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Habitat modelling of 'functional reef' and broad-scale ecosystem components for temperate Australian waters (NESP MaC 2.1)

This record describes the outputs of two different modelling exercises that were used to characterise the seafloor habitats for temperate Australian waters. The modelled area includes all shelf waters (<250m depth) in southern Australia south of the Tropic of Capricorn. Bioregional benthic habitat maps were constructed using (1) the Geoscience Australia 250m 2023 grid (Beaman 2023); (2) ground-truthing observations derived from horizontally facing imagery from stereo-BRUV and BOSS camera systems; and (3) several physical datasets as covariates in model development (all oceanographic variables smoothed to 250m resolution). Source data is available from Geoscience Australia's eCat: https://doi.org/10.26186/148758 (bathymetry), Squidle+: (benthic imagery annotations), and (3) AODN Portal: https://portal.aodn.org.au/search (IMOS oceanographic datasets).


The specific subset of GA observations used in this modelling exercise is available from https://github.com/UWA-Marine-Ecology-Group-projects/nesp-2.1/blob/main/data/tidy/NESP-2.1_broad-habitat.csv. See the NESP Mac Project 2.1 final report for a description of the sampling design for ground-truthing observations and annotation technique.


-----Functional Reef model (binomial)-----

This model discriminates ‘functional reef’ from sediment (non-reef) ecosystem types. Functional reef is defined by this project as “any seabed area functioning as a reef, which may include dense beds of sessile invertebrates or molluscs”. This term was chosen because much of the continental shelf is dominated by sediment yet is stable enough to support emergent sessile biota that provide structure and resources for “reef-affiliated” species. The modelling approach uses a Bayesian representation of a Binomial generalised linear model. For ground-truthing benthic annotations, the following benthic categories were collapsed into the ‘functional reef’ classification: sessile invertebrates, bare rocky reef (consolidated), macroalgae, Amphibolis spp. and Thalassodendron spp. All other benthic classifications were assigned to the ‘non-reef’ category.


-----Ecosystem Component model (multinomial)-----

This model discriminates between five broad habitat types (hereafter ‘ecosystem components’): seagrass, macroalgae, sessile invertebrates, bare consolidated substrata, bare unconsolidated substrata. The modelling approach uses a Bayesian implementation of a Multinomial generalised linear model. For ground-truthing benthic annotations, benthic annotations for mobile species (e.g. echinodermata) were discarded. All remaining annotations were collapsed into the five broad ecosystem components.


A selection of mapping (WMS) services are listed in the 'Downloads & Links' section of this record. See the 'Lineage' section for a full description of the data packages available for download, and for more visualisation options.

Simple

Identification info

Date (Creation)
2024-05-13

Identifier

Title
Information and documentation - Digital object identifier system
Citation identifier
ISO 26324:2012

Code
10.25959/BVJ7-D984
Codespace
doi.org
Description
Digital Object Identifier (DOI)

Principal investigator

Institute for Marine and Antarctic Studies - Monk, Jacquomo (Project leader)
University of Tasmania
Tasmania
Australia
ROR ID >

ORCID >

Principal investigator

Oceans Institute - Langlois, Tim (Project co-lead)
The University of Western Australia
Western Australia
Australia
ROR ID >

ORCID >

Collaborator

Oceans Institute - Spencer, Claude (Field collection)
The University of Western Australia
ROR ID >

ORCID >

Collaborator

Data61 - Wooley, Skipton (Ecosystem modelling)
CSIRO
ROR ID >

ORCID >

Contributor

Institute for Marine and Antarctic Studies - Flukes, Emma (Data processing and visualisations)
University of Tasmania
ROR ID >

ORCID >

Contributor

Oceans Institute - Gibbons, Brooke
The University of Western Australia
ROR ID >

ORCID >

Contributor

Institute for Marine and Antarctic Studies - Bastiaansen, Ashlee (Data processing)
University of Tasmania
ROR ID >

ORCID >

Contributor

Institute for Marine and Antarctic Studies - Hulls, Justin (Field collection)
University of Tasmania
ROR ID >

ORCID >

Contributor

Institute for Marine and Antarctic Studies - Lucieer, Vanessa (Expert knowledge)
University of Tasmania
ROR ID >

ORCID >

Contributor

The University of Adelaide - Grammer, Gretchen (Expert knowledge)
ROR ID >

ORCID >

Contributor

Data61 - Hayes, Keith (Modelling input)
CSIRO
ROR ID >

ORCID >

Contributor

CSIRO Environment - Dunstan, Piers (Expert input)
ROR ID >

ORCID >

Contributor

Institute for Marine and Antarctic Studies - Barrett, Neville
University of Tasmania
ROR ID >

ORCID >

Credit
National Environmental Science Program (NESP) Marine and Coastal Hub
Credit
Department of Climate Change, Energy, the Environment and Water (DCCEEW), Australian Government
Credit
In addition to NESP (DCCEEW) funding, this project is matched by an equivalent amount of in-kind support and co-investment from project partners and collaborators.
Status
complete

Point of contact

Institute for Marine and Antarctic Studies - Monk, Jacquomo (Project leader)
Tasmania
Australia
ROR ID >

ORCID ID >

Point of contact

Oceans Institute - Langlois, Tim (Project co-lead)
The University of Western Australia
Western Australia
Australia
ROR ID >

ORCID ID >

Topic category
  • Biota
  • Environment

Extent



Temporal extent

Time period
2020-01-01 2024-04-30

Vertical element

Minimum value
10
Maximum value
250
Identifier
EPSG::5715
Name
MSL depth
Maintenance and update frequency
none-planned

Resource format

Date
Keywords (Theme)
  • National Environmental Science Program (NESP) Marine and Coastal Hub
NASA/GCMD Keywords, Version 8.5
  • KELP FOREST
  • SPONGES
  • MACROALGAE (SEAWEEDS)
  • SEAGRASS
  • BENTHIC
  • MARINE ECOSYSTEMS
  • DIGITAL ELEVATION/TERRAIN MODEL (DEM)
Australian and New Zealand Standard Research Classification (ANZSRC): Fields of Research
  • Conservation and Biodiversity
  • Environmental Science and Management not elsewhere classified
  • Marine and Estuarine Ecology (incl. Marine Ichthyology)

Resource constraints

Classification
Unclassified

Resource constraints

Linkage
http://i.creativecommons.org/l/by/4.0/88x31.png

License Graphic

Title
Creative Commons Attribution 4.0 International License


>

Website
http://creativecommons.org/licenses/by/4.0/

License Text

Other constraints
Cite data as: Monk, J., Langlois, T., Spencer, C., Woolley, S., Flukes, E., Gibbons, B., Bastiaansen, A., Hulls, J., Lucieer, V., Grammer, G., Hayes, K., Dunstan, P., & Barrett, N. (2024). Habitat modelling of 'functional reef' and broad-scale ecosystem components for temperate Australian waters [Data set]. Institute for Marine and Antarctic Studies & NESP Marine and Coastal Hub. https://doi.org/10.25959/BVJ7-D984

Resource constraints

Other constraints
This dataset is hosted by the Institute for Marine and Antarctic Studies (IMAS), University of Tasmania, on behalf NESP Marine and Coastal Hub Project 2.1.

Resource constraints

Use limitation
Data was sourced from the NESP Marine and Coastal Hub – the Marine and Coastal Hub is supported through funding from the Australian Government’s National Environmental Science Program (NESP), administered by the Department of Climate Change, Energy, the Environment and Water (DCCEEW).
Language
English
Character encoding
UTF8

Distribution Information

Distribution format
  • GeoTIFF

OnLine resource
DATA ACCESS - Explore and individually download individual data files, ReadMe etc.

OnLine resource
DATA ACCESS - Full data package (.zip of above)

OnLine resource
View & explore Functional Reef model outputs in Seamap Australia

OnLine resource
View & explore Ecosystem Component model outputs in Seamap Australia

Additional outputs available under Seafloor Habitat > Predicted Habitats > Bivariate probability..., or search for 'bivariate probability'

OnLine resource
Reproducible code for synthesising and categorising benthic annotations

OnLine resource
Project page on NESP Marine and Coastal Hub website

OnLine resource
TemperateAus_broadscale_predArea_binomial_reef

MAP - Functional Reef mean prediction

OnLine resource
TemperateAus_binomial_predicted_reef_ERROR

MAP - Functional Reef bivariate probability

OnLine resource
TemperateAus_broadscale_predArea_bivariateProb_reef

MAP - Functional Reef bivariate probability of occurrence

OnLine resource
TemperateAus_broadscale_predArea_multinomial_habitat

MAP - Ecosystem Components mean prediction [combination view]

OnLine resource
TemperateAus_broadscale_predArea_bivariateProb_sessile_inverts

MAP - Sessile Invertebrates bivariate probability of occurrence

OnLine resource
TemperateAus_broadscale_predArea_bivariateProb_seagrass

MAP - Seagrass bivariate probability of occurrence

OnLine resource
TemperateAus_broadscale_predArea_bivariateProb_macroalgae

MAP - Macroalgae bivariate probability of occurrence

OnLine resource
TemperateAus_broadscale_predArea_bivariateProb_consolidated

MAP - Bare Consolidated (bare rocky reef) bivariate probability of occurrence

OnLine resource
TemperateAus_broadscale_predArea_bivariateProb_unconsolidated

MAP - Bare Unconsolidated (bare sediment) bivariate probability of occurrence

Resource lineage

Statement
See NESP Marine and Coastal Project 2.1 final report for a full for a description of the sampling design, annotation technique, and modelling approach. A key objective of this modelling approach was to effectively report the spatial uncertainty associated with model predictions to assist with conservation and management assessments. The outputs from both the Functional Reef and Ecosystem Component models is presented in two alternative ways. VISUALISATION OPTION #1 The first approach presents model outputs as a map of the mean probability of occurrence for reef or each ecosystem class, with uncertainty (inter-quartile range (IQR) error of prediction) shown as a separate map that can be viewed in parallel. The data packages for both the binomial reef and multinomial ecosystem models contain ReadMe files describing the data structure: -----Functional Reef (binomial)----- https://data.imas.utas.edu.au/attachments/seamap_predicted_habitat/temperate_aus/model_outputs/reef_binomial/ProbabilityOfOccurrence -----Ecosystem Components (multinomial)----- https://data.imas.utas.edu.au/attachments/seamap_predicted_habitat/temperate_aus/model_outputs/ecosystemComponents_multinomial/ProbabilityOfOccurrence VISUALISATION OPTION #2 The second uncertainty mapping approach reports a map of the expected probability of occurrence (mean prediction) combined with the IQR error of prediction in a single raster, where each combination of mean x error (10 error quantiles x 10 mean quantiles = 100 unique raster values) is plotted along a bivariate colour gradient. The colour scales are shown on two axes, with y showing the probability of occurrence (or “likelihood”) and x representing the error in those predictions (or “(un)certainty”). The data package for both the binomial reef and multinomial ecosystem models contain ReadMe files describing the data structure: -----Functional Reef (binomial)----- https://data.imas.utas.edu.au/attachments/seamap_predicted_habitat/temperate_aus/model_outputs/reef_binomial/BivariateUncertainty -----Ecosystem Components (multinomial)----- https://data.imas.utas.edu.au/attachments/seamap_predicted_habitat/temperate_aus/model_outputs/ecosystemComponents_multinomial/BivariateUncertainty
Hierarchy level
Dataset

Metadata

Metadata identifier
urn:uuid/b349c610-32c5-4574-ae8e-43cbf204e8bc

Language
English
Character encoding
UTF8

Point of contact

Institute for Marine and Antarctic Studies (IMAS), University of Tasmania (UTAS) - Emma Flukes (NESP Marine and Coastal Hub Data Manager (Southern node))
Parent metadata
  • NESP MaC Project 2.1 - Mapping temperate continental shelf seabed habitats

Type of resource

Resource scope
Dataset
Metadata linkage
https://metadata.imas.utas.edu.au/geonetwork/srv/eng/catalog.search#/metadata/b349c610-32c5-4574-ae8e-43cbf204e8bc

Point of truth URL of this metadata record

Date info (Creation)
2024-05-13T11:44:25
Date info (Revision)
2025-04-04T21:26:39

Metadata standard

Title
ISO 19115-3:2018
 
 

Overviews

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Spatial extent

Keywords

National Environmental Science Program (NESP) Marine and Coastal Hub
Australian and New Zealand Standard Research Classification (ANZSRC): Fields of Research
Conservation and Biodiversity Environmental Science and Management not elsewhere classified Marine and Estuarine Ecology (incl. Marine Ichthyology)
NASA/GCMD Keywords, Version 8.5
BENTHIC DIGITAL ELEVATION/TERRAIN MODEL (DEM) KELP FOREST MACROALGAE (SEAWEEDS) MARINE ECOSYSTEMS SEAGRASS SPONGES

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Read here the full details and access to the data.

Associated resources

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