Adam D. Miller’s research while affiliated with Flinders University and other places

Understanding the biological connections between populations is essential to wildlife management and conservation. Genetic studies play a central role in characterizing these connections, but typically require stratified sampling regimes to assess the spatial extent and strength of gene flow, and the relative influences of sex and ontogeny on patterns of connectivity. Yet, this can be challenging in some study systems, particularly in large marine species such as sharks, where genetic studies often rely on opportunistic and/or sampling conducted over large spatial scales. We demonstrate the importance of stratified sampling to identify previously undetected genetic structure in tiger sharks (Galeocerdo cuvier) off eastern Australia, where panmixia has been previously reported. We performed population genomic analyses on 414 tiger sharks, representing males and females and both juvenile‐subadult and adult‐life stages, and 21 locations spanning approximately 3000 km of eastern Australia and the Indo‐Pacific region. Similar to previous studies, we demonstrate a lack of overall genetic structure across the sampling area; however, our analysis shows evidence of spatial autocorrelation and local genetic structuring in juvenile‐subadult female tiger sharks. These results point to potential influences of sex and ontogeny on patterns of population genetic structure and connectivity in Australian tiger sharks. We discuss these findings in the context of essential habitats supporting tiger shark populations and risks of overstating the strength of biological connections among shark populations in the absence of appropriate sampling regimes.

Bottlenecks pose a major threat to species persistence by reducing genetic diversity and increasing inbreeding. Although evolutionary theory suggests these constraints can be overcome, empirical evidence has largely come from invasive species. Here, we analyse whole-genome data from 418 koalas (Phascolarctos cinereus) across 27 populations to reconstruct demographic histories and examine rare genetic variation. We find that northern populations retain higher genetic diversity, while southern populations, despite severe bottlenecks, exhibit larger and increasing effective population sizes (Ne). This apparent contradiction is explained by increased reshuffling of genetic variation through recombination, and the accumulation of rare alleles during recent demographic expansion. Our findings demonstrate that rapid population growth can substantially elevate Ne, offering an evolutionary pathway by which threatened populations may escape the genetic risks of inbreeding.

Bather protection programmes rely heavily on surveillance tools capable of detecting the presence of shark species that are known to physically interact with humans. This study investigates the potential for environmental DNA (eDNA) technologies to improve shark detection capabilities and complement current survey methods. We conducted a 14-month monitoring programme at two white shark (Carcharodon carcharias) visitation hotspots in eastern Australia and assessed spatio-temporal patterns of near-shore visitation using a species-specific eDNA assay, SMART (Shark-Management-Alert-in-Real-Time) drumline captures, and acoustic telemetry data from tagged white sharks. We observed higher shark detection frequencies across both survey locations using eDNA compared to the SMART drumline and telemetry survey methods. Specifically, eDNA surveys provided relatively constant rates of detection across the survey period, whereas SMART drumline and telemetry detections were highly seasonal and largely restricted to the austral winter–spring period. Findings from the eDNA surveys are consistent with current assumptions about white shark spatial ecology with year-long presence of white sharks in near-shore subtropical habitats in eastern Australia but suggest that shark presence during the summer–autumn months is possibly more prevalent than currently assumed. Overall, this study highlights the value of eDNA as a tool for enhancing shark detection capabilities, and the importance of adopting multiple complementary survey methods when assessing shark visitation rates. We discuss the implications of these findings for bather protection and white shark mitigation programmes in Australia and overseas.

Aim The white shark (Carcharodon carcharias) is one of the world's largest and most recognisable marine predators but has suffered significant declines since the mid‐twentieth century. Conservation efforts remain complicated by persistent knowledge gaps associated with white shark biology and ecology, including the biological connectedness of white shark populations. We re‐assess patterns of population genetic structure in Australian white sharks, where two subpopulations—eastern and southern‐western—are currently recognised based on previous animal tracking and genetic assessments. Methods Population genomic analyses are performed using tissues from ~650 individual white sharks and ~7000 single nucleotide polymorphism (SNP) loci generated through reduced genome representation sequencing. We test for evidence of genetic structure and relatedness among sharks from eastern and southern Australia and use population genetic simulations to assess the likely strength of inter‐generational migration between regions. Results This study challenges the current paradigm of population structure in Australian white sharks, showing a lack of genetic structure between white sharks from eastern and southern Australia. These findings are further supported by population genetic simulations and kinship analyses indicating high levels of intergenerational migration and relatedness between regions. Consistent with recent reports from eastern Australia, we also detected high levels of relatedness among juvenile and subadult white sharks and estimated the overall effective population size (Ne) of Australian white sharks to be less than 500 individuals. Furthermore, we provide evidence of a potential reduction in Ne over the last two generations. Main Conclusions Overall, these findings highlight the need to consider this revised estimate of genetic structure when discussing the management and conservation of the species. Our results also raise concerns for the conservation of Australian white sharks highlighting risks of potential inbreeding, and reductions in population fitness and resilience. We discuss the need for further research and the importance of ongoing population monitoring.

Killer whales (Orcinus orca) have been documented to prey on white sharks (Carcharodon carcharias), in some cases causing localised shark displacement and triggering ecological cascades. Notably, a series of such predation events have been reported from South Africa over the last decade, with killer whales specifically targeting sharks' liver. However, observations of these interactions are rare, and knowledge of their frequency across the world's oceans remains limited. In October 2023, a 4.7 m (total length) white shark carcass washed ashore in southeastern Australia, coinciding with reports from citizen scientists of killer whales hunting a large, unidentified prey item in the area. Visual inspection of the carcass revealed that the liver, digestive, and reproductive organs were missing, and the presence of four distinctive bite wounds, one of which was characteristic of killer whale liver extraction as seen in South Africa. Genomic analyses performed on swabs taken from the bite wounds confirmed the presence of killer whale DNA in the major bite area, while the other bites were embedded with genetic material from the scavenging broadnose sevengill shark (Notorynchus cepedianus). These results provide confirmed evidence of killer whale predation on white sharks in Australia and the likely selective consumption of the liver, suggesting predations of this nature are more globally prevalent than currently assumed.

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.

Ocean warming and extreme heatwaves threaten marine species supporting commercial fisheries and aquaculture. Predicting the responses of these industries to chronic and acute warming depends on understanding which life stages are most vulnerable, the potential for stocks to adapt to changing thermal environments, and the availability of thermally adapted genotypes to help enhance stock resilience through strategic interventions. Here, we shed light on some of these knowledge gaps by quantifying the critical thermal maximum (CTmax) of ~ 10–210 g hybrid abalone (Haliotis rubra × H. laevigata) from two farms representing contrasting thermal environments from south-eastern Australia. CTmax was not dependent on body size or provenance (farm) when heating rates were rapid (1 °C per h), but a significant relationship between CTmax and body size was observed when heating rates were slower and more ecologically realistic (1 °C per 12 h). Histological analyses revealed a negative relationship between CTmax and the stage of gonadal development when abalone were exposed to chronic thermal stress conditions. These results suggest that marine heatwaves and ongoing ocean warming might favour smaller, less fecund animals in natural and farm settings. This could potentially impact future harvestable biomass, recruitment and population dynamics in wild-capture fisheries, and production of larger, high-value animals in farm settings. This study adds to a growing body of literature pointing to complex and often negative effects of climate change on commercial fisheries, and the potential need for interventions aimed at bolstering fisheries resilience against the effects of ocean warming.