Rhys Coleman

Balancing genetic uniqueness and genetic variation in determining conservation and translocation strategies: a comprehensive case study of threatened dwarf galaxias, Galaxiella pusilla (Mack) (Pisces: Galaxiidae)

Genetic markers are widely used to define and manage populations of threatened species based on the notion that populations with unique lineages of mtDNA and well‐differentiated nuclear marker frequencies should be treated separately. However, a danger of this approach is that genetic uniqueness might be emphasized at the cost of genetic diversity, which is essential for adaptation and is potentially boosted by mixing geographically separate populations. Here, we re‐explore the issue of defining management units, focussing on a detailed study of Galaxiella pusilla, a small freshwater fish of national conservation significance in Australia. Using a combination of microsatellite and mitochondrial markers, 51 populations across the species range were surveyed for genetic structure and diversity. We found an inverse relationship between genetic differentiation and genetic diversity, highlighting a long‐term risk of deliberate isolation of G. pusilla populations based on protection of unique lineages. Instead, we adopt a method for identifying genetic management units that takes into consideration both uniqueness and genetic variation. This produced a management framework to guide future translocation and re‐introduction efforts for G. pusilla, which contrasted to the framework based on a more traditional approach that may overlook important genetic variation in populations.

Microsatellite markers and mtDNA data indicate two distinct groups in dwarf galaxias, Galaxiella pusilla (Mack) (Pisces: Galaxiidae), a threatened freshwater fish from south-eastern Australia

Galaxiella pusilla is a small, non-migratory freshwater fish, endemic to south-eastern Australia and considered nationally threatened. To assist in the conservation of the species, microsatellite markers were developed and used to characterize genetic variation in 20 geographically distinct populations across its range. Substantial genetic differentiation was found between an eastern (Victoria east of the Otway Ranges and Tasmania) and western (South Australia and Victoria west of, and including, the Otway Ranges) region. This major separation was also observed in data from a mitochondrial gene and supports a previously proposed split. Populations from the eastern region had overall lower genetic diversity for both the microsatellite and mtDNA markers. There was substantial genetic differentiation between populations within the two regions, suggesting that gene flow is limited by the isolation of freshwater streams. Genetic structure, consistent with an isolation-by-distance model, was also evident in both regions. Patterns of genetic variation in this threatened species are compared to those obtained for other taxa across the same region. The need to consider separate conservation strategies for the two sets of populations is emphasized.

REVIEW: Identifying, preventing and mitigating ecological traps to improve the management of urban aquatic ecosystems

Summary 1. Urbanization alters the environmental characteristics of aquatic ecosystems, often reducing the availability and quality of habitats for animals. Improving the condition of urban waterbodies is increasingly important, but management activities could have unintended outcomes that increase the extinction risk for animals. 2. A mismatch can exist between human perceptions of habitat quality, and what represents functional habitats for animals. This can lead to animals not responding to management activities, if presumed high-quality habitats are unsuitable. More seriously, the fitness of animals could be compromised by management activities, especially if animals prefer threatening habitats resulting in an ecological trap. 3. Ecological traps can drive populations to extinction and may arise directly from management activities. However, there has been limited work on how to best manage traps despite their important implications for the conservation and management of animal populations. 4. We illustrate how urban management activities could cause ecological traps, and potential ways that traps could be managed. We outline a decision framework to identify, prevent and mitigate ecological traps, and illustrate this framework using stormwater wetlands as a case study. Stormwater wetlands have many features of natural wetlands but accumulate pollutants as part of the stormwater treatment process and there is a high likelihood some are traps. If so, this will be an important environmental issue, given the rate at which these wetlands are being created around many cities. 5. Synthesis and application. Ecological traps that arise as unintended outcomes of management activities could represent a serious but currently underappreciated environmental problem. Our study will help minimize the risk that management activities inadvertently decouple habitat selection cues from habitat quality, and mitigate the potential consequences for animals when this does occur. This is an important step to ensure that management activities achieve desired ecological outcomes and do not result in unintentional environmental degradation.

Source tracking using microbial community fingerprints: Method comparison with hydrodynamic modelling

Urban estuaries around the world are experiencing contamination from diffuse and point sources, which increases risks to public health. To mitigate and manage risks posed by elevated levels of contamination in urban waterways, it is critical to identify the primary water sources of contamination within catchments. Source tracking using microbial community fingerprints is one tool that can be used to identify sources. However, results derived from this approach have not yet been evaluated using independent datasets. As such, the key objectives of this investigation were: (1) to identify the major sources of water responsible for bacterial loadings within an urban estuary using microbial source tracking (MST) using microbial communities; and (2) to evaluate this method using a 3-dimensional hydrodynamic model. The Yarra River estuary, which flows through the city of Melbourne in South-East Australia was the focus of this study. We found that the water sources contributing to the bacterial community in the Yarra River estuary varied temporally depending on the estuarys hydrodynamic conditions. The water source apportionment determined using microbial community MST correlated to those determined using a 3-dimensional hydrodynamic model of the transport and mixing of a tracer in the estuary. While there were some discrepancies between the two methods, this investigation demonstrated that MST using bacterial community fingerprints can identify the primary water sources of microorganisms in an estuarine environment. As such, with further optimization and improvements, microbial community MST has the potential to become a powerful tool that could be practically applied in the mitigation of contaminated aquatic systems.

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.

Integrated conceptual modelling of faecal contamination in an urban estuary catchment

Urban stormwater is regarded as a key input of faecal contamination in receiving water bodies and therefore, a major concern for health risks associated with aquatic recreation. Wastewater leakages, cross connections and overflows, together with faeces washed from surfaces during rainfall events, are possible origins of faecal contamination which enter these water bodies through stormwater drains. This paper applies conceptual models to a case study of the Yarra River estuary to understand the relative importance of fluxes derived from an urban creek and the 219 urban stormwater pipes which drain directly to the estuary as compared with other inputs, such as the Yarra River itself. Existing hydrologic-microorganism models were used for the estimation of the inputs from riverine and urban stormwater fluxes. These predictions were applied as boundary conditions for a new, highly simplified, model which accounts for the transport and survival of faecal microorganisms in the estuary. All models were calibrated using a rich dataset, containing over 2,000 measured Escherichia coli concentrations. Mass balances from the riverine and stormwater models indicate the limited influence of urban stormwater drains on the estuary during dry weather; less than 0.05% to 10% (5th and 95th percentile; median 0.5%) of the total daily E. coli load entering the estuary was derived from urban stormwater drains. While wet weather contributions from stormwater drains could be more significant (2% to 50%; 5th and 95th percentile), the average contribution remained marginal (median 10%). Sensitivity testing of the estuarine microorganism model by switching off stormwater boundary conditions resulted in minimal model efficiency reduction; this may reflect the low average daily contribution from urban stormwater drains. While these results confirm previous studies which show that E. coli loads derived from stormwater drains are dwarfed by other inputs, it is essential to note that these results also demonstrate that some conditions reveal the opposite; high proportions from stormwater are possible when combined with low riverine inputs and high urban rainfall. Furthermore, this study focuses on the overall impacts of direct urban stormwater inputs on the faecal contamination levels within the estuary, and localized impacts would certainly require further investigation.

Presence and survival of culturable Campylobacter spp. and Escherichia coli in a temperate urban estuary

Urban estuaries throughout the world typically contain elevated levels of faecal contamination, the extent of which is generally assessed using faecal indicator organisms (FIO) such as Escherichia coli. This study assesses whether the bacterial FIO, E. coli is a suitable surrogate for Campylobacter spp., in estuaries. The presence and survival dynamics of culturable E. coli and Campylobacter spp. are compared in the water column, bank sediments and bed sediments of the Yarra River estuary (located in Melbourne, Australia). The presence of E. coli did not necessarily indicate detectable levels of Campylobacter spp. in the water column, bed and bank sediments, but the inactivation rates of the two bacteria were similar in the water column. A key finding of the study is that E. coli and Campylobacter spp. can survive for up to 14days in the water column and up to 21days in the bed and bank sediments of the estuary. Preliminary data presented in this study also suggests that the inactivation rates of the two bacteria may be similar in bed and bank sediments. This undermines previous hypotheses that Campylobacter spp. cannot survive outside of its host and indicates that public health risks can persist in aquatic systems for up to three weeks after the initial contamination event.

Tidal fluctuations influence E. coli concentrations in urban estuaries

This study investigated the influence of water level and velocity on Escherichia coli levels over multiple tidal cycles in an urban microtidal estuary in Melbourne, Australia. Over 3,500 E. coli samples and high resolution water level and velocity measurements from two locations within the estuary were used for the analysis. E. coli negatively correlated with water level in the upper estuary which was proposed to be linked to increased resuspension of estuarine sediments during low tide. No relationship was found in the lower estuary, likely due to wet weather inputs dwarfing subtler tidal-related processes. Removal of wet weather data enabled significant relationships to emerge in the lower estuary: 1) positive with water level (when a 9-h shift applied corresponding to the phase shift between water levels and velocities) and; 2) positive with velocity (no shift applied). This supports a link between increased E. coli levels and tidal-related resuspension.

Spatial variability of E. coli in an urban salt-wedge estuary

This study investigated the spatial variability of a common faecal indicator organism, Escherichia coli, in an urban salt-wedge estuary in Melbourne, Australia. Data were collected through comprehensive depth profiling in the water column at four sites and included measurements of temperature, salinity, pH, dissolved oxygen, turbidity, and E. coli concentrations. Vertical variability of E. coli was closely related to the salt-wedge dynamics; in the presence of a salt-wedge, there was a significant decrease in E. coli concentrations with depth. Transverse variability was low and was most likely dwarfed by the analytical uncertainties of E. coli measurements. Longitudinal variability was also low, potentially reflecting minimal die-off, settling, and additional inputs entering along the estuary. These results were supported by a simple mixing model that predicted E. coli concentrations based on salinity measurements. Additionally, an assessment of a sentinel monitoring station suggested routine monitoring locations may produce conservative estimates of E. coli concentrations in stratified estuaries.

Taking advantage of adaptations when managing threatened species within variable environments: the case of the dwarf galaxias, Galaxiella pusilla (Teleostei, Galaxiidae)

Native fish are threatened globally by invasive species, and management actions largely focus on detecting and eradicating invaders before they become established. However, once established, invaders might also be controlled by taking advantage of adaptations of threatened species to local conditions. This strategy was explored in dwarf galaxias (Galaxiella pusilla) a freshwater-dependent species of national conservation significance in Australia, threatened by invasive eastern gambusia (Gambusia holbrooki). Most habitats occupied by G. pusilla experience a seasonally variable and unpredictable hydrologic regime, where water levels substantially contract during dry periods and expand during wet periods. It was hypothesised that they are likely to have developed adaptations to surviving in these habitats by persisting without surface water. In contrast to G. holbrooki, we found that G. pusilla could withstand longer periods without surface water, including air breathing and higher respiration rates in air, than could G. holbrooki. We showed, within a single G. pusilla population, large inter-annual variability in fish densities linked to natural wetting and drying regimes. These findings indicate that periodic drying provides a way of protecting G. pusilla in water bodies where G. holbrooki has invaded, representing a strategy that takes advantage of local adaptation and metapopulation structure of G. pusilla.