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

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Publications (79)


Map of tiger shark sampling locations labeled with site codes (see Table 1) along the eastern seaboard of Australia and the Indo‐Pacific.
Spatial autocorrelation coefficient (r) for SNP data over a range of geographic distance classes spanning 700 km for adult females (top left), adult males (bottom left), juvenile‐subadult females (top right), and juvenile‐subadult males (bottom right).
Evidence of Fine‐Scale Genetic Structure in Tiger Sharks (Galeocerdo cuvier) Highlights the Importance of Stratified Sampling Regimes
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  • Full-text available

June 2025

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79 Reads

Jessica J. Fish

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Christine Dudgeon

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Adam D. Miller

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.

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Figure 1.
Escaping inbreeding: the demographic path to genetic recovery

May 2025

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55 Reads

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.


Improving white shark detection capabilities in an Australian bather protection programme using environmental DNA

April 2025

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24 Reads

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1 Citation

ICES Journal of Marine Science

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.


Assumed population subdivision of Australian white sharks (Carcharodon carcharias), where sharks from eastern and southern‐western Australia are considered isolated gene pools. Regions encompassing sampling locations are shown in orange shaded boxes, and total sample sizes and representative animal total length (average total length including standard error, and length ranges) for each region are provided.
Simulated effects of varying number of white sharks (Carcharodon carcharias) migrants per generation on global FST among eastern and southern Australia (n = 2) with effective population sizes (Ne) of 250, 500 and 1000, and simulations run for 10 generations (left), 50 generations (centre) and 100 generations (right). * indicates where the predicted the FST is less than the observed FST value of 0.003 (95% CIs: 0.002–0.003).
Genomic Assessment of Australian White Sharks (Carcharodon carcharias) Challenges Previous Evidence of Population Subdivision

February 2025

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168 Reads

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3 Citations

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.


White shark carcass (Carcharodon carcharias) with bite wounds attributed to killer whale (Orcinus orca) predation. (A) Killer whales Ripple (EA_0005) and Bent Tip (EA_0007), known for their long‐term association, photographed together in Port Phillip Bay, Victoria, Australia, in 2015 (source: Karl Bromelow). (B) White shark carcass found at Bridgewater Bay, Victoria, Australia, on 17th October 2023 (source: Ben Johnson, Portland Bait and Tackle). (C) Bite wound at the pectoral girdle where killer whale DNA was detected (source: Adam Miller). (D) Bite wounds 2, 3, and 4 where broadnose sevengill shark DNA was found (source: Adam Miller).
Genetic Evidence of Killer Whale Predation on White Sharks in Australia

January 2025

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287 Reads

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 analyses indicate resilience of a commercially and culturally important marine gastropod snail to climate change

November 2023

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114 Reads

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2 Citations

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.


Single experimental aquarium from experimental system (2 × 150 L aquaria and 1 × 150 L sump), with nylon gutter brush attached to PVC pipe frames, restricting animal movement to faces of the aquaria. Abalone are adhered to the front (ventral view) and back (dorsal view) aquaria faces
Linear regressions comparing body mass and CTmax of abalone subjected to a acute thermal ramping (1 °C per hour; n = 81) and b chronic thermal ramping (1 °C per 12 h; n = 92). Pearson’s correlation coefficient significance values and linear equations, and mixed model ANOVA significance values are depicted in the bottom right of each plot
Boxplots comparing farm of origin and CTmax of abalone subjected to acute thermal ramping (purple; 1 °C per hour; n = 81) and chronic thermal ramping (orange; 1 °C per 12 h; n = 92). Mixed model ANOVA significance values for provenance effect on CTmax are depicted in the top right of the plot. Asterisks represent outliers and black dots represent the mean
Boxplots comparing gonad development stages of all abalone and CTmax of abalone subjected to chronic thermal ramping (1 °C per 12 h; n = 93). One-way ANOVA significance values are depicted in the top right of the plot. Asterisks represent outliers and black dots represent the mean
Size-dependent thermal limits in Australian hybrid abalone: implications for productivity shifts with ocean warming

November 2023

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209 Reads

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1 Citation

Reviews in Fish Biology and Fisheries

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.


Citations (64)


... A study of shark DNA found in seawater supports this conclusion. Samples of sea water tested for eDNA shed by white sharks along the same stretch of coast (Clark et al 2025) confirms that only a small minority of sharks are being relocated. ...

Reference:

Shark Mitigation for Surfing: Science, Technology, and Praxis
Improving white shark detection capabilities in an Australian bather protection programme using environmental DNA
  • Citing Article
  • April 2025

ICES Journal of Marine Science

... Population structure of the Australian white shark population is complex, with early tracking studies McAuley et al. 2017;Bruce et al. 2019) and genetic analyses using nuclear and mitochondrial markers (Blower et al. 2012) suggesting a subdivision between an east and southwest subpopulation on either side of Bass Strait. However, documented movements across Bass Strait Spaet et al. 2020) and lack of population structure evidenced by recent genomic analyses of ~650 individuals genotyped at ~7000 single-nucleotide polymorphisms (SNPs) (Clark et al. 2025) challenge the current subpopulation paradigm. Characterising the extent of resource-habitat divergence over ontogeny for individuals either side of Bass Strait has yet to be undertaken, but could provide further insight into the ecological population structure of white sharks in this region. ...

Genomic Assessment of Australian White Sharks (Carcharodon carcharias) Challenges Previous Evidence of Population Subdivision

... In contrast, the burnt plots initially had higher soil nutrient content due to the combustion of the post-harvest residues, however, they lacked organic substrates. This limited the types of fungi that could colonize these plots (Dove and Hart, 2017), such as pyrophytic fungal species (Johnston et al., 2024;Tomao et al., 2020). Thus, burnt plots had lower fungal biodiversity, with only 96/ 130 exclusive OTUs compared to 257/210 in the mulched immediately planted plots. ...

Impacts of planned burning on the fungal diversity and vascular plants in a heathy woodland
  • Citing Article
  • July 2024

Forest Ecology and Management

... Thus, adult movement would likely facilitate connectivity to only localised areas of suitable habitat, but haphazardly. T. militaris are not genetically differentiated across NSW (Nimbs et al. 2023), so populations at isolated rocky shores would need to be linked by larval supply. ...

Genomic analyses indicate resilience of a commercially and culturally important marine gastropod snail to climate change

... These limitations highlight a pressing need for comprehensive monitoring of environmental conditions across NSW estuaries and how these might affect seagrass persistence and adaptation. This need is particularly important given that southeast Australia is a climate change hotspot (Hobday and Pecl 2014) already experiencing extreme heatwaves, likely close to the upper limits of thermal maxima leading to changes in reproductive biology for taxa (e.g., Holland et al. 2024). Such monitoring is essential to determine the impacts of long-term climate change patterns and extreme climate events (e.g., heatwaves, floods), which are projected to increase in frequency and intensity under future climate scenarios (Dey et al. 2019;Oliver et al. 2019). ...

Size-dependent thermal limits in Australian hybrid abalone: implications for productivity shifts with ocean warming

Reviews in Fish Biology and Fisheries

... In avian species, eDNA has been utilized to identify a terrestrial bird at its drinking sites (Day et al. 2019), elusive marshland birds from water or soil samples (Neice and McRae 2021, Feist et al. 2022, Guan et al. 2023, and the critically endangered Strigops habroptilus (Kākāpō) from soil samples (Urban et al. 2023), as well as a swan and a few geese species . Avian species have also been detected in metabarcoding studies targeting water, air, airborne dust, soil, leaf swabs, flowers, and spider webs (Ushio et al. 2018, Clare et al. 2022, Lynggaard et al. 2022, Coleman et al. 2023, Johnson et al. 2023, Jønsson et al. 2023, Lynggaard et al. 2023, Newton et al. 2023, Zhang et al. 2023, Lynggaard et al. 2024, Newton et al. 2024, Tetzlaff et al. 2024. ...

Contrasting patterns of biodiversity across wetland habitats using single‐time‐point environmental DNA surveys

Aquatic Conservation Marine and Freshwater Ecosystems

... This is somewhat surprising since the procedure is relatively simple to perform, does not require specialist equipment and animals can be released afterward. Gastric lavage also remains more cost-effective than other emerging techniques, such as identifying prey items from cloacal swabs with DNA metabarcoding (Clark et al., 2023;Olin et al., 2023). ...

Insights into the diet and trophic ecology of white sharks ( Carcharodon carcharias ) gained through DNA metabarcoding analyses of cloacal swabs

... However, this potential climate maladaptation seems primarily driven by expected climate warming in these areas. Since the Western ESU is currently adapted to warmer environments than the Eastern ESU, the introduction of adaptive variation via gene flow from the former to the latter might make populations more resistant to warmer future climates, avoiding local extinctions 64,65 . Furthermore, the long migration distance of the Eastern ESU is expected to increase in the foreseeable future, unless a switch to novel non-breeding areas, located closer to the breeding sites, occurs. ...

Genetic offset and vulnerability modelling: misinterpretations of results and violations of evolutionary principles
  • Citing Preprint
  • June 2023

... We suggest a forensic carbon accounting method [38] be applied to seaweed carbon sequestration. This method can utilise novel forms of measuring seaweed carbon export such as using eDNA in deep sea sediment cores and modelling of fatty acids signatures to predict macroalgal carbon in marine sediments [39,40]. This method can use international collaboration to build from the J-Blue Japanese methodology for seaweed carbon credits [41], which has proved successful. ...

Patterns and drivers of macroalgal ‘blue carbon’ transport and deposition in near-shore coastal environments
  • Citing Article
  • May 2023

The Science of The Total Environment

... A similar finding of the negative association between trait plasticity and integration was also reported in a recent study on the eco-physiological responses of two wetland plant species to water table decline . More recently, however, some researchers have challenged this notion, arguing that phenotypic integration did not constitute an inherent constraint to plasticity; instead, there might be a positive association between phenotypic plasticity and integration for plants in coping with environmental heterogeneity Oyanoghafo et al., 2023;Shi et al., 2023). Therefore, it is yet undetermined whether phenotypic integration hinders the expression of plasticity. ...

Contributions of phenotypic integration, plasticity and genetic adaptation to adaptive capacity relating to drought in Banksia marginata (Proteaceae)