The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment "The state and trends of quality of species and groups – Epipelagic fish species". The full Expert Assessment, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Expert Assessment are accessible through the "On-line Resources" section of this record. DESCRIPTION OF ECOLOGICAL SPECIES/COMMUNITY FOR EXPERT ASSESSMENT Australia’s coastal small pelagic fishes (<50 cm) include species such as Australian Sardines, Maray, Blue and Sandy Sprats, Australian anchovy, scads, Jack Mackerel, hardyheads, silversides, Blue mackerel, Australian Herring and Redbait. Tropical and temperate assemblages are comprised of different species and there are also regional differences in species composition (Hobday et al. 2009). This assessment refers only to temperate species in the East, South-east and South-west regions. Blue Mackerel, Common Jack Mackerel, Redbait and Australian Sardine (off eastern Australia only) are targeted by the Commonwealth Small Pelagic Fishery. The SPF is managed in two Zones: East spanning half of the East and eastern South-east regions and the West spanning the South west and western half of South-east). State fisheries primarily target Australian Sardine but may also take Australian Anchovy, Blue Mackerel, sprats and Maray. DATA STREAM(S) USED IN EXPERT ASSESSMENT The assessment is based on data and analyses published in the peer review literature, stock assessment reports and minutes of the meetings of the Small Pelagic Fishery Scientific Panel. Details of specific data sets used to generate the assessment have not been provided. 2016 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details] • 2016 • Assessment grade: Good Assessment trend: Stable Confidence grade: Adequate high quality evidence and high level of consensus Confidence trend: Adequate high quality evidence and high level of consensus Comparability: Grade and trend are comparable to the 2011 assessment • 2011 • Assessment grade: Good Assessment trend: Stable Confidence grade: Adequate high quality evidence and high level of consensus Confidence trend: Limited evidence or limited consensus CHANGES SINCE 2011 SOE ASSESSMENT Additional fishery catch data, more recent stock assessments.

The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment "The state and trends of quality of species and groups – whales". The full Expert Assessment, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Expert Assessment are accessible through the "On-line Resources" section of this record. DESCRIPTION OF TAXONOMIC GROUP FOR EXPERT ASSESSMENT A total of 24 species of whales (two of which comprise two subspecies) have been documented from Australian waters with a further one (Omura’s whale) likely to occur, but yet to be definitively confirmed. A number of these species (e.g. sperm whale) are distributed nationally, others are restricted to particular latitudes (e.g. Bryde’s whale) and others consist of populations that only seasonally utilise Australian waters (e.g. some of the baleen whale species). DATA STREAM(S) USED IN EXPERT ASSESSMENT This assessment is based on peer-review papers and reports provided by a series of researchers working on whales in Australia. Details on the specific data products used in this assessment have not been provided. 2016 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details] • 2016 • Assessment grade: Good Assessment trend: Unclear Confidence grade: Limited evidence or limited consensus Confidence trend: Limited evidence or limited consensus Comparability: Grade and trend are somewhat comparable to the 2011 assessment • 2011 • Baleen whales Assessment grade: Poor Assessment trend: Stable Confidence grade & trend: Limited evidence or limited consensus • 2011 • Humpback whales Assessment grade: Good Assessment trend: Increasing Confidence grade & trend: Limited evidence or limited consensus • 2011 • Toothed whales Assessment grade: Poor Assessment trend: Stable Confidence grade & trend: Limited evidence or limited consensus CHANGES SINCE 2011 SOE ASSESSMENT The 2011 assessment was split across three categories. Given the lack of data on status and trends for most species it was considered more appropriate to provide one assessment, highlighting the increasing trends for humpback and southern right whales. Anecdotal information suggests that populations of most whales are stable and so it was considered more appropriate to assign status as good. With very little information on most species abundances, limited evidence of any change in populations and no long-term monitoring of populations with which clear trends could be determined, trend was identified as ‘unclear’ rather than ‘stable’.

The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment "The state and trends of quality of species and groups – sea snakes". The full Expert Assessment, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Expert Assessment are accessible through the "On-line Resources" section of this record. DESCRIPTION OF ECOLOGICAL PROCESS FOR EXPERT ASSESSMENT Assessing the status of sea snakes is a priority based on evidence of significant declines in some populations (e.g., Guinea 2007, 2013, Lukoschek et al. 2007, 2013). Australia has approximately 32 sea snake species, more than half of global diversity, including 13 endemic species. Sea snakes occur in a variety of shallow-water marine habitats in northern Australia, including estuaries, reefs, soft-sediment habitats, and seagrass meadows. Two endemic species are listed as Critically Endangered under the EPBC Act and IUCN Red List, a further two endemics listed as Endangered and Near Threatened by IUCN have not been assess under the EPBC Act. DATA STREAM(S) USED IN EXPERT ASSESSMENT • Data primarily collected from an expert panel of sea snake researchers and marine resource managers during an IUCN Sea Snake Specialist Group Red List workshop in February 2009. • Updated status of sea snake populations from coastal WA and off-shore Timor Sea Reefs obtained from reports and publications by Michael Guinea, Vimoksalehi Lukoschek, Blanche D’Anastasi and Kate Sanders 2016 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details] Status and trends within the Australian EEZ are largely unknown but likely to vary between species and bioregions. Species have almost disappeared from Ashmore Reef, Timor Sea, the reasons for which are unknown. CHANGES SINCE 2011 SOE ASSESSMENT Largely agrees with 2011 SOE assessment with the addition of the declines reported from the NW Shelf.

The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment "The state and trends of non-indigenous/non-endemic species – number and abundance of introduced species". The full Expert Assessment, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Expert Assessment are accessible through the "On-line Resources" section of this record. DESCRIPTION OF ECOLOGICAL PROCESS FOR EXPERT ASSESSMENT There are over 250 introduced marine plants and animals established in Australian waters (see marine pests.gov.au). Some have hitch-hiked to Australian waters on the hulls of vessels of all types from yachts to commercial ships, or in their ballast water. Others have been introduced to support local aquaculture, with the aquarium industry another vector. Some species are listed on the National Introduced Marine Pest Information System and are assessed under the ‘Number and abundance of NIMPIS-listed species’ assessment. This assessment covers those species not currently on the list. DATA STREAM(S) USED IN EXPERT ASSESSMENT This assessment is based on peer-review papers and reports as well as information on the marine pests website: see http://www.marinepests.gov.au. 2016 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details] • 2016 • Assessment grade: Good Assessment trend: Unclear Confidence grade: Limited evidence or limited consensus Confidence trend: Evidence or consensus too low to make an assessment Comparability: Grade and trend are comparable to the 2011 assessment • 2011 • Assessment grade: Good Assessment trend: Unclear Confidence grade: Limited evidence or limited consensus Confidence trend: Evidence or consensus too low to make an assessment CHANGES SINCE 2011 SOE ASSESSMENT The 2016 assessment is similar to the 2011 assessment. With very little information on most species abundances and no long-term monitoring of populations with which clear trends could be determined it was considered appropriate to assign a trend of ‘unclear’.

The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment "The state and trends of quality of species and groups - inner shelf reef fish species". The full Expert Assessment, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Expert Assessment are accessible through the "On-line Resources" section of this record. DESCRIPTION OF ECOLOGICAL SPECIES/COMMUNITY FOR EXPERT ASSESSMENT Bony and cartilaginous fish assemblages found on coastal rocky and coral reefs <25 m depth, around the Australian continent. This includes all species (most not exploited). DATA STREAM(S) USED IN EXPERT ASSESSMENT Reef Life Survey visual census data were used for the current status assessment, with extensive spatial coverage of sites around the continent. Temporal trend information came from a combination of RLS, LTTRMP and AIMS long-term GBR monitoring datasets at 16 particular locations (MPA locations include the broader region and sites inside and outside sanctuary zones): NSW: Batemans Marine Park, Jervis Bay Marine Park, Sydney, Lord Howe Island, Port Stephens VIC: Beware Reef, Port Phillip Heads SA: Encounter Bay (Fleurieu Peninsula) WA: Rottnest Island, Jurien Marine Park, Ningaloo Marine Park QLD: Capricorn-Bunker, Southern GBR, Central GBR, Northern GBR TAS: Maria Island 2016 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details] • 2016 • Assessment grade: Poor Assessment trend: Deteriorating Confidence grade: Adequate high quality evidence and high level of consensus Confidence trend: Adequate high quality evidence and high level of consensus Comparability: Grade and trend are somewhat comparable to the 2011 assessment • 2011 • Assessment grade: Poor Assessment trend: Stable Confidence grade: Limited evidence or limited consensus Confidence trend: Limited evidence or limited consensus CHANGES SINCE 2011 SOE ASSESSMENT Unclear what the 2011 assessment was based on.

The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment "The state and trends of quality of species and groups – dolphins and porpoises". The full Expert Assessment, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Expert Assessment are accessible through the "On-line Resources" section of this record. DESCRIPTION OF TAXONOMIC GROUP FOR EXPERT ASSESSMENT Following taxonomic standards, 20 dolphin species in the Family Delphinidae and one species in the Family Phocoenidae occur in Australian waters. A number of these species (e.g. common bottlenose dolphins) are distributed nationally, others are restricted to particular latitudes (e.g. dusky dolphin) and others consist of populations that are highly restricted to embayments and tributaries within particular regions (e.g. the endemic snub-fin dolphin). DATA STREAM(S) USED IN EXPERT ASSESSMENT This assessment is based on peer-review papers and reports provided by a series of researchers working on dolphin and porpoises in Australia. Data on state and trends and associated spatial and temporal coverage are detailed in the publications provided in the reference list. Specific data products used to generate the assessment are not listed. 2016 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details] • 2016 • Assessment grade: Good Assessment trend: Unclear Confidence grade: Limited evidence or limited consensus Confidence trend: Limited evidence or limited consensus Comparability: Grade and trend are somewhat comparable to the 2011 assessment • 2011 • Assessment grade: Good Assessment trend: Stable Confidence grade: Limited evidence or limited consensus Confidence trend: Limited evidence or limited consensus CHANGES SINCE 2011 SOE ASSESSMENT The 2016 assessment is similar to the 2011 assessment. With very little information on most species abundances and no long-term monitoring of populations with which clear trends could be determined it was considered appropriate to alter the trend assignment to ‘unclear’ rather than ‘stable’.

The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment "The state and trends of ecological processes – trophic structures and relationships". The full Expert Assessment, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Expert Assessment are accessible through the "On-line Resources" section of this record. DESCRIPTION OF ECOLOGICAL PROCESS FOR EXPERT ASSESSMENT For this assessment, food web structure and function as defined by diet and modelling studies (which synthesis much of the available information) have been used to evaluate the status and trends for trophic structures and relationships. The status and outlook for the structure of Australian marine ecosystems is highly variable. Food webs are naturally dynamic, through time and space (e.g. Griffiths et al. 2009), and human pressure on them has varied around Australia over the past two centuries, altering trophic structures to differing degrees (Dell et al. 2013, GBRMPA 2014). Food webs studies have primarily focused on coastal and shelf waters (e.g. Salini et al 1998, Bulman et al. 2001, DofWWA 2009), with much less coverage of deep water food webs. Diet studies have only occurred intermittently and few studies have been subsequently repeated (e.g. recent resampling of fish diets on the shelf of SE Australia; CSIRO unpublished). Consequently, understanding the true magnitude of inter-annual variation in diets is low and there is little capacity to be sure of dietary changes through time. Modelling studies (Fulton et al. 2005, Klaer 2005) suggest there has been trophic restructuring of food webs in south-eastern Australia over the last century, particularly as a result of the intensification of commercial fisheries up to the 1990s. The reduction in fishing pressure, particularly over the last 5-10 years (Flood et al. 2014, Patterson et al. 2015) will likely, eventually, allow the recovery of trophic structures. However, a complete recovery is unlikely given the multitude of on-going pressures (e.g. remaining fishing pressure, both recreational and commercial, shipping, coastal habitat modification, pollution, etc.) and because some highly depleted species (e.g. eastern gemfish) have failed to recover from past overexploitation; which itself may be related to shifts in trophic connections with predators and prey (TSSC 2009). In addition, climate change is reshaping south eastern ecosystems, with shifts in species ranges (Sunday et al. 2015) and the realisation of new trophic interactions (e.g. shifts in octopus diets; Briceno et al. 2015), as omnivorous species appear to shift more rapidly than carnivores (Sunday et al. 2015). Eastern Australian ecosystems, including the Great Barrier Reef are highly modified (Butler and Jernakoff 1999, GBRMPA 2014). Amongst the most obviously shifted systems are around population centres and in the southern Great Barrier Reef (GBRMPA 2014). As elsewhere, fishing pressure has eased over the past 5 years, but other pressures (e.g. from increasing development) have increased (AIMS 2014). Overall trophic structures likely remain highly modified, both by past and present removal of predatory species and shifts in abundance of basal species, due to eutrophication or habitat removal (GBRMPA 2014, Fulton and Gorton 2014). The ecosystems of northern, western, southwestern and southern Australia see less direct, and spatially more variable, pressure than those in the east and south east. Over the past 3 decades, fishing pressure in the region has significantly declined, and has continued to do so (though at a reduced rate) over the past 5 years (Prince et al. 2008, Patterson et al. 2014, Fletcher and Santoro 2015). Development of other sectors (e.g. shipping) has grown, but largely concentrated on specific locations (AIMS

The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment "The state and trends of ecological communities – algal beds". The full Expert Assessment, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Expert Assessment are accessible through the "On-line Resources" section of this record. DESCRIPTION OF ECOLOGICAL COMMUNITY FOR EXPERT ASSESSMENT Algal beds are generally thought of as algae associated with hard substratum such as rocky reefs that provides a strong point of attachment for algae to grow and maintain position. The majority of Australia’s algal beds are found in temperate waters and are in many cases replaced as the major habitat forming benthic organisms by corals in more tropical environments where intense grazing by herbivorous fishes contains algal biomass, particularly in clear offshore waters. The changeover from temperate algal covered reefs to coral dominated reefs is a gradual transition, but, as a broad generalisation, is considered to be in the vicinity of the Abrohlos Islands in Western Australia and Brisbane in Queensland, and is driven by the northern limit of the canopy forming kelp, Ecklonia radiata. Throughout this range, algal beds are found from the intertidal zone down to approximately 30 m depth where light availability limits growth. Despite this, lower limits may be much reduced in turbid or coloured water, or substantially exceed this in clear offshore water. Algal beds are composed of many constituent species with more than 1500 species of red, brown and green algae known from temperate and tropical Australia. Despite this, the overall canopy forming species are dominated by a far smaller subset of species, including Ecklonia radiata (the common kelp) which tends to be the dominant habitat former and most conspicuous species on temperate reefs, particularly on moderate to high energy coasts where it can form an extensive monospecific canopy above other algae. Given this ecological dominance which is consistent at continental scales, the overall health and extent of Ecklonia is considered to be a suitable indicator of the state of algal beds in general. Despite this, Ecklonia is typically replaced as a dominant species by Sargassum and Cystophora species in sheltered waters such as the Tasmanian north coast and upper reaches of South Australian gulfs, and may replace other species that are under stress (such as Macrocystis pyrifera in Tasmania, the giant kelp or Scytothalia dorycarpa in Western Australia). Hence understanding the condition of algal beds can often require a region-specific knowledge of trends in key species in addition to Ecklonia. DATA STREAM(S) USED IN EXPERT ASSESSMENT The assessment is predominantly based on data and analyses published in peer review papers. Data has been used from IMOS, The Reef Life Survey, and various state based ecological monitoring programs associated with the establishment of coastal MPAs. Details of specific data sets used to generate the assessment have not been provided. 2016 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details] • 2016 • Assessment grade: Good Assessment trend: Stable to deteriorating Confidence grade: Adequate high quality evidence and high level of consensus Confidence trend: Adequate high quality evidence and high level of consensus Comparability: Grade and trend are somewhat comparable to the 2011 assessment • 2011 • Assessment grade: Very good Assessment trend: Stable Confidence grade: Limited evidence or limited consensus Confidence trend: Adequate high quality evidence and high level of consensus CHANGES SINCE 2011 SOE ASSESSMENT Uncertain.

The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment "The state and trends of habitats and communities - water column, inner shelf (0 - 25 m)". The full Expert Assessment, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Expert Assessment are accessible through the "On-line Resources" section of this record. DESCRIPTION OF HABITAT/COMMUNITY FOR EXPERT ASSESSMENT Based on biomass the major communities found in the water column are phytoplankton>bacteria>zooplankton>fish (Marchant 2002). The water column is the habitat and the major determinants of quality for most pelagic organisms can be considered to be temperature (T), salinity (S), light, nutrients, dissolved oxygen (DO), pH, and food availability. The inner shelf waters around Australia are generally warm, mostly saline, well illuminated, low in nutrients, and phytoplankton, zooplankton and fish abundance. The inner shelf is also the pelagic marine habitat most exposed to human induced pressures and has local habitats that range from heavily disturbed to pristine. The capability of this habitat to support the existing flora and fauna can be considered to be under threat (e.g. Game et al. 2009) from: inputs from the terrestrial environment (e.g. sediments in runoff or due to increased erosion, nutrients, wastes), harvesting of biota, invasive species, infrastructure development (e.g. impoundments, harbours, hardening), mariculture, mining, oil and gas extraction, climate change (warming, falling DO, decreasing pH). There are many areas of local habitat degradation, with the most impacted areas tending to be embayments and estuaries with significant population pressures and limited exchange (e.g. Alyazichi et al., 2015; Mckinley et al., 2011). In spite of improvements in the management of these types of pressures the magnitude of the growth in mineral exports, agriculture exports and population growth would suggest that development impacts will have risen. At the same time across many jurisdictions improvements in sewage treatment and disposal mean that potentially dangerous pathogens are increasingly rare. For example in 2015 96% of NSW open beaches with high rates of recreational use were rated good or very good (NSW EPA, 2015). At a larger geographic scale our shelf waters are experiencing increasing impacts from global pressures such as warming. Shelf waters from Port Hedland to Cape Howe have risen ~ 1°C from 1993 to 2013 (Foster et al., 2014), and portions of the SW region were 3°C warmer during February 2011 than normal (Pearce and Feng 2013). There is evidence that dissolved oxygen has declined (Thompson et al. 2009) and will continue to decline due to warming (Talley et al., 2016). This is likely to lead to more losses of marine fauna due to low oxygen; such as the unprecedented event during 2015 in Cockburn Sound (Pattiaratchi 2016). Recent blooms of toxic phytoplankton in regions where they never bloomed before (Campbell et al., 2013) and the SE shellfish that have suffered badly from disease outbreaks (Hooper et al., 2007; Lewis et al., 2012). There is evidence of widespread responses to climate related pressures across the major types of biota, phytoplankton, zooplankton and fish (e.g. Johnson et al. 2011, Thompson et al. 2016) as well as our coral reefs under increased stress from rising temperatures and declining pH (Mongin et al., 2016). DATA STREAM(S) USED IN EXPERT ASSESSMENT Data are computed from the level 3 (L3) daily global products using one merging method following Maritorena and Siegel, (2005). Details can be found at http://www.globcolour.info/products_description.html Phytoplankton and zooplankton data are from Australia’s National Reference Stations operated by the Integrated Marine Observing System. 2016 SOE ASSESSMENT

The Marine chapter of the 2016 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment "The state and trends of habitats and communities - water column, slope (250 m -700 m)". The full Expert Assessment, including figures and tables (where provided), is attached to this record. Where available, the Data Stream(s) used to generate this Expert Assessment are accessible through the "On-line Resources" section of this record. DESCRIPTION OF HABITAT/COMMUNITY FOR EXPERT ASSESSMENT The major determinants of pelagic habitat can be considered to be temperature (T), salinity (S), light, nutrients, dissolved oxygen (DO), pH, and food availability. The slope waters around Australia are generally warm, saline, well illuminated, low in nutrients, phytoplankton, zooplankton and fish. The primary pressures affecting the pelagic biota in slope waters are related to climatic cycles (e.g. ENSO) and long term climate change impacting on T, S, DO, pH and fishing. The slope waters are particularly sensitive to changes in our boundary currents, the EAC and the Leeuwin which generally flow south, seaward of the shelf break. The pelagic productivity of the slope waters provides most of the food to animals in these waters and on the bottom. The shelf edge canyons can enhance upwelling or ‘capture’ eddies that act to focus phytoplankton into these features. Data collection is sparse but IMOS continuous plankton recorder (CPR) routes around Australia sample largely from this region. DATA STREAM(S) USED IN EXPERT ASSESSMENT Data are computed from the level 3 (L3) daily global products using one merging method following Maritorena and Siegel, (2005). Details can be found at http://www.globcolour.info/products_description.html 2016 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details] • 2016 • Assessment grade: Good Assessment trend: Unclear Confidence grade: Limited evidence or limited consensus Confidence trend: Limited evidence or limited consensus Comparability: Grade and trend are comparable to the 2011 assessment • 2011 • Assessment grade: Good Assessment trend: Stable Confidence grade: Limited evidence or limited consensus Confidence trend: Limited evidence or limited consensus CHANGES SINCE 2011 SOE ASSESSMENT This assessment uses observations from a greater range of spatial and temporal scales allowing a much better assessment of current state and trends to be made. There is also a statistical analysis of temporal change in zooplankton biomass.