A risk assessment approach to manage inundation of Elseya albagula nests in impounded waters: a win-win situation?

Environmental DNA analysis confirms extant populations of the cryptic Irwin’s turtle within its historical range

Background

Approximately 50% of freshwater turtles worldwide are currently threatened by habitat loss, rural development and altered stream flows. Paradoxically, reptiles are understudied organisms, with many species lacking basic geographic distribution and abundance data. The iconic Irwin’s turtle, Elseya irwini, belongs to a unique group of Australian endemic freshwater turtles capable of cloacal respiration. Water resource development, increased presence of saltwater crocodiles and its cryptic behaviour, have made sampling for Irwin’s turtle in parts of its range problematic, resulting in no confirmed detections across much of its known range for > 25 years. Here, we used environmental DNA (eDNA) analysis for E. irwini detection along its historical and contemporary distribution in the Burdekin, Bowen and Broken River catchments and tributaries. Five replicate water samples were collected at 37 sites across those three river catchments. Environmental DNA was extracted using a glycogen-aided precipitation method and screened for the presence of E. irwini through an eDNA assay targeting a 127 base pair-long fragment of the NADH dehydrogenase 4 (ND4) mitochondrial gene.

Results

Elseya irwini eDNA was detected at sites within its historic distribution in the lower Burdekin River, where the species had not been formally recorded for > 25 years, indicating the species still inhabits the lower Burdekin area. We also found higher levels of E. iriwni eDNA within its contemporary distribution in the Bowen and Broken Rivers, matching the prevailing scientific view that these areas host larger populations of E. irwini.

Conclusions

This study constitutes the first scientific evidence of E. irwini presence in the lower Burdekin since the original type specimens were collected as part of its formal description, shortly after the construction of the Burdekin Falls Dam. From the higher percentage of positive detections in the upper reaches of the Broken River (Urannah Creek), we conclude that this area constitutes the core habitat area for the species. Our field protocol comprises a user-friendly, time-effective sampling method. Finally, due to safety risks associated with traditional turtle sampling methods in the Burdekin River (e.g., estuarine crocodiles) we propose eDNA sampling as the most pragmatic detection method available for E. irwini.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02009-6.

Adaptive Management to Reduce Nest Inundation of a Critically Endangered Freshwater Turtle: Confirming the Win-win

Inundation of Australian freshwater turtle nests has been identified as a threat to recruitment and long-term viability of species such as the critically endangered white-throated snapping turtle (Elseya albagula). Water level fluctuations within water storage infrastructure can inundate significant proportions of E. albagula nests in any year. Using an ecological risk assessment framework, operating rules for a water storage in the Burnett River (South East Queensland, Australia) were implemented to support nesting of E. albagula. Turtles were encouraged to nest at higher elevations on riverbanks by maintaining higher water levels in the impoundment during the nesting season, followed by lowering of water levels during the incubation period to minimise rates of nest inundation from riverine inflows. To verify the success of the new rules, a three-year confirmation monitoring program of nest heights and water levels was undertaken. Results of confirmation monitoring showed that 3% (2018), 11% (2019) and 0% (2020) of E. albagula nests were inundated under the new operating rules, compared to previously estimated nest inundation rates of >20% in ~24% of years of a 118-year simulation period (1890-2008) under previous storage operating rules. Emergency releases from an upstream storage in 2019 and 2020 for dam safety did not affect the success of the rule, demonstrating its resilience to natural and artificial flow regimes. This study demonstrates the importance of confirmation monitoring in verifying the efficacy of targeted changes to water management, and highlights potential application across other water storage infrastructure with threatened freshwater turtle populations requiring adaptive management.

A Risk-Based Ecohydrological Approach to Assessing Environmental Flow Regimes

For several decades there has been recognition that water resource development alters river flow regimes and impacts ecosystem values. Determining strategies to protect or restore flow regimes to achieve ecological outcomes is a focus of water policy and legislation in many parts of the world. However, consideration of existing environmental flow assessment approaches for application in Queensland identified deficiencies precluding their adoption. Firstly, in managing flows and using ecosystem condition as an indicator of effectiveness, many approaches ignore the fact that river ecosystems are subjected to threatening processes other than flow regime alteration. Secondly, many focus on providing flows for responses without considering how often they are necessary to sustain ecological values in the long-term. Finally, few consider requirements at spatial-scales relevant to the desired outcomes, with frequent focus on individual places rather than the regions supporting sustainability. Consequently, we developed a risk-based ecohydrological approach that identifies ecosystem values linked to desired ecological outcomes, is sensitive to flow alteration and uses indicators of broader ecosystem requirements. Monitoring and research is undertaken to quantify flow-dependencies and ecological modelling is used to quantify flow-related ecological responses over an historical flow period. The relative risk from different flow management scenarios can be evaluated at relevant spatial-scales. This overcomes the deficiencies identified above and provides a robust and useful foundation upon which to build the information needed to support water planning decisions. Application of the risk assessment approach is illustrated here by two case studies.

The influence of a new water infrastructure development on the relative abundance of two Australian freshwater turtle species

Development of water infrastructure benefits water security and agriculture but poses risks to habitat and aquatic fauna. Wyaralong Dam was constructed on Teviot Brook in 2010 to provide future urban water supplies for South East Queensland, Australia. Construction of the dam created a large impoundment area and environmental impact assessment predicted significant impacts upon resident freshwater turtle species and their habitats. Differences in habitat requirements, life-history characteristics and sensitivity to change between the Macquarie River turtle (Emydura macquarii macquarii) and the common saw-shelled turtle (Myuchelys latisternum) were expected to influence the impact of the dam on the spatial and temporal abundance of these species. The relative abundance of each species was monitored at sites located within, upstream and downstream of the impoundment across wet and dry seasons during the dam’s first five years of operation. The results of this monitoring program indicate that spatial and temporal variability in the relative abundance of E. macquarii macquarii and M. latisternum occurred during the study but not all expected impacts were realised. Contrary to expectation, the relative abundance of E. macquarii macquarii did not increase over time within, upstream or downstream of the dam. M. latisternum showed greater temporal variability at some sites; however, no clear relationship between relative abundance and operational years was observed during the monitoring program. Spatial variability in relative abundance between sites was dependent upon season, with trends generally consistent across both turtle species. Where differences between species were observed, these are suspected to have resulted from the influence of environmental conditions on species-specific movement behaviours. The monitoring program confirmed the use of the upper limits of the impoundment and the plunge pool below the dam wall by both turtle species but relative abundance within the main body of the impoundment remained low throughout monitoring. The results of the study allow for consideration of the suitability of predefined management measures and the development of recommendations for future monitoring programs prescribed for water infrastructure developments.

Nesting behaviour of the endangered Mary River turtle: monitoring and modelling to inform e-flow strategies

The Mary River turtle (Elusor macrurus) is an endemic, monotypic species with multiple impacts across its life-history, including overharvesting of eggs, nest predation and habitat degradation. Long-term recruitment failure has led to protection measures established under state, federal and international authority. Previous research has demonstrated that E. macrurus lives instream but nests on river banks, requiring specific habitat for breeding, nesting and recruitment. Ecohydrological rules represent the critical water requirements contributing to a species’ life history and can be used to develop and assess environmental flow strategies for species affected by water resource development. This study investigated the nesting behaviour of E. macrurus, including the environmental drivers that affect nest inundation. Monitoring showed that nesting by E. macrurus peaked in October and November, driven by rainfall events (>10 mm), with potential impacts from flow events (20% of nests established <2.5 m above water level at time of nesting). These ecohydrological rules were modelled against 109 years of simulated natural flow and rainfall data. The ‘potential nesting and nest inundation’ (PNNI) indicator revealed that nesting for E. macrurus was assured in a majority of years under the natural flow scenario. The results of this study will inform the development and assessment of e-flow strategies for nesting by E. macrurus in terms of current, and future water resource development, along with climate change impacts.