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This dataset contains information on specimens of Southern Ocean Pycnogonida (Arthropoda), that were collected from ten different research cruises, spanning 13 years. The individual aims and objectives of each cruise can be found in their cruise reports. The specimens have been collated into a single dataset, forming the basis of J. Maxwell’s PhD. The dataset will be used to investigate the community structure of Antarctic pycnogonids and the factors which influence its composition. This dataset is published by SCAR-AntOBIS under the licence CC-BY 4.0. Please follow the guidelines from the SCAR and IPY Data Policies (https://www.scar.org/excom-meetings/xxxi-scar-delegates-2010-buenos-aires-argentina/4563-scar-xxxi-ip04b-scar-data-policy/file/) when using the data. If you have any questions regarding this dataset, please do not hesitate to contact us via the contact information provided in the metadata or via data-biodiversity-aq@naturalsciences.be.This dataset adds vital occurrence and abundance data for pycnogonids from 10 previously unexamined research cruises from the Weddell Sea, Antarctic Penisula and the islands of the Scotia Arc. It includes the first pycnogonid data from the Prince Gustav Channel. The 197 sampling stations within this dataset represent an 11% increase in the number of stations where pycnogonids have been recorded in the Southern Ocean, southern South America and New Zealand waters and an 18% increase for above 60 degrees latitude. Presence data for any observed epifauna are also included.

The Southern Ocean is a productive and biodiverse region, but it is also threatened by anthropogenic pressures. Protecting the Southern Ocean should start with well-informed Marine Ecosystem Assessments of the Southern Ocean (MEASO) being performed, a process that will require biodiversity data. In this context, open geospatial biodiversity databases such as OBIS and GBIF provide good avenues, through aggregated geo-referenced taxon locations. However, like most aggregated databases, these might suffer from sampling biases, which may hinder their usability for a MEASO. Here, we assess the quality and distribution of OBIS and GBIF data in the context of a MEASO. We found strong spatial, temporal and taxonomic biases in these data, with several biases likely emerging from the remoteness and inaccessibility of the Southern Ocean (e.g., lack of data in the dark and ice-covered winter, most data describing charismatic or well-known taxa, and most data along ship routes between research stations and neighboring continents). Our identification of sampling biases helps us provide practical recommendations for future data collection, mobilization, and analyses.

IntroductionMesopelagic fishes play a central role in the transfer of energy through open-ocean food webs, particularly in the Southern Ocean where they are both important predators of zooplankton and a key prey group for many higher predators. However, they are notoriously difficult to sample, which has limited our understanding of the bio-physical predictors of their abundance and spatiotemporal variability. Species distribution models can be used to help understand species’ ecological requirements by relating records of their presence or abundance to environmental data.MethodsHere, we used data from Myctobase – a new circumpolar database of mesopelagic fishes – to model patterns in abundance of eight key myctophid species (family Myctophidae) and the genus Bathylagus in the Southern Ocean south of 45°S. We developed species-specific boosted regression tree models to obtain circumpolar predictions of abundance. Average daytime and night-time summer predictions for the period 1997 to 2011 at 0 to 200m depths were generated for each species.ResultsDepth and solar position were important predictors and species were stratified in their depth distribution. For all species, except for G. nicholsi, there was an interaction between depth of capture and solar position, reflecting diel vertical migration. Other important variables included sea surface temperature, dissolved oxygen at 200 m, chlorophyll a, and sea surface height, indicating an association with water mass properties. Circumpolar patterns of abundance varied between species with some displaying affinities for oceanic regions at Antarctic latitudes (e.g., E. antarctica and Bathylagus spp.) or sub-Antarctic latitudes (e.g., K. anderssoni and P. tenisoni); and affinities for shelf regions (e.g., P. boliniand G. nicholsi).DiscussionOur findings suggest that the abundance of mesopelagic fish is influenced by diel vertical migration and meso- and sub-mesoscale oceanographic features, with the Polar Front being a major delimiting feature. Our study showed contrasting patterns in community composition with higher species diversity north of the Polar Front that might be indicative of latitudinal variability in food web structure. Our spatial analysis is an important step toward resolving what determines important habitat for mesopelagic fishes, providing foundational information for understanding shifting food web dynamics into the future.

Abstract Background Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. Results In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. Conclusions Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.

Globally important services are supported by Southern Ocean ecosystems, underpinned by the structure, function, and dynamics of complex interconnected and regionally distinctive food webs. These food webs vary in response to a combination of physical and chemical processes that alter productivity, species composition and the relative abundance and dynamics of organisms. Combined with regional and seasonal variability, climate-induced changes and human activities have and are expected to continue to drive important structural and functional changes to Southern Ocean food webs. However, our current understanding of food web structure, function, status, and trends is patchy in space and time, and methods for systematically assessing and comparing community-level responses to change within and across regional and temporal scales are not well developed. Insights gained from food web modelling studies—ranging from theoretical analyses of ecosystem resilience and adaptation, to qualitative and quantitative descriptions of the system—can assist in resolving patterns of energy flow and the ecological mechanisms that drive food web structure, function, and responses to drivers (such as fishing and climate change). This understanding is required to inform robust management strategies to conserve Southern Ocean food webs and the ecosystem services they underpin in the face of change. This paper synthesises the current state of knowledge regarding Southern Ocean pelagic food webs, highlighting the distinct regional food web characteristics, including key drivers of energy flow, dominant species, and network properties that may indicate system resilience. In particular, the insights, gaps, and potential integration of existing knowledge and Southern Ocean food web models are evaluated as a basis for developing integrated food web assessments that can be used to test the efficacy of alternative management and policy options. We discuss key limitations of existing models for assessing change resulting from various drivers, summarise priorities for model development and identify that significant progress could be made to support policy by advancing the development of food web models coupled to projected biogeochemical models, such as in Earth System models.

Southern Ocean ecosystems offer numerous benefits to human society and the global environment, and maintaining them requires well-informed and effective ecosystem-based management. Up to date and accurate information is needed on the status of species, communities, habitats and ecosystems and the impacts of fisheries, tourism and climate change. This information can be used to generate indicators and undertake assessments to advise decision-makers. Currently, most marine assessments are derivative: reliant on the review of published peer-reviewed literature. More timely and accurate information for decision making requires an integrated Marine Biological Observing and Informatics System that combines and distributes data. For such a system to work, data needs to be shared according to the FAIR principles (Findable, Accessible, Interoperable, and Reusable), use transparent and reproducible science, adhere to the principle of action ecology and complement global initiatives. Here we aim to provide an overview of the components of such a system currently in place for the Southern Ocean, the existing gaps and a framework for a way forward.

Southern Ocean ecosystems are globally important and vulnerable to global drivers of change, yet they remain challenging to study. Fish and squid make up a significant portion of the biomass within the Southern Ocean, filling key roles in food webs from forage to mid-trophic species and top predators. They comprise a diverse array of species uniquely adapted to the extreme habitats of the region. Adaptations such as antifreeze glycoproteins, lipid-retention, extended larval phases, delayed senescence, and energy-conserving life strategies equip Antarctic fish and squid to withstand the dark winters and yearlong subzero temperatures experienced in much of the Southern Ocean. In addition to krill exploitation, the comparatively high commercial value of Antarctic fish, particularly the lucrative toothfish, drives fisheries interests, which has included illegal fishing. Uncertainty about the population dynamics of target species and ecosystem structure and function more broadly has necessitated a precautionary, ecosystem approach to managing these stocks and enabling the recovery of depleted species. Fisheries currently remain the major local driver of change in Southern Ocean fish productivity, but global climate change presents an even greater challenge to assessing future changes. Parts of the Southern Ocean are experiencing ocean-warming, such as the West Antarctic Peninsula, while other areas, such as the Ross Sea shelf, have undergone cooling in recent years. These trends are expected to result in a redistribution of species based on their tolerances to different temperature regimes. Climate variability may impair the migratory response of these species to environmental change, while imposing increased pressures on recruitment. Fisheries and climate change, coupled with related local and global drivers such as pollution and sea ice change, have the potential to produce synergistic impacts that compound the risks to Antarctic fish and squid species. The uncertainty surrounding how different species will respond to these challenges, given their varying life histories, environmental dependencies, and resiliencies, necessitates regular assessment to inform conservation and management decisions. Urgent attention is needed to determine whether the current management strategies are suitably precautionary to achieve conservation objectives in light of the impending changes to the ecosystem.

Antarctic specimens collected during various research expeditions are preserved in natural history collections around the world potentially offering a cornucopia of morphological and molecular data. Historical samples of marine species are, however, often preserved in formaldehyde which may render them useless for genetic analysis. We sampled stomachs and hindguts from 225 Trematomus specimens from the Natural History Museum London. These samples were initially collected between 20 and 100 years ago and fixed in either formaldehyde or ethanol. A 313 bp fragment of the cytochrome c oxidase subunit I (COI) was amplified and sequenced for prey item identification in the stomach and a 450 bp region of the 16S rRNA gene to investigate microbiome composition in the gut system. Both data sets were characterized by large dropout rates during extensive quality controls. Eventually, no unambiguous results regarding stomach content (COI) were retained, possibly due to degraded DNA, inefficient primers and contamination. In contrast, reliable microbiome composition data (16S rRNA) was obtained from 26 samples. These data showed a correlation in change of microbiome composition with fish size as well as year of the catch, indicating a microbiome shift throughout ontogeny and between samples from different decades. A comparison with contemporary samples indicated that the intestinal microbiome of Trematomus may have drastically changed within the last century. Further extensive studies are needed to confirm these patterns with higher sample numbers. Molecular analyses of museum stored fish can provide novel micro evolutionary insights that may benefit current efforts to prioritize conservation units in the Southern Ocean.

Small mesopelagic fish are ubiquitous in the ocean, representing an important trophic link between zooplankton and tertiary consumers such as larger fish, marine mammals and birds. Lanternfishes (Myctophidae) are common worldwide as well as in the Southern Ocean. However, only 17 of the approximately 250 myctophid species occur exclusively in sub-Antarctic or Antarctic waters. It is unclear whether they colonized these latitudes once and diversified from there, or whether multiple colonization events took place in which multiple ancestral phenotypes entered the Southern Ocean at various times. Phylogeographic patterns have been investigated for individual myctophid species, but so far no study has compared species across the Southern Ocean. Here, we present a dataset with previously unpublished cytochrome c oxidase I (COI; n = 299) and rhodopsin (rh1; n = 87) gene sequences from specimens collected at various locations in the Southern Ocean. Our data extend the DNA barcode library of Antarctic mesopelagic fish substantially. Combined morphological and molecular taxonomy lead to confident species level identification in 271 out of 299 cases, providing a robust reference dataset for specimen identification, independently of incomplete morphological characters. This is highly topical in light of prospective ecological metabarcoding studies. Unambiguous sequences were subsequently combined with publicly available sequences of the global DNA barcode library yielding a dataset of over 1,000 individuals for phylogenetic and phylogeographic inference. Maximum likelihood trees were compared with results of recent studies and with the geographical origin of the samples. As expected for these markers, deep phylogenetic relationships remain partially unclear. However, COI offers unmatched sample and taxon coverage and our results at the subfamily to genus level concur to a large extent with other studies. Southern Ocean myctophids are from at least three distant subfamilies suggesting that colonization has occurred repeatedly. Overall, spatial divergence of myctophids is rare, potentially due to their enormous abundance and the homogenizing force of ocean currents. However, we highlight potential (pseudo-)cryptic or unrecognized species in Gymnoscopelus bolini, Lampanyctus achirus, and the non-myctophid genus Bathylagus.

Major climatic changes in the Pleistocene had significant effects on marine organisms and the environments in which they lived. The presence of divergent patterns of demographic history even among phylogenetically closely-related species sharing climatic changes raises questions as to the respective influence of species-specific traits on population structure. In this work we tested whether the lifestyle of Antarctic notothenioid benthic and pelagic fish species from the Southern Ocean influenced the concerted population response to Pleistocene climatic fluctuations. This was done by a comparative analysis of sequence variation at the cyt b and S7 loci in nine newly sequenced and four re-analysed species. We found that all species underwent more or less intensive changes in population size but we also found consistent differences between demographic histories of pelagic and benthic species. Contemporary pelagic populations are significantly more genetically diverse and bear traces of older demographic expansions than less diverse benthic species that show evidence of more recent population expansions. Our findings suggest that the lifestyles of different species have strong influences on their responses to the same environmental events. Our data, in conjunction with previous studies showing a constant diversification tempo of these species during the Pleistocene, support the hypothesis that Pleistocene glaciations had a smaller effect on pelagic species than on benthic species whose survival may have relied upon ephemeral refugia in shallow shelf waters. These findings suggest that the interaction between lifestyle and environmental changes should be considered in genetic analyses.