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Ocean–atmosphere climatic interactions, such as those resulting from El Niño Southern Oscillation (ENSO) are known to influence sea level, sea surface temperature, air temperature, and rainfall in the western Pacific region, through to the north-west Australian Ningaloo coast. Mangroves are ecologically important refuges for biodiversity and a rich store of blue carbon. Locations such as the study site (Mangrove Bay, a World Heritage Site within Ningaloo Marine Park and Cape Range National Park) are at the aridity range-limit which means trees are small in stature, forests small in area, and are potentially susceptible to climate variability such as ENSO that brings lower sea level and higher temperature. Here we explore the relationship between mangrove dieback, and canopy condition with climatic variables and the Southern Oscillation Index (SOI)—a measure of ENSO intensity, through remote sensing classification of Landsat satellite missions across a 29 year period at a north-west Australian site. We find that the SOI, and seasonal mean minimum temperature are strongly correlated to mangrove green canopy (as indicator of live canopy) area. This understanding of climate variations and mangrove temporal heterogeneity (patterns of abundance and condition) highlights the sensitivity and dynamics of this mangrove forest and recommends further research in other arid and semi-arid tropical regions at mangrove range-limits to ascertain the extent of this relationship.

As some types of disturbance to coral reefs are attenuated with depth, the resilience of herbivorous fish species utilizing shallow areas ( 30 m) reef areas. Scraper herbivores were associated with the reef crest (

The effective management of marine species relies on a comprehensive understanding of how the environment can influence biodiversity and distributions. This study quantified the biodiversity of invertebrates across the phyla Arthropoda, Echinodermata, Mollusca and Porifera from 132 sampling stations along the coast of the Ningaloo Marine Park (NMP) and across depths ranging from 30 to 123 m, providing a broad assessment of the biodiversity of marine invertebrates in mesophotic habitats of the NMP. Benthic sleds were used to sample biodiversity and specimens identified to the highest taxonomic resolution. Single-beam and multibeam surveys of the seabed were performed to derive 58 spatial and bathymetric variables used to assess their relevance to the distributions of benthic diversity. A total of 787 taxa were identified across the four phyla, of which 51% were rare and sampled from a single station. Latitude and depth were significant in structuring the invertebrate diversity in the mesophotic, with Point Cloates notably identified as a significant geographical feature in partitioning diversity to the north and south of the NMP. Depth was more influential at structuring diversity in the northern section of the NMP due to the narrower Ningaloo Shelf, and southern localities including Turtles and Red Bluff were identified as biodiversity hotspots for benthic invertebrates. Importantly, comparisons of diversity within ‘no-take’ and ‘general use’ zones along the NMP indicate that sanctuary zones represent the diversity contained in the marine park, thus highlighting their importance in the protection and conservation of invertebrate diversity for the region.

Novel tools and methods for monitoring marine environments can improve efficiency but must not compromise long-term data records. Quantitative comparisons between new and existing methods are therefore required to assess their compatibility for monitoring. Monitoring of shallow water coral reefs is typically conducted using diver-based collection of benthic images along transects. Diverless systems for obtaining underwater images (e.g. towed-cameras, remotely operated vehicles, autonomous underwater vehicles) are increasingly used for mapping coral reefs. Of these imaging platforms, towed-cameras offer a practical, low cost and efficient method for surveys but their utility for repeated measures in monitoring studies has not been tested. We quantitatively compare a towed-camera approach to repeated surveys of shallow water coral reef benthic assemblages on fixed transects, relative to benchmark data from diver photo-transects. Differences in the percent cover detected by the two methods was partly explained by differences in the morphology of benthic groups. The reef habitat and physical descriptors of the site—slope, depth and structural complexity—also influenced the comparability of data, with differences between the tow-camera and the diver data increasing with structural complexity and slope. Differences between the methods decreased when a greater number of images were collected per tow-camera transect. We attribute lower image quality (variable perspective, exposure and focal distance) and lower spatial accuracy and precision of the towed-camera transects as the key reasons for differences in the data from the two methods and suggest changes to the sampling design to improve the application of tow-cameras to monitoring.

Marine reserves are a key tool for the conservation of marine biodiversity, yet only ~2.5% of the world's oceans are protected. The integration of marine reserves into connected networks representing all habitats has been encouraged by international agreements, yet the benefits of this design has not been tested empirically. Australia has one of the largest systems of marine reserves, providing a rare opportunity to assess how connectivity influences conservation success. An Australia‐wide dataset was collected using baited remote underwater video systems deployed across a depth range from 0 to 100 m to assess the effectiveness of marine reserves for protecting teleosts subject to commercial and recreational fishing. A meta‐analytical comparison of 73 fished species within 91 marine reserves found that, on average, marine reserves had 28% greater abundance and 53% greater biomass of fished species compared to adjacent areas open to fishing. However, benefits of protection were not observed across all reserves (heterogeneity), so full subsets generalized additive modelling was used to consider factors that influence marine reserve effectiveness, including distance‐based and ecological metrics of connectivity among reserves. Our results suggest that increased connectivity and depth improve the aforementioned marine reserve benefits and that these factors should be considered to optimize such benefits over time. We provide important guidance on factors to consider when implementing marine reserves for the purpose of increasing the abundance and size of fished species, given the expected increase in coverage globally. We show that marine reserves that are highly protected (no‐take) and designed to optimize connectivity, size and depth range can provide an effective conservation strategy for fished species in temperate and tropical waters within an overarching marine biodiversity conservation framework., An Australia‐wide dataset was collected using baited remote underwater video systems deployed across a depth range from 0 to 100 m to assess the effectiveness of marine reserves for protecting fished species. A meta‐analytical comparison of 73 fished species within 91 marine reserves found that, on average, marine reserves had 28% greater abundance and 53% greater biomass of fished species compared to adjacent areas open to fishing. We show that marine reserves that are highly protected (no‐take) and designed to optimize connectivity, size and depth range can provide an effective conservation strategy for fished species in temperate and tropical waters.

Made available in DSpace on 2021-06-25T12:19:58Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-09-24 Australian Government's National Environmental Science Program Australian Research Data Commons GorgonBarrow Island Gorgon Barrow Island Net Conservation Benefits Fund Baited remote underwater stereo-video systems (stereo-BRUVs) are a popular tool to sample demersal fish assemblages and gather data on their relative abundance and body size structure in a robust, cost-effective and non-invasive manner. Given the rapid uptake of the method, subtle differences have emerged in the way stereo-BRUVs are deployed and how the resulting imagery is annotated. These disparities limit the interoperability of datasets obtained across studies, preventing broadscale insights into the dynamics of ecological systems. We provide the first globally accepted guide for using stereo-BRUVs to survey demersal fish assemblages and associated benthic habitats. Information on stereo-BRUVs design, camera settings, field operations and image annotation are outlined. Additionally, we provide links to protocols for data validation, archiving and sharing. Globally, the use of stereo-BRUVs is spreading rapidly. We provide a standardized protocol that will reduce methodological variation among researchers and encourage the use of Findable, Accessible, Interoperable and Reusable workflows to increase the ability to synthesize global datasets and answer a broad suite of ecological questions. Univ Western Australia, UWA Oceans Inst, Perth, WA, Australia Univ Western Australia, Sch Biol Sci, Perth, WA, Australia Dept Biodivers Conservat & Attract, Marine Sci Program, Biodivers & Conservat Sci, Kensington, WA, Australia Curtin Univ, Sch Mol & Life Sci, Perth, WA, Australia Univ Tasmania, Inst Marine & Antarctic Studies, Hobart, Tas, Australia Silliman Univ, Angelo King Ctr Res & Environm Management, Dumaguete, Philippines NOAA Inouye Reg Ctr, NOAA Fisheries, Pacific Isl Fisheries Sci Ctr, Sci Operat Div, Honolulu, HI USA Univ Hawaii Manoa, Joint Inst Marine & Atmospher Res, Honolulu, HI 96822 USA South African Inst Aquat Biodivers, Grahamstown, South Africa Rhodes Univ, Dept Zool & Entomol, Grahamstown, South Africa Univ St Andrews, Ctr Res Ecol & Environm Modelling, Sch Math & Stat, St Andrews, Fife, Scotland Indian Ocean Marine Res Ctr, Australian Inst Marine Sci, Perth, WA, Australia Australian Inst Marine Sci, Townsville, Qld, Australia Govt Western Australia, Western Australian Fisheries & Marine Res Labs, Dept Primary Ind & Reg Dev, North Beach, WA, Australia NSW Dept Primary Ind, Fisheries Res, Taylors Beach, NSW, Australia Dept Environm & Water, Marine Sci Program, Sci & Corp Serv Div, Adelaide, SA, Australia Flinders Univ S Australia, Southern Shark Ecol Grp, Coll Sci & Engn, Bedford Pk, SA, Australia Deakin Univ, Sch Life & Environm Sci, Ctr Integrat Ecol, Warrnambool, Vic, Australia NSW Dept Primary Ind, Fisheries Res, Huskisson, NSW, Australia Coral Reef Res Fdn, Koror, Palau NSW Dept Primary Ind, Fisheries Res, Coffs Harbour, NSW, Australia Ctr Environm Fisheries & Aquaculture Sci, Lowestoft, Suffolk, England Sao Paulo State Univ, Elasmobranch Res Lab, Inst Biosci, Sao Vicente, SP, Brazil Massey Univ, Sch Nat & Computat Sci, Auckland, New Zealand Sao Paulo State Univ, Elasmobranch Res Lab, Inst Biosci, Sao Vicente, SP, Brazil

Increasing sea surface temperature and extreme heat events pose the greatest threat to coral reefs globally, with trends exceeding previous norms. The resultant mass bleaching events, such as those evidenced on the Great Barrier Reef in 2016, 2017, and 2020 have substantial ecological costs in addition to economic and social costs. Advancing remote (nanosatellites, rapid revisit traditional satellites) and in-field (drones) technological capabilities, cloud data processing, and analysis, coupled with existing infrastructure and in-field monitoring programs, have the potential to provide cost-effective and timely information to managers allowing them to better understand changes on reefs and apply effective remediation. Within a risk management framework for monitoring coral bleaching, we present an overview of how remote sensing can be used throughout the whole risk management cycle and highlight the role technological advancement has in earth observations of coral reefs for bleaching events.

There is a growing emphasis on formally recognizing the connection to the marine environment of Indigenous peoples and the traditional ecological knowledge (TEK) these strong connections cultivate. The potential for TEK to significantly enrich the scientific comprehension of the marine environment, whilst also celebrating the rich bio-cultural knowledge in its own right, is indisputable. Here, we present a scientifically robust and culturally appropriate participatory mapping methodology for the marine environment which can effectively achieve genuine cross-cultural ecological knowledge transfer between scientists and Indigenous Peoples. Through a case study working with the Anindilyakwa people of the Groote Eylandt Archipelago, we mapped the TEK of benthic habitats off Australia’s poorly surveyed northern coast. Representatives from 14 Anindilyakwa clan groups participated in the marine mapping (n = 53), resulting in 22 individual maps. Eleven broad-scale habitat classifications, predominately in the intertidal and nearshore marine environment, were described in both Anindilyakwa and English. The information gathered was then used to develop benthic habitat maps covering a combined area of ∼1800 km2 and was assessed for accuracy against in situ observations. We found that despite the difficulties in working across two different world views, through the application of this carefully refined methodology, scientists can effectively document the rich TEK of the marine environment in a manner suitable for conservation and management planning while also supporting the prioritization of Indigenous values within the decision-making process.

Canopy-forming macroalgae can construct extensive meadow habitats in tropical seascapes occupied by fishes that span a diversity of taxa, life-history stages and ecological roles. Our synthesis assessed whether these tropical macroalgal habitats have unique fish assemblages, provide fish nurseries and support local fisheries. We also applied a meta-analysis of independent surveys across 23 tropical reef locations in 11 countries to examine how macroalgal canopy condition is related to the abundance of macroalgal-associated fishes. Over 627 fish species were documented in tropical macroalgal meadows, with 218 of these taxa exhibiting higher local abundance within this habitat (cf. nearby coral reef) during at least one life-history stage. Major overlap (40%-43%) in local fish species richness among macroalgal and seagrass or coral reef habitats suggest macroalgal meadows may provide an important habitat refuge. Moreover, the prominence of juvenile fishes suggests macroalgal meadows facilitate the triphasic life cycle of many fishes occupying diverse tropical seascapes. Correlations between macroalgal canopy structure and juvenile abundance suggests macroalgal habitat condition can influence levels of replenishment in tropical fish populations, including the majority of macroalgal-associated fishes that are targeted by commercial, subsistence or recreational fisheries. While many macroalgal-associated fishery species are of minor commercial value, their local importance for food and livelihood security can be substantial (e.g. up to 60% of landings in Kenyan reef fisheries). Given that macroalgal canopy condition can vary substantially with sea temperature, there is a high likelihood that climate change will impact macroalgal-associated fish and fisheries.

AIM: Understanding the relative importance of climatic and non‐climatic distribution drivers for co‐occurring, functionally similar species is required to assess potential consequences of climate change. This understanding is, however, lacking for most ecosystems. We address this knowledge gap and forecast changes in distribution for habitat‐forming seaweeds in one of the world's most species‐rich temperate reef ecosystems. LOCATION: The Great Southern Reef. The full extent of Australia's temperate coastline. METHODS: We assessed relationships between climatic and non‐climatic environmental data known to influence seaweed, and the presence of 15 habitat‐forming seaweeds. Distributional data (herbarium records) were analysed with MAXENT and generalized linear and additive models, to construct species distribution models at 0.2° spatial resolution, and project possible distribution shifts under the RCP 6.0 (medium) and 2.6 (conservative) emissions scenarios of ocean warming for 2100. RESULTS: Summer temperatures, and to a lesser extent winter temperatures, were the strongest distribution predictors for temperate habitat‐forming seaweeds in Australia. Projections for 2100 predicted major poleward shifts for 13 of the 15 species, on average losing 78% (range: 36%–100%) of their current distributions under RCP 6.0 and 62% (range: 27%–100%) under RCP 2.6. The giant kelp (Macrocystis pyrifera) and three prominent fucoids (Durvillaea potatorum, Xiphophora chondrophylla and Phyllospora comosa) were predicted to become extinct from Australia under RCP 6.0. Many species currently distributed up the west and east coasts, including the dominant kelp Ecklonia radiata (71% and 49% estimated loss for RPC 6.0 and 2.6, respectively), were predicted to become restricted to the south coast. MAIN CONCLUSIONS: In close accordance with emerging observations in Australia and globally, our study predicted major range contractions of temperate seaweeds in coming decades. These changes will likely have significant impacts on marine biodiversity and ecosystem functioning because large seaweeds are foundation species for 100s of habitat‐associated plants and animals, many of which are socio‐economically important and endemic to southern Australia.

The authors acknowledge the financial support of Woodside Energy Ltd., operator of permit WA33P, on behalf of the Browse joint venture in the conduct of this research. We wish to thank the Master and crew of RV Solander and staff from ERM (Environmental Resources Management) for support during the field surveys. EC was supported by the ARC Industrial Transformation Research Hub for Offshore Floating Facilities which is funded by the Australian Research Council, Woodside Energy, Shell, Bureau Veritas and Lloyds Register (Grant No. IH140100012). We thank M. Hatch (Woodside) for providing comments on the draft of this manuscript.

Submerged reef ecosystems can be very diverse and may serve as important refugia for shallow-water conspecifics. This study quantified the benthic and fish communities of two proximate, predominantly mesophotic coral ecosystems (MCEs), Glomar Shoal and Rankin Bank, which are geographically isolated from other similar features in the region. Glomar Shoal is identified as a key ecological feature (KEF) in the North West Marine Region of Australia. Multibeam surveys were performed to characterise the seafloor and to derive secondary environmental variables, used to explain patterns in benthic and fish communities. Towed video surveys quantified benthic cover, and stereo baited remote underwater stations were used to survey fish abundance and diversity. Surveys were completed in depths of ~ 20–115 m. The two MCEs exhibited distinct communities; Rankin Bank consistently had higher cover (up to 30×) of benthic taxa across depths, and fish communities that were twice as abundant and 1.5× more diverse than Glomar Shoal. The location of the MCEs, depth and rugosity were most influential in structuring benthic communities. Phototrophic taxa, specifically macroalgae and hard corals, had up to 22 × higher cover at Rankin Bank than at Glomar Shoal and were dominant to 80 m (compared to 60 m at Glomar Shoal), presumably due to greater light penetration (lower turbidity) and lower sand cover at greater depths. The 20% coral cover at Rankin Bank was comparable to that reported for shallow reefs. The cover of sand, hard corals and sponges influenced fish communities, with higher abundance and diversity of fish associated with shallow hard coral habitats. This study demonstrated that the two MCEs were unique within the local context, and when coupled with their geographical isolation and biodiversity, presents compelling support for the additional recognition of Rankin Bank as a KEF.

Aim We used modelled environmental data to identify important drivers of bioregional patterns of demersal fish assemblages characterized by a high proportion of endemic species. Location Of 1,600 km of coastal marine environment in south-western Australia. Methods We compiled data from 1090 stereo-BRUVs samples; a total of ~55,000 individuals belonging to 219 demersal fish species. Multivariate Regression Trees and Distance-based Linear Models distinguished which biological and/or environmental variables, amongst an initial set of 49, were most correlated to observed patterns of demersal fish assemblage structure. Indicator species analysis identified fish species most representative of the assemblage types. Results The most parsimonious model (constrained by five benthic variables and one spatial variable) explained 42% of the variation in spatial patterns of fish community structure. Canopy-forming seaweeds were the major benthic drivers, and, when found on structurally complex hard habitat, supported the highest diversity of species after sites dominated by hard coral cover. Indicator species analysis revealed that 28 of 35 significant species for this habitat type were endemics with fish assemblages associated with these habitats often spatially restricted to tens of kilometres. Main conclusions Demersal fish assemblage composition and biogeographical ranges in south-western Australia are strongly influenced by the presence of canopy-forming macroalgae. Canopy-dominated habitats have already been subject to catastrophic temperature-related die-offs in the northern part of this study, indicating its vulnerability to temperature-driven climate change. These results highlight not only the crucial role of this habitat in supporting endemic fish communities in the region, and the tenuous nature of their existence, but also the challenges facing marine managers who, unable to manipulate the influence of climate change variables, can only focus on alleviating stresses operating on local scales.

Identifying and protecting nursery habitats for species is a key conservation strategy for the long-term sustainability of populations. In tropical ecosystems, macroalgal habitats have recently been identified as nurseries for fish of commercial and conservation significance. Here, we explore how local-scale variations in seaweed habitat quality interact with large-scale climatic conditions (Southern Oscillation Index, SOI) to influence the recruitment of three tropical fish species (Lethrinus spp.), often targeted by fishers. New fish recruits and juveniles of all species were almost exclusively found in macroalgal nursery habitats, while adults of two of these species were predominantly found on adjacent coral reefs. Annual supply rates of new recruits were found to be strongly correlated to variations in the SOI, with La Nina conditions associated with higher recruitment. However, local rates of recruitment were generally poor predictors of older juvenile abundance. Instead, local juvenile abundance was more closely related to structural characteristics of macroalgae nursery habitat quality (density, canopy height, canopy cover) and/or predator biomass, at the time of survey, with species-specific habitat associations apparent. Given the dynamic nature of fish recruitment supply to the SOI, coupled with the effects of climatic and oceanic processes on the structure of macroalgal patches, these results suggest protection of macroalgal nursery habitats that maintain high canopy density, height and cover is critical to supporting the conservation of fish populations.

This paper provides a first assessment of fish communities associated with the submerged oceanic banks and shoals in north-west Australia. Until recently, little was known about these deeper and more inaccessible reefs. The mesophotic coral-reef habitats (20–80 m) were a major reservoir of marine biodiversity, with unique and exceptionally high fish diversity and abundance. Species richness in the study region was 1.4 times, and abundance almost twice, that recorded for similar mesophotic habitats on the Great Barrier Reef in north-east Australia. A review of the published literature revealed that Australia’s NW oceanic shoals support the highest fish species richness reported for mesophotic reefs to date. We made regional comparisons of fish community structure (species composition, richness and abundance) and assessed the influence of depth, substrate and location. The presence of consolidated calcareous reef, depth and aspect (a surrogate for exposure) had the greatest influence on species richness. In contrast, aspect and the presence of benthic biota had the greatest influence on fish abundance. Sites most exposed to the prevailing currents (facing north-east) had lowest fish abundance, while highest abundances were recorded on moderately exposed sites (along the north-west and south-east edges). The most abundant species were small (Pomacentrus coelestis) and large (Naso hexacanthus) planktivorous fish. Currently, 29.3% of NE Australia mesophotic reefs are within no-take management zones of the Great Barrier Reef. In contrast, just 1.3% of the NW oceanic shoals are designated as no-take areas. The location and extent of mesophotic reefs remain poorly quantified globally. Because these habitats support significant biodiversity and have the potential to act as important refugia, understanding their extent is critical to maintaining coral-reef biodiversity and resilience and supporting sustainable management.

International audience; The most western little penguin colony globally, and the most northern in Western Australia (WA) is found on Penguin Island, WA. The penguins use coastal bays that are also used extensively by recreational watercraft. These penguins have been found to either dive predominantly to shallow depths of 1–5 m or to depths >8 m. It is thus hypothesized that (a) both the shallow and deeper diving penguins can potentially be disturbed or injured by these watercraft but that the risk will differ between the two diving strategies, and (b) that risk of injury for both is greater during the summer and autumn, when people are more likely to use watercraft. This was tested by attaching data loggers to little penguins during chick rearing and by investigating necropsy records. Diving activity was studied for the very shallow and relatively deeper diving penguins separately, and we considered the penguins were vulnerable to interactions with watercraft when they were within the top 2 m of the water column or at the surface. Shallow‐diving penguins executed >1,200 dives per day, 64% of dives occurred within the top 2 m, and they were vulnerable for approximately two‐thirds of their time at sea. The deeper diving penguins executed fewer dives. Almost half of dives were to ≥10 m, yet they were vulnerable for almost one‐third of their time at sea. Their post‐dive recovery was also longer. Thus, the risk of interaction from watercraft differs depending on the diving behaviour. This study highlights the potential impact to little penguins throughout Australia and New Zealand.

Tropical cyclones generate extreme waves that can damage coral reef communities. Recovery typically requires up to a decade, driving the trajectory of coral community structure. Coral reefs have evolved over millennia with cyclones. Increasingly, however, processes of recovery are interrupted and compromised by additional pressures (thermal stress, pollution, diseases, predators). Understanding how cyclones interact with other pressures to threaten coral reefs underpins spatial prioritization of conservation and management interventions. Models that simulate coral responses to cumulative pressures often assume that the worst cyclone wave damage occurs within ~100 km of the track. However, we show major coral loss at exposed sites up to 800 km from a cyclone that was both strong (high sustained wind speeds=33 m/s) and big (widespread circulation~300 km), using numerical wave models and field data from northwest Australia. We then calculate the return time of big and strong cyclones, big cyclones of any strength and strong cyclones of any size, for each of 150 coral reef ecoregions using a global data set of past cyclones from 1985 to 2015. For the coral ecoregions that regularly were exposed to cyclones during that time, we find that 75% of them were exposed to at least one cyclone that was both big and strong. Return intervals of big and strong cyclones are already less than 5 years for 13 ecoregions, primarily in the cyclone-prone NW Pacific, and less than 10 years for an additional 14 ecoregions. We identify ecoregions likely at higher risk in future given projected changes in cyclone activity. Robust quantification of the spatial distribution of likely cyclone wave damage is vital not only for understanding past coral response to pressures, but also for predicting how this may change as the climate continues to warm and the relative frequency of the strongest cyclones rises.

Many marine fish populations have declined due to the individual or cumulative impacts of increasing water temperatures, ocean acidification, overfishing and other human-induced impacts such as land run-off, dredging and habitat alteration. Some solutions may be offered by ecosystem-based fisheries and conservation management. However, understanding their effectiveness relies on the availability of good quality data on the size distributions and abundance of fish populations and assemblages, collected at appropriate temporal and spatial scales. Since the early 2000s, baited remote underwater video systems (BRUVs) have become a popular tool for collecting data on fish assemblages across a range of depths and habitats. In Australia, this technique has been adopted by many different agencies and institutions, creating a unique opportunity to compile a continental-scale synthesis of fish data using a standardised sampling technique. Key Australian researchers and managers were invited to contribute to a synthesis workshop on baited underwater video in Albany, Western Australia between the 4th and 8th of February 2018. Data from 19,939 BRUVs deployments, collected between 2000 and 2017 around Australia, were compiled using GlobalArchive (globalarchive.org). The workshop identified and prioritised several key research themes that would contribute to the conservation and sustainable management of focal species and broad assemblages. Our goal is to describe where and when the data were collected, the type of equipment used and how the imagery was analysed. We also discuss the types of questions that can be addressed by analysing these standardised datasets and the potential benefits to conservation and fisheries management.

The value of subsea pipelines as habitat for fish and benthic species is being considered, particularly by the oil and gas industry as they look to decommission seafloor infrastructure reaching the end of production. We investigated fish and benthic communities along a ca.345 km section of offshore pipeline in remote northern Australia to compare pipeline communities with those in surrounding areas and provide context for decommissioning risk assessments. We surveyed pipeline and adjacent natural seabed ecosystems at five locations on the continental shelf using remote video technology to quantify fish and benthic communities and modelled predicted fish communities across the study locations. We found that the pipeline supported turfing and low-relief biota (e.g. coralline algae, ascidians, bryozoans, small/encrusting sponges and soft coral or mixed filter feeder communities) with cover >75%. Pipeline benthic communities differed from those in adjacent ecosystems. Within 6 km of the pipeline, the seabed was predominantly sand/silt with only sparse biota; natural hard substrate (e.g. shoal features within 3 km of the pipeline) supported diverse coral and filter feeder communities (average 10–25% cover). Fish abundance and assemblage composition on the pipeline also differed from those in surrounding high- and low-complexity habitats. This difference was driven by high abundance and biomass of commercially important fish species near the pipeline and sand-affiliated species elsewhere. Our study provides important new insights into the marine communities associated with a subsea pipeline in northern Australia; with this artificial habitat observed to support a subset of species known to inhabit the area, but effectively representing a unique assemblage within the region.

Species with specialized resource use can display strong spatial heterogeneity in abundance according to the availability of their preferred habitats. If these preferences shift with ontogeny, then a wide range of habitats may need to be protected in order to support both adult populations and their replenishment. We explored whether microhabitat selectivity interacts with habitat availability to provide an effective suite of indicators for regional fish abundance and replenishment, using offshore rocky reefs in south-eastern Australia as a case study. We examined generalized additive mixed models (GAMMs) in a full subsets approach to infer the best predictors for adult and juvenile fish density in four diverse families (Labridae, Odacidae, Pomacentridae, Serranidae), based on rapid underwater visual surveys across transects (⿼500 m 2 ), wave exposures (0.3⿿1 km), and sites (0.3⿿48 km). We then examined whether these regional fish-habitat models aligned with the microhabitat electivity of individuals (at scale of 2 ). Microhabitat selection by reef fishes at the local scale underpinned the most effective habitat indicators for regional heterogeneity in fish abundance, and pointed to critical nursery habitats that support hotspots of juvenile recruitment. Strong species-habitat relationships, such as these, can be combined with broad-scale habitat mapping to assess the potential carrying capacity of focal areas, spatial management zone placements, and nursery habitats that warrant special protection. A number of emerging threats to these key habitat types indicates an urgent need for habitat-based protection and monitoring as a key part of holistic marine ecosystem conservation and management.

A major limitation to fully integrated ecosystem based fishery management approaches is a lack of information on the spatial distribution of marine species and the environmental conditions shaping these distributions. This is particularly problematic for deep-water species that are hard to sample and are data poor. The past decade has seen the rapid development of a suite of advanced species distribution, or ecological niche, modelling approaches developed specifically to support efficient and targeted management. However, model performance can vary significantly and the appropriateness of which methods are best for a given application remains questionable. Species distribution models were developed for three commercially valuable Hawaiian deep-water eteline snappers: Etelis coruscans (Onaga), Etelis carbunculus (Ehu) and Pristipomoides filamentosus (Opakapaka). Distributional data for these species was relatively sparse. To identify the best method, model performance and distributional accuracy was assessed and compared using three approaches: Generalised Additive Models (GAM), Boosted Regression Trees (BRT) and Maximum Entropy (MaxEnt). Independent spatial validation data found MaxEnt consistently provided better model performance with ‘good’ model predictions (AUC =>0.8). Each species was influenced by a unique combination of environmental conditions, with depth, terrain (slope) and substrate (low lying unconsolidated sediments), being the three most important in shaping their distributions. Sustainable fisheries management, marine spatial planning and environmental decision support systems rely on an understanding species distribution patterns and habitat linkages. This study demonstrates that predictive species distribution modelling approaches can be used to accurately model and map sparse species distribution data across marine landscapes. The approach used herein was found to be an accurate tool to delineate species distributions and associated habitat linkages, account for species-specific differences and support sustainable ecosystem-based management.

Aim: The dispersal and distribution patterns of many marine organisms are driven by oceanographic conditions, which are influenced by global climate. Climate-driven oceanographic changes are thus likely to result in biogeographical changes. We assess how recent and predicted oceanographic changes affect the dispersal capacities and distributions of ecologically important (especially habitat-forming) marine organisms. Location: We include studies from tropical, temperate and sub-polar regions to draw globally relevant conclusions. Methods: We review biogeographical, biological and oceanographic studies to critically evaluate emerging trends in biogeographical responses to climate-driven oceanographic changes, and predict how future changes will affect marine ecosystems. Results: Many oceanic dispersal pathways are being altered by climate change. These changes will affect marine ecosystems by differentially affecting the replenishment potential and connectivity of key habitat-forming species. In particular, the length of propagule pre-competency periods, propagule behaviour and the geographical distance between areas of suitable habitat will be critical in determining how oceanographic changes affect the pattern and success of dispersal events, including the likelihood of species experiencing poleward range shifts in response to a warming climate. Main conclusions: Future climate-driven oceanographic changes are likely to strengthen or weaken different oceanic dispersal pathways, which will either increase or decrease the potential for dispersal and connectivity in various marine taxa according to the interaction between the local oceanographic, geographical and taxon-specific biological factors. A key focus for future work should be the development of fine-scale near-shore ocean circulation models that can be used to assess the dispersal response of key marine taxa under various marine climate change scenarios.

Tropical reefs have been subjected to a range of anthropogenic pressures such as global climate change, overfishing and eutrophication that have raised questions about the prominence of macroalgae on tropical reefs, whether they pose a threat to biodiversity, and how they may influence the function of tropical marine ecosystems. We synthesise current understanding of the structure and function of tropical macroalgal reefs and how they may support various ecosystem goods and services. We then forecast how key stressors may alter the role of macroalgal reefs in tropical seascapes of the Anthropocene. High levels of primary productivity from tropical canopy macroalgae, which rivals that of other key producers (e.g., corals and turf algae), can be widely dispersed across tropical seascapes to provide a boost of secondary productivity in a range of biomes that include coral reefs, and support periodic harvests of macroalgal biomass for industrial and agricultural uses. Complex macroalgal reefs that comprise a mixture of canopy and understorey taxa can also provide key habitats for a diverse community of epifauna, as well as juvenile and adult fishes that are the basis for important tropical fisheries. Key macroalgal taxa (e.g., Sargassum) that form complex macroalgal reefs are likely to be sensitive to future climate change. Increases in maximum sea temperature, in particular, could depress biomass production and/or drive phenological shifts in canopy formation that will affect their capacity to support tropical marine ecosystems. Macroalgal reefs can support a suite of tropical marine ecosystem functions when embedded within an interconnected mosaic of habitat types. Habitat connectivity is, therefore, essential if we are to maintain tropical marine biodiversity alongside key ecosystem goods and services. Consequently, complex macroalgal reefs should be treated as a key ecological asset in strategies for the conservation and management of diverse tropical seascapes. A plain language summary is available for this article.

Many fishes undergo ontogenetic habitat shifts to meet their energy and resource needs as they grow. Habitat resource partitioning and patterns of habitat connectivity between conspecific fishes at different life-history stages is a significant knowledge gap. Species distribution models were used to examine patterns in the relative abundance, individual biomass estimates and environmental niche associations of different life stages of three iconic West Australian fishes. Continuous predictive maps describing the spatial distribution of abundance and individual biomass of the study species were created as well predictive hotspot maps that identify possible areas for aggregation of individuals of similar life stages of multiple species (i.e. spawning grounds, fisheries refugia or nursery areas). The models and maps indicate that processes driving the abundance patterns could be different from the body size associated demographic processes throughout an individual’s life cycle. Incorporating life-history in the spatially explicit management plans can ensure that critical habitat of the vulnerable stages (e.g. juvenile fish, spawning stock) is included within proposed protected areas and can enhance connectivity between various functional areas (e.g. nursery areas and adult populations) which, in turn, can improve the abundance of targeted species as well as other fish species relying on healthy ecosystem functioning.

Information on habitat associations from survey data, combined with spatial modelling, allow the development of more refined species distribution modelling which may identify areas of high conservation/fisheries value and consequentially improve conservation efforts. Generalised additive models were used to model the probability of occurrence of six focal species after surveys that utilised two remote underwater video sampling methods (i.e. baited and towed video). Models developed for the towed video method had consistently better predictive performance for all but one study species although only three models had a good to fair fit, and the rest were poor fits, highlighting the challenges associated with modelling habitat associations of marine species in highly homogenous, low relief environments. Models based on baited video dataset regularly included large-scale measures of structural complexity, suggesting fish attraction to a single focus point by bait. Conversely, models based on the towed video data often incorporated small-scale measures of habitat complexity and were more likely to reflect true species-habitat relationships. The cost associated with use of the towed video systems for surveying low-relief seascapes was also relatively low providing additional support for considering this method for marine spatial ecological modelling.

Creating large conservation zones in remote areas, with less intense stakeholder overlap and limited environmental information, requires periodic review to ensure zonation mitigates primary threats and fill gaps in representation, while achieving conservation targets. Follow-up reviews can utilise improved methods and data, potentially identifying new planning options yielding a desirable balance between stakeholder interests. This research explored a marine zoning system in north-west Australia–a biodiverse area with poorly documented biota. Although remote, it is economically significant (i.e. petroleum extraction and fishing). Stakeholder engagement was used to source the best available biodiversity and socio-economic data and advanced spatial analyses produced 765 high resolution data layers, including 674 species distributions representing 119 families. Gap analysis revealed the current proposed zoning system as inadequate, with 98.2% of species below the Convention on Biological Diversity 10% representation targets. A systematic conservation planning algorithm Maxan provided zoning options to meet representation targets while balancing this with industry interests. Resulting scenarios revealed that conservation targets could be met with minimal impacts on petroleum and fishing industries, with estimated losses of 4.9% and 7.2% respectively. The approach addressed important knowledge gaps and provided a powerful and transparent method to reconcile industry interests with marine conservation.

Prioritising biodiversity conservation requires knowledge of where biodiversity occurs. Such knowledge, however, is often lacking. New technologies for collecting biological and physical data coupled with advances in modelling techniques could help address these gaps and facilitate improved management outcomes. Here we examined the utility of environmental data, obtained using different methods, for developing models of both uni- and multivariate biodiversity metrics. We tested which biodiversity metrics could be predicted best and evaluated the performance of predictor variables generated from three types of habitat data: acoustic multibeam sonar imagery, predicted habitat classification, and direct observer habitat classification. We used boosted regression trees (BRT) to model metrics of fish species richness, abundance and biomass, and multivariate regression trees (MRT) to model biomass and abundance of fish functional groups. We compared model performance using different sets of predictors and estimated the relative influence of individual predictors. Models of total species richness and total abundance performed best; those developed for endemic species performed worst. Abundance models performed substantially better than corresponding biomass models. In general, BRT and MRTs developed using predicted habitat classifications performed less well than those using multibeam data. The most influential individual predictor was the abiotic categorical variable from direct observer habitat classification and models that incorporated predictors from direct observer habitat classification consistently outperformed those that did not. Our results show that while remotely sensed data can offer considerable utility for predictive modelling, the addition of direct observer habitat classification data can substantially improve model performance. Thus it appears that there are aspects of marine habitats that are important for modelling metrics of fish biodiversity that are not fully captured by remotely sensed data. As such, the use of remotely sensed data to model biodiversity represents a compromise between model performance and data availability.

Niche requirements and habitat resource partitioning by conspecific fishes of different sizes are significant knowledge gaps in the species distribution modelling domain. Management actions and operations are typically concentrated on static habitats, or specific areas of interest, without considering movement patterns of species associated with ontogenetic shifts in habitat usage. Generalized additive models were used to model the body-length-habitat relationships of six fish species. These models were used to identify subsets of environmental parameters that drive and explain the continuous length-habitat relationships for each of the study species, which vary in their degree of ecological and/or commercial importance. Continuous predictive maps of the length distributions for each of the six study species across approximately 200 km2 of the study area were created from these models. The spatial patterns in habitat partitioning by individuals of different body lengths for all six study species provide strong evidence for ontogenetic shifts. This highlights the importance of considering ontogenetic processes for marine spatial management. Importantly, predictive hotspot maps were created that identify potential areas that accumulate individuals of similar life stages of multiple species (e.g., multispecies nursery areas). In circumstances where limited resources are available for monitoring and management of fish resources, predictive modelling is a valuable tool for studying previously overlooked processes such as ontogenetic habitat shifts. Predictive modelling provides crucial information that elucidates spatial patterns in community composition across mosaics of benthic habitats. This novel technique can contribute to the spatial management of coastal fish and fisheries by identifying areas that are important for different life history stages of multiple fish species.

Species habitat associations are often complex, making it difficult to assess their influence on populations. Among coral reef fishes, habitat requirements vary among species and with ontogeny, but the relative importance of nursery and adult-preferred habitats on future abundances remain unclear. Moreover, adult populations may be influenced by recruitment of juveniles and assessments of habitat importance should consider relative effects of juvenile abundance. We conducted surveys across 16 sites and 200 km of reef to identify the microhabitat preferences of juveniles, sub-adults and adults of the damselfish Pomacentrus moluccensis . Microhabitat preferences at different life-history stages were then combined with 6 years of juvenile abundance and microhabitat availability data to show that the availability of preferred juvenile microhabitat (corymbose corals) at the time of settlement was a strong predictor of future sub-adult and adult abundance. However, the influence of nursery microhabitats on future population size differed spatially and at some locations abundance of juveniles and adult microhabitat (branching corals) were better predictors of local populations. Our results demonstrate that while juvenile microhabitats are important nurseries, the abundance of coral-dependent fishes is not solely dependent on these microhabitats, especially when microhabitats are readily available or following large influxes of juveniles.

Ecosystem reconfigurations arising from climate-driven changes in species distributions are expected to have profound ecological, social, and economic implications. Here we reveal a rapid climate-driven regime shift of Australian temperate reef communities, which lost their defining kelp forests and became dominated by persistent seaweed turfs. After decades of ocean warming, extreme marine heat waves forced a 100-kilometer range contraction of extensive kelp forests and saw temperate species replaced by seaweeds, invertebrates, corals, and fishes characteristic of subtropical and tropical waters.This community-wide tropicalization fundamentally altered key ecological processes, suppressing the recovery of kelp forests., This work was funded by the Australian Research Council (T.W., G.A.K.), the Hermon Slade Foundation (T.W., S.B.), a U.K. Natural Environment Research Council Independent Research Fellowship (D.A.S.), the Australian Institute of Marine Science (T.W., M.D., B.R.), the Australian National University (C.J.F.), the Western Australian Museum (J.F.), the Department of Parks and Wildlife (T.H.H., S.W.), CSIRO Oceans and Atmosphere (R.C.B., F.D., M.A.V.), Fisheries Research and Development Corporation project no. 2008/013 (R.K.H., G.A.K.), The Marsden Fund of The Royal Society of New Zealand (M.S.T.), and the WA Strategic Research Fund for the Marine Environment (R.B., M.A.V., J.F.).

Tropical cyclone (TC) waves can severely damage coral reefs. Models that predict where to find such damage (the ‘damage zone’) enable reef managers to: 1) target management responses after major TCs in near-real time to promote recovery at severely damaged sites; and 2) identify spatial patterns in historic TC exposure to explain habitat condition trajectories. For damage models to meet these needs, they must be valid for TCs of varying intensity, circulation size and duration. Here, we map damage zones for 46 TCs that crossed Australia’s Great Barrier Reef from 1985–2015 using three models – including one we develop which extends the capability of the others. We ground truth model performance with field data of wave damage from seven TCs of varying characteristics. The model we develop (4MW) out-performed the other models at capturing all incidences of known damage. The next best performing model (AHF) both under-predicted and over-predicted damage for TCs of various types. 4MW and AHF produce strikingly different spatial and temporal patterns of damage potential when used to reconstruct past TCs from 1985–2015. The 4MW model greatly enhances both of the main capabilities TC damage models provide to managers, and is useful wherever TCs and coral reefs co-occur.