AndreaBozzo/ceres-open-data-index huggingface dataset:
NERP TE Project 3.2 - What is a risk? Identifying rainforest refugia and hotspots of plant genetic diversity in the Wet Tropics and Cape York Peninsula, 2011-2014 (JCU)

This project will map the genetic and phylogenetic diversity of northeast Queensland rainforest plants and fungi with a focus on the mountaintop species, which are regarded as among the most at risk from climate warming. The project consists of two nested subprojects. 

Project ‘a’ (PD analysis) will provide a broad scale analysis of patterns of genetic diversity across the NE Qld rainforests. This study will investigate the relative performance of taxonomic richness and phylogenetic diversity measures for conservation priority setting in the Wet Tropics and Cape York rainforest contexts. We will use the results to identify and map areas of high biodiversity significance and investigate correlations with environmental and ecological variables. Preliminary results to date show that areas with higher PD than expected contain a higher proportion of immigrant plant lineages dispersed mostly from Southeast Asia within the past few million years. Our results demonstrate how the integration of historical data and PD can more effectively inform conservation priority setting particularly in biomes with complex evolutionary histories. 

Project ‘b’ (mountain-top diversity) takes a finer scale look at population-level genetic diversity in one highly restricted rainforest ecosystem – mountain-top rainforest – projected to be most threatened by climate change. We will combine emerging genetic technologies with environmental, ecological and morphological information to: 1) elucidate the location and relative importance of high altitude refugia for plants in the Wet Tropics and Cape York Peninsula Bioregions and the mechanisms that influence the survival of populations and species; and 2) document the fungal biodiversity of the mountain tops.

Tags: National Environmental Research Program Tropical Ecosystems Hub, marine
Organization: Australian Ocean Data Network
Temperate Australian quantitative spatial and temporal abundance data for rocky reef biota (biodiversity): long-term Tasmanian MPAs - Tinderbox

The data is quantitative abundance of fish and megafaunal invertebrates and algal % cover derived from transect based counts at a wide range of locations across Temperate Australia. The methods are described in detail in Edgar and Barrett (1997). Primarily the data are derived from transects at 5 m depth and/or 10 m depth at each site surveyed. Methods were initially developed for research on temporal changes following protection in Tasmanian long-term MPAs (Maria Is, Tinderbox, Ninepin Point, Governor Island), and the data represented by this record has been collected at Tinderbox. 

In many cases the dataset involves temporal replication (year scale), particularly for the core Tasmanian MPAs represented by this record.

Tags: Abundance - fish, Abundance - invertebrates, Carapace length - rock lobster, Fish size class, Percentage cover algal species, Shell length - abalone
Organization: Australian Ocean Data Network
IMOS - National Reef Monitoring Network Sub-Facility - Image Annotation Protocol Manual

Various methods in image annotation are possible, this protocol provides a method of producing standardised habitat cover data compatible with previous work. This allows data synthesis over broad scales, contributing to downstream platforms for reef reporting, such as the Reef Life Explorer, and enhancing the Findability, Accessibility, Interoperability and Reusability (FAIR) of data.

This document forms part of the National Reef Monitoring Network Sub-Facility data. The National Reef Monitoring Network provides publicly accessible data for shallow reef biodiversity on a global scale, integrating high quality compatible data from long-term scientific monitoring programs and citizen science programs globally.

Organization: Australian Ocean Data Network
Spatial distribution of killer whales (Orcinus orca) in the Bremer Marine Park and adjacent areas (NESP Emerging Priorities EP2)

This dataset relates to statistical models of killer whale (Orcinus orca) occurrence in the Bremer Sub-Basin developed from vessel-based and aerial survey data collected  between 2015 and 2017.

Further information can be found in:
Salgado-Kent C, Parnum I, Wellard R, Erbe C, Fouda L. 2017. Habitat preferences and distribution of killer whales (Orcinus orca) in the Bremer Sub-Basin, Australia. Report to the National Environmental Science Programme Marine Biodiversity Hub (CMST 2017-15), 37 p.

Tags: Killer whale, Orcinus orca
Organization: Australian Ocean Data Network
NESP MB Project D3 - Implementing monitoring of AMPs and the status of marine biodiversity assets on the continental shelf

This record provides an overview of the scope and research output of NESP Marine Biodiversity Hub Project D3 - "Implementing monitoring of AMPs and the status of marine biodiversity assets on the continental shelf". For specific data outputs from this project, please see child records associated with this metadata.



There is a significant need to support Parks Australia in the establishment of an inventory and monitoring program for Australian Marine Park (AMP) networks, and ensure it is integrated within broader national monitoring frameworks.

The first part of this project provided a national collation all known mapping data from government and industry (including data acquired during CERF and NERP Hubs) to improve understanding of the distribution and extent of this key habitat around Australia, and to identify critical gaps in this knowledge to be filled by targeted surveys. This significantly improved understanding of KEF boundaries and conservation values or assets within Commonwealth Marine Reserves on Australia’s continental shelf. A classification system was developed for these reefs, and matched with refinement of inventory and monitoring approaches to track reef health through time, including standard approaches to SOE understanding and reporting consistent with measures developed for coastal systems within NESP (i.e. see project C2). This also involved collation of all mapping data on non-reef hard substrate, and all non-reef soft substrate, with this information also being available as a significant output.

The second part of this project initiates a series of surveys, utilising standard operating procedures (SOPs), to demonstrate a sustainable path for a national survey program. By facilitating national approaches, including a standards-based approach to collecting new marine data, project outcomes will include key steps to assist Parks Australia to implement and initiate an AMP monitoring program, new knowledge to inform AMP management, a national integrated framework for State of Environment (SOE) reporting, and collaboration between State-based and Commonwealth-based programs. 

Planned Outputs
• National-scale map of the distribution and extent of reef/non-reef habitat on the Aus continental shelf
• Collation of all available mapping data for the Aus continental shelf
• Detailed reports specific to each AMP survey, including a plain English summary
• Survey data stored in national databases and portals
• New multibeam mapping data from AMP survey areas and adjacent waters 
• New data on benthic invertebrate cover obtained from AUV imagery surveys
• New data on benthic fish abundance obtained by BRUV surveys

Tags: Commonwealth Marine Reserve (CMR), Conservation and Biodiversity, Key Ecological Feature (KEF), Marine and Estuarine Ecology (incl. Marine Ichthyology), National Environmental Science Program (NESP) Marine Biodiversity Hub, Natural Resource Management, biodiversity, monitoring, rocky reef
Organization: Australian Ocean Data Network
Fast Repetition Rate Fluorometry (FRRF) data collected on the RV L'Astrolabe from 14/01/2007 to 19/01/2007 (Hobart - Dumont d'Urville)

These data were collected on the RV L'Astrolabe (platform code: FHZI) from 14/01/2007 to 19/01/2007 on a trip from Hobart to Dumont D'Urville.

Maximum photochemical efficiency of photosystem II (PSII), also called maximum quantum yield of PSII (Fv/Fm), has become one of the most widely utilized fluorescence parameters in phytoplankton research. It represents the potential photochemical efficiency, which is the probability that the light energy captured by the photosynthetic apparatus is being utilized as photochemistry. Fv/Fm has been shown to have an instant response to variations in physical and chemical properties and is interpreted as a diagnostic of the overall health or competence of phytoplankton. Together with the absorption cross section area of PSII and chlorophyll concentration, it can be used to measure primary production (Cheah et al. 2011, Deep Sea Research).

Seawater from 3 m depth was supplied continuously from the ship’s clean seawater line. FRR fluorescence yields were measured continuously at 1 minute intervals in dark-adapted state (! 15 minutes dark-adaptation) using a flash sequence consisting of a series of 100 subsaturation flashlets (1.1 μs flash duration and 2.8 μs interflash period) and a series of 20 relaxation flashlets (1.1 μs flash duration and 51.6 μs interflash period).

Tags: Continents | Antarctica, Countries | Australia, Fast Repetition Rate Fluorometer (FRRF), Global/Oceans | Southern Ocean, Instrument's photomultiplier electronic sensitivity (1-256), Latitude, Longitude, Maximum quantum yield (Fv/Fm), Minimum fluorescence in the light chamber of the FRRF (also used as a proxy for biomass), Oceans | Ocean Temperature | Sea Surface Temperature, Oceans | Salinity/density | Salinity, Photosynthesis, connectivity between PSII reaction centres under actinic light, functional absorption cross section of PSII (measure of the proportion of light harvested for photoc, maximum fluorescence in the light chamber of the FRRF, maximum quantum yield of photosystem II ( (FmL - FoL) / FmL), primary production, time constant of electron transport from PSII to PSI, variable fluorescence (FmL - FoL)
Organization: Australian Ocean Data Network
Management options to minimise formation of urchin barrens: using belt transect surveys to monitor benthic community structure

Belt transect surveys (50m) were used to monitor the benthic community structure through time at experimental (lobster additions/ research reserve sites or abalone diver urchin culls) and control sites in eastern Tasmania. Measures of percentage cover of key algal guilds, percentage of reef grazed by sea urchins, number of sea urchins (Centrostephanus rodgersii, Heliocidaris erythrogramma), Abalone (Haliotis Rubra), Rock lobsters (Jasus edwardsii) and type of substratum were recorded.

Tags: Algal coverage, Centrostephanus rodgersii, Coverage of urchin barrens, Ecklonia radiata, Haliotis rubra, Heliocidaris erythrogramma, Jasus edwardsii, Jasus edwardsii (rock lobster) carapace length, Macrocystis pyrifera, Phyllospora comosa, Temperate Reef, Urchin barrens, coverage
Organization: Australian Ocean Data Network
Surveys to locate juvenile crown-of-thorns starfish (Acanthaster planci) on the Great Barrier Reef

In 1989, reefs in the central GBR were surveyed to locate high density populations of larger (5-15 cm) juvenile crown-of-thorns starfish (Acanthaster planci). Preliminary surveys were undertaken at two inshore reefs (Hayman Island and Reef No. 20-019) in October 1989. During November 1989, searches were carried out at different depths at 45 sites on 12 reefs. The reefs surveyed were 19-123, 19-124, 19-131, 19-138, Bait, Bowden, Davies, Hope, Little, Oublier, Rafter and Stanley.All reefs surveyed were relatively small and had supported large numbers of starfish during the 1970s. At the time of survey they either supported large numbers of adult starfish or were located immediately to the south of the main concentration of reefs with outbreaks. A range of reef types across the continental shelf were surveyed. The perimeter of each reef was surveyed by manta tow to identify sites with relatively high live coral cover and small areas of dead coral then 3 or 6 sites were selected for more intensive SCUBA swim searches.SCUBA searches were undertaken by divers along 4 depth contours at each site: reef crest/flat, 5m, 10m and 15m. Where this was impractical, the divers swam parallel to each other and covered the maximum practical depth range between the crest and the base of the reef slope. The four divers swam slowly along their respective depth contours for a set period of twenty minutes, covering a distance of approximately 100m. Whilst swimming, each diver scanned approximately 1m either side of the swim path looking for any small starfish or evidence of their presence. All small areas of recently dead coral were closely examined and if no starfish were found, then an attempt was made to determine the cause of mortality. The following observations were recorded during each 20 minute swim search: number of adult crown-of-thorns starfish, number and size of juvenile (Additional dives were undertaken at night on Stanley and Bait Reefs, in areas where numerous small coral scars had been recorded during the day. These involved 5 divers who searched for juveniles within an area approximately 100x50m, over a 90 minute period.
 Surveys were undertaken to locate high density populations of juvenile crown-of-thorns starfish (Acanthaster planci), which could be used in further studies of recruitment, predation and population dynamics of the juvenile stage this starfish.
 Only 14 juvenile starfish were found in the 1989 survey.Observations have been expanded since 1989 and some aspects have been incorporated into the ongoing AIMS Long Term Monitoring Program - refer to the separate metadata record on 'Agents of coral mortality'.

Organization: Australian Ocean Data Network
Seafloor bathymetry of the Gifford Marine Park

Flythrough movie of Gifford Marine Park, which is located 700 km east of Brisbane, Australia. The park is situated about halfway along the Lord Howe Rise seamount chain on the western flank of the Lord Howe Rise. Seamounts along this chain formed from Miocene volcanism via a migrating magma source (“hotspot”) after the opening of the Tasman Sea. Two large, flat-topped volcanic seamounts dominate the park. Their gently sloping summits have accumulated veneers of sediment, which in places have formed fields of bedforms. Steep cliffs, debris and large mass movement scars encircle each seamount, and contrast with the lower gradient abyssal plains from which they rise. Spanning over 3 km of ocean depths, the seamounts are likely to serve multiple and important roles as breeding locations, resting areas, navigational landmarks or supplementary feeding grounds for some cetaceans (e.g. humpback whales, sperm whales). They may also act as important aggregation points for other highly migratory pelagic species. The bathymetry shown here was collected on two surveys - the first in 2007 by Geoscience Australia and the second in 2017 by Geoscience Australia in collaboration with the Japan Agency for Marine-Earth Science and Technology. The Gifford Marine Park has also been the focus of a study undertaken by the Marine Biodiversity Hub as part of the National Environmental Science Program.
This research is supported by the National Environmental Science Program (NESP) Marine Biodiversity Hub through Project D1.

Tags: Marine Biodiversity Hub, National Environmental Science Program, Published_External, biodiversity, geomorphology, marine
Organization: Australian Ocean Data Network
Mangroves of North-western Australia mapped with multi-dimensional space–time remote sensing (ICoAST)

Mangroves are a globally important ecosystem subject to significant anthropogenic and climate impacts. Tidally submerged forests and those that occur in arid and semi-arid regions are particularly susceptible to sea level rise or are growing at the margins of their their ecophysiological limits. The spatial extent of these types of mangroves over broad scales are typically poorly documented as their structural and environmental characteristics make them difficult to detect using remote sensing models.

This study utilised the entire Landsat 8 satellite collection between January 2014 and June 2021. A new cloud-based time-series method was used that accounts for tidal variance in detecting mangrove areas that are periodically inundated and have historically been difficult to detect with traditional remote sensing methods. A habitat area model was derived for remote North-western Australia and detected an additional 32% (76,048 hectares) of mangroves that were previously undocumented. The accuracy of the model was assessed within the distinct geomorphic zones of the region through visual validation from high-resolution imagery.

See accompanying report for full methodology:
Hickey, S.M.; Radford, B. Turning the Tide on Mapping Marginal Mangroves with Multi-Dimensional Space–Time Remote Sensing. Remote Sens. 2022, 14, x. https://doi.org/10.3390/rs14143365

Tags: Great Barrier Reef, Landsat, benthic habitat, mangrove habitat, remote sensing
Organization: Australian Ocean Data Network
Fish and benthic surveys around remote Timor Sea Shoals, using baited remote underwater video stations (BRUVS) (TM)

BRUVS (TM) were deployed in 3 depth zones, 20-30 m, 40-60 m and 90-110 m at 3 shoals near Evans Shoal, 6 Karmt shoals and 6 Sahul shoals as well as 4 adjacent sites in 96-100 m on the shelf in the Timor Sea. A series of 6 BRUVS (TM) were set in a line at each site and depth.Sampling positions, depth, time and associated operational data were secured at the time of deployment. The parameters recorded during the tape reading process were:- classification of the habitat (a still image is grabbed for each set)- identification to species level of all vertebrates observed (following the CAABCodes Australian standard naming convention)- the relative abundance of each species (recorded as 'maxN' - the maximum number visible at one time at any point on the tape)- the 'time of arrival' (Tarr) of each fish species- the life stage of each species (adult or juvenile)- the time elapsed before maxN (TmaxN) and feeding (Tf) was observed for each species
 The purpose of this project was to record the fish, shark, ray and sea snake faunas, and associated benthic habitats, of the major clusters of Timor Sea shoals at 3 depth zones, 20-30 m, 40-60 m and 90-110 m.
 Towed camera footage was also recorded in the areas where BRUVS (TM) were deployed.

Organization: Australian Ocean Data Network
Seafloor bathymetry of the Gascoyne Marine Park

This flythrough highlights canyon environments within the Gascoyne Marine Park offshore northwestern Australia. The Cape Range Canyon is a relatively narrow, linear canyon that initiates on the continental slope, but is connected to the shelf via a narrow channel. The walls of the canyon are steep and reveal a history of slumping and retrogressive failure, that have broadened the canyon over time. The floor contains a series of deep plunge pools, indicative of the action of sediment-laden turbidity currents in further eroding this canyon. 
Epibenthos within the canyons was relatively sparse and likely regulated by disturbance associated with sedimentation in the canyons. Rock overhangs often supported the highest densities of benthic suspension feeders, including glass sponges, octocorals, and ascidians. 
Bathymetry data and seafloor imagery for this flythrough was collected by the Schmidt Ocean Institute during survey FK200308. Funding was provided by Schmidt Ocean Institute, Geoscience Australia, the Australian Government’s National Environmental Science Program (NESP) Marine Biodiversity Hub, the Director of National Parks, and the Foundation for the WA Museum through a Woodside Marine Biodiversity Grant.

Tags: Bathymetric grids, Bathymetry, EARTH SCIENCES, Geomorphology and Regolith and Landscape Evolution, Marine, Multibeam, Published_External
Organization: Australian Ocean Data Network
Assessing the effects of changes in Great Barrier Reef Marine Park Zoning plans on southern mid-shelf shoals using towed video (Towvid) (MTSRF Project 4.8.2)

Towed video (Towvid) surveys were undertaken in February/March 2007 and August/September 2007 on two pairs of discrete deepwater shoals in the mid-shelf section of the southern Great Barrier Reef. Within each pair, one shoal was from a 'green zone' (closed to all fishing) and the other from a 'blue zone' (open to fishing), based on the rezoning of the Great Barrier Reef Marine Park, carried out in 2004. The pairs of reefs chosen were: East Warregos (green) and West Warregos (blue); Barcoo Bank (green) and Karamea Bank (blue). A lightweight towed video system developed by AIMS was used to survey seabed habitats on and around the four shoal sites. The camera was deployed and towed from the stern of RV Cape Ferguson while maintaining a speed of approximately two to three knots. During camera deployment an observer used custom software developed for use with the towed video system to conduct a real-time seabed classification based on biotic and abiotic habitat components. The classification data was logged simultaneously with GPS position, depth sounder data and time. The resultant habitat observations were thus geo-referenced for later spatial analysis.
 Towed video surveys were undertaken to characterise the habitat on features identified from the digital terrain models produced from multibeam acoustic mapping, as likely productive fish habitat. This information was then used to determine placement of BRUVS (TM).
 This is one component of a series of surveys conducted as part of this MTSRF project, see also separate metadata records on:Reef base shoals (Capricorn-Bunker, Pompey and Swains Groups) Shoals off Cardwell Shoals off Cairns Magnetic Shoals (Townsville)

Organization: Australian Ocean Data Network
Coral Sea - Fregetta Seamount - Geomorphology and Surface Classification

Voyage IN2019_V04 contributed an additional 29,000 kms2 of seafloor survey data to the Coral Sea knowledge base. From this new bathymetric data individual seamounts have been extracted and have been classified to the Geoscience Australia Geomorphology Classification Scheme. This dataset contains two layers representing the classification layers- 1) Surface (Plain, Slope, Escarpment) and 2) fine scale Geomorphology of the seamount for the Fregetta Seamount.
Ongoing research with this survey data will provide new insights into the detailed geomorphic shape and spatial relationships between adjacent seabed features. This information will be released in future publications to show the potential of how the scale of such seafloor data can be used for predictive habitat modelling when analysed with the biological data overlays.

Organization: Australian Ocean Data Network
NERP TE Project 6.2 - Drivers of juvenile shark biodiversity and abundance in inshore ecosystems of the Great Barrier Reef, 2011-2014 (JCU)

Sharks play an important role in marine ecosystems but are facing increasing pressure from fishing and other anthropogenic factors. Along the Queensland coast inshore waters play an important role as nursery areas for sharks. However, the same inshore waters are also most prone to fisheries exploitation and effects of freshwater discharge from coastal streams and rivers. This project will examine the importance of different types of inshore habitat (protected bay vs. open coastline) and marine park zoning (open and closed to fishing), and how environmental factors such as freshwater discharge from rivers effect how these nursery areas function. The project has two broad objectives:

A. Investigate the spatial and temporal changes in the biodiversity and abundance of sharks in inshore nursery areas along the central GBR coast.
B. Determine the effect of environmental drivers on inshore shark biodiversity along the central GBR coast.

Results from the project will be used to improve the information available to fisheries and marine park managers on the relative importance of inshore habitats, the role of areas closed to fishing, and the sustainability of inshore shark populations.

Tags: National Environmental Research Program Tropical Ecosystems Hub, marine
Organization: Australian Ocean Data Network