Adam D. Miller's research while affiliated with Deakin University and other places

Publications (63)

Article
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Aim Kelp forests throughout temperate regions of the world serve as foundation species that play a critical role in sustaining the health and function of marine ecosystems but are experiencing declines in abundance due to a loss in resilience as the ocean climate changes. Ocean warming along southeast Australia has already been linked to dramatic l...
Technical Report
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The use of molecular assays to assess the presence of species using environmental DNA (eDNA) and RNA (eRNA) as analytes has diversified as the field of environmental surveillance advances. These methods can be used, for example, to screen for pest species as part of biosecurity measures and risk management, to screen for threatened species as part...
Technical Report
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The use of environmental DNA (eDNA) and RNA (eRNA) methods is a rapidly advancing field that provides fast, cost-effective, non-invasive methods to identify the presence of target species. These methods can be used, for example, to screen for pest species as part of biosecurity measures and risk management, to screen for threatened species as part...
Article
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Oil spills pose a significant threat to marine biodiversity. Crude oil can partition into sediments where it may be persistent, placing benthic species such as decapods at particular risk of exposure. Transcriptomic and histological tools are often used to investigate the effects of hydrocarbon exposure on marine organisms following oil spill event...
Technical Report
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To assist with management and conservation, the Action Plan compiles existing knowledge on taxonomy, conservation status, description, cultural significance, distribution and habitat, biology and ecology as well as threats, conservation priorities and knowledge gaps for each priority Euastacus
Article
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Infectious diseases are recognised as one of the greatest global threats to biodiversity and ecosystem functioning. Consequently, there is a growing urgency to understand the speed at which adaptive phenotypes can evolve and spread in natural populations to inform future management. Here we provide evidence of rapid genomic changes in wild Australi...
Article
The spread of marine pests is occurring at record rates due to globalisation and increasing trade. Environmental DNA (eDNA) is an emerging tool for pest surveillance, allowing for the detection of genetic material shed by organisms into the environment. However, factors influencing the spatial and temporal detection limits of eDNA in marine environ...
Article
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• Dispersal is a critically important process that dictates population persistence, gene flow, and evolutionary potential, and is an essential element for identifying species conservation risks. This study aims to investigate the contributions of dispersal syndromes and hydrographic barriers on patterns of population connectivity and genetic struct...
Preprint
Infectious diseases are recognised as one of the greatest global threats to biodiversity and ecosystem functioning. Consequently, there is a growing urgency to understand the speed at which adaptive phenotypes can evolve and spread in natural populations to inform future management. Here we provide evidence of rapid genomic changes in wild Australi...
Article
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The irregular supply of natural mussel seed for aquaculture has seen an increase in the establishment of hatcheries to produce a reliable source of mussel seed. While many of the factors influencing fertilisation and early survival of hatchery-produced mussel larvae have been explored, little is known about the factors influencing the success of la...
Article
Worldwide, rising ocean temperatures are causing declines and range shifts in marine species. The direct effects of climate change on the biology of marine organisms are often well documented, yet knowledge on the indirect effects, particularly through trophic interactions, is largely lacking. We provide evidence of ocean warming decoupling critica...
Article
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Cosmopolitan marine pelagic species display variable patterns of population connectivity among the world’s major oceans. While this information is crucial for informing management, information is lacking for many ecologically important species, including apex predators. In this study we examine patterns of genetic structure in the broadnose sevengi...
Article
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The number of human–shark interactions has increased worldwide during the past decade resulting in injuries and fatalities. In Australia, the white shark (Carcharodon carcharias), tiger shark (Galeocerdo cuvier), and bull shark (Carcharhinus leucas) are responsible for the majority of fatal incidents. On the southeast coast of Australia, monitoring...
Article
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The health of the world’s oceans are intrinsically linked to the biodiversity of the ecosystems they sustain. The importance of protecting and maintaining ocean biodiversity has been affirmed through the setting of the UN Sustainable Development Goal 14 to conserve and sustainably use the ocean for society’s continuing needs. The decade beginning 2...
Article
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Animal and plant species around the world are being challenged by the deleterious effects of inbreeding, loss of genetic diversity, and maladaptation due to widespread habitat destruction and rapid climate change. In many cases, interventions will likely be needed to safeguard populations and species and to maintain functioning ecosystems. Strategi...
Article
Global climate change poses a significant threat to natural communities around the world, with many plant species showing signs of climate stress. Grassland ecosystems are not an exception, with climate change compounding contemporary pressures such as habitat loss and fragmentation. In this study we assess the climate resilience of Themeda triandr...
Article
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Habitat fragmentation imperils the persistence of many functionally important species, with climate change a new threat to local persistence due to climate‐niche mismatching. Predicting the evolutionary trajectory of species essential to ecosystem function under future climates is challenging but necessary for prioritizing conservation investments....
Article
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Seagrasses are important marine ecosystems situated throughout the world’s coastlines. They are facing declines around the world due to global and local threats such as rising ocean temperatures, coastal development and pollution from sewage outfalls and agriculture. Efforts have been made to reduce seagrass loss through reducing local and regional...
Article
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Rising ocean temperatures and extreme temperature events have precipitated declines and local extinctions in many marine species globally, but patterns of loss are often uneven across species ranges for reasons that are poorly understood. Knowledge of the extent of local adaptation and gene flow may explain such patterns and help predict future tra...
Article
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Warming from climate change and resulting increases in energy stored in the oceans is causing changes in the hydrodynamics and biogeochemistry of marine systems, exacerbating current challenges facing marine fisheries. Although studies have evaluated effects of rising temperatures on marine species, few have looked at these impacts along with other...
Preprint
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Fragmented grassland ecosystems, and the species that shape them, are under immense pressure. Restoration and management strategies should include genetic diversity and adaptive capacity to improve success but these data are generally unavailable. Therefore, we use the foundational grass, Themeda triandra , to test how spatial, environmental, and p...
Article
Revegetation plantings are a key management tool for ecological restoration. Revegetation success is usually measured using ecological traits, however, genetic diversity should also be considered as it can influence fitness, adaptive capacity and long-term viability of revegetation plantings and ecosystem functioning. Here we review the global lite...
Article
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The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected stud...
Article
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Characterising adaptive genetic divergence among conspecific populations is often achieved by studying genetic variation across defined environmental gradients. In marine systems this is challenging due to a paucity of information on habitat heterogeneity at local and regional scales and a dependency on sampling regimes that are typically limited t...
Article
Crude oil is a key contaminant in aquatic environments entering via natural and anthropogenic sources, causing toxicity in marine organisms. Traditionally, biomarkers have been utilised to determine crude oil exposure and effects in aquatic organisms, however advances in genomic technologies has led to increased adoption of transcriptomic approache...
Article
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The Brolga (Antigone rubicunda) is a large Australian crane species with a broad distribution spanning from the tropical north to the south-eastern regions of the continent. Brolga populations throughout New South Wales, Victoria and South Australia have been in decline since the early twentieth century, with the species being listed as vulnerable...
Article
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Background: Understanding the mechanisms that underlie the diversification of herbivores through interactions with their hosts is important for their diversity assessment and identification of expansion events, particularly in a human-altered world where evolutionary processes can be exacerbated. We studied patterns of host usage and genetic struc...
Article
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The whale shark (Rhincodon typus) is an iconic and endangered species with a broad distribution spanning warm-temperate and tropical oceans. Effective conservation management of the species requires an understanding of the degree of genetic connectivity among populations, which is hampered by the need for sampling that involves invasive techniques....
Article
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The Australasian fucoid, Hormosira banksii, commonly known as ‘Neptune’s necklace’ or ‘bubbleweed’ is regarded as an autogenic ecosystem engineer with no functional equivalents. Population declines resulting from climate change and other anthropogenic disturbances pose significant threats to intertidal biodiversity. For effective conservation strat...
Article
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Background Australian scorpions have received far less attention from researchers than their overseas counterparts. Here we provide the first insight into the molecular variation and evolutionary history of the endemic Australian scorpion Urodacus yaschenkoi . Also known as the inland robust scorpion, it is widely distributed throughout arid zones...
Working Paper
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Background. Australian scorpions have received far less attention from researchers than their overseas counterparts. Here we provide the first insight into the molecular variation and evolutionary history of the endemic Australian scorpion Urodacus yaschenkoi. Also known as the inland robust scorpion, it is widely distributed throughout arid zones...
Preprint
Full-text available
Background. Australian scorpions have received far less attention from researchers than their overseas counterparts. Here we provide the first insight into the molecular variation and evolutionary history of the endemic Australian scorpion Urodacus yaschenkoi . Also known as the inland robust scorpion, it is widely distributed throughout arid zones...
Article
Full-text available
Habitat fragmentation is a major threat to biodiversity, as it can alter ecological processes at various spatial and trophic scales. At the species level, fragmentation leading to the isolation of populations can trigger reductions in genetic diversity, potentially having detrimental effects on population fitness, adaptability and ultimately popula...
Article
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Understanding dispersal traits and adaptive potential is critically important when assessing the vulnerability of freshwater species in highly modified ecosystems. The present study investigates the population genetic structure of the Murray crayfish Euastacus armatus in the southern Murray–Darling Basin. This species has suffered significant popul...
Article
AimThe invasion pathways of pest arthropods can be traced using genetic tools to develop an understanding of the processes that have shaped successful invasions and to inform both pest management and conservation strategies in their non-native and native ranges, respectively. The redlegged earth mite, Halotydeus destructor, is a major economic pest...
Article
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The Australian freshwater crayfish species, Cherax quadricarinatus Von Martens, 1868, is an important commercial and invasive species that is also being increasingly used as a model organism to address important and interesting questions in crustacean biology. Through deep sequencing of the transcriptome of C. quadricarinatus from the hepatopancrea...
Article
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Background Mountain landscapes are topographically complex, creating discontinuous `islands¿ of alpine and sub-alpine habitat with a dynamic history. Changing climatic conditions drive their expansion and contraction, leaving signatures on the genetic structure of their flora and fauna. Australia¿s high country covers a small, highly fragmented are...
Article
The red crab, Gecarcoidea natalis, is endemic to Christmas Island in the Indian Ocean and largely responsible for shaping the unique ecosystem found throughout the island's rainforests. However, the introduction and establishment of supercolonies of the highly invasive yellow crazy ant, Anoplolepis gracilipes, has decimated red crab numbers over th...
Article
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Comparative phylogeographic analyses of alpine biota from the Northern Hemisphere have linked patterns of genetic diversification to glacial expansion and contraction events in the Pliocene and Pleistocene. Furthermore, the extent of diversification across species groups appears to be associated with vagility. In this study we test whether these pa...
Article
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The Glenelg spiny freshwater crayfish Euastacus bispinosus is a large endangered freshwater invertebrate of southeastern Australia that has suffered major population declines over the last century. Disjunct populations in the state of South Australia are in a particularly critical condition, restricted to a few isolated rising-spring habitats and i...
Article
The wheat curl mite (WCM), Aceria tosichella Keifer (Trombidiformes: Eriophyidae), is a major pest in cropping regions of the world and is recognised as the primary vector of several yield-reducing pathogens, primarily affecting wheat. Management of WCM is complicated due to several aspects of the mite’s biology and ecology; however, commercially v...
Article
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The complete mitochondrial genome and a set of polymorphic microsatellite markers were identified by 454 pyrosequencing (1/16th of a plate) for the New Caledonian rainforest spider-ant Leptomyrmex pallens. De novo genome assembly recovered the entire mitochondrial genome with mean coverage of 8.9-fold (range 1-27). The mitogenome consists of 15,591...
Article
The eastern barred bandicoot, Perameles gunnii, has undergone a dramatic decline in distribution and abundance on the mainland of Australia during the twentieth century. In 1988 a captive breeding program was initiated to reduce the chance of extinction. With the extinction of the last wild mainland population in the early 1990s, reintroductions fr...
Article
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The Glenelg spiny crayfish, Euastacus bispinosus, is an iconic freshwater invertebrate of south eastern Australia and listed as ‘endangered’ under the Environment Protection and Biodiversity Conservation Act 1999, and ‘vulnerable’ under the International Union for Conservation of Nature’s Red List. The species has suffered major population declines...
Article
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Major disjunctions among marine communities in southeastern Australia have been well documented, although explanations for biogeographic structuring remain uncertain. Converging ocean currents, environmental gradients, and habitat discontinuities have been hypothesized as likely drivers of structuring in many species, although the extent to which s...
Article
A suite of polymorphic microsatellite markers and the complete mitochondrial genome sequence was developed by next generation sequencing (NGS) for the critically endangered orange-bellied parrot, Neophema chrysogaster. A total of 14 polymorphic loci were identified and characterized using DNA extractions representing 40 individuals from Melaleuca,...
Article
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Barred galaxias, Galaxias fuscus, is an endangered freshwater fish confined to headwaters of mountain streams in the Goulburn River system in central Victoria, Australia. Next generation DNA sequencing was used to develop a suite of microsatellite markers that can be used for future population genetic assessments of G. fuscus. A total of 24 polymor...
Article
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Next Generation DNA sequencing was used to develop a suite of microsatellite markers for the marine mollusk, Donax deltoides. A total of 20 polymorphic loci were identified and 12 characterized using 30 individuals from a single population (Venus Bay) in south eastern Australia. We observed moderate to high genetic variation across most loci (mean...
Article
Macroinvertebrates can be successfully used as biomonitors of pollutants and environmental health because some groups are sensitive whereas, others are relatively tolerant to pollutants. An issue of ongoing debate is what constitutes an appropriate group for biomonitoring; should the group represent species, genera or higher taxonomic levels? A phy...
Article
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The complete mitochondrial DNA sequence was determined for the Australian giant crab Pseudocarcinns gigas (Crustacea: Decapoda: Menippidae) and the giant freshwater shrimp Macrobrachium rosenbergii (Crustacea: Decapoda: Palaemonidae). The Pse gigas and Mrosenbergii mitochondrial genomes are circular molecules, 15,515 and 15,772 bp in length, respec...
Article
The complete mitochondrial DNA sequence was determined for the Australian freshwater crayfish Cherax destructor (Crustacea: Decapoda: Parastacidae). The 15,895-bp genome is circular with the same gene composition as that found in other metazoans. However, we report a novel gene arrangement with respect to the putative arthropod ancestral gene order...
Article
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Miller, A.D., Waggy, G., Ryan, S.G., and Austin, C.M. 2004. Mitochondrial 12S rRNA sequences support the existence of a third species of freshwater blackfish (Percicthyidae: Gadopsis) from south-eastern Australia. Memoirs of Museum Victoria 61(2): 121-127. Fish of the genus Gadopsis are a distinctive component of the freshwater fish fauna of south-...

Citations

... Conversely, rivers that drain the Kimberley and Arnhem plateaus in the northwest are highly isolated from one another under current sea-level heights, running more steeply through well-defined rivers characterized by deep sandstone gorges, numerous waterfalls and a lack of flat, lowland areas that would allow for overland connectivity between catchments during floods. Consequently, dispersal between catchments is negligible in all but the most vagile species under current sea-level conditions [39,46]. These contrasting regional features imply that vicariant allopatric speciation during periods of high sea-level isolation would be the stronger mechanism in the northwest. ...
... In extreme cases, intensified grazing by over-abundant sea urchins has depleted kelp communities at both local and regional scales, converting once kelp-dominated reef communities into urchin barrens where kelp recovery is unlikely to occur in the absence of intervention (Rogers- Bennett & Catton, 2019). The loss of kelps through the establishment of urchin barrens has cascading ecological effects on marine ecosystems and economic values, including important fisheries species such as abalone that depend on kelp for habitat and food (Holland et al., 2021;Rogers-Bennett & Catton, 2019). ...