This restriction site associated DNA sequencing (RAD-seq) dataset for Antarctic krill (Euphausia superba) includes raw sequence data and summaries for 148 krill from 5 Southern Ocean sites. A detailed README.pdf file is provided to describe components of the dataset. DNA library preparation was carried out in two separate batches by Floragenex (Eugene, Oregon, USA). RAD fragment libraries (SbfI) were sequenced on an Illumina HiSeq 2000 using single-end 100 bp chemistry. As there is no reference genome for Antarctic krill, a set of unique 90 bp sequences (RAD tags) was assembled from 17.3 million single-end reads from an individual krill. We obtained over a billion raw reads from the 148 krill in our study (a mean of 6.8 million reads per sample). The reference assembly contained 239,441 distinct RAD tags. The core genotype dataset exported for downstream data filtering included just those SNPs with genotype calls in at least 80% of the krill samples and contained 12,114 SNPs on 816 RAD tags. Sample collection table (comma separated): Southern Ocean Location, Sample Size, Austral Summer, Latitude, Longitude, ID East Antarctica (Casey), 21, 2010/2011, 64S, 100E, Cas East Antarctica (Mawson), 22, 2011/2012. 66S, 70E, Maw Lazarev Sea, 38, 2004/2005 and 2007/2008, 66S, 0E, Laz Western Antarctic Peninsula, 16, 2010/2011, 69S, 76W, WAP Ross Sea, 23, 2012/2013, 68S, 178E, Ross

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.

Metadata record for data from ASAC Project 484 See the link below for public details on this project. ---- Public Summary from Project ---- Emperor penguins are the only birds that breed in the Antarctic winter. They feed mainly on fish and squid but also ingest krill. Changes in food availability due to oceanographic or climatic factors, or to the extent of sea ice (through the processes of global warming) will have a direct impact on the breeding success and population size of the penguins. By counting the number of males that incubate at mid-winter each year, we can monitor trends in their population size. Counts of fledglings in spring (November) tell us how successful the penguins bred. The download file contains an excel spreadsheet which presents a summary of known Emperor Penguin colonies in the area of the Australian Antarctic Territory (AAT), and a file which details counts of male emperor penguins at the Taylor Glacier colony. A description of the column headings used in the spreadsheet is below. Colony: Colony name lat, long: latitude and longitude of colony discovered: date colony was discovered current est pop (BP): Current estimated population size in breeding pairs - current as at date the colony was last seen last seen: date the colony was last seen counting method: method used to count the breeding pairs in the colony comments: any applicable comments reference: references relating to the colony Taken from the 2009-2010 Progress Report: Public summary of the season progress: Population size of colonies fluctuates which is why long term monitoring studies are necessary to detect trends. At the emperor penguin colony at Taylor Glacier, monitored continuously since 1988, a slight downward trend is apparent but is not (yet?) statistically significant. The colony was visited three times: once in winter to obtain an estimate of the number of adults in the colony (roughly equivalent to the number of breeding pairs), and twice during the late chick rearing season to estimate breeding success. The count of adults in 2009 was the lowest on record. Reasons for this are still unknown.

Metadata record for data from AAS (ASAC) project 3010. Public Pycnogonids are primitive, bizarre arthropods. Found worldwide, Antarctic pycnogonids are the most diverse, abundant, and include some of the most spectacular forms. Near 250 species from the region are known, many in need for taxonomic revision, and more species new to science likely to be found. This project will document diversity of pycnogonids and target widely distributed species to obtain morphological, genetic and ecological information on distribution patterns and evolutionary history. This combined approach should provide a better insight of the roles of sea spiders in Antarctic biodiversity and the evolution and radiation of Antarctic marine benthic fauna. Project objectives: 1. To document the diversity of Australian Antarctic pycnogonids at species level and to target species with potential to investigate ecological interactions, zoogeographical patterns and genetic variability. To examine connectivity patterns and genetic differentiation in populations of target species of pycnogonids across large spatial scales inferring diversification processes and possibly speciation rates. To investigate the distribution patterns and possible mechanisms of dispersal of species with apparent wide distributions (e.g. circumpolar distribution, Antarctic -Pacific distribution and Antarctic-Arctic), based on molecular tools. To explore how sea spiders fit evolutionary models testing the origin of deep sea fauna and proposing hypothesis for colonisation mechanisms and radiation processes, as many pycnogonid taxa from the deep sea are also represented on the continental shelf. To resolve phylogenetic questions regarding the affinities among Antarctic species and lower latitude species to understand the evolutionary history of a highly diverse and cosmopolitan lineage (Callipallenidae-Nymphonidae). Details from previous years are available for download from the provided URL. Taken from the 2009-2010 Progress Report: Objective 1 - During this second year of the project more than 500 lots of unsorted samples of pycnogonids are being sorted and identified, many to species level. -In July 2009, 130 lots from the Ross Sea and Subantarctic areas deposited at NIWA in NZ, were sorted, identified and many of them barcoded. Some material has been requested on loan to continue taxonomic studies probably leading to description of new species. -In November 2009, more than 330 lots of CEAMARC samples of sea spiders were received on loan from the Natural History Museum in Paris, where they were deposited in 2008. This material is extremely relevant not only for its diversity but also numbers of individuals per sample. CEAMARC samples (including additional 136 samples from AAD) have provided a unique opportunity to obtain appropriate numbers of individuals of target species such Nymphon australe, with more than 1000 individuals collected. This material is currently being used in analyses about genetic differentiation and diversity at different spatial scales. -Current work in progress on the species level identification of the CEAMARC material would lead to a proper characterisation of the pycnogonid fauna from an extremely important area of the Australian Antarctic territory. We have identified Nymphon australe, Colossendeis megalonyx, Nymphon spp., Austropallene spp. and Pallenopsis spp, as the most frequent and abundant Australian Antarctic pycnogonids and it is expected to correlate abundance and occurrence patterns to other biotic and abiotic parameters that could explain the numbers and diversity of these taxa in the area. I co-authored a pioneering paper with H. Griffiths (senior author) from BAS and others, on the diversity and biogeography of Antarctic pycnogonids, which was submitted last month to journal Ecography. At least two new species to science are to be described based on CEAMARC material currently studied. Objective 2 -There is a publication in press (Arango et al.) in

RNA was extracted from pooled gonad tissues and tails of five sexually mature males and females, respectively, originating from the krill aquarium at the AAD in Tasmania, Australia. For RNA extractions, RNeasy mini kits (QIAGEN) were used and total RNA (8 micrograms each) was sent to Geneworks, South Australia (www.geneworks.com.au), for Illumina TruSeq 75 bp paired-end sequencing in two technical replica. Reads Yield Total Yield Krill_Male_sex_a_read1_sequence.txt 8,120,993 609,074,475 bases 1,218,148,950 bases Krill_Male_sex_a_read2_sequence.txt 8,120,993 609,074,475 bases Krill_Male_sex_b_read1_sequence.txt 10,465,586 784,918,950 bases 1,569,837,900 bases Krill_Male_sex_b_read2_sequence.txt 10,465,586 784,918,950 bases Krill_Male_tissue_a_read1_sequence.txt 7,867,804 590,085,300 bases 1,180,170,600 bases Krill_Male_tissue_a_read2_sequence.txt 7,867,804 590,085,300 bases Krill_Male_tissue_b_read1_sequence.txt 10,956,251 821,718,825 bases 1,793,118,450 bases Krill_Male_tissue_b_read2_sequence.txt 10,956,251 821,718,825 bases Krill_Female_sex_read1a_sequence.txt 29,447,654 2,208,574,050 bases 4,417,148,100 bases Krill_Female_sex_read2a_sequence.txt 29,447,654 2,208,574,050 bases Krill_Female_sex_read1b_sequence.txt 18,223,515 1,366,763,625 bases 2,733,527,250 bases Krill_Female_sex_read2b_sequence.txt 18,223,515 1,366,763,625 bases The insert size for these libraries is approx 160bp.

Metadata record for data from ASAC Project 2794 See the link below for public details on this project. Public: This study will use innovative technology to measure the winter spatial foraging patterns and net energy gain of adult female elephant seals (and potentially Weddell seals), while simultaneously providing high-resolution data on the physical nature of the water column in which the seals live. By combining biological and physical data with satellite derived sea-ice information, this study will improve our understanding of predator foraging success (and therefore mechanisms which regulate population trajectories) and provide physical oceanographers with fundamental data on the importance mechanisms that determine the winter ice and bottom water formation that under-pin the Antarctic marine ecosystem. Project objectives: The extent and nature of Antarctic winter sea ice is thought to have profound impacts on biological productivity, the recruitment of Antarctic krill, and the flow-on effects through the Antarctic marine food web. 1. Winter sea-ice formation is also hypothesised to play an important, yet highly-variable role in ocean circulation patterns through the production of cold, dense winter bottom water. 2. The mechanisms determining the inter-annual variation in winter ice formation are poorly understood, as are the complex feedback processes involved, but they are nonetheless recognised as being vulnerable to human-induced climate change. 3. Given the dynamically-linked nature of winter-ice and biological productivity, long-term climatic changes will have broad scale influences on Antarctic biota. This study will use innovative technological developments to quantify the response of one of the major Antarctic marine predators, the southern elephant seal (Mirounga leonina), to inter-annual variation in winter ice conditions. We will measure the winter spatial foraging patterns and net energy gain of adult female elephant seals while simultaneously providing high-resolution data on the physical nature of the water column in which the seals are living. The combination of these biological and physical data with satellite-derived sea-ice information will relate variation in the winter-ice to broad scale biological production through the foraging success (maternal investment and therefore demographic performance) of a top Antarctic marine predator, as well as providing physical oceanographers with fundamental data on the important mechanisms that determine the winter ice and bottom water formation that under-pin the Antarctic marine ecosystem. The specific objectives are to: Measure the foraging performance of the seals in terms of spatially-specific net energy gain while at sea, in relation to intra- and inter-annual variation in sea-ice and oceanic processes. Use newly-developed (and tested) animal-borne satellite-linked Conductivity-Temperature-Depth Satellite Relay Data Loggers (CTD-SRDLs) to provide oceanographic quality data on local physical characteristics (temperature and salinity). Record fine-scale foraging parameters (dive depth, duration, swimming speed) using "Dead-Reckoning" Data Loggers (DRDLs) and feeding events using Stomach Temperature Sensors (STSs). Integrate these data collected in years and regions of different winter ice extent and conditions. Assess diet during the winter months using stable isotope and fatty acid signature analysis. Combine the biological and physical information to refine current models of predator performance based on annual climatic features. These models will be used to examine a range of climate-change scenarios, initially for elephant seals but with a view to broadening the species application at a later stage. Taken from the 2008-2009 Progress Report: Progress against objectives: Due to logistic constraints, no satellite telemetry was conducted at Casey or Macquarie Island this year, but preliminary surveys of the region were conducted for both elephant and Weddell

A spreadsheet detailing the analysis of humpback whale biopsy samples including the field: Sample ID Duplicate (notes field) Location sample was taken Collection date (UTC) Collection latitude and longitude Sex Haplotype DLOOP sequence Microsatellite sequence Single nucleotide polymorphism (SNP) markers

Distribution and abundance of breeding seabirds in the AAT. This dataset comprises a broad range of component datasets derived from ground surveys aerial photography and oblique photography. Aerial and oblique photography has been used to obtain supplementary information on distribution and abundance of seabirds in the region. Recent surveys, 2000/01 onwards, have made use of GPS for more precise geographic information on seabird nests and colonies. At present there are a number of child metadata records attached to this record. See the link above for details.

The dataset contains boundaries of Adelie penguin breeding colonies at numerous breeding sites across east Antarctica. The boundary data were obtained using a range of methods which are detailed in separate spatial group-season accounts. The database of potential Adelie penguin breeding habitat in Southwell et al. (2016a) was used to associate colony boundaries to a particular breeding site and structure how the boundaries are stored. The breeding site database has a unique identifying code of every site of potential breeding habitat in East Antarctica, and the sites are aggregated into spatial sub-groups and then spatial groups. The file structure in which the boundaries are stored has a combination of 'group' and 'split-year breeding season' at the top level (eg VES 2015-16 contains all boundaries in spatial group VES (Vestfold Hills and islands) taken in the 2015-16 breeding season). Within each group-year folder are sub-folders for each breeding site where photos were taken (eg IS_72276 is Gardner Island in the VES group). Please refer to the Seabird Conservation Team Data Sharing Policy for use, acknowledgement and availability of data prior to downloading data.

This indicator is no longer maintained, and is considered OBSOLETE. INDICATOR DEFINITION Demographic parameters for the Adelie penguin at Bechervaise Island near Mawson. TYPE OF INDICATOR There are three types of indicators used in this report: 1.Describes the CONDITION of important elements of a system; 2.Show the extent of the major PRESSURES exerted on a system; 3.Determine RESPONSES to either condition or changes in the condition of a system. This indicator is one of: CONDITION RATIONALE FOR INDICATOR SELECTION The Adelie penguin is a relatively long lived sea bird dependent on krill. It is expected that major changes in the availability of food (krill) to sea birds will be reflected ultimately in recruitment into the breeding population. Causes of changes in the availability of krill relate directly to changes in both the biological and physical environment brought about by man made or natural means. Ageing populations may give an outward appearance of stability in terms of numbers at a breeding colony but such a condition may mask a decline in recruitment. To determine whether there are environmental influences on the population it is necessary to undertake detailed demographic studies. Demographic studies carried out over many years on animal populations comprising known age cohorts are required to determine those factors responsible for any observed changes in recruitment and/or mortality. Population reconstruction techniques provide estimates of recruitment and mortality and relate these functions to population size and/or population trends. These studies may alert us to possible changes in the ecosystem particularly related to the availability of food to the penguins or changes to the physical environment. The identification of the cause of changes must come from detailed investigations of food availability and the environment carried out at the same time. Annual breeding success at Bechervaise Island (eggs laid to chicks fledged) varies enormously from 0 in catastrophic years to above 1 for good seasons. The population at Bechervaise Island near Mawson has been monitored since 1990 as part of the CCAMLR Ecosystem Monitoring Program. Chicks and adults have been tagged annually. The number of breeding pairs has increased slightly between 1990-2001, but changes in the non -breeding population are unknown. Demographic studies based on the return rate of birds tagged as chicks provide information on trends in the overall population and the net rate of recruitment. Since it is intended that this program be undertaken indefinitely it makes this population an excellent subject for monitoring in the context of the SOE. DESIGN AND STRATEGY FOR INDICATOR MONITORING PROGRAM Spatial Scale: Restricted to the Mawson region. Similar studies are carried out by other national research programs at Terra Nova Bay (Italy) and on the Antarctic Peninsula (USA). Frequency: Annual Measurement Technique: The Adelie penguin population at Bechervaise Island consists of approximately 1800 breeding pairs. Each breeding season since 1990/91 in excess of 250 chicks have been given implanted electronic identification tags. The return of birds to their natal colony has been detected automatically by the Automated Penguin Monitoring System (APMS)or by checking all birds with a hand held tag reader. Additional and associated biological data as prescribed by CCAMLR (1997 are collected to aid interpretation of demographic and other trends. To detect trends in the population size and in demographic parameters, particularly of recruitment, it will be necessary to maintain an annual tagging program of chicks and recording of all tagged birds. RESEARCH ISSUES comprehensive analysis of the data collected over the duration of this study is required to determine natural variation and potential anthropogenic influences affecting Adelie penguin population dynamics. LINKS TO OTHER INDICATORS Sea-ice extent and concentration.