Native freshwater fish of Australia have a diverse but largely undescribed endemic pathogen and parasite fauna. However, due to long-shared evolutionary histories and virulence/transmissibility trade-offs, effects of these endemic pathogens and parasites appear to be subtle: significant impacts are rarely observed and epizootics have not been recorded. In contrast, a number of alien pathogens and parasites are now established across southern Australia, causing manifestly harmful effects to native fish species and known or suspected epizootics in native fish populations. Undetected and/or undescribed alien viral pathogens are also suspected of being present. Alien pathogens and parasites were introduced to Australia with imports of live alien fish or their fertilised eggs. A review of the scientific and historical evidence indicates that they have had, and continue to have, greater impacts on native fish species than previously realised—especially for freshwater species. This review also documents a previously unknown, Murray-Darling-Basin-wide epizootic of Murray cod Maccullochella peelii in 1929–30, which may have contributed to strong declines in the related eastern freshwater cod Maccullochella ikei. A serious Chilodonella epizootic of M. peelii in 1982 is also examined. In addition, a possible role for alien viruses of the family Iridoviridae (Ranavirus and Megalocytivirus) in the general decline of the critically endangered silver perch Bidyanus bidyanus, and the rapid collapse of two specific native fish populations—upper Murrumbidgee River B. bidyanus and Shoalhaven River Macquarie perch Macquaria australasica—is suggested. It is argued that the severity of the impact of the virulent alien oomycete Saprolegnia parasitica, both historical and present day, has been underestimated. Finally, action is recommended against emerging new pathogen and parasite threats, and the extreme risk current alien fish importations pose in introducing them. These will further threaten already stressed native fish populations in southern Australia, particularly across the Murray-Darling Basin.

Researchers have hypothesised that influxes of pelagic zooplankton to river channels after floods and high flows are necessary for strong recruitment of some native fish species, including Murray cod (Maccullochella peelii peelii) (Mitchell), in the Murray-Darling river system, Australia. This study investigated the composition of the diet and gut fullness of drifting Murray cod larvae weekly during two spawning seasons with contrasting flows, to determine if pelagic zooplankton comprised a greater proportion of the gut contents and guts were fuller in a high flow (2000) than in a low flow (2001) year. Gut fullness and yolk levels of 267 larvae were ranked, and prey identified to family level. Approximately 40 and 70% of individuals had been feeding in 2000 and 2001, respectively. Gut fullness increased with declining yolk reserves. Larvae in both the years had an almost exclusively benthic diet, irrespective of the flow conditions at the time. Substantial inundation of dry ground in 2000, albeit restricted to in-channel benches, anastomosing channels and oxbow lakes, did not lead to an influx of pelagic, floodplain-derived zooplankton subsequently exploited by Murray cod larvae. These results have the implications for the management of regulated temperate lowland rivers: high flows cannot automatically be assumed to be beneficial for the fish larvae of all species and their food resources, and caution should be exercised with the timing of flow releases.

Context. The Murray-Darling Basin -Australia's largest river systemis heavily dominated by alien fish. Native fish species have suffered numerous localised extinctions and ~47% are listed on federal and/or state threatened species lists. Aims. This paper explores the hypothesis that alien fish and alien fish stockings can be the primary cause of decline and localised extinction of large-bodied native fish species, as opposed to habitat degradation and river regulation. The Lower Goodradigbee River, which is unregulated, in excellent instream health over the great majority of its course, and replete with high quality habitat, is utilised as a case study. Methods. I investigated the hypothesis by synthesising historical records with contemporary scientific research and recent field observations. The role of alien fish species, particularly alien trout species (Oncorhynchus mykiss and Salmo trutta) and constant stockings of them, were closely examined. Results. Data support the hypothesis that domination by alien trout species and their continual stocking have lead to historical declines and localised extinctions of large-bodied native fish species. Continued alien trout stockings, along with more recent invasions of alien carp (Cyprinus carpio) and alien redfin perch (Perca fluviatilis), are inhibiting native fish recovery. A suspected field sighting of the alien fish pathogen atypical Aeromonas salmonicida is reported, and the status of the declining native crayfish Murray cray (Euastacus armatus), and potential alien fish impacts upon them, are examined. Conclusions. The impacts of alien fish and alien fish stocking in Australia require major re-evaluation and dedicated research. Implications. It is strongly recommended that stocking of alien trout into the Lower Goodradigbee River for angling cease in order to conserve surviving native fish and Murray cray populations. Conservation stockings to effect a Murray cod (Maccullochella peelii) recovery in the Lower Goodradigbee River are warranted.