand/Australia collaborative mooring array spanning two gaps in the Macquarie Ridge north of Macquarie Island, and 2. occupation of a CTD transect running south from New Zealand to 60o S along the Macquarie Ridge. Eight of the nine moorings were successfully recovered. The mooring at site number 3 (NIWA gear) was unrecoverable, with acoustic release communication indicating only the bottom portion of the mooring remaining and lying flat on the ocean floor. Complete details of the mooring work are included in a separate mooring recovery report. Mooring instruments were downloaded on the ship, with a very high percentage of successful data recording. Ship maneouvering and deck operations all went well throughout the recoveries. Shiptime at the mooring locations was well spent, with daylight hours dedicated to mooring recovery, and night time used for nearby CTD, swath mapping, coring and sea mount activities, and for unspooling of mooring line. The additional container space created on the top deck portside (above the trawldeck) proved extremely valuable for stowage of mooring gear. 58 CTD's were completed during the cruise, including 54 along the main transect, and 4 at coring locations (part of the geology program). Main transect CTD's included 2 across the northern mooring group, and 3 across the southern mooring group. Most casts were to within 25 metres of the bottom. Instrument problems resulted in incomplete casts at the following locations: CTD 9, CTD 11 and CTD 27. CTD 46 was skipped due to bad weather, while further instrument problems prevented a cast at the southernmost site (CTD 50). Niskin bottles were sampled at each station for dissolved oxygen and salinity, with a subset of stations selected for 18O sampling. Some stations were additionally sampled for DIC, alkalinity, 13C, silicate, and U/Th, as part of the geology program. Note that dissolved oxygen data have been removed from this data set, as oxygen bottle samples were never analysed.