Dean M. Gilligan

Islands of water in a sea of dry land: hydrological regime predicts genetic diversity and dispersal in a widespread fish from Australia’s arid zone, the golden perch (Macquaria ambigua)

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 isolated waterholes connected during unpredictable floods. These conditions cause boom/bust cycles in the population dynamics of taxa, but their influence on spatial genetic diversity is largely unknown. We used a landscape genetics approach to assess the effect of hydrological variability on gene flow, spatial population structure and genetic diversity in an Australian freshwater fish, Macquaria ambigua. Our analysis is based on microsatellite data of 590 samples from 26 locations across the species range. Despite temporal isolation of populations, the species showed surprisingly high rates of dispersal, with population genetic structure only evident among major drainage basins. Within drainages, hydrological variability was a strong predictor of genetic diversity, being positively correlated with spring‐time flow volume. We propose that increases in flow volume during spring stimulate recruitment booms and dispersal, boosting population size and genetic diversity. Although it is uncertain how the hydrological regime in arid Australia may change under future climate scenarios, management strategies for arid‐zone fishes should mitigate barriers to dispersal and alterations to the natural flow regime to maintain connectivity and the species’ evolutionary potential. This study contributes to our understanding of the influence of spatial and temporal heterogeneity on population and landscape processes.

The role of anthropogenic vs. natural in-stream structures in determining connectivity and genetic diversity in an endangered freshwater fish, Macquarie perch (Macquaria australasica)

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 approach, we assessed the impact of habitat availability on population genetic diversity and connectivity of an endangered Australian freshwater fish Macquarie perch, Macquaria australasica (Percichthyidae). The relative contribution of anthropogenic versus natural in‐stream habitat structures in shaping genetic structure and diversity in M. australasica was quite striking. Genetic diversity was significantly higher in locations with a higher river slope, a correlate of the species preferred habitat – riffles. On the other hand, barriers degrade preferred habitat and impede dispersal, contributing to the degree of genetic differentiation among populations. Our results highlight the importance of landscape genetics to understanding the environmental factors affecting freshwater fish populations and the potential practical application of this approach to conservation management of other freshwater organisms.

Phylogeography of a threatened freshwater fish (Mogurnda adspersa) in eastern Australia: conservation implications

Phylogeography is a field that has the potential to provide an integrative approach to the conservation of threatened species. The southern purple spotted gudgeon, Mogurnda adspersa, is a small freshwater fish that was once common and widely distributed throughout south-eastern Australia. However, habitat alteration has dramatically reduced the size and the range of Murray-Darling Basin populations, which are now classified as endangered. Here patterns of genetic structure and evolutionary history of M. adspersa in southern Queensland and the Murray-Darling Basin are elucidated using three regions of the mitochondrial DNA, the ATPase 6 and 8 and the control region. Murray-Darling Basin populations are characterised by lineages with highly localised endemism, very low genetic diversity and restricted gene flow. Phylogenetic reconstructions show that Murray-Darling Basin populations comprise a monophyletic clade that possibly originated by range expansion from the coast around 1.6 million years ago. It is proposed that the divergent Murray-Darling Basin clade is of high conservation priority and requires separate management. The present study further exemplifies the role of drainage rearrangement in driving evolutionary diversification in Australian freshwater fishes, an historical process with profound implications for conservation management.

Mortality of larval Murray cod (Maccullochella peelii peelii) and golden perch (Macquaria ambigua) associated with passage through two types of low-head weirs

Determining factors responsible for increases in the mortality of freshwater fish larvae are important for the conservation of recruitment processes and for the long-term sustainability of freshwater fish populations. To assess the impact of one such process, Murray cod (Maccullochella peelii peelii Mitchell) and golden perch (Macquaria ambigua Richardson) larvae were arranged into treatment and control groups and passed through different configurations (overshot and undershot) of a low-level weir. Passage through an undershot weir resulted in the death of 95 ± 1% golden perch and 52 ± 13% Murray cod. By comparison, mortality was significantly lower in the overshot treatment and both controls. The relatively large number of undershot weirs within the known distribution of these species could impact upon recruitment over a large scale. It is therefore recommended that water management authorities consider the potential threats of operating undershot gated weirs on the survival of larval fish until further research determines appropriate mitigatory measures for these and other species.

Experimental Infection of Australian Freshwater Fish with Epizootic Haematopoietic Necrosis Virus (EHNV)

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, 12 ecologically or economically important freshwater fish species from southeastern Australia were exposed experimentally to the virus. A bath-challenge model at 18 ± 3°C was employed with limited use of intraperitoneal inoculation to determine if a species was likely to be susceptible to EHNV. Of the species tested, Murray-Darling Rainbowfish Melanotaenia fluviatilis and Dewfish Tandanus tandanus (also known as Freshwater Catfish) were considered to be potentially susceptible species. EHNV was isolated from approximately 7% of surviving Eastern Mosquitofish Gambusia holbrooki, indicating this widespread alien fish species is a potential carrier. The infection of Silver Perch Bidyanus bidyanus and Macquarie Perch Macquaria australasica and the lack of infection in Murray Cod Maccullochella peelii peelii and Golden Perch Macquaria ambigua ambigua after exposure to EHNV via water confirmed earlier data from Langdon (1989). Five other species of native fish were potentially not susceptible to the virus or the fish were able to recover during the standard 35-d postchallenge observation period. Overall, it appeared that EHNV was less virulent in the present experimental model than in previous studies, but the reasons for this were not identified. Received May 21, 2012; accepted November 1, 2012.

Recovery of the endangered trout cod, Maccullochella macquariensis: what have we achieved in more than 25 years?

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 years) are assessed, documenting changes to population distribution and abundance and updating ecological knowledge. Increased knowledge (especially breeding biology and hatchery techniques, movements, habitats and genetics) has greatly influenced recovery actions and the use of a population model was developed to assist with management options and stocking regimes. Key recovery actions include stocking of hatchery-produced fish to establish new populations, regulations on angling (including closures), education (particularly identification from the closely related Murray cod, M. peelii) and habitat rehabilitation (especially re-instatement of structural woody habitats). In particular, the establishment of new populations using hatchery stocking has been a successful action. The importance of a coordinated long-term approach is emphasised and, although there is uncertainty in ongoing resourcing of the recovery program, much has been achieved and there is cautious optimism for the future of this species.

Historic divergence with contemporary connectivity in a catadromous fish, the estuary perch (Macquaria colonorum)

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 connectivity in 17 populations (n = 354) of estuary perch from the southeast and southern coasts of Australia. The mtDNA data showed a latitudinal disjunction in haplotype frequencies that divided populations into two groups (ΦST = 0.419), in a pattern suggestive of isolation by geographic distance. However, no marked structure or correlation with distance was apparent within each group, a result consistent with microsatellite data that showed high contemporary population connectivity across large distances. This was contrary to expectations that the species would exhibit moderate to strong genetic structure consistent with a one-dimensional stepping stone pattern. Coales...

Optimising an integrated pest-management strategy for a spatially structured population of common carp (Cyprinus carpio) using meta-population modelling

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 sampling biases and yield from available carp-control tools. We simulated proposed carp-removal activities and also the potential effects of biological-control options; cyprinid herpesvirus-3 (CHV-3) and daughterless-carp gene technology. Outputs compared the population abundance before carp control (before 2009) and after a ~70-year period of sustained management. Models suggest that the proposed levels of carp removal may reduce biomass by ~50%. Although substantial, this control level may not be sufficient to reduce carp biomass densities below thresholds associated with ecological damage. In contrast, a CHV-3 bio-control program has potential to reduce carp biomass densities to, or exceeding, target levels, if mortality rates exceed 30% and broad-scale outbreaks occur in at least 40% of years, despite the likely development of resistance. A synergistic bio-control program using CHV-3, followed by a gene technology-based sex-ratio distortion program, is potentially the most effective strategy for reducing carp biomass by over 90% in the long term.

Genome-wide data delimits multiple climate-determined species ranges in a widespread Australian fish, the golden perch (Macquaria ambigua)

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 distribution across arid and semi-arid regions of Australia. We generated ddRAD data (18,979 filtered SNPs and 1.725million bp of sequences) for samples from 27 localities spanning the native range of golden perch, Macquaria ambigua (Teleostei; Percichthyidae). Our analytical framework uses population genomics to assess connectivity and population structure using model-based and model-free approaches, phylogenetics to clarify evolutionary relationships, and a coalescent-based Bayesian species delimitation method to assess statistical support of inferred species boundaries. Addressing uncertainties regarding range limits and taxonomy is particularly relevant for this iconic Australian species because of the intensive stocking activities undertaken to support its recreational fishery and its predicted range shifts associated with ongoing climate change. Strong population genomic, phylogenetic, and coalescent species delimitation support was obtained for three separately evolving metapopulation lineages, each lineage should be considered a distinct cryptic species of golden perch. Their range limits match the climate-determined boundaries of main river basins, despite the ability of golden perch to cross drainage divides. We also identified cases suggestive of anthropogenic hybridization between lineages due to stocking of this recreationally important fish, as well as a potential hybrid zone with a temporally stable pattern of admixture. Our work informs on the consequences of aridification in the evolution of aquatic organisms, a topic poorly represented in the literature. It also shows that genome-scale data can substantially improve and rectify inferences about taxonomy, hybridization and conservation management previously proposed by detailed genetic studies.

Severe consequences of habitat fragmentation on genetic diversity of an endangered Australian freshwater fish: A call for assisted gene flow

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 (e.g. via translocations) can reverse these trends, but lack of data on fitness loss and fear of impairing population “uniqueness” often prevents managers from acting. Here, we use population genetic and riverscape genetic analyses and simulations to explore the consequences of extensive habitat loss and fragmentation on population genetic diversity and future population trajectories of an endangered Australian freshwater fish, Macquarie perch Macquaria australasica. Using guidelines to assess the risk of outbreeding depression under admixture, we develop recommendations for population management, identify populations requiring genetic rescue and/or genetic restoration and potential donor sources. We found that most remaining populations of Macquarie perch have low genetic diversity, and effective population sizes below the threshold required to retain adaptive potential. Our simulations showed that under management inaction, smaller populations of Macquarie perch will face inbreeding depression within a few decades, but regular small‐scale translocations will rapidly rescue populations from inbreeding depression and increase adaptive potential through genetic restoration. Despite the lack of data on fitness loss, based on our genetic data for Macquarie perch populations, simulations and empirical results from other systems, we recommend regular and frequent translocations among remnant populations within catchments. These translocations will emulate the effect of historical gene flow and improve population persistence through decrease in demographic and genetic stochasticity. Increasing population genetic connectivity within each catchment will help to maintain large effective population sizes and maximize species adaptive potential. The approach proposed here could be readily applicable to genetic management of other threatened species to improve their adaptive potential.