Phylogeography of the widespread Australian freshwater prawn, Macrobrachium australiense (Decapoda, Palaemonidae)

Aim To investigate the phylogeographic structure of the widespread freshwater prawn, Macrobrachium australiense, within and between major Australian drainage basins using mitochondrial sequence data. This will enable the investigation of historical connections between major drainages and examination of hypotheses of biogeographic associations among Australian freshwater basins. Location Inland, eastern and northern Australia. Methods Sequencing 16S rRNA and ATPase 6 protein coding mitochondrial DNA genes from M. australiense from 19 locations from inland, eastern and northern Australia. Results Within drainage basins, haplotype trees are monophyletic, with the exception of the Finke River from the Lake Eyre Basin. Macrobrachium australiense from the two main inland drainages, the Murray–Darling and Lake Eyre Basin are divergent from each other and do not form a monophyletic group, instead the Murray–Darling Basin haplotypes clade with eastern coastal haplotypes. Haplotypes from neighbouring eastern coastal drainages were found to be quite divergent from each other. Main conclusions The phylogeographic relationships among M. australiense suggest that the two major inland drainages, the Murray–Darling Basin and the Lake Eyre Basin, are not biogeographically closely associated to each other. Instead the Murray–Darling Basin is more closely allied with the eastern coastal drainages across the Great Dividing Range. Despite their proximity the neighbouring southeast Queensland coastal Mary and Brisbane Rivers are also biogeographically divergent from each other. The results also indicate that the Finke River appears to have been isolated from the remainder of the Lake Eyre Basin catchment for a significant period of time.     

Review of cold water pollution in the Murray–Darling Basin and the impacts on fish communities

The release of water from deep below the surface of large dams causes significant disturbance to water temperature regimes in downstream river channels with consequent impacts upon aquatic biota and river health. The Murray–Darling Basin (MDB) has a large number of dams, which are known to cause cold water pollution (CWP) in the downstream reaches of the impounded rivers. This study reviews the situation with regard to CWP in the MDB including the location, magnitude and extent of temperature suppression, the impacts upon fish, constraints and progress towards ameliorating the problem.     

Ecological impacts of dams,water diversions and river management on floodplain wetlands in Australia

Australian floodplain wetlands are sites of high biodiversity that depend on flows from rivers. Dams, diversions and river management have reduced flooding to these wetlands, altering their ecology, and causing the death or poor health of aquatic biota. Four floodplain wetlands (Barmah‐Millewa Forest and Moira Marshes, Chowilla floodplain, Macquarie Marshes, Gwydir wetlands) illustrate these effects with successional changes in aquatic vegetation, reduced vegetation health, declining numbers of water‐birds and nesting, and declining native fish and invertebrate populations. These effects are likely to be widespread as Australia has at least 446 large dams (>10 m crest height) storing 8.8 × 10⁷ ML (10⁶ L) of water, much of which is diverted upstream of floodplain wetlands. More than 50% of floodplain wetlands on developed rivers may no longer flood. Of all of the river basins in Australia, the Murray‐Darling Basin is most affected with dams which can store 103% of annual runoff and 87% of divertible water extracted (1983–84 data). Some floodplain wetlands are now permanent storages. This has changed their biota from one tolerant of a variable flooding regime, to one that withstands permanent flooding. Plans exist to build dams to divert water from many rivers, mainly for irrigation. These plans seldom adequately model subsequent ecological and hydrological impacts to floodplain wetlands. To avoid further loss of wetlands, an improved understanding of the interaction between river flows and floodplain ecology, and investigations into ecological impacts of management practices, is essential.     

Reducing the perversion of diversion: Applying world‐standard fish screening practices to the Murray–Darling Basin

Summary The impact of water diversion on fish populations is a global issue. Many countries have invested substantial funding into research and implementation strategies to ensure fish are protected at diversions that take water out of rivers for agriculture and other human uses. The most common management action is the installation of fish screens, and a wide range of designs are presently available that suit a large range of diversions. The Murray–Darling Basin is the largest catchment in Australia and has been substantially developed over the past 100 years to store and divert water for that protect fish from escaping into the irrigation systems. Recent studies have determined that water diversions have substantial impacts on native fish populations, but there are presently no coordinated efforts for mitigation strategies. The purpose of this review is to highlight aspects of successful screening programmes worldwide and identify those that could be directly applied to the Murray–Darling Basin. The development of similar programmes in the United States, New Zealand and the United Kingdom has identified that sufficient information and technology exists to inform the development of fish screening programmes. There is no need to commence implementation from first principles, and substantial progress can be achieved by applying successful aspects of other programmes. By identifying existing designs, defining ecological targets, developing generalised guidelines appropriate for local conditions and engaging the community, a co‐ordinated and successful fish screening programme could be directly applied to the Murray–Darling Basin. This would have substantial benefits for the long‐term sustainability of native fish without compromising water supply requirements.     

The effect of landscape processes upon gene flow and genetic diversity in an Australian freshwater fish, Neosilurus hyrtlii

1. Flow regime and riverine architecture are two important landscape characteristics that influence genetic diversity and gene flow in riverine species.
2. Using population genetic markers (mtDNA, microsatellites and allozymes), this study aimed to investigate genetic diversity and gene flow in the freshwater fish, Neosilurus hyrtlii , across two major drainage divisions in northern and central Australia (the Gulf of Carpentaria and Lake Eyre basins). These basins lie adjacent to each other and differ in their hydrological inputs and riverine structure, providing an ideal opportunity to identify the impact of landscape processes upon population dynamics of freshwater fish.
3. Populations were strongly structured among basins, among catchments within basins and were weakly structured within catchments in the Lake Eyre Basin, providing support for the Stream Hierarchy Model.
4. Interestingly, mtDNA and microsatellite diversity was much higher in the Gulf of Carpentaria Basin compared to the Lake Eyre Basin. It was concluded that this difference was due to the extreme hydrological variability in this basin and boom-bust population cycles resulting in smaller effective population sizes in the Lake Eyre Basin.     

Clarifying an ambiguous evolutionary history: range‐wide phylogeography of an Australian freshwater fish,the golden perch (Macquaria ambigua)

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)] of eastern Australia. Methods A total of 590 samples were collected from across the entire species’ distribution and a section of the mitochondrial DNA control region was sequenced. In order to reconstruct the evolutionary history of M. ambigua a comprehensive suite of phylogeographic analyses was conducted, including nested clade phylogeographic analysis, mismatch analysis and isolation‐with‐migration model simulations. Results Three major lineages corresponding to the major drainage basins, FITZ, MDB and LEB/BULL, were identified (Φ_ST = 0.92). Lineages from the coastal basin (FITZ) were highly divergent from those of the inland basins (up to 6%). Levels of genetic diversity in the inland basins were relatively low and our analyses indicate that these populations experienced both demographic and range expansions during the Pleistocene. Main conclusions Investigation of the range‐wide phylogeography of M. ambigua has revealed new insights into the biogeography of the Australian arid zone, particularly with regard to evolutionary events chronologically associated with cyclical moist and dry conditions. We propose that M. ambigua originated on the east coast (FITZ) and crossed a major geographic barrier, the Great Dividing Range (GDR), to colonize the inland basins (MDB, LEB and BULL). We infer a series of demographic and range expansion events for M. ambigua consistent with a scenario of moister Pleistocene conditions and increased connectivity of freshwater environments, both within and among drainage basins. Major lineages then diversified following isolation of freshwater environments under increasingly arid climate conditions. We suggest that management priorities for M. ambigua should include the resolution of taxonomic uncertainties and the maintenance of genetic diversity of both stocked populations in the MDB and native populations of the LEB that may be at risk of further isolation and reduced gene flow due to increased aridification under future climate change scenarios.     

Genetic diversity of Eucalyptus camaldulensis Dehnh. following population decline in response to drought and altered hydrological regime

The river red gum (Eucalyptus camaldulensis Dehnh.) inhabits riparian zones and associated floodplains throughout Australia. Following changes to hydrological regime due to river regulation and prolonged drought in south‐eastern Australia, river red gum populations within the Murray–Darling Basin have suffered substantial decline. To better understand the effect of drought on river red gum genetic diversity, we examined single nucleotide polymorphism (SNP) variation in 12 candidate genes among six red gum floodplain forest sites in Yanga National Park, which had experienced contrasting levels of drought and associated decline over an eight‐year period. We also examined genetic diversity using these markers in five additional river red gum populations from the Murray–Darling Basin to place genetic diversity results from Yanga in a regional context. Tree condition was significantly lower and mortality higher in the most drought affected sites; however, differences in overall genetic diversity and divergence were not detected among sites. No evidence of genetic adaptation in response to drought in this set of candidate genes was detected when differentiation at individual SNP loci was examined. While the overall condition of E. camaldulensis was strongly influenced by hydrological regime, our results suggest the evolutionary potential of floodplain forests in Yanga were not immediately impacted by population decline linked with drought and changes in hydrological regime. We propose that due to low genetic structure among populations in the region, genetic diversity of river red gums within the Murray–Darling Basin might be effectively conserved during periods of extended drought by protecting representative populations.     

Extreme water level decline effects sediment distribution and composition in Lake Alexandrina,South Australia

Water level decline affects the biophysical environment of shallow lakes. Unprecedented drought in Australia’s Murray–Darling Basin resulted in extreme water level drawdown in the large, shallow Lake Alexandrina at the end of the River Murray. Surface sediment was collected from 22 sites in the lake before and after water levels declined to assess the integrated limnological changes over the period of drawdown. Results indicate an increase in the proportion of organic particles in profundal sediments, as well as an increase of fine particles (<19.9 μm) in peripheral sediments. These changes to sediment composition corresponded to higher concentrations of suspended particles at low water levels. Increased autochthony and a shift in primary production from macrophytes to phytoplankton in Lake Alexandrina support these findings. Inorganic carbon and other nutrients were lost from sandy sediments most likely through carbonate dissolution driven by a localized decrease in pore water pH from increased mineralisation of organic matter.     

Effects of flooding on recruitment and dispersal of the Southern Pygmy Perch (Nannoperca australis) at a Murray River floodplain wetland

Summary With limited evidence linking Australia's Murray‐Darling Basin fish species and flooding, this study assessed annual variation in abundance and recruitment levels of a small‐bodied, threatened floodplain species, the Southern Pygmy Perch (Nannoperca australis), in floodplain habitats (creeks, lakes and wetlands) in the Barmah‐Millewa Forest, Murray River, Australia. Spring and summer sampling over a 5‐year period encompassed large hydrological variation, including 1 year of extended floodplain inundation which was largely driven by an environmental water release, and 2 years of severe regional drought. Recruitment and dispersal of Southern Pygmy Perch significantly increased during the floodplain inundation event compared with the other examined years. This study provides valuable support for an environmental water allocation benefiting a native species, and explores the link between flooding and its advantages to native fish. This suggests that the reduced flooding frequency and magnitude as a result of river regulation may well be a major contributing factor in the species’ decline in the Murray‐Darling Basin.     

Length–length and length–weight relationships of fish species from the Lake Eyre Basin,Australia

The Lake Eyre Basin in central Australia is one of the world's last unregulated dryland river systems. To facilitate future research in this area, the relationships between total length, standard length, and wet weight for 10 widespread, large‐bodied freshwater fish species are presented. All linear relationships were strong (r² > 0.90) and values of the exponent b of the length–weight relationships ranged from 2.786 to 3.336. These results provide novel baseline data for species in this area.     

Optimising hydrological conditions to sustain wintering waterbird populations in Poyang Lake National Natural Reserve: implications for dam operations

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Tree health and regeneration response of Black Box (Eucalyptus largiflorens) to recent flooding

Black Box (Eucalyptus largiflorens) is a dominant floodplain tree in the Murray–Darling Basin. In northern Victoria, the health of Black Box woodlands has declined as a consequence of river regulation and drought. This has raised concern about the long‐term survival of populations. Although tree health and regeneration of this species are entwined with flooding, there is limited knowledge of its response to environmental watering. This inhibits the effective implementation of management actions to secure the long‐term survival of floodplain Black Box populations. We investigated the effect of flooding history on Black Box tree health, population status and regeneration at 26 sites within the Murray Sunset National Park, Victoria. Sites were assessed under two flooding treatments: (1) ‘recently flooded’ (sites frequently flooded within the last 5 years and (2) ‘historically flooded’ (sites not flooded since 1993). Black Box populations in recently flooded sites had a greater range of life stages present and fewer dead trees, indicating a healthier and more sustainable population structure. In addition, trees were in better health with higher canopy condition and reproductive output (e.g. flowers and fruits), and the average tree diameter was greater than in historically flooded sites. Seedlings and saplings were present only at recently flooded sites, indicating that water availability and tree health are a strong determinant of regeneration in these landscapes. Flooding is an important factor in the sustainability of Black Box populations in this Victorian semi‐arid floodplain. A key recommendation is that managed flows should be implemented to target populations in poor condition. Although regular flooding is required to maintain or improve the health of Black Box populations, developing the optimum flow regime (timing, frequency and duration) to facilitate this outcome requires further investigation.     

Spangled perch (Leiopotherapon unicolor) in the southern Murray‐Darling Basin: Flood dispersal and short‐term persistence outside its core range

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’ following widespread flooding during 2010 and 2011. Although records of the species declined over 2013, L. unicolor remained resident in the southern Murray‐Darling Basin as of April 2014. The species persisted in several locations for three consecutive winters with recruitment documented at two sites. This study represents the first identification of the dispersal of large numbers of L. unicolor into the southern Murray‐Darling Basin, persistence beyond a single winter, and recruitment by the species in habitats south of its recognized ‘core adult range’. Targeted research would determine the potential for predicted environmental changes (artificially warmer drainage wetlands, climate change and greater floodplain connectivity) to facilitate longer term persistence and range expansion by the species in the southern Murray‐Darling Basin.     

National Agricultural Productivity & Reconciliation Ecology Centre conference

The National Agricultural Productivity & Reconciliation Ecology Centre (NAPREC) held its inaugural conference in Deniliquin in the southern Murray–Darling Basin, NSW, Australia, 4–5 October 2017, and attracted an engaged group of farmers, researchers, industry and government representatives. The theme of the conference was ‘Positive Partnerships for Pathways to Sustainable Agriculture and Biodiversity’. It explored the application of Reconciliation Ecology and the value of the human elements of natural resource management within the context of the southern Murray–Darling Basin.     

Bird responses to riparian management of degraded lowland streams in southeastern Australia

We assessed the degree to which fencing, livestock exclusion, and replanting of riparian zones affected avian assemblages in massively cleared landscapes. Measurements were made at three creeks in the southern Murray–Darling Basin in southeastern Australia, each of which had circa 1‐km long treated sections and paired “untreated” circa 1‐km sections, where no fencing, planting, or stock exclusion was done. We measured the change in vegetation characteristics and abundances of native birds for up to 8 years after works were completed. Prior to data collection, we developed expected responses of bird species based on the anticipated time‐courses of change in vegetation structure. We used hierarchical Bayesian models to explore the effects of the management actions, and to account for within‐site variation in vegetation characteristics. There were major changes in vegetation structure (reductions in bare ground and increases in shrubs and tree recruitment) but avian responses generally were small and not as expected. There are at least four possible reasons for the limited avian responses: (1) there has been a long‐term decline in woodland birds across the region; (2) the study was conducted during the longest drought in the instrumental record in the study region; (3) the total amount of replanted vegetation was small in a massively denuded region; and (4) monitoring may have been over too short a term to detect responses to longer‐term changes in structural vegetation.     

Ecological monitoring to support Water Sharing Plan evaluation and protect wetlands of inland New South Wales,Australia

Government‐funded flow response monitoring and modelling programmes (flow science) provided by the New South Wales Office of Water (NOW) have supported water resource management since 1997. Flow science has a core technical component defined by hypothesis‐driven long‐term monitoring and analysis, but it also represents many activities that support committees involved in environmental flow management. This is done through collaborations and contracting and has fostered considerable research and analysis into flow ecology, including modelling for the recent Murray–Darling Basin Plan. We describe the performance of environmental flows against legislated wetland objectives to improve wetland function and diversity using flow science. On‐ground monitoring at wetland sites has largely ceased but the flow science done so far indicates that the environmental flow rules written into Water Sharing Plans improve wetland diversity and function. Determination of the long‐term flow needs of NSW wetlands, including how well current Water Sharing Plans aid the delivery of environmental flows, requires finding the means to build on current flow science knowledge from across Australia.     

Hypoxic blackwater event severely impacts Murray crayfish (Euastacus armatus) populations in the Murray River,Australia

Prolonged flooding in 2010/11 ended a decade of drought and produced a large‐scale hypoxic blackwater event across the southern Murray‐Darling Basin, Australia. The hypoxic conditions caused fish kills and Murray crayfish Euastacus armatus to emerge from the water onto the river banks to avoid the poor water quality. This study examined the medium‐term impact of this blackwater event on Murray crayfish populations in the Murray River, where approximately 1800 km of the main channel were affected by hypoxia. Murray crayfish populations were surveyed in July 2012, along a 1100‐km section of the Murray River at 10 sites affected by hypoxic blackwater and six sites that were not affected, and data were compared with surveys of the same sites undertaken in July 2010, four months before the hypoxic blackwater event (before‐after‐control‐impact experimental design). Murray crayfish abundance in 2012 (post‐blackwater) was significantly lower at blackwater affected sites (81% reduction from 2010), but not at non‐affected sites. The hypoxic blackwater impacted Murray crayfish of both sexes and all size‐classes in a similar manner. The results demonstrate that prolonged periods of hypoxia can markedly impact populations of the long‐lived and slow‐growing Murray crayfish despite the species ability to emerge from hypoxic water. The findings highlight important challenges for the management of both the recreational fishery for this species and riverine flows in relation to hypoxic blackwater events.     

Host-dependent genetic variation in freshwater pearl mussel (Margaritifera margaritifera L.)

Freshwater fishes are vulnerable to changes in water quality, physical habitat and connectivity resulting from drought, particularly in regulated rivers. When adequate river flows return, the recovery of populations might depend on the duration and consequences of drought. Rivers of the highly regulated Murray–Darling Basin in south-eastern Australia terminate at two large, shallow lakes that are separated from the estuary by tidal barrages. Over-abstraction of water and widespread prolonged drought (1997–2010) placed the lakes under severe environmental stress, culminating in critical water level recession from 2007 to 2010. Concurrently, most freshwater fish populations collapsed. We investigate shifts in fish assemblages resulting from habitat inundation in the lakes following the drought. The inundation and re-connection of the lakes and fringing habitats led to a substantial reduction of salinity throughout the region, and aquatic vegetation shifted from salt-tolerant to freshwater species. Fish assemblages became increasingly characterized by common freshwater taxa (ecological generalists), including high proportions of alien species. There were no indications of population recovery for three threatened species. The findings emphasize that short-lived fishes with specialized habitat requirements are vulnerable to severe population declines during prolonged drought in regulated rivers, which might restrict their recovery when adequate flows return.     

Ecoacoustics can detect ecosystem responses to environmental water allocations

1. Globally, water abstraction for human consumption and irrigated agriculture leads to significant changes in aquatic ecosystems. To counter these detrimental effects, water releases—often termed environmental water allocations—restore overbank flow or are delivered to artificially disconnected wetlands. While a suite of monitoring methods is available, few programmes track continuous change in biota, mainly because repeated remote site visits can be prohibitively expensive.
2. In this paper, we propose a new approach to environmental flow monitoring, using ecoacoustic methods. We test acoustic monitoring of frog and waterbird responses to environmental water deliveries in the Goulburn Broken, a valley in the southern Murray–Darling river system. Response to three major environmental water deliveries within 2 years was monitored at four sites along Reedy swamp. Every 2 weeks, 30 s were recorded every 30 min, for a total of 24 hr.
3. We used two analysis strategies—manual counts of bird calls, as well as ecoacoustic indices, which describe the sonic properties of the acoustic spectrum at a site. Manual counts demonstrated that water-dependent birds were clearly responding to environmental water deliveries, whereas non-water-dependent species did not show any increases in activity. After restricting the analysis to the dawn chorus of birds and frogs, two acoustic indices (the median amplitude and the acoustic complexity index) showed responses to watering events.
4. Ecoacoustic methods show promise for continuous response monitoring to environmental water allocations. However, the first strategy—manual annotation of calls—might be too labour intensive for standard monitoring programmes. The second strategy—index-based approaches—can also detect ecological responses, although further investigation using control sites is needed. Automated call classifiers are an alternative that is currently being developed for endangered species. We also encourage simultaneous monitoring of the soundscape above and under water.

     

Relationships between lotic macroinvertebrate traits and responses to extreme drought

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