Data stored in a Dryad package (doi:10.5061/dryad.c75sj) associated with the publication: Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples Authors: Bruce Deagle , Laurence Clarke , John Kitchener, Andrea Polanowski, Andrew Davidson. Molecular Ecology Resources. The Continuous Plankton Recorder (CPR) has been used to characterise zooplankton biodiversity along transects covering hundreds of thousands of kilometres in the Southern Ocean CPR survey. Plankton collected by the CPR is currently identified using is classical taxonomy (i.e. using a microscope and morphological features). We investigated the potential to use DNA metabarcoding (species identification from DNA mixtures using high-throughput DNA sequencing) as a tool for rapid collection of taxonomic data from CPR samples. In our study, zooplankton were collected on CPR silks along two transects between Tasmania and Macquarie Island. Plankton were identified using standard microscopic methods and by sequencing a mitochondrial COI marker. Data provided in the Dryad Data entry include the DNA sequences (Illumina MiSeq) recovered, the morphological identifications and the R-code used to analyse these data. The results from our study show that a DNA-based approach increased the number of metazoan species identified and provided high resolution taxonomy of groups problematic in conventional surveys (e.g. larval echinoderms and hydrozoans). Metabarcoding also generally produced more detections than microscopy, but this sensitivity may make cross-contamination during sampling a problem. In some samples, the prevalence of DNA from larger plankton (such as krill) masked the presence of smaller species. Overall, the genetic data represents a substantial shift in perspective, making direct integration into current long-term time-series challenging. We discuss a number of hurdles that exist for progressing this powerful DNA metabarcoding approach from the current snapshot studies to the requirements of a long-term monitoring program.

Human impacts threaten not only species, but also entire ecosystems. Ecosystems under stress can collapse or transition into different states, potentially reducing biodiversity at a variety of scales. Here we examine the vulnerability of shallow invertebrate-dominated ecosystems on polar seabeds, which may be threatened for several reasons. These unique communities consist of dark-adapted animals that rely on almost year-round sea-ice cover to create low-light shallow marine environments. Climate change is likely to cause early sea-ice break-out in some parts of Antarctica, which will dramatically increase the amount of light reaching the seabed. This will potentially result in ecological regime shifts, where invertebrate-dominated communities are replaced by macroalgal beds. Habitat for these endemic invertebrate ecosystems is globally rare, and the fragmented nature of their distribution along Antarctic coast increases their sensitivity to change. At the same time, human activities in Antarctica are concentrated in areas where these habitats occur, compounding potential impacts. While there are clear mechanisms for these threats, lack of knowledge about the current spatial distribution of these ecosystems makes it difficult to predict the extent of ecosystem loss, and the potential for recovery. In this paper we describe shallow ice-covered ecosystems, their association with the environment, and the reasons for their vulnerability. We estimate their spatial distribution around Antarctica using sea-ice and bathymetric data, and apply the IUCN Red List of Ecosystems criteria to formally assess their vulnerability. We conclude that shallow ice-covered ecosystems should be considered near threatened to vulnerable in places, although the magnitude of risk is spatially variable. This dataset comprises two files. Both are provided in netCDF format in polar stereographic project (see nc file for projection details). light_budget_6km.nc : this gives the estimated annual light budget (in mol photons/m^2/year) at the surface of the water column, having been adjusted for sea ice cover (see paper for details). This is calculated on the 6.25km grid associated with the sea ice concentration data. benthic_light_500m.nc : this gives the estimated annual light budget (in mol photons/m^2/year) at the sea floor, having been further adjusted for water depth. It is provided on a 500m grid (as per the IBCSO bathymetry used). Areas deeper than 200m are given no-data values, and areas outside of the coverage of the sea ice grid are assigned a value of -999. See paper for details.