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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.

Globally, river degradation has decimated freshwater fish populations. To help reverse this trend in a southeastern Australia river, we used multiple restoration actions, including reintroduction of instream woody habitat, riparian revegetation, removal of a weir hindering fish movement, fencing out livestock, and controlling riparian weeds. We monitored the responses of native fish at the segment scale (20 km) and reach scale (0.3 km) over 7 years to assess the effectiveness of the different restoration strategies. Two closely related species, Murray cod Maccullochella peeli and trout cod Maccullochella macquariensis, increased at the restored segment compared with the control segment. However, inherent differences between river segments and low sample size hampered assessment of the mechanisms responsible for segment‐scale changes in fish abundance. In contrast, at the reach scale, only M. peeli abundance significantly increased in reaches supplemented with wood. These differential responses by 2 closely related fish species likely reflect species‐specific responses to increased habitat availability and enhanced longitudinal connectivity when the weir improved passage around a fishway. Changes in M. peeli abundance in segments supplemented with and without wood suggest an increase in carrying capacity and not simply a redistribution of individuals within the segment, facilitated the observed expansion. Our findings confirm the need to consider individual fish species' habitat preferences carefully when designing restoration interventions. Further, species‐specific responses to restoration actions provide waterway managers with precise strategies to target fish species for recovery and the potential to predict fish outcomes based on ecological preferences.

In many animal populations, demographic parameters such as survival and recruitment vary markedly with age, as do parameters related to sampling, such as capture probability. Failing to account for such variation can result in biased estimates of population‐level rates. However, estimating age‐dependent survival rates can be challenging because ages of individuals are rarely known unless tagging is done at birth. For many species, it is possible to infer age based on size. In capture–recapture studies of such species, it is possible to use a growth model to infer the age at first capture of individuals. We show how to build estimates of age‐dependent survival into a capture–mark–recapture model based on data obtained in a capture–recapture study. We first show how estimates of age based on length increments closely match those based on definitive aging methods. In simulated analyses, we show that both individual ages and age‐dependent survival rates estimated from simulated data closely match true values. With our approach, we are able to estimate the age‐specific apparent survival rates of Murray and trout cod in the Murray River, Australia. Our model structure provides a flexible framework within which to investigate various aspects of how survival varies with age and will have extensions within a wide range of ecological studies of animals where age can be estimated based on size.

Recognition that many species share key life-history strategies has enabled predictions of responses to habitat degradation or rehabilitation by these species groups. While such responses have been well documented for freshwater fish that exhibit 'periodic' and 'opportunistic' life-history strategies, this is rare for 'equilibrium' life-history, due largely to their longevity and by comparison, more regular and stable levels of recruitment. Unfortunately, this limits the confidence in using life-history strategies to refine water management interventions to rectify the negative impacts of river regulation for these species. We addressed this knowledge gap for Murray cod Maccullochella peelii, a high-profile, long-lived recreationally popular equilibrium species in south-eastern Australia. We used monitoring data collected across a gradient of hydrologically altered rivers over two decades, to test various hypotheses linking recruitment strength with key attributes of the flow regime. Although Murray cod recruited in most years, as expected for an equilibrium species, responses to flow varied among and within rivers among years. We found links between recruitment strength and the magnitude and variation in discharge during the spring spawning period, as well as flows experienced by juvenile fish during summer and winter - the hydrological components most affected by river regulation. However, the specific slopes and directions of some of these links varied idiosyncratically across rivers. Our results emphasise the importance of accounting for flows that influence each of the key life stages during the recruitment process and lend support for managing rivers in accordance with the natural flow regime. It also shows the need for waterway-specific studies and further refinement of existing flow metrics to allow more credible transferability of results. The approach used in this study can also be applied to other species sharing life-history strategies for which long-term monitoring data has been compiled and length-at-age relationships established.

Introduced species are a major threat to freshwater biodiversity. Often eradication is not feasible, and management must focus on reducing impacts on native wildlife. This requires an understanding of how native species are affected but also how environmental characteristics influence population dynamics of both invasive and native species. Such insights can inform how to manipulate systems in order to take advantage of life-history traits native species possesses that invaders do not. The highly invasive fish, Gambusia holbrooki, has been implicated in the decline of many freshwater fish and amphibians. In south-eastern Australia, one of these is the threatened native fish, Galaxiella pusilla. As G. pusilla can survive periods without surface water, this presents an opportunity for adaptive management, given G. holbrooki lack these adaptations. We develop a stochastic population model to explore the impact of G. holbrooki on G. pusilla and test the feasibility of both natural and management-induced drying to protect this species. Our results support recent empirical studies showing G. holbrooki are a serious threat to G. pusilla persistence, especially through impacts on larval survival. While persistence is more likely in water bodies that frequently dry out, even optimal natural drying regimes may be insufficient when impacts from G. holbrooki are high. However, management-induced drying may allow persistence of G. pusilla in sites inhabited by both species. Given our model outcomes, the biology of these species and the habitats they occupy, we recommend maintaining or restoring aquatic and riparian vegetation and natural drying regimes to protect G. pusilla from G. holbrooki, in addition to undertaking management-induced drying of invaded water bodies. Our results provide insights into how the effects of G. holbrooki may be mitigated for other native species, which is important given this species is perhaps the most pervasive invader of freshwater ecosystems. We conclude with a discussion of the potential for using disturbance processes in the management of invasive species more broadly in freshwater and terrestrial systems.

Increasing demand for water and a desire for greater human water security has facilitated the global expansion of dams, with river regulation acknowledged as the leading cause of biodiversity decline in rivers. Native biota within these stressed systems are also impacted by reductions in habitat availability, decreased hydraulic diversity, increased sedimentation, movement barriers, invasive species and altered flows that may profoundly change the character and functioning of rivers. Construction or enlargement of reservoirs is continuing, and whilst downstream impacts are often considered, upstream impacts receive far less attention. We develop a population model to examine the impacts of reservoir expansion on a threatened riverine species in South Eastern Australia: the two-spined blackfish. We examined two processes, loss of breeding habitat and increased predation, directly linked to reservoir expansion as well as a broader threat of recruitment failure due to sedimentation. These threatening processes were assessed using the expected minimum population size as an indicator of risk. As is often the case for threatened species, limited data were used to parameterise the model and sensitivity analysis performed to assess the appropriateness of the model parameterisation. The outcomes indicate that the two-spined blackfish population is vulnerable to the loss of breeding habitat particularly if two-spined blackfish are unable to spawn in the larger dam, although this vulnerability is ameliorated if the whole river is accounted for. Including possible impacts from the resident trout population for the whole river, indicates the two-spined blackfish to be vulnerable to low level predation particularly if the trout population have a high growth rate. Population modelling has rarely been used to predict the consequences of dam construction on aquatic species/communities. The example here shows it to be a powerful tool to visualise and quantify potential biodiversity outcomes.

Fish species that have no commercial or recreational value are often overlooked in conservation management, despite serious threats to their long-term future. This can be termed the ‘small threatened freshwater fishes’ paradigm. Population viability analysis (PVA) is a useful technique to assess threatened species and conservation management options. While the development and use of population models and population viability analysis is common in conservation, and often used for larger fishes, this has not been so for small threatened freshwater species. This study uses the PVA process to develop a stochastic population model for Nannoperca australis (southern pygmy perch) in temperate south-eastern Australia. The model was most sensitive to early life-history survival rates, for which there were no estimates from field data, compared with other model uncertainty. This study also found that the oldest age class had the highest reproductive value, providing unique support to the value of big, old, fat and fecund fish (BOFFFs) in sustaining natural populations. Modelling indicated that a population in stable habitat supporting about 2000 female adults would likely to be viable, able to withstand some disturbance and possibly be used as a source population for reintroductions. In reality, however, there are few populations in the wild of sufficient size to withstand such take for translocations and hence the production of fish through hatchery means may be required. This type of approach should prove useful for the conservation management of many similar species globally.

Most assessments of the effectiveness of river restoration are done at small spatial scales (

Overabundant herbivorous mammals can increase the mortality rates of preferred food species, causing long-term changes to plant communities. When lethal control of the herbivore is not possible, fertility control is often advocated as a management solution. There is, however, little empirical evidence that fertility control is a viable option for managing the impacts of open populations of polygynous mammals. We evaluated the effectiveness of two long-term fertility control programs implemented to reduce overabundant koala (Phascolarctos cinereus) populations and their impacts on preferred food trees (manna gum, Eucalyptus viminalis): one in Victoria (10 years) and one in South Australia (17 years). Fertility control reduced koala recruitment such that population densities more than halved at both sites. Mortality rates of manna gum trees were significantly reduced at one site, and trees with light or moderate defoliation recovered at both sites. Relationships between koala population density and canopy defoliation suggest that if management wishes to alleviate moderate browsing pressure then koala density should be maintained below 1.0 koala/ha. We conclude that population-level fertility control can significantly reduce overabundant koala populations and some of their impacts on food trees. Our empirical study demonstrates that long-term fertility control can reduce the undesirable impacts of open populations of polygynous mammals.

Globally, freshwater crayfish are imperilled, particularly large species harvested for human consumption. Crustacean fisheries typically rely on size- and sex-specific harvest regulations to counterbalance the adverse effects of over-harvesting which manifests within populations as disparate size truncation, and uneven sex ratios. A stochastic population model was used to examine the risk from harvest pressure on a threatened crayfish Euastacus armatus in south-eastern Australia. We compared a new indicator, size at functional reproduction (SFR – females with eggs), with the contemporary index of size at onset of maturity (SOM) when applying the current regulations of no-take for females with eggs. SOM under estimates risk compared with SFR. This risk difference was amplified with increasing harvest pressure, proving SOM inadequate for characterizing risk. Variable and increasing adult sex ratios with size was thought to indicate past harvest pressure and signs of recovery from harvest over-exploitation. However, in conjunction with evidence of differential encounter rates between female and male crayfish, we show that high sex ratios in catch data were not due to harvest pressure, pointing to problems with using sex ratio as a measure of exploitation and recovery. Our modelled results were unable to produce high sex ratios in catch data without a differential encounter rate included. If differential encounter rates exist, of the scenarios explored, the greatest risk was associated with the current harvest regulations. With recent declines in distribution and abundance, we argue that either the harvestable slot limit length be altered to account for our SFR results or that all female E. armatus be protected until the numerous uncertainties outlined herein are resolved. Finally, as SFR directly represents the biology of a species and will not inappropriately characterize risk compared with SOM, the new indicator SFR must replace SOM for monitoring, conservation and fisheries management of all decapods.

Reserve systems are part of biodiversity conservation planning. However, reserves are rarely assessed for their contribution to population persistence. Here we address knowledge gaps on reserve effectiveness by developing a new approach to model protected area efficacy as a function of habitat suitability and natural disturbance regimes. We demonstrate the utility of the model through a detailed case study of the critically endangered Leadbeater⿿s possum ( Gymnobelideus leadbeateri) in south⿿eastern Australia. We defined reserve effectiveness for the species to be when there was no more than 5% probability of populations falling to (or below) 500 adult females in 40 generations. A reserve system established specifically for Leadbeater⿿s possum was found inadequate to ensure population persistence for the next 40 generations, given historical disturbance, habitat decline, and future fires. Simulation modelling of potential areas of reserve suggests that, depending on management risk tolerance, between 30% to 100% of current forest extent within the range of the species may be required to ensure population persistence. This study exemplifies the need to consider the size of reserves prior to their establishment to ensure an adequate reserve design that will be effective against future disturbance for conserving threatened species.

Aim: The koala is a widely distributed Australian marsupial with regional populations that are in rapid decline, are stable or have increased in size. This study examined whether it is possible to use expert elicitation to estimate abundance and trends of populations of this species. Diverse opinions exist about estimates of abundance and, consequently, the status of populations. Location: Eastern and south-eastern Australia Methods: Using a structured, four-step question format, a panel of 15 experts estimated population sizes of koalas and changes in those sizes for bioregions within four states. They provided their lowest plausible estimate, highest plausible estimate, best estimate and their degree of confidence that the true values were contained within these upper and lower estimates. We derived estimates of the mean population size of koalas and associated uncertainties for each bioregion and state. Results: On the basis of estimates of mean population sizes for each bioregion and state, we estimated that the total number of koalas for Australia is 329,000 (range 144,000-605,000) with an estimated average decline of 24% over the past three generations and the next three generations. Estimated percentage of loss in Queensland, New South Wales, Victoria and South Australia was 53%, 26%, 14% and 3%, respectively. Main conclusions: It was not necessary to achieve high levels of certainty or consensus among experts before making informed estimates. A quantitative, scientific method for deriving estimates of koala populations and trends was possible, in the absence of empirical data on abundances.

The koala (Phascolarctos cinereus), one of the world's most iconic faunal species, was recently listed under Australian government legislation as vulnerable in the northern states of Queensland and New South Wales and in the Australian Capital Territory, but not in the southern states of Victoria and South Australia. This review synthesises empirical evidence of regional koala population trends, their conservation outlook, and associated policy challenges. Population declines are common in the northern half of the koala's range, where habitat loss, hotter droughts, disease, dog attacks and vehicle collisions are the major threats. In contrast, some southern populations are locally overabundant and are now subject to managed declines. The koala presents the problem of managing a wide-ranging species that now primarily occurs in human-modified landscapes, some of which are rapidly urbanising or subject to large-scale agricultural and mining developments. Climate change is a major threat to both northern and southern populations. The implementation of policy to conserve remaining koala habitat and restore degraded habitat is critical to the success of koala conservation strategies, but habitat conservation alone will not resolve the issues of koala conservation. There needs to be concerted effort to reduce the incidence of dog attack and road-related mortality, disease prevalence and severity, and take into account new threats of climate change and mining. Many of the complex conservation and policy challenges identified here have broader significance for other species whose population trends, and the nature of the threatening processes, vary from region to region, and through time.

Understanding why related species have differing population-level responses to threats can be key to identifying conservation options for declining populations. However, this is difficult when multiple threats are implicated. Chytrid fungus (Batrachochytrium dendrobatidis: Bd) is implicated in at least 500 amphibian population declines globally, although few tangible options exist to mitigate pathogen impacts. Other threatening processes also invariably operate on most amphibians. Non-native fish, for example, can contribute to amphibian declines and may exacerbate Bd impacts. We disentangled the impacts of Bd and non-native fish upon two stream breeding frog species with differing conservation statuses to reveal vital rates that are crucial for species persistence. Litoria spenceri are threatened and historically occurred at elevations between 300–1100 m asl in southeastern Australia. Litoria lesueurii are non-threatened and sympatric with L. spenceri at some sites. Using mark-recapture derived demographic rates known to correlate with climate and elevation, discrete-time deterministic population models were constructed for each species at high, moderate and low elevation sites, and multiple management scenarios. Our study reveals that age to maturation, clutch size and egg-year 1 survival influenced interspecific and intraspecific population-level responses of the two frogs to Bd impacts. Importantly, our results highlight that an amphibian population’s capacity to counteract Bd-mediated adult mortality is clearly constrained by other threats and environment interactions that moderate species recruitment. Furthermore, understanding limits to recruitment may help identify Bd mitigation strategies. In our study, disease mitigation may be best achieved at some sites by enhancing recruitment through non-native fish management.

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.

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.

Globally, overharvest contributes to population declines of fish and invertebrates. Quantifying the effects of fishing and associated harvest is essential to preventing such declines. Murray crayfish Euastacus armatus exhibit slow growth and late age at maturity, and were historically abundant in Australia’s Murray–Darling Basin, but river regulation, pollution and overfishing have reduced their range and abundance. Diminished recreational fisheries still exist, but data to quantify catch, effort and harvest are not available to inform management decisions. We used a population model to assess the status of a harvested Murray crayfish population, informed by data collected from a fishery-dependant survey. Quantitative fisher surveys were undertaken in the Murrumbidgee River during the 2012 Murray crayfish open season (May–August inclusive). Shortly after the surveys, and in light of fishery-independent data that indicated a Murray crayfish decline, the crayfish recreational fishery was spatially reduced and shortened to a 3-month season (June–August), bag limits were reduced and size limits were changed from a minimum length limit of 90mm to a harvest-slot length limit (HSLL) of 100–120mm. Modelling of the Murray crayfish population indicated it was most likely to be relatively small with a mean population size of 2777 individuals and affected by a high rate of crayfish harvest (harvest probability 0.4), indicating vulnerability to further decline should fishing effort and harvest persist. The population model was used to assess the regulation change to a HSLL, with the results supporting the regulation change and indicating that implementation of the HSLL would stabilise the population, albeit over many years. This study demonstrates that empirical data and population modelling are crucial to inform fishery regulations for threatened species.

The number of threatened species continues to increase due to a range of anthropogenic disturbances, and many species continue to decline increasing their risk of extinction. Translocation is a widely used management technique to establish new populations to reduce the risk of extinction. There are, however, a range of issues to be considered. For example, for some species the donor population may be impacted by translocation, for other species it must be decided whether to translocate adults or juveniles to establish new populations. The question then becomes who do you move? The endangered Macquarie perch in south-eastern Australia is continuing to decline, with the recent Millennium Drought (1997–2010) and associated events (e.g., bushfires) contributing to dramatic local declines and the need for emergency responses. Successful historic translocations of this species involved adult fish, however the removal of significant numbers of adult fish may now impact source populations and alternative translocation approaches needed investigating. The use of sub-adult or juvenile fish, that would be expected to experience higher mortality, may be an approach to establishing new populations which would have less severe impacts on source populations. However, the number of fish required, frequency of translocation and likelihood of population establishment are unknown. This study outlines the development of a population model to assist in trialling translocation scenarios for establishing new populations of Macquarie perch. The model predicts that translocations of young-of-year fish (age 0+) is unlikely to be successful unless ∼600 females are released annually for five years. If translocating yearling (age 1+) fish, annual translocations of >100 females is required to achieve success, with stocking for at least five consecutive years required. If the frequency of recruitment failure or magnitude of Allee effects increases, then translocations of increased numbers of yearlings or prolonged stocking (10 years) is required to achieve success. The addition of small numbers of adult fish in combination with yearlings decreases the number of yearlings required, and increases the chance of success under more stressful scenarios.

To quantify how electrofishing capture probability varies over time and across physiochemical and disturbance gradients in a turbid lowland river, we tagged between 68 and 95 fish·year−1 with radio transmitters and up to 424 fish·year−1 with external and passive integrated transponder (PIT) tags. We surveyed the site noninvasively using radiotelemetry to determine which of the radio-tagged fish were present (effectively closing the radio-tagged population to emigration) and then electrofished to estimate the proportion of available fish that were captured based on both this and standard mark–recapture methods. We replicated the electrofishing surveys three times over a minimum of 12 days each year, for 7 years. Electrofishing capture probability varied between 0.020 and 0.310 over the 7 years and between four different large-bodied species (Murray cod (Maccullochella peelii), trout cod (Maccullochella macquariensis), golden perch (Macquaria ambigua ambigua), and silver perch (Bidyanus bidyanus)). River turbidity associated with increased river discharge negatively influenced capture probability. Increasing fish length increased detection of fish up to 500 mm for Murray cod, after which capture probability decreased. Variation in capture probability in large lowland rivers results in additional uncertainty when estimating population size or relative abundance. Research and monitoring programs using fish as an indicator should incorporate strategies to lessen potential error that might result from changes in capture probabilities.

Sustainable management of natural resources requires robust and timely information inputs, particularly in multispecies or cross-jurisdictional fisheries such as the Murray-Darling Basin's (MDB) recreational fishery. Innovative data collection and monitoring approaches, management tools and cooperative efforts enable the requirements of fisheries managers to be met efficiently and cost-effectively. This paper considers a number of pioneering initiatives operationalised under the Native Fish Strategy that have helped inform sustainable management outcomes for the recreational fishery in the MDB.

Managing fisheries using length-based harvest regulations is common, but such policies often create trade-offs among conservation (e.g. maintaining natural agestructure or spawning stock biomass) and fishery objectives (e.g. maximizing yield or harvest numbers). By focusing harvest on the larger (older) fish, minimumlength limits are thought to maximize biomass yield, but at the potential cost of severe age and size truncation at high fishing mortality. Harvest-slot-length limits (harvest slots) restrict harvest to intermediate lengths (ages), which may contribute to maintaining high harvest numbers and a more natural age-structure. However, an evaluation of minimum-length limits vs. harvest slots for jointly meeting fisheries and conservation objectives across a range of fish life-history strategies is currently lacking. We present a general age- and size-structured population model calibrated to several recreationally important fish species. Harvest slots and minimum-length limits were both effective at compromising between yield, numbers harvested and catch of trophy fish while conserving reproductive biomass. However, harvest slots consistently produced greater numbers of fish harvested and greater catches of trophy fish while conserving reproductive biomass and a more natural population age-structure. Additionally, harvest slots resulted in less waste in the presence of hooking mortality. Our results held across a range of exploitation rates, life-history strategies and fisheries objectives. Overall, we found harvest slots to represent a valuable option to meet both conservation and recreational fisheries objectives. Given the ubiquitous benefits of harvest slots across all life histories modelled, rethinking the widespread use of minimum-length limits is warranted.

Carp are a highly successful invasive fish species, now widespread, abundant and considered a pest in south-eastern Australia. To date, most management effort has been directed at reducing abundances of adult fish, with little consideration of population growth through reproduction. Environmental water allocations are now an important option for the rehabilitation of aquatic ecosystems, particularly in the Murray–Darling Basin. As carp respond to flows, there is concern that environmental watering may cause floodplain inundation and provide access to spawning habitats subsequently causing unwanted population increase. This is a management conundrum that needs to be carefully considered within the context of contemporary river flow management (natural, environmental, irrigation). This paper uses a population model to investigate flow-related carp population dynamics for three case studies in the Murray–Darling Basin: (1) river and terminal lakes; (2) wetlands and floodplain lakes; and (3) complex river channel and floodplain system. Results highlight distinctive outcomes depending on site characteristics. In particular, the terminal lakes maintain a significant source carp population regardless of river flow; hence any additional within-channel environmental flows are likely to have little impact on carp populations. In contrast, large-scale removal of carp from the lakes may be beneficial, especially in times of extended low river flows. Case studies 2 and 3 show how wetlands, floodplain lakes and the floodplain itself can now often be inundated for several months over the carp spawning season by high volume flows provided for irrigation or water transfers. Such inundations can be a major driver of carp populations, compared to within channel flows that have relatively little effecton recruitment. The use of a population model that incorporates river flows and different habitats for this flow-responsive species, allows for the comparison of likely population outcomes for differing hydrological scenarios to improve the management of risks relating to carp reproduction and flows.

Murray cod Maccullochella peelii (Mitchell) is a large, iconic Australian fish species targeted by anglers but also listed as nationally threatened. A consultative process that included conservation and fishery interests helped to develop a population model for this species and agree on management scenarios to be tested. The modelled scenarios illustrated that threats to populations (risk of decline) can be substantially reduced and catch rates increased through harvest slot length limits (HSLL) rather than minimum legal limits (MLL). A 600- to 1000-mm HSLL provided lower risk of decline and greater catch rates than the existing 500-mm MLL, but better results were achieved with a 400- to 600-mm HSLL. Importantly, a range of other impacts (fish kills, stocking, thermal impacts, larval mortalities, habitat changes) were recognised and incorporated. This study provides an example of the utility of a population model to improve management decision-making for both conservation and fishery objectives.

Forest management decisions are characterised by a high level of uncertainty because responses reflect a range of interacting ecological processes. Faced with this situation, modelling can be a useful tool for characterising that uncertainty and for predicting its impacts on management decisions. In the adaptive management paradigm, different model structures are essentially hypotheses of system behaviour that are formulated to encapsulate structural uncertainty about the system. Here we report upon the initial stages of a management-scale experiment designed to increase our understanding of the effects of deer control on forest ecosystems in New Zealand. Using a modelling approach based on fuzzy cognitive maps (FCM) we were able to formalise expert knowledge and explore how growth rates of tree seedlings would respond to lower deer densities, with or without responses by other plants in the forest understorey. Alternative models predicted that the response of seedling growth and biomass in small (16 m 2 ) plots used in the experiment were dependent on hypotheses about the strength of plant competition for soil nutrients and moisture which, in turn, were conditional on light availability in the plot. To learn about which model best may describe the system, we used recently proposed methods in Approximate Bayesian Computation (ABC) to perform model selection and inference using a simulated data set generated from one of our candidate models. Using a novel Markov chain Monte Carlo algorithm together with ABC model selection on our simulated data we show that these procedures provide reliable model selection and parameter inference and hence, should be suitable for confronting our candidate FCM models with data collected at the end of the experiment.

Oil spill responders require information on the relative toxicity of dispersed and un-dispersed oil in order to make informed decisions regarding the use of chemical dispersants during spill events. Toxicity of the water-accommodated fraction (WAF) and the chemically-enhanced WAF (CEWAF; via the dispersant Corexit 9500) of weathered Prudhoe Bay crude oil was investigated using adult and embryonic topsmelt; topsmelt are an ecologically important atherinid in California bays and estuaries and an important indicator species. Following 96-h exposures, metabolite profiles were measured using 1D 1 H nuclear magnetic resonance (NMR) spectroscopy and compared via principal component analysis. Similar metabolic profiles were obtained between WAF- and CEWAF-exposed adults and embryos. Although metabolic changes, for the adults lacked significance, significant increasing and decreasing metabolic changes were observed for embryos directly exposed. Furthermore, no mortality was observed for embryos, exposed to WAF and normal development occurred, whereas CEWAF exposed embryos lead to mortality and cardiovascular abnormalities. Observed toxicological information, specifically for developing fish, can aide resource managers in the relative risk of treating oil spills with dispersant.

With maritime transport of crude oil from Alaska to California, there is significant potential for a catastrophic spill which could impact migrating salmon. Therefore, this study compared the lethal and sublethal metabolic actions of the water-accommodated fraction (WAF) and the chemically enhanced WAF (CEWAF, via Corexit 9500) of Prudhoe Bay crude oil in smolts of Chinook salmon (Onchorhyncus tshawytscha). After 96-h exposure to the CEWAF, the resulting LC50 was some 20 times higher (i.e., less toxic) than that of the WAF. Muscle and liver samples from surviving fish were collected and low-molecular weight metabolites were analyzed using one-dimensional (1)H and projections of two-dimensional (1)H J-resolved NMR. Principal component analysis (PCA), employed to analyze NMR spectra and identify most variance from the samples, revealed age-related metabolic changes in the fish within the replicated studies, but few consistent metabolic effects from the treatments. However, ANOVA results demonstrated that the dose-response metabolite patterns are both metabolite- and organ-dependent. In general, exposure to either WAF or CEWAF resulted in an increase of amino acids (i.e., valine, glutamine and glutamate) and a decrease of both organic osmolytes (i.e., glycerophosphorylcholine) and energetic substrates (i.e., succinate). The simultaneous increase of formate and decrease of glycerophosphorylcholine in the liver, or the decrease of glycerophosphorylcholine in muscle, may serve as sensitive sublethal biomarkers for WAF or CEWAF exposures, respectively. In conclusion, dispersant treatment significantly decreased the lethal potency of crude oil to salmon smolts, and the NMR-based metabolomics approach provided a sensitive means to characterize the sublethal metabolic actions.

Summary 1 Koala Phascolarctos cinereus populations sometimes exhibit eruptive dynamics, increasing to peak abundance and then crashing to low abundance. This dynamic is considered unacceptable because koalas die from starvation and food trees are killed by defoliation. There is concern that such dynamics may be occurring at a number of sites in south-eastern Australia. The only management option is fertility control of females. 2 We constructed a simulation model of koalas interacting with their food supply (manna gum Eucalyptus viminalis) in Mount Eccles National Park, Victoria, Australia. The amount of manna gum leaves consumed changed the survival and fecundity rates of koalas, and the amount of leaves removed changed the survival and transition rates of manna gums. 3 Without fertility control the koala population was predicted to increase to peak abundance within 10–18 years before crashing. The predicted dynamics of manna gum were more variable but abundance increased in most simulations for up to c. 5 years before declining to c. 25% of peak abundance within 20–30 years and then increasing subsequently. The maximum rate of koala population decline was an important determinant of the interaction between koalas and manna gum. 4 The best management strategy that was analysed involved estimating the number of unsterilized females in the population annually and then sterilizing a variable number to maintain a population of 1000 koalas: this strategy generated the least decline in manna gum at a consistently low cost. However, there was a delay between imposing fertility control and consequent reduction in koala abundance because of high adult female survival rates. Hence manna gum was predicted to decline for 5–10 years before increasing. 5 Synthesis and applications. Our results highlight important time-lags between implementing fertility control, reducing the abundance of a herbivore with high survival rates and subsequent changes in the abundance of its food supply. Our model is useful for understanding how controlling ‘overabundant’ herbivores impacts upon the dynamics of both the herbivore and its food supply.

A one-dimensional hydrodynamic reservoir model is coupled with a stochastic fish population model to examine the impacts of cold water pollution (CWP) on the Australian freshwater fish, Murray cod, downstream of Hume Dam, Australia. Mitigation of CWPthroughtheintroductionofselectivewithdrawalcapabilitiestoaccessnear-surfacewaterispredictedtoincreasedischarge temperatures during the crucial spring-early summer post-spawning period by 4‐68C for normal operating conditions, that is, a full reservoir in early spring. No improvement in discharge temperature was predicted for drought conditions characterized by relatively low storage levels in early spring. The predicted temperature increase using selective withdrawal increased the predicted average minimum female population abundance by 30‐300% depending on the assumed spawning behaviour. Increased discharge temperatures appear to be achievable and are expected to reduce the stress currently impacting Murray cod populations due to CWP during crucial post-spawning periods. This provides evidence that mitigation of this problem may assistinrehabilitatingMurraycodpopulationsintheMurrayRiverdownstreamofHumeDam.Copyright#2007JohnWiley& Sons, Ltd.

The effects of cold water releases, as a by-product of storing irrigation water in large dams, has been a source of great concern for its impact on native freshwater fish for some time. The Mitta Mitta River, northeast Victoria, is impacted by altered thermal regimes downstream of the fourth largest dam in Australia, Dartmouth dam, with some daily temperatures 10–12°C below normal. Murray cod (Maccullochella peelii peelii) were endemic to the Mitta Mitta River; however, resident Murray cod have not been found in this river since 1992. The response of eggs and hatched larvae from Murray cod to different temperature gradients of water were measured and the post-spawning survival recorded. As a case study, post-spawning survival was then inferred from flow data for each year of operation of Dartmouth Dam, recorded since first operation in 1978, and included in a stochastic population model to explore the impact of the altered (historical) thermal regime on population viability. Experimental results revealed no egg and larval survival below 13°C and predicted historical temperature regimes point to more than 15 years of low temperatures in the Mitta Mitta River. Population modelling indicates that the impact of cold water releases on post-spawning survival is a significant threatening process to the viability of a Murray cod population. Additionally, we consider changes to the thermal regime to explore how the thermal impact of large dams may be minimized on downstream fish populations through incrementally increasing the temperature of the releases. The modelled Murray cod population responds to minor increases in the thermal regime; however, threats are not completely removed until an increase of at least 5–6°C. Copyright © 2005 John Wiley & Sons, Ltd.

Summary Adaptive management (AM) remains a commonly cited, yet frequently misunderstood, management approach. The aim of AM is to improve environmental management through ‘learning by doing’ and understand the impact of incomplete knowledge, but AM more commonly consists of ad hoc changes in managing environmental resources in the absence of adequate planning and monitoring. Here, we trace and review the development of AM, the central roles of consultation, collaboration and of monitoring, and of quantitative models and simulations. We identify a series of formalized, structured steps included in one AM cycle and review how current AM programs build upon such cycles. We conclude that the best AM outcomes require rigorous and formalized approaches to planning, collaboration, modelling and evaluation. Finally, simulating potential outcomes of an AM cycle in the presence of existing uncertainty can help to identify management strategies that are most likely to succeed in relation to clearly articulated goals.

A stochastic population model has been developed for exploring the conservation management of the endangered fish trout cod (Maccullochella macquariensis) in the circumstances of incomplete understanding of the ecology of the species as well as the absence of appropriate data for the estimation of some vital rates. The model includes a stage-structured approach with environmental and demographic variation, and examines three types of density dependence: Beverton–Holt, Ricker and a biomass approach that we have developed to incorporate intraspecific competition beyond recruitment to 1-year olds. The stochastic model was used to explore the current and future status of the protected and last self-sustaining natural population of trout cod, restricted to a 200 km section of the Murray River in south-eastern Australia, under the different density-dependent mechanisms. Current practices for reintroducing trout cod were also evaluated. The analysis indicates that the protected natural population may be stable provided that it remains free from any significant disturbance. However, the analysis also indicates that trout cod may be very sensitive to any reduction in adult survival and remain potentially vulnerable to continued anthropogenic disturbance, in particular fishing. The analysis also indicates that the current practice of releasing fingerlings to establish a reintroduced population was more likely to fail than releasing on-grown 1-year-old fish at reintroduction sites. Furthermore, the traditional density-dependent mechanisms have less support than the applied biomass approach. The stochastic population model developed becomes a resource for guiding the conservation management and further research into the ecology of trout cod.

We comment on a recent article by Newton (Environ. Model. Softw. (2010), 25, 15-23), which proposed a method, based on a Bayesian belief networks, for classifying the threat status of species under the IUCN Red List Categories and Criteria, and compared this method to an earlier one that we had developed that is based on fuzzy logic. There are three types of differences between the results of the two methods, the most consequential of which is different threat status categories assigned to some species for which the input data were uncertain. We demonstrate that the results obtained using the fuzzy logic approach are consistent with IUCN Red List criteria and guidelines. The application of Bayesian Networks to the IUCN Red List criteria to assist uncertain risk assessments may yet have merit. However, in order to be consistent with IUCN Red List assessments, applications of Bayesian approaches to actual Red List assessments would need an explicit and objective method for assigning likelihoods based on uncertain data.

As part of an ongoing program of management for a critically endangered fish, we explored adaptive management as a method to overcome pervasive uncertainty regarding the reintroduction of trout cod (Maccullochella macquariensis Cuvier). We simulated the entire adaptive management cycle to explore the suitability of the approach for guiding threatened species management and to identify problems and barriers to "learning by doing". During the planning phase, a number of compromises were identified between specification of goals and objectives, the available management options, and current monitoring capacity. Undertaking a simulation of the implementation of alternate adaptive approaches to this reintroduction provided a number of insights into adaptive management in general. First, identifying the weak link in the process of inference emphasized the need to consider whether goals and objectives are achievable and meaningful and whether they complement monitoring and (or) any other limitations of the system. Second, in natural resource management, it is crucial to negotiate objectives in the light of what one can measure. Third, although there are lessons to be learned from each stage of the adaptive management cycle, there is value in simulating the entire adaptive management cycle, including management actions, monitoring, and the states of the system that lead to management intervention.

In 1998 the protected population of Perameles gunnii (eastern barred bandicoot) at Woodlands Historic Park, Victoria, Australia became functionally extinct following removals of individuals for translocation between 1994 and 1996. Population viability analysis and data collected whilst the population was in decline are used to explore the impact that these removals had on the decline of the P. gunnii population at Woodlands. Due to some ambiguities in the life history of P. gunnii at Woodlands, two structurally different population models were used. Explicitly including the removal of animals in the analysis indicates that there may be at least a three-fold increase in the risk of quasiextinction due to removals. In some scenarios, over 17% of the trajectories decrease to a level less than or equal to 10 females within the observed time period of the collapse of the population, that is by April 1998. The modelling approach identified a number of critical factors in the decline of the population, such as variation in survival rates. By representing the life history strategy using two alternate models, quantitative statements about the impact that removals had on the population decline at Woodlands are made. While removals probably contributed to the collapse of the population, removals were not the sole cause of population decline. The real reasons for decline remain unknown; however, it is likely to be closely linked to habitat decline, difficult environmental conditions and predation. If P. gunnii are reintroduced to Woodlands again, then the models presented here may help to develop management strategies to establish a self sustaining population, as well as exploring translocations options.

A problem for population modellers in undertaking quantitative population viability analysis has been restricting survival rates to the unit interval and retaining the specified mean and standard deviation. In order to overcome this problem, we have developed a general method for generating correlated survival rates. The method consists of applying the transformation Φ x , the cumulative distribution function of the standard normal distribution, to suitably correlated normal variates X1, X2, …, Xk. The means, standard deviations and correlation coefficients of X1, X2, …, Xk are calculated so that the transformed results have the desired means, standard deviations and correlations for the survival rates. This method allows the full spectrum of correlations among different ages/stages to be considered, as well as the flexibility of a range of differently shaped distributions. The method proposed may generally apply to any function that satisfies the definition of a cumulative distribution function for which a derivative and inverse exist. A case study using the Φ x transform exemplifies these advantages, especially in comparison with the typical process of limiting random deviates to the unit interval currently in use. The case study emphasises the point that the limiting of random deviates may lead to an under-estimation of the specified variation and, as a result, simulated risk curves exhibiting a smaller range in possible outcomes compared with our method. This has particular importance when developing population viability analysis models to assess the risk of extinction or quasiextinction of a population.

Uncertainty about which model structure best describes the life history of a species may be a problem for the development of some population viability analysis (PVA). This paper describes the development and exploration of two structurally different stochastic population models when there is uncertainty about the life history of a species. Delayed reproduction was observed in a protected population of the small marsupial Perameles gunnii (eastern barred bandicoot) at Woodlands Historic Park, Victoria, Australia. This previously undocumented feature of P. gunnii may be considered to be either a component of the seasonal breeding cycle or it may be delayed development to sexual maturity. A delayed development model is compared to a standard development model where the parameter estimates of each model were obtained from a long-term mark-recapture study at Woodlands Historic Park. While the growth rate of the delayed development model is less than that of the standard model, the predicted risks of extinction/quasiextinction were higher for the standard model. This discrepancy is the result of different interpretations placed upon the available data underpinning the two models, the most important of which is the difference between the estimated variance in survivorship of the sub-adult stage. The results highlight the need for conservation assessments based on stochastic modelling to explore the degree to which the predicted extinction risk is affected by the incomplete knowledge of the species’ basic biology and parameter values.

The World Conservation Union (IUCN) defined a set of categories for conservation status supported by decision rules based on thresholds of parameters such as distributional range, population size, population history, and risk of extinction. These rules have received international acceptance and have become one of the most important decision tools in conservation biology because of their wide applicability, objectivity, and simplicity of use. The input data for these rules are often estimated with considerable uncertainty due to measurement error, natural variation, and vagueness in definitions of parameters used in the rules. Currently, no specific guidelines exist for dealing with uncertainty. Interpretation of uncertain data by different assessors may lead to inconsistent classifications because attitudes toward uncertainty and risk may have an important influence on the classification of threatened species. We propose a method of dealing with uncertainty that can be applied to the current IUCN criteria without altering the rules, thresholds, or intent of these criteria. Our method propagates the uncertainty in the input parameters and assigns the evaluated species either to a single category (as the current criteria do) or to a range of plausible categories, depending on the nature and extent of uncertainties. Resumen: La Union Mundial para la Conservacion (IUCN) definio un grupo de categorias referentes a estados de conservacion sustentadas en reglas de decision basadas en umbrales de parametros como son el rango de distribucion, el tamano poblacional, la historia poblacional y el riesgo de extincion. Estas reglas han recibido aceptacion internacional y se han convertido en una de las herramientas mas importantes para la toma de decisiones en biologia de la conservacion debido a su amplia aplicabilidad, objetividad y simplicidad de uso. Los datos requeridos para estas reglas son frecuentemente estimados con una incertidumbre considerable debido a errores de medicion, variacion natural y vaguedad en la definicion de los parametros usados en las reglas. Actualmente no existen lineamientos especificos para enfrentar la incertidumbre. La interpretacion de datos inciertos por diferentes estimadores puede conducir a clasificaciones inconsistentes debido a que ciertas actitudes hacia la incertidumbre y el riesgo pueden tener una influencia importante en la clasificacion de especies amenazadas. Proponemos un metodo para enfrentar a la incertidumbre que puede ser aplicado a los criterios actuales de IUCN sin alterar las reglas, los umbrales, o la intencion de estos criterios. Nuestro metodo propaga la incertidumbre en los parametros usados y asigna a la especie evaluada a una sola categoria (a como lo hace el criterio actual) o a un rango de categorias plausibles, dependiendo de la naturaleza y la extension de las incertidumbres.

The classification of species with respect to their conservation status using the IUCN criteria is an important process in many countries, providing a guide for setting conservation priorities. Recent advances have resulted in several approaches to dealing with uncertainty in data used to classify species. These methods demand an unambiguous and transparent logical structure for the criteria. We suggest some changes to the ways in which the criteria are represented that correct an unnecessary inconsistency and which may serve to avoid important errors when uncertainty in the data is considered explicitly.

Decision rule sets are used widely to classify the conservation status of species. These classifications are intended to approximate the relative degree of threat faced by different species. They are important because they play a role in setting conservation priorities. It is suggested that such rule sets should take into account estimates of the statistical distribution and confidence intervals reported for each of the parameters. Examples are provided for three threatened Australian plant species.

Most current methods available for assessing the conservation status of a species do not take into account the underlying uncertainty inherent in the data. A point estimate approach is generally adopted to interpret the data used in these assessments. For species that are not well known, the paucity of quality data produces an unreliable estimate of the species’ status. The assessment of threat, based upon a range of values reflecting the uncertainty in parameter estimates, can be undertaken within the framework of fuzzy sets and used to broaden the evaluation of a species. When the parameter estimates of two biological variables are combined, the use of fuzzy sets in conjunction with a point scoring convention generates a range of plausible outcomes, rather than a single outcome that would result from the point estimate approach. Different types of uncertainty, including probabilistic uncertainty and reasonable bounds for expert judgment, can be interpreted and used to provide a measure of reliability of the outcomes. The measure of reliability ranks each outcome and provides a statement about which outcome best represents the level of threat faced by a species. The incorporation of fuzzy sets into a current convention shows that consideration of uncertainty may change the assessment of a species and accordingly the conservation priorities. Evalacion de la Amenaza y las Prioridades de Conservacion Bajo Niveles Realistas de Incertidumbre y Confiabilidad Los metodos mas comunmente utilizados para determinar el estado de una especie para su conservacion no consideran la incertidumbre existente en los datos disponibles para dicho analisis. Estos metodos generalmente utilizan estimados puntuales en la interpretacion de los datos y por esto resultan inadecuados cuando son aplicados a especies poco conocidas dado que la escasez de datos confiables puede llevar a conclusiones incorrectas sobre el estado de la especie. La evaluacion del riesgo de una especie basada en el uso de intervalos que reflejan la incertidumbre de los parametros estimados, puede ser llevada a cabo usando “intervalos difusos” (fuzzy sets). Cuando los parametros estimados de dos o mas variables biologicas son combinanados, el uso de intervalos difusos en combinacion con metodos basados en estimados puntuales, aumenta el espectro de resultados posibles en la evaluacion del estado de la especie. Distintos tipos de incertidumbre, incluyendo la incertidumbre probabilistica y las razonables dudas asociadas a las estimaciones de los expertos, pueden ser interpretadas y utilizadas para evaluar la validez de los resultados. Las medidas de confianza en los datos otorgan un orden a cada resultado y ademas proveen un criterio para decidir cual de los resultados representa mejor el nivel de riesgo de la especies en consideracion. La incorporacion de los intervalos difusos en los metodos convencionales demuestra que la inclusion de incertidumbre en los datos puede cambiar las interpretaciones sobre el estado de las especies y de esta manera, los criterios y prioridades para su conservacion.

Crude oil spills from tankers remain a serious threat along coastal California. Resource managers require information on the acute toxicity of treated and untreated oil, and their sublethal effects on wildlife. This investigation compared the toxic actions of the water-accommodated fraction (WAF) and the chemically-enhanced WAF (CEWAF; Corexit 9500) of Prudhoe Bay crude oil in pre-smolt Chinook salmon ( Oncorhynchus tshawytscha ) via nuclear magnetic resonance (NMR)-based metabolomics. Metabolite profiles from muscle samples, after 96 h exposures, were measured using 1D 1 H NMR and compared via principal component analysis. It was determined that both WAF and CEWAF produced similar profiles in which amino acids, lactate and ATP comprised the highest intensity signals. Overall, metabolic substrates and growth measurements did not show residual effects of short-term exposure on long-term development. In conclusion, the 96 h LC 50 s indicate dispersant application significantly decreased hydrocarbon potency and identified metabolites may be bio-indicators of hydrocarbon stress from hydrocarbon exposure.