Hamish A. Malcolm’s research while affiliated with New South Wales Department of Primary Industries and other places

Genomic vulnerability analyses are being increasingly used to assess the adaptability of species to climate change and provide an opportunity for proactive management of harvested marine species in changing oceans. Southeastern Australia is a climate change hotspot where many marine species are shifting poleward. The turban snail, Turbo militaris is a commercially and culturally harvested marine gastropod snail from eastern Australia. The species has exhibited a climate-driven poleward range shift over the last two decades presenting an ongoing challenge for sustainable fisheries management. We investigate the impact of future climate change on T. militaris using genotype-by-sequencing to project patterns of gene flow and local adaptation across its range under climate change scenarios. A single admixed, and potentially panmictic, demographic unit was revealed with no evidence of genetic subdivision across the species range. Significant genotype associations with heterogeneous habitat features were observed, including associations with sea surface temperature, ocean currents, and nutrients, indicating possible adaptive genetic differentiation. These findings suggest that standing genetic variation may be available for selection to counter future environmental change, assisted by widespread gene flow, high fecundity and short generation time in this species. We discuss the findings of this study in the content of future fisheries management and conservation.

Turban snails are targeted for their high-quality meat and, consequently, are often subjected to heavy harvesting pressure. Managing recreational and small-scale fisheries is challenging, partly due to a lack of biological data underpinning certain regulatory measures. This study aimed to fill current knowledge gaps on the reproductive cycle of the recreationally and culturally harvested Australian turbinid, Turbo militaris. The objectives were to investigate the reproductive timing of T. militaris in New South Wales (NSW) and identify likely environmental drivers of reproductive period-icity. Oocytes and gonads were sampled from wild animals monthly over 15 months at two sites separated by $500 km. Analysis of oocyte size frequency and gonadoso-matic index revealed that T. militaris has a pattern of extended reproduction, which is synchronous between sexes. Turbo militaris was ripest during summer, and spawning appears to have occurred over multiple events, although primarily during winter. Reproductive timing was associated with environmental explanatory variables, including sea surface temperature, wave height, salinity, phytoplankton and nitrate concentration, together accounting for 81% of the variation in oocyte size frequency and 67% in the gonadosomatic index. Reproductive periodicity was correlated with wave conditions and phytoplankton concentrations inconsistently between sites, indicating that the effect of some environmental conditions may be unpredictable or site-specific. Reproductive timing was asynchronous between two sites in the NSW fishery, posing challenges for designing seasonal fishing closures and community-based harvesting rules. Spatial closures for species with spawning over extended timeframes, or spatially asynchronous reproductive cycles, are potentially more suitable for achieving fisheries management objectives.

The persistent exposure of coral assemblages to more variable abiotic regimes is assumed to augment their resilience to future climatic variability. Yet, while the determinants of coral population resilience across species remain unknown, we are unable to predict the winners and losers across reef ecosystems exposed to increasingly variable conditions. Using annual surveys of 3171 coral individuals across Australia and Japan (2016–2019), we explore spatial variation across the short‐ and long‐term dynamics of competitive, stress‐tolerant, and weedy assemblages to evaluate how abiotic variability mediates the structural composition of coral assemblages. We illustrate how, by promoting short‐term potential over long‐term performance, coral assemblages can reduce their vulnerability to stochastic environments. However, compared to stress‐tolerant, and weedy assemblages, competitive coral taxa display a reduced capacity for elevating their short‐term potential. Accordingly, future climatic shifts threaten the structural complexity of coral assemblages in variable environments, emulating the degradation expected across global tropical reefs.

Climate change is modifying marine species' distribution with consequences for the structure and function of ecosystems. The warming and strengthening East Australian Current (EAC) is driving the tropicalisation of subtropical marine ecosystems through changing overwinter survival of tropical species. However, this can be complex for obligate symbionts, such as anemonefishes. Here, we documented fine-scale temporal changes in the density of anemonefishes and assessed the influence of latitude, temperature, and the availability of host sea anemones. Juvenile, subadult and adult Amphiprion akindynos and A. latezonatus occurred at all study locations: North Solitary Island (equatorward), South Solitary Island, and Fish Rock (poleward). While the sea anemone Heteractis crispa was readily available at Fish Rock, we found that a lack of another sea anemone Entacmaea quadricolor hindered the establishment of adult A. akindynos and A. latezonatus populations. Minimum water temperature was also a bottleneck for the tropical anemonefish A. akindynos, but not for the subtropical A. latezonatus. Our findings suggest anemonefishes are capable of contributing to the tropicalisation of the east coast of Australia. However, poleward establishment is currently limited by the absence of the preferred host sea anemone.

The current exposure of species assemblages to high environmental variability may grant them resilience to future increases in climatic variability. In globally threatened coral reef ecosystems, management seeks to protect resilient reefs within variable environments. Yet, our lack of understanding for the determinants of coral population performance within variable environments hinders forecasting the future reassembly of coral communities. Here, using Integral Projection Models, we compare the short- ( i.e. , transient) and long-term ( i.e. , asymptotic) demographic characteristics of tropical and subtropical coral assemblages to evaluate how thermal variability influences the structural composition of coral communities over time. Exploring spatial variation across the dynamics of functionally different competitive, stress-tolerant, and weedy coral assemblages in Australia and Japan, we show that coral assemblages trade-off long-term performance for transient potential in response to thermal variability. We illustrate how coral assemblages can reduce their susceptibility towards environmental variation by exploiting volatile short-term demographic strategies, thus enhancing their persistence within variable environments. However, we also reveal considerable variation across the vulnerability of competitive, stress-tolerant, and weedy coral assemblages towards future increases in thermal variability. In particular, stress-tolerant and weedy corals possess an enhanced capacity for elevating their transient potential in response to environmental variability. Accordingly, despite their current exposure to high thermal variability, future climatic shifts threaten the structural complexity of coral assemblages, derived mostly from competitive coral taxa within highly variable subtropical environments, emulating the degradation expected across global coral communities.

Marine fisheries in coastal ecosystems in many areas of the world have historically removed large‐bodied individuals, potentially impairing ecosystem functioning and the long‐term sustainability of fish populations. Reporting on size‐based indicators that link to food‐web structure can contribute to ecosystem‐based management, but the application of these indicators over large (cross‐ecosystem) geographical scales has been limited to either fisheries‐dependent catch data or diver‐based methods restricted to shallow waters (<20 m) that can misrepresent the abundance of large‐bodied fished species. We obtained data on the body‐size structure of 82 recreationally or commercially targeted marine demersal teleosts from 2904 deployments of baited remote underwater stereo‐video (stereo‐BRUV). Sampling was at up to 50 m depth and covered approximately 10,000 km of the continental shelf of Australia. Seascape relief, water depth, and human gravity (i.e., a proxy of human impacts) were the strongest predictors of the probability of occurrence of large fishes and the abundance of fishes above the minimum legal size of capture. No‐take marine reserves had a positive effect on the abundance of fishes above legal size, although the effect varied across species groups. In contrast, sublegal fishes were best predicted by gradients in sea surface temperature (mean and variance). In areas of low human impact, large fishes were about three times more likely to be encountered and fishes of legal size were approximately five times more abundant. For conspicuous species groups with contrasting habitat, environmental, and biogeographic affinities, abundance of legal‐size fishes typically declined as human impact increased. Our large‐scale quantitative analyses highlight the combined importance of seascape complexity, regions with low human footprint, and no‐take marine reserves in protecting large‐bodied fishes across a broad range of species and ecosystem configurations.

Anthropocene coral reefs are faced with increasingly severe marine heatwaves and mass coral bleaching mortality events. The ensuing demographic changes to coral assemblages can have long-term impacts on reef community organisation. Thus, understanding the dynamics of subtropical scleractinian coral populations is essential to predict their recovery or extinction post-disturbance. Here we present a 10-yr demographic assessment of a subtropical endemic coral, Pocillopora aliciae (Schmidt-Roach et al. in Zootaxa 3626:576–582, 2013) from the Solitary Islands Marine Park, eastern Australia, paired with long-term temperature records. These coral populations are regularly affected by storms, undergo seasonal thermal variability, and are increasingly impacted by severe marine heatwaves. We examined the demographic processes governing the persistence of these populations using inference from size-frequency distributions based on log-transformed planar area measurements of 7196 coral colonies. Specifically, the size-frequency distribution mean, coefficient of variation, skewness, kurtosis, and coral density were applied to describe population dynamics. Generalised Linear Mixed Effects Models were used to determine temporal trends and test demographic responses to heat stress. Temporal variation in size-frequency distributions revealed various population processes, from recruitment pulses and cohort growth, to bleaching impacts and temperature dependencies. Sporadic recruitment pulses likely support population persistence, illustrated in 2010 by strong positively skewed size-frequency distributions and the highest density of juvenile corals measured during the study. Increasing mean colony size over the following 6 yr indicates further cohort growth of these recruits. Severe heat stress in 2016 resulted in mass bleaching mortality and a 51% decline in coral density. Moderate heat stress in the following years was associated with suppressed P. aliciae recruitment and a lack of early recovery, marked by an exponential decrease of juvenile density (i.e. recruitment) with increasing heat stress. Here, population reliance on sporadic recruitment and susceptibility to heat stress underpin the vulnerability of subtropical coral assemblages to climate change.

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.

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.

Worldwide, several countries have established coherent, representative, and large-scale networks of marine reserves to conserve biodiversity. Very few have, however, published systematic assessments of the ecological responses to this network protection, hindering broad understanding of their generality, utility, and efficacy. We present data collected from systematic sampling of rocky reef fish assemblages at sites across a network of 27 no-take marine reserve areas (NTMR) and 27 partially protected areas (PPA) nested within multiple marine parks (regional networks) across three Australian bioregions spanning >1000 km of coastline (7° latitude) to test the generality of ecological change across this network. We also sampled 18 reference areas (outside of the marine parks) to provide an independent assessment of potential NTMR effects and also to assess whole marine park effects. Baited remote underwater video (BRUV) was used to sample fishes between depths of 20–40 m over austral winters in four years (2010, 2011, 2015, and 2016). Despite substantial bioregional differences in fish assemblages, large and consistent effects of NTMR protection were detected across all bioregions for a key commercially and recreationally harvested species, Chrysophrys auratus (pink snapper). There were substantial increases in relative abundance of C. auratus in NTMR compared with fished zones through time (effect sizes >150%). The wider assemblage of targeted fish (excluding C. auratus) only showed relatively small effects of protection (~11%) with trends observed for site-attached wrasses (labrids) and planktivores (e.g., commercially fished Scorpis lineolata) that are recreationally and commercially harvested. Furthermore, the relative abundance of non-target or by-catch species generally did not differ among management zones across the bioregional network. These results highlight how NTMR can be used to assess the ecological effects of fishing and wider environmental management, and can be incorporated into ecosystem-based management for reef species more generally. Importantly, the provision of robust evidence of the performance and generality of NTMR over large-spatial scales (e.g., bioregions) provides greater confidence in the expected outcomes from marine reserve networks as a conservation management approach.