The use of historical environmental monitoring data to test predictions on cross-scale ecological responses to alterations in river flows

Biological invasions are among the biggest threats to freshwater biodiversity. This is increasingly relevant in the Murray–Darling Basin, Australia, particularly since the introduction of the common carp (Cyprinus carpio). This invasive species now occupies up to ninety per cent of fish biomass, with hugely detrimental impacts on native fauna and flora. To address the ongoing impacts of carp, cyprinid herpesvirus 3 (CyHV-3) has been proposed as a potentially effective biological control agent. Crucially, however, it is unknown whether CyHV-3 and other cyprinid herpesviruses already exist in the Murray–Darling. Further, little is known about those viruses that naturally occur in wild freshwater fauna, and the frequency with which these viruses jump species boundaries. To document the evolution and diversity of freshwater fish viromes and better understand the ecological context to the proposed introduction of CyHV-3, we performed a meta-transcriptomic viral survey of invasive and native fish across the Murray–Darling Basin, covering over 2,200 km of the river system. Across a total of thirty-six RNA libraries representing ten species, we failed to detect CyHV-3 nor any closely related viruses. Rather, meta-transcriptomic analysis identified eighteen vertebrate-associated viruses that could be assigned to the Arenaviridae, Astroviridae, Bornaviridae, Caliciviridae, Coronaviridae, Chuviridae, Flaviviridae, Hantaviridae, Hepeviridae, Paramyxoviridae, Picornaviridae, Poxviridae, Reoviridae and Rhabdoviridae families, and a further twenty-seven that were deemed to be associated with non-vertebrate hosts. Notably, we revealed a marked lack of viruses that are shared among invasive and native fish sampled here, suggesting that there is little virus transmission from common carp to native fish species, despite co-existing for over fifty years. Overall, this study provides the first data on the viruses naturally circulating in a major river system and supports the notion that fish harbour a large diversity of viruses with often deep evolutionary histories.

Generalized and quantitative relationships between flow and ecology are pivotal to developing environmental flow standards based on socially acceptable ecological conditions. Informing management at regional scales requires compiling sufficient hydrologic and ecological sources of information, identifying information gaps, and creating a framework for hypothesis development and testing. We compiled studies of empirical and theoretical relationships between flow and ecology in the South Atlantic region (SAR) of the United States to evaluate their utility for the development of environmental flow standards. Using database searches, internet searches, and agency contacts, we gathered 186 sources of information that provided a qualitative or quantitative relationship between flow and ecology within states encompassing the SAR. A total of 109 of the 186 sources had sufficient information to support quantitative analyses. Ecological responses to natural changes in flow magnitude, frequency, and duration were highly variable regardless of the direction and magnitude of changes in flow. In contrast, the majority of ecological responses to anthropogenic-induced flow alterations were negative. Fish abundance, diversity, reproduction, and habitat consistently showed negative responses to anthropogenic flow alterations, whereas other ecological categories (e.g., macroinvertebrates and riparian vegetation) showed somewhat variable responses and even positive responses (e.g., algal abundance). Fish and organic matter had sufficient sample sizes to stratify natural flow-ecology relationships by specific flow categories (e.g., high flow, baseflows) or by physiographic province (e.g., Coastal Plain, Piedmont). After stratifying relationships, we found that significant correlations existed between changes in natural flow and fish responses. In addition, a regression tree explained 57% of the variation in fish responses to anthropogenic and natural changes in flow. Altogether, our results suggested that the source of flow change and the ecological category of interest played primary roles in determining the direction and magnitude of ecological responses. Furthermore, our results suggest that developing broadly generalized relationships between ecology and changes in flow at a regional scale is unlikely unless relationships are placed within meaningful contexts, such as environmental flow components or geomorphic settings.

In recent decades, the ecological condition of the Murray-Darling Basin of eastern Australia has been in focus as the effects of drought and long-term over-extraction have resulted in a stressed, degraded river system. Within the Basin, the climate is highly variable (seasonally and decadally), the river system is highly regulated with large storages in the headwaters of most catchments, and regulation of flows is dominated by irrigation demands, both in terms of volume and timing. While many of the catchments have some environmental flow rules built into the river operations, these have been, in the main, ineffective in maintaining or improving condition. The recent long-term drought has exacerbated the situation, with irrigators and environmental assets alike suffering from reduced, and unreliable, water allocations. The Australian Government has been responsive to these concerns and has mandated the development of a Basin Plan to protect, restore and provide for the ecological values and ecosystem services of the Basin, without unduly compromising the net economic returns to the Australian community from the use and management of the Basin water resources. The requirement to balance the triple bottom-line - namely environmental, social and economic - means that the benefits from returning water to the environment, especially if it is at the expense of other uses, must be quantifiable and realisable. This requires an understanding of the relationship between the wetting requirements of water-dependent ecosystems; and the ability of the river system (and its management) to deliver water, in-channel and overbank, in a way (timing and volume) that is informed by these needs. The Murray-Darling Basin Floodplain Inundation Model (MDB-FIM) maps spatial extent of floodplain inundation under ecologically significant flood return periods to derive spatial inundation patterns over time across the Murray-Darling Basin under different climate and development scenarios. Model development, as a proof-of-concept, is reported in Doody et al. (2009). Such a model can be extended to provide the spatial framework for implementing floodplain ecohydrology models that predict the likely ecological response of a selected set of key habitats, assets and/or regions from changes in flow, expressed as average flow return periods. This paper reports on the initial phase of such an application. A project commenced to enumerate the environmental, social and economic benefits of returning water to the environment as prescribed in the Basin Plan, under a range of alternate flow scenarios. MDB-FIM was selected as a candidate foundation framework to provide the spatial relationships between river volumes and ecologically-relevant flood return periods as commonly used when expressing environmental water requirements. The first stage involved re-processing the MDB-FIM input data to include recent flood events (2010-2011). This extends MDB-FIM's spatial coverage to include many high floodplains that had not been inundated for many decades. In other words, this enhances MDB-FIM's ability to underpin the development of ecological response models for such areas which typically have different vegetation communities to low floodplains and riparian zones. The second stage required working with ecologists and hydrologists to match MDB-FIM's spatial and temporal resolutions with that required by the ecological response models. It is anticipated that the use of MDB-FIM will provide for a whole-of-Basin quantitative assessment of floodplain ecosystems and environmental assets. This in turn can be used to support the assessment of the benefits of returning water to these environments.

Context The Murray–Darling Basin serves as a crucial habitat for aggregating waterbirds; however, decades of large-scale regulation of rivers and water resources have adversely affected waterbird breeding in the Basin. Aims To understand the characteristics of wetlands that attract and support aggregating waterbirds, focusing on identifying environmental conditions conducive to waterbird breeding. Methods In total, 52 wetland sites across the Murray–Darling Basin, with high waterbird abundances, were identified, of which 26 supported waterbird breeding. Classification models were developed using temporally static and dynamic environmental datasets to discern wetland characteristics associated with waterbird breeding. Key results Analyses showed that wetlands supporting waterbird breeding contained a maximum inundated area of ‘other shrublands’ exceeding 3.635 km2 and variation in normalised difference vegetation index, possibly reflective of a ‘boom and bust’ ecological response. Conclusions Understanding the habitat requirements of wetlands to prompt waterbird breeding is critical for effective environmental water management and conservation strategies. Implications Targeted wetland management and environmental water allocation to support waterbird breeding populations in the Murray–Darling Basin is essential for continued waterbird breeding. There is a need for continued research to refine management strategies and ensure the long-term sustainability of waterbird populations in the face of ongoing environmental challenges.

This paper investigates the accessibility and usefulness of the Ecosystem Services (ES) framework to policy analysts. Using a mixed methods approach of document analysis and semi-structured interviews we examine how an ES assessment of the benefits of restoring water to the Murray-Darling Basin (MDB) in Australia has been used by government agencies in policy and planning. The ES assessment links changes in water management under the Basin Plan with modelled changes in water quality, river flows and inundation patterns and in turn to modelled freshwater and estuarine ecosystem response. These ecological responses were expressed in terms of incremental ES benefits which were valued monetarily using a variety of valuation techniques. To investigate how these pieces of information were used in the policy debate around the re-allocation of water in the MDB, semi-structured interviews were conducted with 20 Australian, State, and local government officials as well as academics and consultants. The interviews were designed to uncover the complex information dissemination process through networks within and among agencies. The results are mixed as to whether the assessment served to influence public policy. The report has been utilized and cited by Australian federal agencies, the downstream State of South Australia and conservation-based NGOs in their position statements and as such has been used as evidence in support of re-allocation of water in the MDB. A number of interview participants commented that the ES assessment raised awareness and this may lead to broader usage of the information and framework in the implementation phase of MDB water reform.

On improving the science and practice of riparian restoration

The Murray–Darling Basin (MDB) is Australia’s food bowl, contributing 40% of agricultural production and supporting a population of over 4 million people. Historically, the MDB supported a unique native fish community with significant cultural, subsistence, recreational, commercial and ecological values. Approximately one-quarter of the MDB’s native species are endemic. Changes to river flows and habitats have led to a >90% decline in native fish populations over the past 150 years, with almost half the species now of conservation concern. Commercial fisheries have collapsed, and important traditional cultural practices of First Nations People have been weakened. The past 20 years have seen significant advances in the scientific understanding of native fish ecology, the effects of human-related activities and the recovery measures needed. The science is well established, and some robust restoration-enabling policies have been initiated to underpin actions. What is now required is the political vision and commitment to support investment to drive long-term recovery. We present a summary of 30 priority activities urgently needed to restore MDB native fishes.

Chapter 10 - Active management of environmental water in 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.

Globally, there is growing concern on the negative impacts of species invasions and habitat disturbance because these have been shown to have the potential to disrupt native community structure and function. In some instances, these two stressors can occur in concert, such as in river systems associated with inter-basin water transfer (IBWT) schemes. The Great Fish River in the Eastern Cape, South Africa, is an example of a system affected by both habitat modification and multiple fish invasions largely because of an IBWT scheme. The opening of the Orange-Fish IBWT, which transfers water from the Orange River to the Great Fish River, modified the latter’s natural flow regime from irregular seasonal to perennial. In addition, the IBWT facilitated translocations of five fish species from the Gariep Dam (Orange River system) into the Great Fish River system. Proliferation of these non-native fish species, along with that of other fish species introduced for angling and biological control, raise questions on the mechanisms facilitating their existence within this highly modified river system. This thesis explored mechanisms associated with co-occurrences of these multiple non-native fishes within the Great Fish River. A comparison of historical and contemporary records on the ichthyofauna of the Great Fish River revealed that, of the 11 non-native fishes reported in this system, seven have established successfully, three have failed to establish and the status of one was uncertain. The Orange-Fish IBWT and angling were the main vectors of these invasions, accounting for 36% and 46%, respectively. The study also found that most established non-native fish species were large sized, had high longevity and wide habitat tolerance. Trait-based approaches were employed to investigate the role of functional diversity of non-native and native fishes in relation to their composition, distribution and environmental relationships. Although considerable interspecific variation in body morphology-related functional traits among species were observed, there was no clear distinction in these traits between native and non-native fish assemblages on a trait-ordination space. Furthermore, there were weak species-trait-environment relationships, suggesting that environmental filtering was less plausible in explaining the occurrence patterns of these fishes. Stable isotope-based trophic relationships were evaluated in three invaded sections: the upper (UGFR) mainstem sections of the Great Fish River; and lower (LGFR) mainstem sections of the Great Fish River; and its tributary, the Koonap River. It was observed that native and non-native fish assemblages exhibited variation in isotopic diversity typified by low isotopic diversity overlaps in UGFR and Koonap River, whereas the LGFR was characterised by high isotopic diversity overlap. Within the invaded sections, non-native fishes were found to have isotopic niches characterised by variable isotopic niche sizes and were more isotopically dissimilar with propensity towards trophic differentiation within the UGFR and Koonap River but were mostly characterised by high isotope niche overlaps in the LGFR. Overall, these results provided evidence of trophic niche differentiation as a probable mechanism associated with the co-occurrences of the non-native fishes. However, mechanisms facilitating these co-occurrences within the invaded sections appears to be complex, context-specific and, in some cases, unclear. Lastly, machine learning techniques, boosted (BRT) and multivariate (MRT) regression trees, revealed that the flow-disturbed habitats were invaded by multiple non-native species, whereas the non-disturbed headwaters remained invasion free. In addition, non-native species were predicted to co-occur with native species within the mainstem and large tributary sections of the Great Fish River system. Thus, the IBWT-disturbed mainstem sections were predicted to be more prone to multiple invasions compared to undisturbed headwater tributaries.

<em>Abstract</em> .—The Murray–Darling basin (MDB) in southeastern Australia, covers 1.1 million km<sup>2</sup>, involves six partner jurisdictions with a myriad of different government agencies, and, hence, provides an excellent example of the complexities of multijurisdictional management across a range of social and political tiers. In the MDB, fish and fisheries compete for water with agriculture, which is the traditional water user and is driven by national economics. Murray–Darling basin rivers are now highly regulated and generally in poor health, with native fish populations estimated to be at only about 10% of their pre-European settlement abundances. All native commercial fisheries are now closed, and the only harvest is by a recreational fishery. The six partner jurisdictions developed a Native Fish Strategy (NFS) to rehabilitate native fish populations to 60% of pre-European settlement levels after 50 years of implementation by addressing priority threats through a coordinated, long-term, whole-of-fish-community (all native fishes) approach. As there are a wide range of stakeholders, broad engagement was needed at a broad range of government and community levels. The NFS funding was discontinued after 10 years, not because of its lack of successes or project governance, but due to jurisdictional political changes and funding cuts that resulted in a failure of the collaborative funding structure. The withdrawal of considerable funding by one jurisdiction led to collective decline in monetary contributions and posed a threat to the multijurisdictional structures for both water and natural resource management (NRM) within the MDB. As a consequence, there was a review and reduction in NRM programs and a subsequent reduction in focus to the core business of water delivery. Reflection on the NFS, however, provides some useful insights as to the successes (many) and failures (funding) of this partnership model. Overall, the strategy and its structure was effective, as exhibited by an audit of outputs, outcomes, and networks; by the evident ongoing advocacy by NRM practitioners and the community; and by the continuation of ideas under other funding opportunities. This has provided a powerful legacy for future management of fishes in the MDB.

This paper outlines the hydrological change associated with water resources development for six rivers within the Murray-Darling Basin. Hydrological change was assessed using simulated data from the Integrated Quantity and Quality Model (IQQM) and a range of relatively simple flow statistics: the annual proportional flow deviation; the frequencies of medium or high flow events; and the durations of low or no-flow events. The changes in physical properties, water quality and biological characteristics within the six river systems were assessed from the literature and summarized. This information was used to construct a series of hypothetical curves (reference curves) summarizing ecological response to hydrological change. The suitability of these response curves was then checked using data from a seventh river, Cooper Creek, a relatively major pristine endorheic system in central Australia. Reference curves appear to be an effective tool for assessing the likely ecological responses of river systems to increased hydrological change. Copyright © 2000 John Wiley & Sons, Ltd.

ESR Endangered Species Research Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials ESR 16:165-181 (2012) - DOI: https://doi.org/10.3354/esr00398 Theme Section: Endangered river fish: threats and conservation options A strategy to rehabilitate fishes of the Murray-Darling Basin, south-eastern Australia John D. Koehn1,*, Mark Lintermans2 1Arthur Rylah Institute for Environmental Research, Department of Sustainability and Environment, 123 Brown St, Heidelberg, Victoria 3084, Australia 2Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia *Email: john.koehn@dse.vic.gov.au ABSTRACT: The Native Fish Strategy (NFS) for the Murray-Darling Basin, south-eastern Australia, provides a whole-of-fish-community approach and coordinated direction for the rehabilitation of its severely degraded native fish populations. Together with actions outlined in recovery plans for threatened species, the NFS addresses priority threats identified for native fishes with the aim to rehabilitate native fish populations to 60% (current populations are estimated to be at about 10%) of the levels that existed prior to European settlement. The NFS has a 50 yr time frame and coordinates actions across 6 different management jurisdictions. A key component of the NFS is the engagement of communities and stakeholders, with this being undertaken, in particular, by the use of dedicated coordinators and the development of ‘demonstration reaches’ where rehabilitation can be undertaken using multiple actions, with community involvement. The NFS is supported by targeted research projects and monitoring within an adaptive management framework. The NFS provides an effective partnership model where central coordination, coupled with focused jurisdictional actions, can deliver benefits to all governments. It synthesises and disseminates knowledge, integrates research and management and catalyses actions for priority problems. The need, objectives, evolution and development, achievements, strengths and weaknesses of the NFS are presented. The NFS approach would be suitable for many large river basins throughout the world. KEY WORDS: Australia · Rehabilitation · Fish populations · Native Fish Strategy · Threatened species · Native fish Full text in pdf format PreviousNextCite this article as: Koehn JD, Lintermans M (2012) A strategy to rehabilitate fishes of the Murray-Darling Basin, south-eastern Australia. Endang Species Res 16:165-181. https://doi.org/10.3354/esr00398 Export citation Mail this link - Contents Mailing Lists - RSS Facebook - Tweet - linkedIn Cited by Published in ESR Vol. 16, No. 2. Online publication date: February 29, 2012 Print ISSN: 1863-5407; Online ISSN: 1613-4796 Copyright © 2012 Inter-Research.

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.

Abstract1. Around the globe, instream infrastructures such as dams, weirs, and culverts associated with roads are wide‐spread and continue to be constructed. There is limited documentation of smaller infrastructure because of mixed regulation and laws related to instream construction, as well as difficulty in documentation because of their size and frequency in waterscapes.2. We reviewed evidence of different methods used to quantify environmental and ecological responses (positive, negative, or neutral) to dams, weirs, and culverts.3. Most studies (78% of 87) in our review evaluated dams or weirs, and more than half evaluated environmental or ecological responses at more than one of these structures. More than half of the studies used spatial (disturbed–undisturbed in the same or a different catchment) rather than temporal (before–after construction or before–after destruction) comparative methods. Evaluations also tended to focus on ecological variables, most specifically on fish community responses (just over a quarter) to infrastructure.4. More than half (58%) of the evaluations at dams, weirs, or culverts reported negative environmental or ecological responses. Discrepancies in responses recorded for different infrastructure types could be partially explained by the focus on ecological responses in reviewed studies and related metrics used for evaluations (e.g. biotic groups, richness, and abundance), the imbalance of studies at different infrastructure types, and discrepancies in spatial and temporal scales of evaluations compared to those at which the variables respond to infrastructure.5. Despite the abundance of road culverts greatly exceeding the number of small or large dams worldwide, they were evaluated in only 22% of studies that we reviewed. Our findings underscore the need for studies to not only better understand local but also cumulative impacts of these smaller infrastructure, as these could be greater than those caused by large infrastructure depending on their location, density, and type, among other factors. Such studies are needed to inform infrastructure planning and watershed management.