Dean Gilligan

Dean Gilligan
New South Wales Department of Primary Industries · Fishing and Aquaculture (Fisheries NSW)

About

102
Publications
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Introduction

Publications

Publications (102)
Article
Full-text available
Hatchery production and fisheries stocking is a widespread and high profile management practice because it allows recreational fisheries to continue in threatened species. Human-mediated transfer of fish across the geographic boundaries of intraspecies lineages or closely related species can cause introgression and occasionally outbreeding depressi...
Article
Major knowledge gaps exist regarding the evolution of arid zone organisms. For freshwater species with high dispersal potential, little is known if historical aridification influenced connectivity across drainage divides and impacted on their divergence and diversification. We tested the hypothesis that the historical aridification of Australia pro...
Article
Sex‐specific ecology has management implications, but rapid sex‐chromosome turnover in fishes hinders sex‐marker development for monomorphic species. We used annotated genomes and reduced‐representation sequencing data for two Australian percichthyids, Macquarie perch Macquaria australasica and golden perch M. ambigua, and whole genome resequencing...
Article
• Fish assemblages in dryland rivers have life-history strategies that have evolved in response to environmental conditions and triggers, particularly water temperatures and flow regimes. The regulation of rivers through the construction of dams, weirs and other water diversion structures has altered natural flow regimes and the associated ecologic...
Article
Full-text available
• Environmental DNA (eDNA) monitoring is a useful tool for species detection but its use in addressing management questions remains scarce. One factor limiting the use of eDNA as a routine monitoring tool is uncertainty around the potential of eDNA data to estimate species abundance. While several confounding factors limit the ability of eDNA data...
Preprint
Understanding sex-specific biology can aid conservation management. But understanding genomic sex differences of monomorphic fish species and developing molecular sexing assays is challenged by their diverse sex-determination systems. To facilitate research on Percichthyid fish, predominant in the Australian freshwater biota, we report whole genome...
Article
Full-text available
Epizootic haematopoietic necrosis virus (EHNV) was originally detected in Victoria, Australia in 1984. It spread rapidly over two decades with epidemic mortality events in wild redfin perch (Perca fluviatilis) and mild disease in farmed rainbow trout (Oncorhynchus mykiss) being documented across southeastern Australia in New South Wales (NSW), the...
Article
Full-text available
Aquatic macrophytes are often monitored to detect change in ecosystem function and state, as well as assessing the effectiveness of invasive aquatic plant management. This study compares seven methodologies to monitor the distribution and abundances of aquatic macrophytes. Four line transect methodologies and three spatial mapping techniques were e...
Article
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Monitoring aquatic biodiversity through DNA extracted from environmental samples (eDNA) combined with high-throughput sequencing, commonly referred to as eDNA metabarcoding, is increasing in popularity within the scientific community. However, sampling strategies, laboratory protocols and analytical pipelines can influence the results of eDNA metab...
Article
To facilitate future research in freshwater fish recruitment response to environmental flow delivery, size‐at‐age and growth models are presented for eight fish species occurring in south‐eastern Australia; three small‐bodied species and the juvenile 0+ age classes of five large‐bodied species. Otolith increments were used to estimate the daily age...
Article
Populations that are adaptively divergent but maintain high gene flow may have greater resilience to environmental change as gene flow allows the spread of alleles that have already been tested elsewhere. In addition, populations naturally subjected to ecological disturbance may already hold resilience to future environmental change. Confirming thi...
Article
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Adaptive differences across species’ ranges can have important implications for population persistence and conservation management decisions. Despite advances in genomic technologies, detecting adaptive variation in natural populations remains challenging. Key challenges in gene-environment association studies involve distinguishing the effects of...
Article
Species range limits often fluctuate in space and time in response to variation in environmental factors and to gradual niche evolution due to changes in adaptive traits. We used genome-wide data to investigate evolutionary divergence and species range limits in a generalist and highly dispersive fish species that shows an unusually wide distributi...
Article
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Genetic diversity underpins the ability of populations to persist and adapt to environmental changes. Substantial empirical data show that genetic diversity rapidly deteriorates in small and isolated populations due to genetic drift, leading to reduction in adaptive potential and fitness and increase in inbreeding. Assisted gene flow (i.e. via tran...
Article
Species range limits often fluctuate in space and time in response to variation in environmental factors, and to gradual niche evolution due to changes in adaptive traits. We used genome-wide data to investigate evolutionary divergence and species range limits and in a generalist and highly dispersive fish species that shows an unusually wide distr...
Article
Genetic variation in mitochondrial genes could underlie metabolic adaptations because mitochondrially encoded proteins are directly involved in a pathway supplying energy to metabolism. Macquarie perch from river basins exposed to different climates differ in size and growth rate, suggesting potential presence of adaptive metabolic differences. We...
Article
Full-text available
Carp (Cyprinus carpio L.) is a pest species in Australian waterways, and cyprinid herpesvirus 3 (CyHV-3) is being considered as a potential biological control (biocontrol) agent. An important consideration for any such agent is its target specificity. In this study, the susceptibility to CyHV-3 of a range of non-target species (NTS) was tested. The...
Article
Genetic variation is critical to the persistence of populations and their capacity to adapt to environmental change. The distribution of genetic variation across a species' range can reveal critical information that is not necessarily represented in species occurrence or abundance patterns. We identified environmental factors associated with the am...
Article
The ranavirus epizootic hematopoietic necrosis virus (EHNV) is endemic to Australia and is listed by the Office International des Epizooties. Clinical outbreaks have only been observed in wild populations of Redfin Perch Perca fluviatilis (also known as Eurasian Perch) and farmed populations of Rainbow Trout Oncorhynchus mykiss. The initial outbrea...
Article
Full-text available
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...
Technical Report
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There are obligations under the Basin Plan to report on the contribution of Commonwealth environmental water to environmental objectives. This study was developed to follow guiding principles of the Environmental Outcomes Framework underpinning the management of Commonwealth environmental water. The sampling regime adopted provides an opportunity t...
Article
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Freshwater eel-tailed catfishes (Tandanus spp.) have a complicated phylogenetic structure including several undescribed cryptic species in eastern Australia. This naturally complex phylogeny is further complicated by their phylogeography, with the existence of numerous populations reported to have been subject to historic translocations. The Murray...
Article
The spangled perch Leiopotherapon unicolor is considered a rare vagrant in the southern Murray-Darling Basin, Australia, due to its intolerance of the relatively cool water temperatures that prevail during winter months. This study details 1342 records of the species from 68 locations between 2010 and 2014 outside its accepted ‘core adult range’ fo...
Article
Full-text available
To evaluate strategies within a carp-control plan, we developed a meta-population model of the geographic arrangement, biological connections and ‘unfished’ stock structure of the pest population of common carp (Cyprinus carpio) in a large river catchment. The model was tuned to recent observations of biomass. Published data were used to estimate s...
Article
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Recovery of threatened species is often necessarily a long-term process. The present paper details the progress towards the recovery of trout cod, Maccullochella macquariensis, an iconic, long-lived fish species first listed as threatened in the 1980s. The objectives, actions and progress over three successive national recovery plans (spanning 18 y...
Article
The reference condition of a river ecosystem is often used as a benchmark against which restoration activities are framed. However, the reference condition approach is not suitable for all river health assessments given undisturbed reference sites similar to a test site may not exist. We tested the ability of applying individual Species Distributio...
Article
Full-text available
The contributions of nursery habitats to recruitment of non-native common carp (Cyprinus carpio) were estimated via analysis of water and otolith 87Sr/86Sr and otolith trace element concentrations (Mg:Ca, Mn:Ca, Sr:Ca, Ba:Ca) over 3 years in the Lachlan River, Australia. Water samples and otoliths of postlarval carp were analyzed to characterize 87...
Article
Abstract The ranavirus, epizootic hematopoietic necrosis virus (EHNV), is endemic to southern Australia with natural outbreaks resulting in mass mortality events in wild Redfin Perch Perca fluviatilis (also known as Eurasian Perch) and less severe disease in farmed Rainbow Trout Oncorhynchus mykiss. To further investigate the host range for EHNV, 1...
Article
Full-text available
Interspecies hybridization is of concern for the management of invasive species, as it can allow the exchange of advantageous alleles between introduced species and undermine control efforts. In this study, hybridization between populations of introduced common carp and goldfish in Australia is investigated. Common carp and goldfish were sampled ex...
Article
The presence and distribution of hybrid individuals and the existence of a hybrid zone between the catadromous Australian bass Macquaria novemaculeata and estuary perch Macquaria colonorum were investigated throughout the range of both species in Australia. Bayesian analyses and genotypic simulations identified 140 putative hybrids (11·5% of the to...
Article
Abstract Habitat fragmentation is one of the leading causes of population declines, threatening ecosystems worldwide. Freshwater taxa may be particularly sensitive to habitat loss as connectivity between suitable patches of habitat is restricted not only by the natural stream network but also by anthropogenic factors. Using a landscape genetics app...
Article
Over the past three decades the Booroolong Frog (Litoria booroolongensis) has declined across the majority of its range, with predation from introduced fish hypothesized as contributing to this decline. In this study we undertook an experiment in artificial enclosures to test the propensity for three introduced fish species (European Carp, Cyprinus...
Article
The estuary perch (Macquaria colonorum) represents an important model for assessing how historical changes in coastal geomorphology and current oceanographic and estuarine conditions may have impacted connectivity in a catadromous fish. A fragment of the mitochondrial control region and six microsatellite DNA markers were used to clarify connectivi...
Article
The Murray crayfish (Euastacus armatus) is a large freshwater species endemic to the Murray-Darling River systems of South Australia, Victoria, New South Wales and the Australian Capital Territory, where it is important for recreational fishing and regional tourism. However, populations have continued to decline due to habitat modification and degr...
Article
Full-text available
The common carp Cyprinus carpio introduced in two drainages in eastern Australia are largely descended from European common carp, and in a third drainage they descend largely from East Asian common carp. The partial genetic differentiation among the species in those drainages is consistent with their origins.
Article
The Australian freshwater catfish (Tandanus tandanus) has suffered a decline in abundance and distribution, and stocking of wild populations with hatchery-bred fish has been suggested to assist with population recovery. Here we describe the isolation and characterisation of eight microsatellite markers that may be used to assess population structur...
Article
Rivers provide an excellent system to study interactions between patterns of biodiversity structure and ecological processes. In these environments, gene flow is restricted by the spatial hierarchy and temporal variation of connectivity within the drainage network. In the Australian arid zone, this variability is high and rivers often exist as isol...
Article
Aim We conducted a range-wide phylogeographic study of a common Australian freshwater fish, the golden perch (Macquaria ambigua), to investigate the relationship between environmental processes and evolutionary history in drainage basins. Location Inland [Lake Eyre (LEB), Murray–Darling (MDB) and Bulloo (BULL)] and coastal basins [Fitzroy (FITZ)] o...
Article
Variable hydrological regimes and habitat availability are factors that affect the distribution of freshwater dependent species and are expected to influence their levels of genetic diversity. Although geologically relatively stable, the south eastern region of Australia has experienced significant changes in hydrological conditions during the Quat...
Article
Full-text available
Common carp Cyprinus carpio were introduced into Australia on several occasions and are now the dominant fish in the Murray-Darling Basin (MDB), the continent's largest river system. In this study, variability at 14 microsatellite loci was examined in C. carpio (n = 1037) from 34 sites throughout the major rivers in the MDB, from 3 cultured populat...