Daniel J. Stoessel

Context: Where conservation efforts are undertaken to decrease downward trends in fish populations, comparatively few resources are directed to small-bodied cryptic species. The true extent of the decline of many of these species is therefore often unknown. Where surveys have occurred, they are frequently limited by budget and hence effort. Consequently, there is a risk that rare species may not be physically captured despite their presence at a site. Such an outcome has dire consequences for the conservation of remnant populations of threatened fish. To counter possible false negative detections, environmental DNA is increasingly being used in conjunction with, or as a precursor to, physical surveys. The Southern Purple-spotted Gudgeon (Mogurnda adspersa) is a small, threatened freshwater fish native to Australia. Recent surveys captured M. adspersa in two highly turbid waterbodies in north-central Victoria. This capture represented the first detection of the species in the state in more than 20 years. Because these waterbodies are part of a network of hydrologically connected systems, it was suspected that the species likely had a broader distribution in the region. Aims: To develop a probe-based eDNA assay for M. adspersa and compare its sensitivity against a physical sampling program. Methods: Detection (presence/absence) between eDNA and traditional surveys was compared across multiple sites. Key results: eDNA presents an effective tool for determining the presence of M. adspersa. The eDNA survey demonstrated significant clustering of eDNA detections towards the outlets of lakes sampled, suggesting concentrated eDNA at this point, or that, due to the channels being shallower, the eDNA of resident individuals may be less diluted. Conclusions: Based on these results, future survey of rare, cryptic species in highly turbid lake systems should in the first instance include a broad scale eDNA survey, with sampling concentrated at outlet channels. Implications: The likely most cost-effective approach to determining the presence/absence of rare species in lake systems is the collection of eDNA samples at outlet channels.

Context: Where water is used to support ecosystem processes under a changing climate, it is vital that it is done efficiently. The Australian bass (Percalates novemaculeata) is a freshwater fish endemic to south-eastern Australia that has been adversely affected by anthropogenic disturbances. This has prompted investigations as to the use of environmental water in support of the species in addition to widespread stocking. Aims: We investigate whether environmental flows and stocking in isolation support a population of Australian bass more effectively than they do in combination, under various climate-change scenarios. We also determine the cost efficiency of each strategy. Methods: We used an age-based stochastic population model to determine outcomes of strategies. Key results: Our model suggested that the application of two or three large environmental flows per year was highly effective in all but the most-extreme climate-change scenarios. Alternatively, the value of stocking increased with an increasing severity of climate change. The cost of delivery of environmental flows far exceeds that of stocking. However, stocking directly benefits only a single species (in this case Australian bass), whereas the provision of environmental water has multi-species benefits, in addition to being vital to maintaining the river ecosystem itself. Conclusions: Under severe climate-change scenarios, stocking, and the use of environmental water in support of populations, may be successful only to a point. Implications: Extreme climate change may therefore negate any attempts to halt the decline of populations of some species.

The release of cold-water from hypolimnetic zones of impoundments sharply reduces downstream riverine water temperature. This cold-water pollution (CWP) can extend for hundreds of kilometres, severely challenging the physiological ability of aquatic fauna, particularly ectotherms such as fish, to maintain essential processes such as metabolism, development and growth and survival. The impact of CWP on native fish, especially early life stages, is poorly known. We investigated the effect of a 24-hour exposure to a range of environmentally-related water temperatures (8, 10, 12, 14, 16, 18 and 20 ?) on three age-classes (< 24-hour-old, 7-day and 14-day-old larvae) of two Australian native fish species: Murray cod (Maccullochella peelii) and Macquarie perch (Macquaria australasica). Overall, larvae of M. peelii were more sensitive to lower water temperatures and hence CWP than M. australasica, indicated by higher rates of equilibrium loss. Larvae of M. peelii were most sensitive to exposure at seven days old whereas M. australasica larvae were most sensitive at < 24-h-old. Using our results, we modelled pre-and post-impoundment temperature scenarios and estimated the downstream CWP footprint for both species in an Australian river reach. Larvae ofM. peelii were predicted to be absent from the first 26 km of river downstream of the impoundment compared with no impact on the distribution of M. australasica. Managing riverine water temperature below impoundments is fundamental to promoting positive outcomes for endemic fish on not only a local, but global basis. This study emphasises the differential impact of CWP among the critical early life stages and fish species and highlights the urgent need to better manage hypolimnetic water releases to improve downstream river ecosystems.

Many freshwater fishes are imperilled globally, and there is a need for easily accessible, contemporary ecological knowledge to guide management. This compendium contains knowledge collated from over 600 publications and 27 expert workshops to support the restoration of 9 priority native freshwater fish species, representative of the range of life-history strategies and values in south-eastern Australia’s Murray–Darling Basin. To help prioritise future research investment and restoration actions, ecological knowledge and threats were assessed for each species and life stage. There is considerable new knowledge (80% of publications used were from the past 20 years), but this varied among species and life stages, with most known about adults, then egg, juvenile and larval stages (in that order). The biggest knowledge gaps concerned early life stage requirements, survival, recruitment, growth rates, condition and movements. Key threats include reduced longitudinal and lateral connectivity, altered flows, loss of refugia, reductions in both flowing (lotic) and slackwater riverine habitats, degradation of wetland habitats, alien species interactions and loss of aquatic vegetation. Examples and case studies illustrating the application of this knowledge to underpin effective restoration management are provided. This extensive ecological evidence base for multiple species is presented in a tabular format to assist a range of readers.

Estuary perch (Percalatescolonorum Gunther) is an estuary dependent fish native to south-eastern Australia that is in decline. There is an increasing emphasis on stocking the species. Understanding the genetic structure across its range is important for guiding optimal stocking strategies. A prior study found some evidence of population genetic structure; however, few genetic markers were used in that assessment. Here, we develop 21 novel polymorphic microsatellite markers to reassess population genetics. Analyses indicate three broad genetic clusters, with populations on mainland Australia exhibiting an isolation by distance pattern. The only known population from Tasmania is genetically and geographically isolated from mainland populations and has very low levels of genetic diversity. We provide recommendations for sourcing broodstock from mainland populations, including describing three broad areas for procuring and releasing broodstock and offspring. The markers and results reported here will prove invaluable for guiding and monitoring the outcomes of stocking and conservation activities.

Devising effective techniques for breeding and rearing rare non-migratory galaxiids is urgently required for conservation purposes where few animals exist in the wild for translocation or reintroduction. The development of such protocols is particularly pertinent in light of recent intense widespread bushfires and long-term drought in southeastern Australia, which have increased the likelihood of the need for captive maintenance to protect and recover remnant species. In this study, we promoted reproductive maturation via manipulation of day length and temperature, and produced viable offspring from two small, endemic freshwater galaxiids, Galaxias fuscus (Mack 1936) and Galaxias longifundus (Raadik 2014) using in vitro propagation techniques. Propagation trials resulted in 425 oocytes being stripped from four ripe G. fuscus females, and 1527 oocytes from three ripe G. longifundus females. Of these, 342 (80.5%) G. fuscus and 968 (63.4%) G. longifundus eggs hatched into larvae. Newly hatched G. fuscus and G. longifundus larvae were transparent, and 8.4–9.7 mm (mean 9.0 mm TL) and 7.1–8.9 mm (mean 8.3 mm TL) consecutively. Absorption of the yolk sac by G. fuscus larvae (1.5–2.0 mm diameter) was complete 6–7 days after hatching, and for G. longifundus (1.0–1.4 mm diameter) 12–13 days after hatching. One-month-old G. fuscus measured ~16 mm and two-month-old larvae ~22 mm, and one-month-old G. longifundus ~11 mm. Methods and techniques employed may aid broader galaxiid conservation efforts.

The worldwide reduction in wetlands has led to the large‐scale decline of wetland‐dependent species. In Australia, to redress some of the decline, partial restoration of the hydrology of a small number of wetlands has been attempted using allocations of environmental water. A common goal of the watering is the maintenance and enhancement of native fish communities, which historically have included populations of the salt tolerant Murray hardyhead (Craterocephalus fluviatilis), a small, short‐lived fish, endemic to the lower Murray–Darling Basin. Despite the addition of environmental water to several sites at which the species is known to persist, populations continue to decline. This decline is, at least in part, suspected to be a consequence of salinities that conflict with the breeding ecology and survival of early life stages. Here the effect of salinity on egg hatch rate and the upper salinity tolerance of larval and juvenile Murray hardyhead was determined under laboratory conditions. It was found that eggs were vulnerable to elevated salinities, whereas juveniles were capable of tolerating salinities up to 105 ppt. Based on the results of the experiment, brackish wetlands managed for Murray hardyhead should be maintained, where possible, between 12 and 45 ppt. Such a salinity regime will necessitate less intensive management of salinity, and a reduced volume of environmental water, providing both environmental and fiscal benefits. The research highlights the benefits of investment in targeted research.

Because fish are sensitive indicators of flow alteration, a detailed knowledge of the response of fish to flows is crucial to the sound management of regulated river systems. Estuary perch are a catadromous, long-lived, estuarine-dependant percichthyid. Here, we relate otolith-derived recruitment and growth histories of individuals of the species in the highly regulated river to hydrologic, climatic and demographic variables. Year class strength was positively related to high flows over the spawning season and in a negative curvilinear way to flows in the austral winter, in addition to cooler annual temperatures in general. Flows benefiting recruitment of estuary perch are best timed to occur in austral winter in addition to the spawning season. Without a substantial increase in the volume of environmental water, large recruitment events will remain dependent on sizable natural catchment-generated inflows. On the basis of our findings, climate change predictions of lower rainfall and higher temperatures in south-east Australia may result in prolonged periods of recruitment failure in the region, and have significant implications for the viability of not only the population of estuary perch in the Snowy River, but also southern populations of the species in general.

Flow regimes have been fundamentally altered in many of the world’s river systems. There is a need to restore components of natural flow variability to protect freshwater biodiversity. The Australian bass is a long-lived, catadromous percichthyid endemic to coastal drainages of south-eastern Australia. Little is known of the timing and magnitude of flows considered important for recruitment and growth of individuals in southern latitudes of the species range. Herein we generate nearly 50 years of otolith-derived recruitment and growth histories for Australian bass and relate these to hydrologic, climatic and demographic variables. We found that younger Australian bass grew fastest in years following a cooler spring, whereas the growth of older fish exhibited little response to temperature. Australian bass year class strength was positively related to high flows in spring and in a negative curvilinear way to spring temperature. A lack of suitable natural flows in spring may be responsible for little to no recruitment of Australian bass in the Genoa River over the past two decades. Based on our findings, the continuing trend of lower rainfall and higher temperatures, coupled with river regulation in some systems in the region, will likely result in depressed juvenile growth and prolonged periods of recruitment failure over the medium to longer term, with significant implications for the viability of populations.