School of Agriculture, Food and Ecosystem Sciences - Research Publications

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    Prediction of Hydrologic Characteristics for Ungauged Catchments to Support Hydroecological Modeling
    Bond, NR ; Kennard, MJ (AMER GEOPHYSICAL UNION, 2017-11)
    Abstract Hydrologic variability is a fundamental driver of ecological processes and species distribution patterns within river systems, yet the paucity of gauges in many catchments means that streamflow data are often unavailable for ecological survey sites. Filling this data gap is an important challenge in hydroecological research. To address this gap, we first test the ability to spatially extrapolate hydrologic metrics calculated from gauged streamflow data to ungauged sites as a function of stream distance and catchment area. Second, we examine the ability of statistical models to predict flow regime metrics based on climate and catchment physiographic variables. Our assessment focused on Australia's largest catchment, the Murray‐Darling Basin (MDB). We found that hydrologic metrics were predictable only between sites within ∼25 km of one another. Beyond this, correlations between sites declined quickly. We found less than 40% of fish survey sites from a recent basin‐wide monitoring program (n = 777 sites) to fall within this 25 km range, thereby greatly limiting the ability to utilize gauge data for direct spatial transposition of hydrologic metrics to biological survey sites. In contrast, statistical model‐based transposition proved effective in predicting ecologically relevant aspects of the flow regime (including metrics describing central tendency, high‐ and low‐flows intermittency, seasonality, and variability) across the entire gauge network (median R2 ∼ 0.54, range 0.39–0.94). Modeled hydrologic metrics thus offer a useful alternative to empirical data when examining biological survey data from ungauged sites. More widespread use of these statistical tools and modeled metrics could expand our understanding of flow‐ecology relationships.
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    Regional-scale extremes in river discharge and localised spawning stock abundance influence recruitment dynamics of a threatened freshwater fish
    Tonkin, Z ; Kearns, J ; Lyon, J ; Balcombe, SR ; King, AJ ; Bond, NR (WILEY, 2017-09)
    Abstract Highly variable recruitment is common for many riverine fish species, governed by a wide range of biotic and abiotic drivers that operate at local and regional scales. The dynamics and drivers of recruitment for many Australian freshwater fish species, particularly those that are rare and long‐lived, are relatively undescribed. This study describes the recruitment dynamics of an endangered riverine fish, Macquarie perch Macquaria australasica, across 5 isolated populations from southeastern Australia, and relates these dynamics to drivers that vary at local and regional scales. We hypothesised large flow events occurring during the core egg, and larval period would be negatively associated with recruitment strength and that recruitment patterns across populations would fluctuate in synchrony in response to extremes in river discharge resulting from regional‐scale climatic patterns. Discharge during the core egg and larval period, which was highly correlated across the region, and a local‐scale variable, spawning stock abundance, were the covariates most important in explaining recruitment strength. We also observed synchronised patterns in recruitment across our populations, thus conforming to predictions of the Moran effect (environmental synchrony). The findings suggest that most remnant populations of Macquarie perch, which are now predominantly isolated within small tributary systems characterised by highly variable flows, face a heightened risk of poor recruitment periods, particularly under climate change predictions. The synchronised patterns in recruitment suggest that threatened freshwater fishes such as Macquarie perch with highly fragmented isolated populations have an increased risk of the regional population becoming imperilled, thus the need for a coordinated multijurisdictional conservation approach.
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    Species distributions represent intraspecific genetic diversity of freshwater fish in conservation assessments
    Hermoso, V ; Kennard, MJ ; Schmidt, DJ ; Bond, N ; Huey, JA ; Mondol, RK ; Jamandre, BW ; Hughes, JM (WILEY, 2016-10)
    Summary Accounting for genetic diversity and evolutionary processes has long been recognised as an important goal in conservation planning. However, because genetic data are often lacking, surrogate approaches are widely used. Few studies have, however, assessed the capacity of surrogate data, such as higher taxonomic levels (e.g. species distributions) to portray intraspecific genetic diversity. Here, we contrast conservation plans based on traditional species distribution data, with those derived from intraspecific genetic data for a smaller subset of species, both using freshwater fish in northern Australia. We modelled the spatial distribution of 46 species and intraspecific genetic diversity within four common species. We then identified priority areas for conservation using both data sets and evaluated the extent to which solutions obtained from species distribution data portrayed genetic diversity. We found that genetic diversity could be adequately represented within priority areas identified using species distribution data, even at low conservation targets and for species with complex genetic structure. However, this was only true when using the entire fish community (i.e. all 46 species). In contrast, a substantial component of the genetic structure would not be represented in conservation priority areas when using a subset of species. Our results have important implications for the use of surrogates for genetic diversity in conservation planning. Sufficient genetic diversity might be represented in conservation priority areas by including a broad range of species with distributions ranging from common to rare elements in the community in the prioritisation analyses. We recommend focusing on improving accuracy of data on species distributions to reduce uncertainties in conservation recommendations derived from commission and omission errors, to avoid misuse of limited conservation funds and potential failure of conservation practice.
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    Go with the flow: the movement behaviour of fish from isolated waterhole refugia during connecting flow events in an intermittent dryland river
    Marshall, JC ; Menke, N ; Crook, DA ; Lobegeiger, JS ; Balcombe, SR ; Huey, JA ; Fawcett, JH ; Bond, NR ; Starkey, AH ; Sternberg, D ; Linke, S ; Arthington, AH (WILEY, 2016-08)
    Summary In many intermittent, dryland rivers, fish are confined to isolated waterholes for much of the year. It is only during brief flow events, which typify the hydrology of these systems, that fish are able to move between waterholes and explore surrounding habitat. Because most of the river channel will dry afterwards, there is a strong advantage for selection of persistent waterholes. Two hundred and fifteen individual fish of three common large‐bodied species were tagged in two isolated waterholes in the Moonie River (Queensland, Australia) over 3 years. Their movements were monitored to identify the flow events that trigger fish movement between waterholes, differences in response among species and size classes and refuge selection preferences. Some individuals of all species moved during flow events and others remained within the same waterhole. There was no clear upstream or downstream preference, and most individuals used a reach of up to 20 km, although some individuals ranged over more than 70 km in only several days. Above a threshold flow of 2 m above commence‐to‐flow level, timing of flow was more important than magnitude, with most movement occurring in response to the first post‐winter flow event, independent of its magnitude and duration. Many of the fish that moved displayed philopatry and subsequently returned to their starting waterhole either by the end of a flow event or on subsequent events, suggesting ability to navigate and a preference for more permanent refuge pools. Maximising survival in a highly variable environment provides a plausible mechanism for maintaining these behaviours. Modifications to both flow regime and hydrological connectivity may reduce movement opportunities for fish in intermittent rivers. Our findings show that fish in intermittent systems use networks of waterholes and that management and conservation strategies should aim to maintain movement opportunities at large spatial scales to preserve population resilience.
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    Development and Application of Predictive Models of Surface Water Extent to Identify Aquatic Refuges in Eastern Australian Temporary Stream Networks
    Yu, S ; Bond, NR ; Bunn, SE ; Kennard, MJ (AMER GEOPHYSICAL UNION, 2019-11)
    Abstract Many organisms living in temporary streams rely on remnant surface water to survive during extended dry periods and recolonize newly established habitats when flow resumes. However, research on the spatiotemporal variations in surface water extent for entire river networks is scarce. In this study, we first present a new field method for rapid surface water assessment. Next, we develop predictive models relating observed water extent to environmental attributes at a large number of surveyed stream segments (n = 241) in eastern Australian coastal catchments. We use the models to predict daily variations in surface water dynamics throughout entire river networks over the period of 1911–2017, based on available long‐term environmental attributes influencing hydrological processes. We find descriptors of surface water extent can be accurately predicted based on robust internal and external validations. Environmental predictor variables representing water gaining processes were more important in predicting surface water extent than variables representing water losses. Simulated long‐term variations in surface water extent were highly dynamic through space and time, particularly in inland streams, which were predicted to be the driest on average. Total stream length with surface water ranged from 8,974 to 13,742 km across the study period. Our study presents a novel and practical approach to quantifying and predicting variations in surface water extent, with potential applicability to other parts of the world. The simulated surface water extent through space and time can be used to identify and prioritize potential aquatic refuge areas that sustain aquatic biodiversity in river networks during extended dry periods.
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    Sediment Respiration Pulses in Intermittent Rivers and Ephemeral Streams
    von Schiller, D ; Datry, T ; Corti, R ; Foulquier, A ; Tockner, K ; Marce, R ; Garcia-Baquero, G ; Odriozola, I ; Obrador, B ; Elosegi, A ; Mendoza-Lera, C ; Gessner, MO ; Stubbington, R ; Albarino, R ; Allen, DC ; Altermatt, F ; Arce, M ; Arnon, S ; Banas, D ; Banegas-Medina, A ; Beller, E ; Blanchette, ML ; Blanco-Libreros, JF ; Blessing, J ; Boechat, IG ; Boersma, KS ; Bogan, MT ; Bonada, N ; Bond, NR ; Brintrup, K ; Bruder, A ; Burrows, RM ; Cancellario, T ; Carlson, SM ; Cauvy-Fraunie, S ; Cid, N ; Danger, M ; de Freitas Terra, B ; Dehedin, A ; De Girolamo, AM ; del Campo, R ; Diaz-Villanueva, V ; Duerdoth, CP ; Dyer, F ; Faye, E ; Febria, C ; Figueroa, R ; Four, B ; Gafny, S ; Gomez, R ; Gomez-Gener, L ; Graca, MAS ; Guareschi, S ; Gucker, B ; Hoppeler, F ; Hwan, JL ; Kubheka, S ; Laini, A ; Langhans, SD ; Leigh, C ; Little, CJ ; Lorenz, S ; Marshall, J ; Martin, EJ ; McIntosh, A ; Meyer, E ; Milisa, M ; Mlambo, MC ; Moleon, M ; Morais, M ; Negus, P ; Niyogi, D ; Papatheodoulou, A ; Pardo, I ; Paril, P ; Pesic, V ; Piscart, C ; Polasek, M ; Rodriguez-Lozano, P ; Rolls, RJ ; Sanchez-Montoya, MM ; Savic, A ; Shumilova, O ; Steward, A ; Taleb, A ; Uzan, A ; Vander Vorste, R ; Waltham, N ; Woelfle-Erskine, C ; Zak, D ; Zarfl, C ; Zoppini, A (AMER GEOPHYSICAL UNION, 2019-10-16)
    Intermittent rivers and ephemeral streams (IRES) may represent over half the global stream network, but their contribution to respiration and carbon dioxide (CO2) emissions is largely undetermined. In particular, little is known about the variability and drivers of respiration in IRES sediments upon rewetting, which could result in large pulses of CO2. We present a global study examining sediments from 200 dry IRES reaches spanning multiple biomes. Results from standardized assays show that mean respiration increased 32-fold to 66-fold upon sediment rewetting. Structural equation modeling indicates that this response was driven by sediment texture and organic matter quantity and quality, which, in turn, were influenced by climate, land use, and riparian plant cover. Our estimates suggest that respiration pulses resulting from rewetting of IRES sediments could contribute significantly to annual CO2 emissions from the global stream network, with a single respiration pulse potentially increasing emission by 0.2–0.7%. As the spatial and temporal extent of IRES increases globally, our results highlight the importance of recognizing the influence of wetting-drying cycles on respiration and CO2 emissions in stream networks.
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    Monitoring age-related trends in genomic diversity of Australian lungfish
    Schmidt, DJ ; Fallon, S ; Roberts, DT ; Espinoza, T ; McDougall, A ; Brooks, SG ; Kind, PK ; Bond, NR ; Kennard, MJ ; Hughes, JM (WILEY, 2018-08)
    An important challenge for conservation science is to detect declines in intraspecific diversity so that management action can be guided towards populations or species at risk. The lifespan of Australian lungfish (Neoceratodus forsteri) exceeds 80 years, and human impacts on breeding habitat over the last half century may have impeded recruitment, leaving populations dominated by old postreproductive individuals, potentially resulting in a small and declining breeding population. Here, we conduct a "single-sample" evaluation of genetic erosion within contemporary populations of the Australian lungfish. Genetic erosion is a temporal decline in intraspecific diversity due to factors such as reduced population size and inbreeding. We examined whether young individuals showed signs of reduced genetic diversity and/or inbreeding using a novel bomb radiocarbon dating method to age lungfish nonlethally, based on 14 C ratios of scales. A total of 15,201 single nucleotide polymorphic (SNP) loci were genotyped in 92 individuals ranging in age from 2 to 77 years old. Standardized individual heterozygosity and individual inbreeding coefficients varied widely within and between riverine populations, but neither was associated with age, so perceived problems with recruitment have not translated into genetic erosion that could be considered a proximate threat to lungfish populations. Conservation concern has surrounded Australian lungfish for over a century. However, our results suggest that long-lived threatened species can maintain stable levels of intraspecific variability when sufficient reproductive opportunities exist over the course of a long lifespan.
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    Science to support the management of riverine flows
    Stoffels, RJ ; Bond, NR ; Nicol, S (WILEY, 2018-08)
    Abstract The last two decades has seen introduction or reform of water legislation in many river basins of the world, and river managers are under increasing pressure to make effective and efficient flow management decisions. To support those decisions, the roles that freshwater scientists must fulfil are rapidly evolving, and now is a good time to ask: What roles must scientists fulfil to best support those decisions? What are the major barriers to seeing those roles fulfilled? How can those barriers be removed? We offer potential answers to these questions. To ensure our arguments are grounded within real policy and decision problems, they are framed within the context of Australia's Murray‐Darling Basin Plan—legislation to guide the management of environmental flows—and its associated Watering Strategy. These problems are not unique, so the challenges and solutions we identify have broader applicability to flow management. Indeed, many of the policy and decision problems we present are common to all ecosystem types, so our arguments will likely be applicable beyond freshwater ecosystems. We argue that scientists must fulfil four roles to support flows management: (1) Monitoring and evaluation of ecosystems to support scientifically defensible reporting of outcomes, and to reduce uncertainty through adaptive management. (2) Modelling to support spatial and temporal projections of ecosystem change under different flow scenarios, resulting in more effective management decisions; improved causal inference about flow effects; identification of threats to the efficacy of flow management; and scaling flow‐response dynamics to broader spatial extents. (3) Fundamental research, resulting in improved outcomes through the identification of non‐flow management interventions that work in synergy with environmental flows and improved understanding of the ecological limitations of current policy. (4) Decision science, leading to more defensible environmental flow decisions and more efficient use of resources. We identify key barriers specific to each role and offer possible remedies. We argue that a major impediment to seeing these roles fulfilled is the ad hoc nature of much of the current research effort. Investment in research must (1) be developed at the basin scale, to ensure science supports decision problems that span multiple scales; (2) be developed as a collaboration between all stakeholders to ensure that science investments remain aligned with decision problems; (3) recognise the need to build and maintain technical capacity within the four roles.
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    Informing Environmental Water Management Decisions: Using Conditional Probability Networks to Address the Information Needs of Planning and Implementation Cycles
    Horne, AC ; Szemis, JM ; Webb, JA ; Kaur, S ; Stewardson, MJ ; Bond, N ; Nathan, R (SPRINGER, 2018-03)
    One important aspect of adaptive management is the clear and transparent documentation of hypotheses, together with the use of predictive models (complete with any assumptions) to test those hypotheses. Documentation of such models can improve the ability to learn from management decisions and supports dialog between stakeholders. A key challenge is how best to represent the existing scientific knowledge to support decision-making. Such challenges are currently emerging in the field of environmental water management in Australia, where managers are required to prioritize the delivery of environmental water on an annual basis, using a transparent and evidence-based decision framework. We argue that the development of models of ecological responses to environmental water use needs to support both the planning and implementation cycles of adaptive management. Here we demonstrate an approach based on the use of Conditional Probability Networks to translate existing ecological knowledge into quantitative models that include temporal dynamics to support adaptive environmental flow management. It equally extends to other applications where knowledge is incomplete, but decisions must still be made.
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    Coupling environment and physiology to predict effects of climate change on the taxonomic and functional diversity of fish assemblages in the Murray-Darling Basin, Australia
    de Oliveira, AG ; Bailly, D ; Cassemiro, FAS ; do Couto, EV ; Bond, N ; Gilligan, D ; Rangel, TF ; Agostinho, AA ; Kennard, MJ ; Silva, DDP (PUBLIC LIBRARY SCIENCE, 2019-11-27)
    This study uses species distribution modeling and physiological and functional traits to predict the impacts of climate change on native freshwater fish in the Murray-Darling Basin, Australia. We modelled future changes in taxonomic and functional diversity in 2050 and 2080 for two scenarios of carbon emissions, identifying areas of great interest for conservation. Climatic-environmental variables were used to model the range of 23 species of native fish under each scenario. The consensus model, followed by the physiological filter of lethal temperature was retained for interpretation. Our study predicts a severe negative impact of climate change on both taxonomic and functional components of ichthyofauna of the Murray-Darling Basin. There was a predicted marked contraction of species ranges under both scenarios. The predictions showed loss of climatically suitable areas, species and functional characters. There was a decrease in areas with high values of functional richness, dispersion and uniqueness. Some traits are predicted to be extirpated, especially in the most pessimistic scenario. The climatic refuges for fish fauna are predicted to be in the southern portion of the basin, in the upper Murray catchment. Incorporating future predictions about the distribution of ichthyofauna in conservation management planning will enhance resilience to climate change.