Knowledge of recruitment dynamics, and in particular trends in recruitment and recruitment variability, are key inputs for integrated assessments of fish stocks. A quantitative longline survey monitoring the recruitment of Antarctic toothfish (Dissotichus mawsoni) in the southern Ross Sea was started in 2012. The survey was expanded in 2016 to monitor trends and biological characteristics in two areas of importance to predators, Terra Nova Bay and McMurdo Sound, and to collect data that would contribute to the research and monitoring plan for the Ross Sea region Marine Protected Area. In most years, the survey was completed as planned, while in three years several factors have constrained the survey from sampling all stations and in the latest two seasons pandemic travel restrictions have necessitated an alternative delivery approach. Between 2012 and 2022, 2 056 tagged Antarctic toothfish have been released on the survey and 21 toothfish have been recaptured. Fifteen pop-up satellite archival tags (PSATs) were deployed on D. mawsoni in 2019 and fifteen skates were tagged in 2020 and 2021. Many tagged toothfish released from the RSSS move from the shelf to the slope. Trends in abundance indices and size and age composition consistently show the progression of strong year classes entering and leaving the survey area and have indicated that recruitment is likely more variable than previously thought. Data from the RSSS have been used to indicate year class strength in Antarctic toothfish stock assessments since 2015. The twelve surveys to date have resulted in a substantive increase in the knowledge and understanding of the distribution and relative abundance of a range of demersal fish species and invertebrate taxa caught on the longlines. Other data routinely collected on the surveys were plankton, temperature, salinity, air quality, cetacean and other marine mammal observations, and photo, video, and echosounder data. The RSSS has provided synergies with other research programmes also addressing CCAMLR objectives, particularly those focused on research and monitoring within the RSrMPA. GET DATA: https://www.ccamlr.org/en/publications/statistical-bulletin

Using seafloor image data to build single-taxon and community distribution models for seabed fauna in New Zealand waters. Understanding the spatial distributions of seabed biodiversity is essential for effective management of the effects of human activities. However, existing knowledge of seabed faunal distributions comes overwhelmingly from records of museum specimens and fisheries and research trawl bycatch. Data from such sources have been used to build models that predict species and community distributions on the basis of correlations with environmental gradients but because these models are based on presence-only data from disparate sources and times, their predictions are considered uncertain. To improve understanding of seabed fauna distributions around New Zealand, we are developing a new database of occurrences and population densities based entirely on quantitative data from seabed photographic surveys designed to sample these fauna. By modelling the spatial relationships between taxon occurrences and environmental gradients across the region, we are able to predict the likelihood of individual taxa and communities being present in as-yet unsampled areas. In the first phase of the project, we concentrated on Chatham Rise; a region of high importance to commercial fisheries and with the highest density of existing seabed imagery. The models developed here were the first abundance-based models of benthic distributions in the New Zealand region at these spatial scales. In the second phase, we expanded the domain of the predictive models to encompass Campbell Plateau, in the south-eastern sector the EEZ. Combining data from Chatham Rise and Campbell Plateau in a single dataset of benthic invertebrate taxon occurrences and population densities enabled development of up-dated predictive distribution models for a range of individual invertebrate taxa, as well as models of the spatial variability in overall community composition. Rasters are in a geotiff format at a 1000 m resolution cell size and have their relevant projections written in their files.

Using seafloor image data to build single-taxon and community distribution models for seabed fauna in New Zealand waters. Understanding the spatial distributions of seabed biodiversity is essential for effective management of the effects of human activities including fishing and mining. To improve understanding of seabed fauna distributions, we are developing a new database of benthic invertebrate occurrences in New Zealand waters by assembling quantitative data from all available seabed photographic surveys. By modelling the spatial relationships between taxon occurrences and environmental gradients across the region, we are able to predict the likelihood of individual taxa and communities being present in as-yet unsampled areas. In the first phase of the project, we concentrated on Chatham Rise; a region of high importance to commercial fisheries and with the highest density of available seabed imagery. Predictions from the models developed here are the first abundance-based models of benthic distributions in the New Zealand region and are the best-informed representations of seabed distributions on Chatham Rise to date, providing a resource that will have applications in marine environmental management and ecosystem research. All rasters are in a geotiff format at a 1000 m resolution cell size and projected to WGS 84 / Mercator 41 - EPSG:3994 coordinate system.

The landmark 518-page publication "Cenozoic Mollusca of New Zealand" by Beu & Maxwell (1990, NZGS Paleontological Bulletin 58) is long out of print. This publication by Beu & Raine (2009, GNS Science Miscellaneous Publication 27) contains revised descriptions and names of all species treated in detail in Paleontological Bulletin 58, arranged in a hypertext format. This guide has been constructed from the text of NZGS Paleontological Bulletin 58, with the figures individually scanned and available alongside the relevant text. Minor changes have been made to the text of morphological descriptions and notes about distribution, but the names of taxa and comparison notes have been extensively updated with taxonomic changes that have been published on Mollusca during the intervening 20 years. DOI:https://doi.org/10.21420/P5FX-VE20 Cite as: Beu, A. G., & Raine, I. J. (2009). Revised descriptions of New Zealand Cenozoic Mollusca from Beu and Maxwell (1990). GNS Science. https://doi.org/10.21420/P5FX-VE20

Radiolarians (holoplanktonic Protozoa) found in marine sediments are commonly used in Southern Ocean as palaeoclimate proxies. Generating such reconstructions of past climate based on radiolarian abundances requires a spatially and environmentally comprehensive reference dataset of modern radiolarian census counts. The Southern Ocean RADiolarian (SO-RAD) dataset includes census counts for 237 radiolarian taxa from 228 surface sediment samples located in the Atlantic, Indian and South-west Pacific sectors of the Southern Ocean. This compilation is the largest radiolarian census dataset derived from surface sediment samples in the Southern Ocean. The SO-RAD dataset may be used as a reference dataset for palaeoceanographic reconstructions, or for studying modern radiolarian biogeography and species diversity. RELATED PUBLICATION: https://doi.org/10.5194/essd-13-5441-2021

This metadata record represents the R phytoclass package. Determine the chlorophyll a (Chl a) biomass of different phytoplankton groups based on their pigment biomarkers. The method uses non-negative matrix factorisation and simulated annealing to minimise error between the observed and estimated values of pigment concentrations (Hayward et al. (2023) https://doi.org/10.1002/lom3.10541). The approach is similar to the widely used 'CHEMTAX' program (Mackey et al. 1996) https://doi.org/10.3354/meps144265), but is more straightforward, accurate, and not reliant on initial guesses for the pigment to Chl a ratios for each phytoplankton group. Further details are provided at: Hayward, A., M. H. Pinkerton, and A. Gutierrez-Rodriguez. 2023. phytoclass: A pigment-based chemotaxonomic method to determine the biomass of phytoplankton classes. Limnol. Oceanogr. Methods 21: 220–241. https://doi.org/10.1002/lom3.10541 GET PACKAGE: https://cran.r-project.org/web/packages/phytoclass/readme/README.html

The major histocompatibility complex (MHC) is a highly polymorphic gene family that is crucial in immunity, and its diversity can be effectively used as a fitness marker for populations. Despite this, MHC remains poorly characterised in non-model species (e.g., cetaceans: whales, dolphins and porpoises) as high gene copy number variation, especially in the fast-evolving class I region, makes analyses of genomic sequences difficult. To date, only small sections of class I and IIa genes have been used to assess functional diversity in cetacean populations. Here, we undertook a systematic characterisation of the MHC class I and IIa regions in available cetacean genomes. We extracted full-length gene sequences to design pan-cetacean primers that amplified the complete exon2 from MHC class I and IIa genes in one combined sequencing panel. We validated this panel in 19 cetacean species and described 354 alleles for both classes. Furthermore, we identified likely assembly artefacts for many MHC class I assemblies based on the presence of class I genes in the amplicon data compared to missing genes from genomes. Finally, we investigated MHC diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. This revealed copy-number variable class I haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. These MHC alleles will form the basis for a cetacean branch of the Immuno-Polymorphism Database (IPD-MHC), a curated resource intended to aid in the systematic compilation of MHC alleles across several species, to support conservation initiatives. The dataset contains 85 fastq files. Each file contains reads of amplicons from five MHC loci (DQA, DQB, DRA, DRB, and class I genes) combined across separate sequencing runs from a single cetacean. Details on individual cetacean sample abbreviations can be found in the manuscript. Reads are paired and merged with the Illumina adapter removed. It also contains one fastq file with all class I alleles found and one fastq file with non-functional DRB alleles found. Alleles are labeled with four letter species abbreviation followed by locus designation (DRB or N for class I) and are numbered in the order they were discovered. Further details are provided at: Heimeier, D., Garland, E. C., Eichenberger, F., Garrigue, C., Vella, A., Baker, C. S., & Carroll, E. L. (2024). A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies. Molecular Ecology Resources, 00, e13955. https://doi.org/10.1111/1755-0998.13955 GET DATA: https://doi.org/10.5061/dryad.wh70rxwvb

In Antarctica, ice shelves such as the Ross Ice Shelf (RIS) fringe 75% of the coastline and cover over 1.5 million km2, creating distinct and largely unexplored marine environments. It is fundamental to characterize the communities under these shelves to understand their biogeochemical role and predict how they might respond to future ice-shelf collapse 1,2. While historical studies suggested the RIS harbors active microorganisms 3–5, nothing is known about the composition of these communities. In this study, we profiled the composition, function, and activities of microbial communities in three seawater samples (400, 550, 700 m depth) underlying the shelf interior. We combined rate measurements with multi-omics (i.e. single-cell genomics, metagenomics, metatranscriptomics, and metaproteomics). Overall, below-shelf waters harbour microbial communities of comparable abundance and diversity to deep pelagic waters. Based on the meta-omic data, the community is inferred to be sustained by dark carbon fixation using ammonia, nitrite, and sulfur compounds as electron donors. In turn, these chemolithoautotrophs are predicted to support the aerobic heterotrophic majority and various trophic interactions. Consistently, this study and previous activity measurements suggest that dark carbon fixation is sufficient to sustain prokaryotic heterotrophic production, making the waters below the RIS presumably the largest chemolithotrophic system in the global ocean. Further details are provided at https://doi.org/10.1038/s41467-021-27769-5 GET DATA: https://www.ebi.ac.uk/ena/browser/view/PRJEB35712 GET DATA: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA593264

Aerial reconnaissance and photography are used in the Ross Sea sector of Antarctica to determine the breeding locations of Adélie penguins and to count the numbers of nests occupied during the early incubation period. From 1981 to present (two-year embargo), all islands and sea coasts between 158°E and 175°E have been searched, and 11 previously unreported breeding colonies discovered. The aim is to census Adélie (Pygoscelis adeliae) populations to provide basic data against which future population levels can be compared in order to monitor environmental change of the Antarctic Ocean ecosystem, both natural and man-induced. GET DATA: https://datastore.landcareresearch.co.nz/en_AU/dataset/adelie-penguin-census-data

Raw images (over approximately 20.000 unique images) collected during the Adelie Penguin Census across 30+ colonies since 1981 (see associated metadata resource for list full list of colonies). Photographs were taken using a black and white film camera from 1981 to 2004 (inclusive) and 2008. Images are available in .tif fomrat. Images are digital from 2005 onwards (except 2008). Raw images are available in cr2/cr3 formats, and processed images are available across tif and jpg formats. High resolution scanning was initiated in 2011 to scan all the negatives in the collection. There are approximately 10,000 negatives in the collection. Images are taken from helicopter at between 2000-2500 feet. All images collected during the 2324 season are georeferenced with latitude and longitude positions in decimal degrees (WGS 84). Camera Settings: ISO = 400 Shutter speed = greater than 1/1000 Focus = manual, pre-focus to 800m Lens = 135mm with UV filter Aperture/ Exposure = F8 (or up to F11) Image Size = Full size White Balance Setting = Daylight Captures per minute = ~80 GET DATA: m.meredyth-young@antarcticanz.govt.nz