The Marine chapter of the 2021 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment "State and Trend of mesopelagic fish species". A PDF of the full Expert Assessment, including figures and tables (where provided) is downloadable in the "On-line Resources" section of this record as "EXPERT ASSESSMENT 2021 - Mesopelagic fish species" DESCRIPTION OF HABITAT/COMMUNITY/PROCESS FOR EXPERT ASSESSMENT Mesopelagic fish species (200 to 1000 m depth) occur throughout the Australian Exclusive Economic Zone (EEZ) region where the seabed depth exceeds 200 m (Flynn and Kloser, 2012; Flynn et al., 2018; Sutton et al., 2018). Mesopelagic fishes reside at depth during the day and a portion migrate to shallower waters to feed at night, revealing diel vertical migration in the sound scattering layer (Figure 1a; Brierley 2014). Ecosystem and carbon models associated with observational studies of mesopelagic fishes highlight their importance to ecosystem services and carbon sequestration role (Fulton et al., 2005; Lehodey et al., 2010; Boyd et al., 2019). This is particularly important for Australia’s continental slope commercial species and other top predators for ecosystem-based management (Smith et al., 2011). The importance of mesopelagic fishes to ecosystem services is recognized yet their biomass and trophic efficiency are uncertain with net and acoustic estimates differing by 2 orders of magnitude in Tasman Sea Australian waters (Kloser et al., 2009; Irigoien et al., 2014). This difference is due to different sampling gear and methods used to interpret the data. DATA STREAM(S) USED IN EXPERT ASSESSMENT The primary data used are the georeferenced, calibrated, and processed single-beam water column volume backscattering coefficient values, representing the linear sum of backscatter from acoustically detectable individual organisms within the sampling volume. The spatial coverage of data used for assessing the state of mesopelagic biogeography is 75oS-45oN and 20oW-330oW with a temporal coverage 2004-2018. The spatial coverage of data used for assessing trends in selected regions is 35oS-50oS and 180oW-220oW with a temporal coverage 2004-2018. 2021 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details] • 2021 • Assessment grade: Very good Assessment trend: Improving Confidence grade: Limited Confidence trend: Somewhat adequate Comparability: Grade and trend are comparable to the 2016 assessment • 2016 • Assessment grade: Very good Assessment trend: Stable 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: Very good Assessment trend: Stable Confidence grade: Limited evidence or limited consensus Confidence trend: Limited evidence or limited consensus CHANGES SINCE 2016 SOE ASSESSMENT The extent of processed bioacoustic data archived under IMOS Bioacoustics sub-Facility is expanding with an improved spatial and temporal coverage, facilitating future state and trend analyses.

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 – 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 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 2021 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment "State and Trend of inner shelf (0-30 m) – reef fish species". A PDF of the full Expert Assessment, including figures and tables (where provided) is downloadable in the "On-line Resources" section of this record as "EXPERT ASSESSMENT 2021 - Inner shelf (0-30 m) – reef fish species" DESCRIPTION OF SPECIES/HABITAT/COMMUNITY/PROCESS FOR EXPERT ASSESSMENT Bony and cartilaginous fish assemblages found on coastal rocky and coral reefs <30 m depth around the Australian continent, including both exploited and unexploited species. DATA STREAM(S) USED IN EXPERT ASSESSMENT Underwater visual census data from Reef Life Survey, the Australian Institute of Marine Science, and the Australian Temperate Reef Collaboration. National synoptic change (mean 2011-2015 period vs mean 2016-2020 period) and 18 long-term monitoring locations spread nationally. See national reefs case study for details. 2021 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details] • 2021 • Assessment grade: Poor Assessment trend: Highly variable among species Confidence grade: Adequate Confidence trend: Adequate Comparability: High. This is the second sequential assessment based on standardised quantitative data from the same sources. • 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 2016 SOE ASSESSMENT not supplied

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 habitats and communities – Seamounts". 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 Seamounts (undersea mountains, often with volcanic origin) provide ‘oasis’ habitats of hard substratum and are widely considered to represent sites of elevated biomass and productivity in the deep ocean. Their habitats can support dense aggregations of corals and associated high biodiversity; these represent vulnerable marine ecosystems (VME) (e.g. UNGA 2006; Clark et al 2011). The geological definition of a seamount (elevation of >1000 m) has no relevance to biodiversity valuation because smaller features are frequently found to support high, if not the highest, biodiversity. An ecological definition (e.g. Pitcher et al. 2007) is recommended. Australia’s marine realm encompasses many seamounts; the best known are the Tasmanian seamounts and the Tasmantid seamount chain. Additional seamounts have been discovered and mapped on the Lord Howe Rise and the Norfolk Ridge, as well as on Australia’s southern margin in the GAB. Seamount communities to ~1500 m depth in the south-east and south-west regions are associated with biogenic habitats formed mostly by the stony coral Solenosmilia variabilis (Koslow et al 2000; Thresher et al. 2014). Its matrix of dead and life coral, built up to a layer of at least 1.6 m thickness in places, forms a habitat for other corals, urchins, brittle- and snakestars and crustaceans (Thresher et al. 2014). Communities and habitats on deeper reaches of seamounts (>1500 m) are less well studied; they are usually less diverse and sparser, although areas of extraordinary high biomass have been observed in the south-east region (Thresher et al. 2014). The seamounts in the Tasmantid chain are mapped and well used by various commercial fisheries, but their epifaunal communities remain poorly documented (Williams et al. 2012). DATA STREAM(S) USED IN EXPERT ASSESSMENT This assessment is based on data derived from Marine National Facility Surveys described in MarLIN (http://www.marine.csiro.au/marlin/search.html) and accessible through the CSIRO Data trawler (http://www.cmar.csiro.au/data/trawler/). Links to specific data sets are provided in the "On-line resources" section of this record. • Voyage of Discovery north-west (SS05/2007) • Voyage of Discovery south-west (SS07/2005 & SS10/2005) • Tasmanian seamounts surveys (SS01/2000, SS04/2006 & SS02/2007, SS01/2008 & TT01/2008) • Habitat Mapping (SS01/2000, SS04/2004) • Habitat and population assessment of giant crabs (2003 - 2005) • NORFANZ survey of Lord Howe Rise and Norfolk Ridge (TAN0308 - NORFANZ) 2016 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details] • 2016 • Assessment grade: Very good-Poor Assessment trend: Stable- Improving 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: Limited evidence or limited consensus CHANGES SINCE 2011 SOE ASSESSMENT There is substantial information on the impact of trawling on seamounts in the South-East Marine Region available.

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 – tuna and billfish". 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 This assessment focuses on those tuna and billfish species that are targeted by commercial fisheries and for which stock assessments are available. These include albacore, bigeye, skipjack, southern bluefin and yellowfin tuna, broadbill swordfish and striped and blue marlin. In Australian waters, southern bluefin tuna are caught predominantly by commercial fisheries in the south-west and temperate east bioregions with recreational catches also occurring in the north-west and south-east bioregions. Yellowfin, bigeye and albacore tuna, swordfish and striped marlin are predominantly caught by commercial and recreational fisheries in the north-west, south-west, temperate east and north east bioregions with recreational catches also occurring in the north and in the south-east seasonally. Blue marlin is caught recreationally in the north-east, temperate east, south-west and north-west bioregions with commercial catches of the species not permitted DATA STREAM(S) USED IN EXPERT ASSESSMENT The assessment is based on stock assessment information produced in working papers provided to the scientific committees of relevant RFMOs and annual reports of the scientific committees and working groups of relevant RFMOs. Assessments are based on a variety of data relating to species population dynamics, spatial dynamics, fishery catches, survey and mark-recapture experiments covering the spatial area of each of the RFMOs and spanning varying temporal periods. 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: 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 notcomparable 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 Since the 2011 chapter, some management frameworks have been modified so both reporting and assessment frameworks have been altered providing clearer views of current stock status. The 2011 assessment doesn’t appear to have referenced available stock assessments which provide the best and most robust indications of status for each of the species. The 2011 assessment stated that there was limited evidence and limited consensus and that the condition of stocks in the south-west was poor and declining, which doesn’t reflect stock assessments conducted at the time. Since the 2011 assessment, stock assessments available for the species have been updated and new data streams are contributing to stock assessments.

The Marine chapter of the 2021 State of the Environment (SoE) report incorporates multiple expert templates developed from streams of marine data. This metadata record describes the Expert Assessment "State and Trend of trophic structures and relationships". A PDF of the full Expert Assessment, including figures and tables (where provided) is downloadable in the "On-line Resources" section of this record as "EXPERT ASSESSMENT 2021 - Trophic structures and relationships" DESCRIPTION OF COMMUNITY/PROCESS FOR EXPERT ASSESSMENT Trophic relationships indicate linkages between species in food webs – who eats who. Consumers in open-ocean pelagic food webs rely on plankton at their base (Griffiths et al.., 2010; Antoine et al., 2020); inshore, benthic food webs may also have a heavy reliance on plankton (Truong et al., 2017) but can also be based on macrophytes, detritus and many invertebrate prey species (Abrantes et al., 2015). Historically, our understanding of these relationships was based on dietary studies (particularly stomach content analysis), which were undertaken sporadically in space and time. More recently, DNA techniques have been applied to stomach contents to detect prey that might not be normally identified from visual analyses, thereby expanding the food web (Berry et al., 2015). These studies may span a large number of species or focus on a subset of interest. Thus, to assemble a food web for a region, and then to assess change, requires many years of sampling, often combining data from different studies. In contrast, diet studies of single species are relatively common, and may be observed through visual observations, imagery, stomach contents, or scat analysis. These studies can reveal geographic, interannual, or long-term change, and indicate wider ecosystem change (e.g. see examples based around little penguins and pinnipeds; Chiaradia et al., 2010; Kirkwood et al., 2008). DATA STREAM(S) USED IN EXPERT ASSESSMENT No raw data analyses were used in this assessment, instead it represents a synthesis of literature published in the last 5 years. 2021 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details] • 2021 • Assessment grade: Poor-good. Variable. Assessment trend: Unclear. Variable. Confidence grade: Adequate Confidence trend: Limited Comparability: Comparable • 2016 • Assessment grade: Poor-Good Assessment trend: Unclear Confidence grade: Adequate high quality evidence or high level of consensus Confidence trend: Adequate high quality evidence or high level of 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 2016 SOE ASSESSMENT Assessment is in line with what was found in 2016.

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 – seabirds". 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 There are presently 57 species of seabirds known to breed in and around Australia and the external territories of Cocos (Keeling) and Christmas Island, Lord Howe and Norfolk Islands, Ashmore and Cartier Islands, and the Coral Sea islands. These 57 species are comprised of penguins (1 species), albatrosses (1 species), petrels, shearwaters and storm-petrels (19 species), boobies, tropicbirds, frigatebirds, cormorants and pelican (16 species) and gulls, tern, and noddies (20 species). Another 130 species of seabirds have been recorded in Australia, either as non-breeding or vagrant. Shorebirds are not considered here, nor are issues associated with nesting or onshore breeding colonies as these are assessed under the Coasts chapter. Species breeding on subantarctic islands and the Antarctic continent are assessed under the Antarctic chapter. DATA STREAM(S) USED IN EXPERT ASSESSMENT The assessment was based on data and analyses published in the peer reviewed literature and agency reports. 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 • 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 Unclear how the 2011 assessment was carried out and on what data. There is very little data on trends in populations available and so the trend cannot be regarded as stable but rather 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 – demersal and benthopelagic fish species, outer shelf (25 m - 250 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 ECOLOGICAL SPECIES/COMMUNITY FOR EXPERT ASSESSMENT Most information on demersal and benthopelagic fish species is derived from fisheries catches. Fishing is predominately concentrated in the south-east (Southern and Eastern Scalefish and Shark Fishery; SESSF) and in the north-east (Queensland State fisheries). The demersal and benthopelagic fished species and populations over the shelf of Australian waters are influenced by changes in the physical environment (warming waters on the east coast, and episodic thermal events on the west coast), by terrestrial sources of pollution, and the effects of extractive industries such as fishing and mining. DATA STREAM(S) USED IN EXPERT ASSESSMENT This assessment is based on fisheries assessments of commercial species. Data on state and trends and associated spatial and temporal coverage are detailed in the publications provided in the reference list. 2016 SOE ASSESSMENT SUMMARY [see attached Expert Assessment for full details] • 2016 • Assessment grade: Poor Assessment trend: Improving Confidence grade: Adequate high-quality evidence or high level of consensus Confidence trend: Limited evidence or limited consensus Comparability: Grade and trend are somewhat comparable to the 2011 assessment • 2011 • Assessment grade: Very good Assessment trend: Stable Confidence grade: Adequate high-quality evidence or high level of consensus Confidence trend: Limited evidence or limited consensus CHANGES SINCE 2011 SOE ASSESSMENT It is not clear how the assessment in 2011 was derived. The 2016 is based on the most recent commercial fisheries assessments.