Habitats serve a variety of functions on the North West Shelf (NWS). They support the life history stages of a diverse suite of tropical species including commercially harvested ones. In addition to natural disturbance regimes, habitats are altered in response to the sectoral uses, which in turn affects the distribution and life histories of species. Habitats thus serve as the nexus linking species with uses and natural disturbance, and different habitats serve different purposes at various stages of the life history of a species. A detailed understanding of habitats, at least at the structural level, is thus a prerequisite for a more comprehensive understanding of ecological structure and functions on the North West Shelf. This component of the North West Shelf Joint Environmental Management Study (NWSJEMS) aimed to collate and integrate data on habitats for the region of the North West Shelf extending from North West Cape to Port Hedland and from the coast to the 200 m isobath. The three main activities of the study were: Development of an integrated collection of information on habitats of the North West Shelf, including expert information; Application of the CSIRO Habitat Classification Framework to the data to determine the spatial nesting and structuring of habitat units on the North West Shelf; and Provision of the habitat structure classification for input into other models developed within NWSJEMS. This record describes data of key benthic marine ecosystems and habitats. These maps and descriptions of their component attributes were designed to assist the process modelling of the ecosystem and impacts of uses, as well as directly supporting planning and management by Western Australian agencies and industries.

As management of marine living resource moves beyond simple single species resource utilisation concerns to ecosystem-based management, consideration of habitat dynamics is becoming an integral part of marine resource management. Previous studies have found that habitat can play a critical role in both single species and community level dynamics of species of commercial concern (Sainsbury, 1987; Sainsbury, 1988; Auster & Malatesta, 1995; Freese et al. 1999; Lindholm et al. 1999; Jackson et al. 2000; Sainsbury et al. 2000). Moreover, benthic habitat is becoming a conservation concern in its own right (Environment Protection and Biodiversity Conservation Act 1999). Useful first steps in understanding local benthic habitat dynamics is to collect observation (preferably through time) of the benthos and then to attempt to create dynamic models that capture the broadscale dynamics of the habitat of interest. Just such an exercise was undertaken for the major benthic habitat types in the North West Shelf of Australia (specifically epibenthic, mainly sponge, habitats, seagrass, macroalgae and mangroves). Between 1983 and 1997 photographic data on benthic habitats were collected on the North West Shelf of Australia by CSIRO Marine Research. These data were used to calculate proportional coverage of small (<25 cm) and large (>25 cm) epibenthos on the seabed between depths of 20 and 200 m. These observations and the fisheries effort data for the Taiwanese (1973 to 1981) and domestic fleets (1987 to 1997) were pooled onto a spatial grid of 10 by 10 nautical minutes with a temporal scale of a year. A multivariate analysis of the main factors associated with the distribution of the benthic habitats was undertaken (as a guide for factors to include in the final habitat dynamics model). The observations suggested that there was a strong depth-dependent gradient in the biomass and coverage of benthic habitat, which did not appear to be related to bottom stress, but may have been associated with sediment substrate properties. Given the importance of bottom stress in shaping benthic habitats in many other locations around Australia (Pitcher et al. 2002; Pitcher et al. 2004a; Pitcher et al. 2004b and Phillip England, CSIRO Marine and Atmospheric Research, pers. comm.) it is surprising that the analyses showed it to be a non-significant physical factor in determining proportional coverage on the North West Shelf (NWS). During the model development phase of the study a dynamic age-structured metapopulation model was created. This habitat model includes depth and substrate dependent recruitment, growth natural mortality and removal rates by fishing and cyclones. The parameters used in this model were either taken from literature or estimated by minimising the sum of squares between the observed and estimated proportional coverage. The model results easily reproduced the observed patterns of strongly depth related recruitment. It also showed that trawl fishing effort (both by Taiwanese and domestic fleets) was probably a significant factor in shaping the current distribution of benthic habitats on the NWS. There were issues with the models ability to predict recovery rates that match the empirical data. This is almost undoubtedly the result of poorly spatially resolved historical catch time series and a too coarse model resolution. Recasting future analyses and modelling efforts on finer (or more irregular) grids should go a long way to rectifying these issues. Nevertheless, even as is, the model still performs acceptably, particularly within an MSE framework. The bulk of the data (and subsequent modelling efforts) dealt with epibenthic (mainly sponge) habitats. The same model was also applied (in a more limited extent) to seagrass, macroalgae and mangroves. There was substantially less data available for these groups and the models were parameterised from the literature and expert knowledge.

The high-level objective of Project 2 was to develop a range of interlinked models of the North West Shelf ecosystem which provide: An understanding of the links between the physical, chemical and biological environments, particularly with respect to primary producers, key species and habitat types; Predictions of the ecosystem response to natural forcing, including seasonal and interannual variability; Predictions of the effects of selected human uses on conservation and other values of the ecosystem, suitable for use in management strategy evaluation and risk assessment; and Identification of environmental quality indicators suitable for monitoring and use in adaptive management. Objectives of Task 2.6 (Trophic modelling) was: Evaluate spatial patterns of fishery production for the main commercial and recreational species, as well as their relationships with spatial patterns of physical variables, nutrients, primary and secondary production, and benthic habitat types. Provide coarse level trophic models support major trophic guilds involved with fishery production. Provide prediction of the impacts of management zoning and fishery targeting on fishery production by major guilds. 1. Prototype fisheries production and trophic models implemented for the coastal region from Exmouth to Port Hedland. 2. Fisheries production and trophic models implemented for the coastal region from Exmouth to Port Hedland. 3. Maps of fishery production and spatial distributions of relative abundance of key commercial fisheries, including relationships with physical factors, primary production, and benthic habitat types (used in Tasks 1.2, 1.3, 2.7, 4.2, 5.1, 5.2, 5.3 and by management agencies). 4. Food web diagrams indicating main trophic interactions and dynamical food web models for the region, including time series of biomass for the main trophic guilds (used in Tasks 1.2, 1.3, 2.7, 5.3, 5.4 and by management agencies). 5. Written report on Fishery Production and Links to Habitats and Food Web Dynamics including model documentation. 2 This report represents the food web dynamics component of these deliverables, i.e. the trophodynamics model implemented for the region from Exmouth Gulf to Port Hedland, food web diagrams, a dynamical food web model for the region including a time series of biomass for the main trophic guilds, and a written report on food web dynamics and model documentation.

The benthic habitats represented in the MSE include continental shelf seabed habitats, coastal seagrass meadows and mangrove forests. A metapopulation model was used. Due to availability of historical data, models were most fully developed for the continental shelf seabed habitats. Parameter values for the remaining habitat types were derived from available NWS data and scientific literature. Historical extent data was augmented by personal communication through workshops and interviews with residents, divers and scientists with long term NWS experience. Each of the habitat types was modelled using the benthic agent model structure.

The NISB Habitat Map was created by the University of Tasmania for a partnership between the Department of Climate Change and the National Land and Water Resources Audit. It supports the DCC/Audit partnership by providing a nationally consistent set of the available mapping data for those habitats that occur between the approximate position of the highest astronomical tide mark (HAT) and the location of the outer limit of the photic benthic zone (approximately at the 50-70 m depth contour). This area is broadly equivalent to the 'inner' and 'mid-shelf' regions identified by Geoscience Australia. The resulting map data set forms a core component of the ECM National Habitat Map Series. The habitat classes include: coral reef, rock dominated habitat, sediment dominated habitat, mangroves, saltmarsh, seagrass, macroalgae and filter feeders (e.g. sponges), as defined in the NISB Habitat Classification Scheme. The scheme is designed to support the development of marine 'ecoregions' or bioregional subregions. Details of the scheme and the process of its development are available in National Intertidal/Subtidal Benthic (NISB) Habitat Classification Scheme Version 1 (Mount, Bricher and Newton, 2007). The NISB Habitat Map consists of two layers for each state. _NISB.shp consists of the entire available habitat mapping at a resolution finer than 1:50 000 (with a few exceptions, outlined in the data quality section below). _NISB_PLUS.shp consists of all the data in _NISB.shp along with coarser resolution data, including NVIS and OzEstuaries data. These layers were used to produce the National ECM Key Habitat Distribution Map Series 10 km and 50 km tile maps. Note: This data is labelled as “NISB_plus”, indicating that it is the NISB Habitat layer plus other lower quality layers.

The North-west Bioregional Profile identifies a number of ecological features that are of conservation value because of the role they play in the environment of the North-west Marine Region. Key ecological features (KEFs) meet one or more of the following criteria: a species, group of species, or a community with a regionally important ecological role (e.g. a predator, prey that affects a large biomass or number of other marine species); a species, group of species, or a community that is nationally or regionally important for biodiversity; an area or habitat that is nationally or regionally important for: a) enhanced or high productivity (such as predictable upwellings - an upwelling occurs when cold nutrient-rich waters from the bottom of the ocean rise to the surface); b) aggregations of marine life (such as feeding, resting, breeding or nursery areas); c) biodiversity and endemism (species which only occur in a specific area); or a unique seafloor feature, with known or presumed ecological properties of regional significance. KEFs have been identified by the Australian Government on the basis of advice from scientists about the ecological processes and characteristics of the area. A workshop held in Perth in September 2007 also contributed to this scientific advice and helped to underpin the identification of key ecological features. Thirteen KEFs have been identified in the North-west Marine Region: Ancient coastline at 125 m depth contour Ashmore Reef and Cartier Island and surrounding Commonwealth waters Canyons linking the Argo Abyssal Plain and Scott Plateau Canyons linking the Cuvier Abyssal Plain and the Cape Range Peninsula Carbonate bank and terrace system of the Sahul Shelf Commonwealth waters adjacent to Ningaloo Reef Continental Slope Demersal Fish Communities Exmouth Plateau Glomar Shoals Mermaid Reed and Commonwealth waters surrounding the Rowley Shoals Pinnacles of the Bonaparte Basin Seringapatam Reef and Commonwealth waters in the Scott Reef Complex Wallaby Saddle In order to create a spatial representation of KEFs for the North-west Marine Region, some interpretation of the information was required. DoE has made every effort to use the best available spatial information, and best judgement on how to spatially represent the features based on the scientific advice provided. This does not preclude others from making their own interpretation of available information.

The NISB Habitat Map was created by the University of Tasmania for a partnership between the Department of Climate Change and the National Land and Water Resources Audit. It supports the DCC/Audit partnership by providing a nationally consistent set of the available mapping data for those habitats that occur between the approximate position of the highest astronomical tide mark (HAT) and the location of the outer limit of the photic benthic zone (approximately at the 50-70 m depth contour). This area is broadly equivalent to the 'inner' and 'mid-shelf' regions identified by Geoscience Australia. The resulting map data set forms a core component of the ECM National Habitat Map Series. The habitat classes include: coral reef, rock dominated habitat, sediment dominated habitat, mangroves, saltmarsh, seagrass, macroalgae and filter feeders (e.g. sponges), as defined in the NISB Habitat Classification Scheme. The scheme is designed to support the development of marine 'ecoregions' or bioregional subregions. Details of the scheme and the process of its development are available in National Intertidal/Subtidal Benthic (NISB) Habitat Classification Scheme Version 1 (Mount, Bricher and Newton, 2007). The NISB Habitat Map consists of two layers for each state. _NISB.shp consists of the entire available habitat mapping at a resolution finer than 1:50 000 (with a few exceptions, outlined in the data quality section below). _NISB_PLUS.shp consists of all the data in _NISB.shp along with coarser resolution data, including NVIS and OzEstuaries data. These layers were used to produce the National ECM Key Habitat Distribution Map Series 10 km and 50 km tile maps. Note: This data is labelled as “NISB_plus”, indicating that it is the NISB Habitat layer plus other lower quality layers.

The West Australia Department of Environmental Protection (DEP) initiated a North West Shelf (NWS) Marine Environmental Management Study in 1998 to develop and consolidate the technical information base, scientific understanding and predictive capabilities required to underpin environmental decision making in both the public and private sectors. Documents, reports and scientific publications pertinent to the North West Shelf are abundant, but vary widely in scope and the degree of relevance to environmental management. Much of the information is from industries and associated government departments involved in exploiting and managing resources, and much of it has been activity specific and/or site specific in nature. This has created rich pockets of specialist knowledge but, unfortunately, the information has not been integrated across industries, government departments or scientific disciplines. Such integration is attractive, but difficult to achieve. As an example, the petroleum industry initiated its own review in the early 1990s to coordinate the then state of knowledge among its members, but has recently identified the need to revisit the process. As a first step in the North West Shelf Marine Environmental Management Study, DEP commissioned the Australian Institute of Marine Science (AIMS) and the Commonwealth Scientific and Industrial Research Organisation (CSIRO) Division of Marine Research to conduct a compilation and review of scientific research and data related to the North West Shelf marine environment. This bibliography is one product of that effort; it provides a compilation of published and unpublished literature generally related to the North West Shelf marine environment and its management. The second product, a review of scientific research and identification of important knowledge gaps, appears as a separate report by Heyward, Revill, and Sherwood (2006), titled Review of Research and Data Relevant to Marine Environmental Management of Australias North West Shelf.