Plenary Speaker: Universal Lessons from Fish Passage Research, Design and Application in Australia

Dr. Mallen-Cooper has been a specialist fishway biologist for 30 years and has designed over 200 fishways in Australia and overseas, from fish locks and fish lifts on large dams to low-level pool-type and nature-like fishways. His approach to projects is to clarify ecological function, develop migration models and integrate fish behavior into all aspects of dam, weir and fishway design. A key aspect of this is integrating biology, hydrology and hydraulics, which has led to new approaches and applications in fishway design and improved ecological function. In the last 10 years Dr. Mallen-Cooper has had a significant focus on broader linkages for fish passage and fish migration within catchments and between rivers and floodplains, and maximizing benefits for fish from environmental flows. Southern Hemisphere fish passage is different although the underlying principles are the same. Coping with small and large fish, upstream, downstream and lateral migrations, highly variable and often very low seasonal flows present challenges that all need to be addressed. Lessons from his experience would assist a more holistic approach to fish passage in the tropics and Northern Hemisphere

Range limit dynamics of biocrusts in a changing climate

Climate change continues to drive a broad range of responses among the world’s biota. For example, there are plants that now flower earlier, animals that have evolved different camouflage, and many species that are shifting their ranges. Range shifting is well-documented for highly mobile taxa such as birds and insects, yet little is known about range shifting in species that form biocrusts—communities of lichens, non-vascular plants, and microbes that live on the soil surface and play important functional roles in nutrient cycling and erosion control. Another key theme of climate change ecology is that some species mediate the responses of other species, for example, by buffering the local microclimate or altering the cycling of nutrients. In line with these two themes, the aim of my thesis is to investigate: 1) what drives range limits in species of biocrust; 2) how biocrust species ranges have responded to recent climate change; 3) how biocrust species ranges are likely to respond to future climate change; and 4) how biocrust species mediate the effects of climate change on soil biota through microclimate buffering. I found that biocrust species are generally carbon limited at their arid range limits (Chapter 2), which suggests that range limits in biocrusts represent the point at which carbon budgets become unsustainable. Chapter 3 describes a field study comparing the modern and historical (25-year-old) distributions of three biocrust species, in which I found no evidence that any species have shifted in space to counteract climate warming. Global species distribution models show that the area of future suitable habitat is likely to be highly variable among biocrust species (Chapter 4), and accessing this habitat will require dispersal over considerable distances (4.6 km yr-1 on average). Finally, I found that tundra lichen mats play a major role in buffering high soil temperatures during summer (Chapter 5). The findings of this thesis are foundational for understanding the spatial aspect of biocrust responses to climate change and can be used to predict and mitigate losses of ecosystem functioning in areas where biocrust species are pushed beyond their niche limits

Introduced plants in the high altitude environments of Kosciusko National Park, South-Eastern Australia

Until recently, most of the available research on the biology of introduced plant species, their interactions with neighbouring species and their responses to a range of environmental conditions has been carried out in an agricultural context. However, the study of introduced plants in natural areas has received increasing attention in the last decade, including the initiation in mid-1982 of a wide-ranging SCOPE programme (Scientific Committee on Problems of the Environment, a subsidiary body of the International Council of Scientific Unions) on the Ecology of Biological Invasions. The research associated with the SCOPE programme has now been published as a series of regional and global reviews (Groves & Burdon, 1986; Kornberg & Williamson, 1986; Macdonald et al., 1986; Mooney & Drake, 1986: Joenje et al., 1987; Usher et al., 1988; Drake et al., 1989). Particular emphasis in these and other studies has been given to factors contributing to the successful establishment of introduced species, and the susceptibility of different communities and ecosystems to introduced species invasions. Natural and semi-natural areas (those areas which are relatively undisturbed by human activities) in most countries are becoming fewer and smaller, and those that remain are subject to increasing visitor use and exploitation. The current concern about the effects of introduced species in natural areas is related to the growing scientific and public awareness of the value of natural areas and their component species. An introduced species is defined in a natural area context as any species which is not native to the region being studied. There are few ecosystems in the world which have not been affected by introduced plant invasions (Usher, 1988; Heywood, 1989). Most of these invasions can be linked either directly or indirectly with human activities, with invasion of undisturbed ecosystems being extremely uncommon (Johnson, 1982; Fox, 1988). Introduced species invading both natural and modified ecosystems vary greatly in their ability to colonise and persist at a site, in their rates of spread and in their effects on the existing plant communities and ecosystem processes (Forcella, 1985; Christensen & Burrows, 1986; Heywood, 1989). Even among the most successful invaders, such as Chrysanthemoides monilifera in coastal areas of southeastern Australia (Weiss & Noble, 1984a & b); Acacia saligna, A. cyclops and A. longifolia in the fynbos biome of southern Africa (Macdonald & Jarman, 1984; Macdonald et al., 1989) and Hypericum perforatum in temperate grassland and woodland communities (Groves, 1989); there appear to be few attributes common to all species which can be used to accurately predict the invasion potential of individual species (Healy, 1969, 1973; Crawley, 1986, 1989; Newsome & Noble, 1986; Williamson & Brown, 1986; Esler, 1988; Noble, 1989)

Exploring ways to deliver better fishway management

Victorian Waterway Management Strategy provides the framework for government, in partnership with the community, to maintain or improve the condition of rivers, estuaries and wetlands so that they can continue to provide environmental, social, cultural and economic values and includes actions specifically aimed at fishway management in Victoria. This presentation discusses the history (and issues) with many of our current fishways and future fishway management in the context of the policy and actions outlined in the Strategy. Actions and approaches to achieve these outcomes include recently released guidelines outlining contemporary performance, design and monitoring of fishways in Victoria and exploring ways to deliver better fishways. These fishway guideline documents are intended to create a consistent approach to fishway management across the state and together with potential future management strategies will ensure improved river connectivity into the future

PacBio amplicon sequencing for metabarcoding of mixed DNA samples from lichen herbarium specimens.

The detection and identification of species of fungi in the environment using molecular methods heavily depends on reliable reference sequence databases. However, these databases are largely incomplete in terms of taxon coverage, and a significant effort is required from herbaria and living fungal collections for the mass-barcoding of well-identified and well-curated fungal specimens or strains. Here, a PacBio amplicon sequencing approach is applied to recent lichen herbarium specimens for the sequencing of the fungal ITS barcode, allowing a higher throughput sample processing than Sanger sequencing, which often required the use of cloning. Out of 96 multiplexed samples, a full-length ITS sequence of the target lichenised fungal species was recovered for 85 specimens. In addition, sequences obtained for co-amplified fungi gave an interesting insight into the diversity of endolichenic fungi. Challenges encountered at both the laboratory and bioinformatic stages are discussed, and cost and quality are compared with Sanger sequencing. With increasing data output and reducing sequencing cost, PacBio amplicon sequencing is seen as a promising approach for the generation of reference sequences for lichenised fungi as well as the characterisation of lichen-associated fungal communities

Flows for native fish in the Murray-Darling Basin: lessons and considerations for future management

Article first published online: 22 APR 2014Increased regulation and extraction of water from rivers has contributed to the decline of fishes, and the use of environmental water allocations (EWAs) is now a key rehabilitation measure. Major reform of water policy in the Murray-Darling Basin (MDB), Australia, has recently provided significant EWAs to improve ecological outcomes. Conflict over water buybacks, the value of the water and the need to maximise environmental benefits and minimise risks of unwanted outcomes has increased the expectation for science to underpin and justify such actions. Recent research has focussed attention on the need to understand fish–flow relationships. The Native Fish Strategy for the Murray-Darling Basin 2003–2013 (NFS), while not specifically targeted at water policy reform or water delivery, has provided fish ecology research and flow restoration experimentation and contributed considerable new scientific knowledge to support flow management. It has contributed to a substantial and positive change in environmental watering for fish, with native fish targets now regularly incorporated into watering objectives. This study documents changes to water management in the MDB, summarises current knowledge of flow-related fish ecology in the MDB, highlights the benefits and risks of some water management practises and provides recommendations for future management and research. A major recommendation is the need for a coordinated, cross-jurisdictional approach to flow restoration for native fish, ensuring that the best available science is being used in all watering allocations. We caution on the use of environmental works such as regulators to artificially inundate floodplains and suggest that such approaches should be viewed as large-scale experiments with the significant risks posed to fish needing to be recognised, adequately monitored and adaptively managed.John D. Koehn, Alison J. King, Leah Beesley, Craig Copeland, Brenton P. Zampatti and Martin Mallen-Coope

The traits of "trait ecologists" : An analysis of the use of trait and functional trait terminology

Trait and functional trait approaches have revolutionized ecology improving our understanding of community assembly, species coexistence, and biodiversity loss. Focusing on traits promotes comparability across spatial and organizational scales, but terms must be used consistently. While several papers have offered definitions, it remains unclear how ecologists operationalize "trait" and "functional trait" terms. Here, we evaluate how researchers and the published literatures use these terms and explore differences among subdisciplines and study systems (taxa and biome). By conducting both a survey and a literature review, we test the hypothesis that ecologists' working definition of "trait" is adapted or altered when confronting the realities of collecting, analyzing and presenting data. From 486 survey responses and 712 reviewed papers, we identified inconsistencies in the understanding and use of terminology among researchers, but also limited inclusion of definitions within the published literature. Discrepancies were not explained by subdiscipline, system of study, or respondent characteristics, suggesting there could be an inconsistent understanding even among those working in related topics. Consistencies among survey responses included the use of morphological, phonological, and physiological traits. Previous studies have called for unification of terminology; yet, our study shows that proposed definitions are not consistently used or accepted. Sources of disagreement include trait heritability, defining and interpreting function, and dealing with organisms in which individuals are not clearly recognizable. We discuss and offer guidelines for overcoming these disagreements. The diversity of life on Earth means traits can represent different features that can be measured and reported in different ways, and thus, narrow definitions that work for one system will fail in others. We recommend ecologists embrace the breadth of biodiversity using a simplified definition of "trait" more consistent with its common use. Trait-based approaches will be most powerful if we accept that traits are at least as diverse as trait ecologists.Peer reviewe

Stratified primary care versus non-stratified care for musculoskeletal pain: findings from the STarT MSK feasibility and pilot cluster randomized controlled trial

Background: Musculoskeletal (MSK) pain from the five most common presentations to primary care (back, neck, shoulder, knee or multi-site pain), where the majority of patients are managed, is a costly global health challenge. At present, first-line decisionmaking is based on clinical reasoning and stratified models of care have only been tested in patients with low back pain. We therefore, examined the feasibility of; a) a future definitive cluster randomised controlled trial (RCT), and b) General Practitioners (GPs) providing stratified care at the point-of-consultation for these five most common MSK pain presentations. Methods: The design was a pragmatic pilot, two parallel-arm (stratified versus nonstratified care), cluster RCT and the setting was 8 UK GP practices (4 intervention, 4 control) with randomisation (stratified by practice size) and blinding of trial statistician and outcome data-collectors. Participants were adult consulters with MSK pain without indicators of serious pathologies, urgent medical needs, or vulnerabilities. Potential participant records were tagged and individuals sent postal invitations using a GP point-of-consultation electronic medical record (EMR) template. The intervention was supported by the EMR template housing the Keele STarT MSK Tool (to stratify into low, medium and high-risk prognostic subgroups of persistent pain and disability) and recommended matched treatment options. Feasibility outcomes included exploration of recruitment and follow-up rates, selection bias, and GP intervention fidelity. To capture recommended outcomes including pain and function, participants completed an initial questionnaire, brief monthly questionnaire (postal or SMS), and 6-month follow-up questionnaire. An anonymised EMR audit described GP decision-making. Results: GPs screened 3063 patients (intervention=1591, control=1472), completed the EMR template with 1237 eligible patients (intervention=513, control=724) and 524 participants (42%) consented to data collection (intervention=231, control=293). Recruitment took 28 weeks (target 12 weeks) with >90% follow-up retention (target >75%). We detected no selection bias of concern and no harms identified. GP stratification tool fidelity failed to achieve a-priori success criteria, whilst fidelity to the matched treatments achieved “complete success”. Conclusions: A future definitive cluster RCT of stratified care for MSK pain is feasible and is underway, following key amendments including a clinician-completed version of the stratification tool and refinements to recommended matched treatments